diff --git a/.github/workflows/integration-testing.yml b/.github/workflows/integration-testing.yml index 3e93dd5b..b211dd53 100644 --- a/.github/workflows/integration-testing.yml +++ b/.github/workflows/integration-testing.yml @@ -13,7 +13,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.9", "3.10", "3.11", "3.12"] + python-version: ["3.10", "3.11", "3.12"] steps: - name: Checkout repository uses: actions/checkout@v4 diff --git a/.github/workflows/unit-testing.yml b/.github/workflows/unit-testing.yml index e2b87dcd..62222e4e 100644 --- a/.github/workflows/unit-testing.yml +++ b/.github/workflows/unit-testing.yml @@ -12,7 +12,7 @@ jobs: strategy: fail-fast: false matrix: - python-version: ["3.9", "3.10", "3.11", "3.12"] + python-version: ["3.10", "3.11", "3.12"] steps: - name: Checkout repository uses: actions/checkout@v4 diff --git a/README.md b/README.md index 5ab4e5f3..4d5ebf4d 100644 --- a/README.md +++ b/README.md @@ -48,6 +48,10 @@ S., & Szalóki, G. (2023). Cavity Characterization in Supramolecular Cages. Journal of chemical information and modeling, 63(12), 3772-3785. . +If you use *PyMOL pyKVFinder Tools*, please also cite: + +Guerra, J. V. da S., Ribeiro Filho, H. V., Bortot, L. O., Honorato, R. V., Pereira, J. G. de C., & Lopes-de-Oliveira, P. S. (2020). ParKVFinder: A thread-level parallel approach in biomolecular cavity detection. In SoftwareX (Vol. 12, p. 100606). Elsevier BV. https://doi.org/10.1016/j.softx.2020.100606. + ## License The software is licensed under the terms of the GNU General Public diff --git a/docs/.buildinfo b/docs/.buildinfo index c5c2bf21..4515d8d0 100644 --- a/docs/.buildinfo +++ b/docs/.buildinfo @@ -1,4 +1,4 @@ # Sphinx build info version 1 # This file hashes the configuration used when building these files. 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100644 --- a/docs/INSTRUCTIONS.rst +++ b/docs/INSTRUCTIONS.rst @@ -8,3 +8,4 @@ To create pyKVFinder documentation as a GitHub page, run: .. code-block:: bash make html + diff --git a/docs/_api_reference/index.html b/docs/_api_reference/index.html deleted file mode 100644 index fe35167d..00000000 --- a/docs/_api_reference/index.html +++ /dev/null @@ -1,203 +0,0 @@ - - - - - - - Functions — pyKVFinder 0.6.14 documentation - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
- -
- -
-
-
-
- - - - \ No newline at end of file diff --git a/docs/_cfg_files/vdw_file_template.html b/docs/_cfg_files/vdw_file_template.html deleted file mode 100644 index 0f2cd1b5..00000000 --- a/docs/_cfg_files/vdw_file_template.html +++ /dev/null @@ -1,160 +0,0 @@ - - - - - - - Van der Waals radii file template — pyKVFinder 0.6.14 documentation - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

Van der Waals radii file template

-

The van der Waals radii file define the radius values for each atom by residue and when not defined, it uses a generic value based on the atom type. The package contains a built-in van der Waals radii file: vdw.dat. However, the user can define its own file with a mandatory format and pass it to pyKVFinder. The format is shown below:

-
>RES
-C       1.66
-CA      2.00
-N       1.97
-O       1.69
-H       0.91
-
-
-
-

Warning

-

The residue name should be in the standard PDB format and each radius value is separated by two tab characters of the atom name.

-
-
- - -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/docs/_images/main_tab_1.png b/docs/_images/main_tab_1.png new file mode 100644 index 00000000..8ae11287 Binary files /dev/null and b/docs/_images/main_tab_1.png differ diff --git a/docs/_images/main_tab_2.png b/docs/_images/main_tab_2.png new file mode 100644 index 00000000..919a1262 Binary files /dev/null and b/docs/_images/main_tab_2.png differ diff --git a/docs/_images/pymol_viewer_1.png b/docs/_images/pymol_viewer_1.png new file mode 100644 index 00000000..155a610d Binary files /dev/null and b/docs/_images/pymol_viewer_1.png differ diff --git a/docs/_images/pymol_viewer_10.png b/docs/_images/pymol_viewer_10.png new file mode 100644 index 00000000..b9ea514b Binary files /dev/null and b/docs/_images/pymol_viewer_10.png differ diff --git a/docs/_images/pymol_viewer_2.png b/docs/_images/pymol_viewer_2.png new file mode 100644 index 00000000..cad58ac1 Binary files /dev/null and b/docs/_images/pymol_viewer_2.png differ diff --git a/docs/_images/pymol_viewer_3.png b/docs/_images/pymol_viewer_3.png new file mode 100644 index 00000000..178b390d Binary files /dev/null and b/docs/_images/pymol_viewer_3.png differ diff --git a/docs/_images/pymol_viewer_4.png b/docs/_images/pymol_viewer_4.png new file mode 100644 index 00000000..f16663be Binary files /dev/null and b/docs/_images/pymol_viewer_4.png differ diff --git a/docs/_images/pymol_viewer_5.png b/docs/_images/pymol_viewer_5.png new file mode 100644 index 00000000..d0e8ebb6 Binary files /dev/null and b/docs/_images/pymol_viewer_5.png differ diff --git a/docs/_images/pymol_viewer_6.png b/docs/_images/pymol_viewer_6.png new file mode 100644 index 00000000..36dba502 Binary files /dev/null and b/docs/_images/pymol_viewer_6.png differ diff --git a/docs/_images/pymol_viewer_7.png b/docs/_images/pymol_viewer_7.png new file mode 100644 index 00000000..5910c105 Binary files /dev/null and b/docs/_images/pymol_viewer_7.png differ diff --git a/docs/_images/pymol_viewer_8.png b/docs/_images/pymol_viewer_8.png new file mode 100644 index 00000000..42d73139 Binary files /dev/null and b/docs/_images/pymol_viewer_8.png differ diff --git a/docs/_images/pymol_viewer_9.png b/docs/_images/pymol_viewer_9.png new file mode 100644 index 00000000..96d7f8f0 Binary files /dev/null and b/docs/_images/pymol_viewer_9.png differ diff --git a/docs/_images/results_tab_1.png b/docs/_images/results_tab_1.png new file mode 100644 index 00000000..2d2c2215 Binary files /dev/null and b/docs/_images/results_tab_1.png differ diff --git a/docs/_images/results_tab_2.png b/docs/_images/results_tab_2.png new file mode 100644 index 00000000..2a7d61a0 Binary files /dev/null and b/docs/_images/results_tab_2.png differ diff --git a/docs/_images/results_tab_3.png b/docs/_images/results_tab_3.png new file mode 100644 index 00000000..0a155c24 Binary files /dev/null and b/docs/_images/results_tab_3.png differ diff --git a/docs/_images/results_tab_4.png b/docs/_images/results_tab_4.png new file mode 100644 index 00000000..0f3ded72 Binary files /dev/null and b/docs/_images/results_tab_4.png differ diff --git a/docs/_images/search_space_tab_1.png b/docs/_images/search_space_tab_1.png new file mode 100644 index 00000000..cd337833 Binary files /dev/null and b/docs/_images/search_space_tab_1.png differ diff --git a/docs/_images/search_space_tab_2.png b/docs/_images/search_space_tab_2.png new file mode 100644 index 00000000..0fe548b7 Binary files /dev/null and b/docs/_images/search_space_tab_2.png differ diff --git a/docs/_installation/index.html b/docs/_installation/index.html deleted file mode 100644 index 0bd71eb1..00000000 --- a/docs/_installation/index.html +++ /dev/null @@ -1,193 +0,0 @@ - - - - - - - Requirements — pyKVFinder 0.6.14 documentation - - - - - - - - - - - - - - - - - - - - -
- - -
- -
-
-
- -
-
-
-
- -
-

Requirements

-

If you don’t have Python v3 and/or SWIG yet, the installation procedure differs depending on the operating system.

-

Python and SWIG can be installed with conda, or with a package manager on Linux and macOS.

-
-

Package managers

-

On Linux:

-
sudo apt install python3 swig
-
-
-

On macOS:

-
brew install python3 swig
-
-
-
-

Note

-

Users can use their preferred package manager to install SWIG and Python v3.

-
-
-
-

Conda

-

If you use conda, you can install Python v3 and SWIG from the defaults channel:

-
# Use an environment rather than install in base environement (recommended)
-conda create -n myenv python=3
-conda activate myenv
-# The SWIG install command
-conda install swig
-
-
-
-
-
-

Installation

-

The prerequisites for installing pyKVFinder is Python v3 and SWIG. If you don’t have Python and/or SWIG yet, please refer to this section.

-

To install the latest release on PyPI, -run:

-
pip install pyKVFinder
-
-
-

Or to install the latest developmental version, run:

-
git clone https://github.com/LBC-LNBio/pyKVFinder.git
-pip install pyKVFinder
-
-
-
- - -
-
- -
-
-
-
- - - - \ No newline at end of file diff --git a/docs/_modules/index.html b/docs/_modules/index.html index 810dff4b..27900ba8 100644 --- a/docs/_modules/index.html +++ b/docs/_modules/index.html @@ -3,7 +3,7 @@ - Overview: module code — pyKVFinder 0.6.14 documentation + Overview: module code — pyKVFinder 0.7.0 documentation @@ -15,8 +15,8 @@ - - + + @@ -36,7 +36,7 @@
- 0.6 + 0.7
@@ -46,40 +46,25 @@
diff --git a/docs/_modules/pyKVFinder/grid.html b/docs/_modules/pyKVFinder/grid.html index 22524f67..40eda70d 100644 --- a/docs/_modules/pyKVFinder/grid.html +++ b/docs/_modules/pyKVFinder/grid.html @@ -3,7 +3,7 @@ - pyKVFinder.grid — pyKVFinder 0.6.14 documentation + pyKVFinder.grid — pyKVFinder 0.7.0 documentation @@ -15,8 +15,8 @@ - - + + @@ -36,7 +36,7 @@
- 0.6 + 0.7
@@ -46,40 +46,25 @@
@@ -129,7 +114,7 @@

Source code for pyKVFinder.grid

 
 
 

-[docs]
+[docs]
 def get_vertices(
     atomic: Union[numpy.ndarray, List[List[Union[str, float, int]]]],
     probe_out: Union[float, int] = 4.0,
@@ -227,7 +212,7 @@ 
Source code for pyKVFinder.grid
 
 
 

-[docs]
+[docs]
 def get_vertices_from_file(
     fn: Union[str, pathlib.Path],
     atomic: Union[numpy.ndarray, List[List[Union[str, float, int]]]],
@@ -691,7 +676,7 @@ 
Source code for pyKVFinder.grid
 
 
 

-[docs]
+[docs]
 def detect(
     atomic: Union[numpy.ndarray, List[List[Union[str, float, int]]]],
     vertices: Union[numpy.ndarray, List[List[float]]],
@@ -1235,7 +1220,7 @@ 
Source code for pyKVFinder.grid
 
 
 

-[docs]
+[docs]
 def spatial(
     cavities: numpy.ndarray,
     step: Union[float, int] = 0.6,
@@ -1458,7 +1443,7 @@ 
Source code for pyKVFinder.grid
 
 
 

-[docs]
+[docs]
 def depth(
     cavities: numpy.ndarray,
     step: Union[float, int] = 0.6,
@@ -1668,7 +1653,7 @@ 
Source code for pyKVFinder.grid
 
 
 

-[docs]
+[docs]
 def constitutional(
     cavities: numpy.ndarray,
     atomic: Union[numpy.ndarray, List[List[Union[str, float, int]]]],
@@ -1953,7 +1938,7 @@ 
Source code for pyKVFinder.grid
 
 
 

-[docs]
+[docs]
 def hydropathy(
     surface: numpy.ndarray,
     atomic: Union[numpy.ndarray, List[List[Union[str, float, int]]]],
@@ -2394,7 +2379,7 @@ 
Source code for pyKVFinder.grid
 
 
 

-[docs]
+[docs]
 def openings(
     cavities: numpy.ndarray,
     depths: Optional[numpy.ndarray] = None,
@@ -2611,7 +2596,7 @@ 
Source code for pyKVFinder.grid
 
 
 

-[docs]
+[docs]
 def export(
     fn: Optional[Union[str, pathlib.Path]],
     cavities: numpy.ndarray,
@@ -2907,7 +2892,7 @@ 
Source code for pyKVFinder.grid
 
 
 

-[docs]
+[docs]
 def export_openings(
     fn: Union[str, pathlib.Path],
     openings: numpy.ndarray,
diff --git a/docs/_modules/pyKVFinder/main.html b/docs/_modules/pyKVFinder/main.html
index 255ffca2..02d0211a 100644
--- a/docs/_modules/pyKVFinder/main.html
+++ b/docs/_modules/pyKVFinder/main.html
@@ -3,7 +3,7 @@
 
   
   
-  pyKVFinder.main — pyKVFinder 0.6.14 documentation
+  pyKVFinder.main — pyKVFinder 0.7.0 documentation
       
       
 
@@ -15,8 +15,8 @@
   
         
         
-        
-        
+        
+        
         
     
     
@@ -36,7 +36,7 @@
               
           
               

-                0.6
+                0.7
               

 

   

@@ -46,40 +46,25 @@
   

 

         

@@ -389,7 +374,7 @@ 
Source code for pyKVFinder.main
 
 
 

-[docs]
+[docs]
 class pyKVFinderResults(object):
     """A class containing pyKVFinder detection and characterization results.
 
@@ -555,7 +540,7 @@ 
Source code for pyKVFinder.main
         return "<pyKVFinderResults object>"
 
 

-[docs]
+[docs]
     def export(
         self,
         output: Union[str, pathlib.Path] = "cavity.pdb",
@@ -609,7 +594,7 @@ 
Source code for pyKVFinder.main
 
 
 

-[docs]
+[docs]
     def write(
         self,
         fn: Union[str, pathlib.Path] = "results.toml",
@@ -659,7 +644,7 @@ 
Source code for pyKVFinder.main
 
 
 

-[docs]
+[docs]
     def plot_frequencies(self, pdf: Union[str, pathlib.Path] = "barplots.pdf"):
         """Plot bar charts of frequencies (residues and classes of residues) in
         a PDF file.
@@ -704,7 +689,7 @@ 
Source code for pyKVFinder.main
 
 
 

-[docs]
+[docs]
     def export_all(
         self,
         fn: Union[str, pathlib.Path] = "results.toml",
@@ -785,7 +770,7 @@ 
Source code for pyKVFinder.main
 
 
 

-[docs]
+[docs]
 def run_workflow(
     input: Union[str, pathlib.Path],
     ligand: Optional[Union[str, pathlib.Path]] = None,
@@ -1326,7 +1311,7 @@ 
Source code for pyKVFinder.main
 
 
 

-[docs]
+[docs]
 class Molecule(object):
     """A class for representing molecular structures.
 
@@ -1660,7 +1645,7 @@ 
Source code for pyKVFinder.main
         return float(padding.round(decimals=1))
 
 

-[docs]
+[docs]
     def vdw(self, step: float = 0.6, padding: Optional[float] = None) -> None:
         """Fill the 3D grid with the molecule as the van der Waals surface representation.
 
@@ -1739,7 +1724,7 @@ 
Source code for pyKVFinder.main
 
 
 

-[docs]
+[docs]
     def surface(
         self,
         step: float = 0.6,
@@ -1883,7 +1868,7 @@ 
Source code for pyKVFinder.main
 
 
 

-[docs]
+[docs]
     def volume(self) -> float:
         """Estimate the volume of the molecule based on the molecular surface representation, ie, vdW, SES or SAS representations.
 
@@ -1909,7 +1894,7 @@ 
Source code for pyKVFinder.main
 
 
 

-[docs]
+[docs]
     def preview(self, **kwargs) -> None:
         """Preview the molecular surface in the 3D grid.
 
@@ -1933,7 +1918,7 @@ 
Source code for pyKVFinder.main
 
 
 

-[docs]
+[docs]
     def export(
         self,
         fn: Union[str, pathlib.Path] = "molecule.pdb",
diff --git a/docs/_modules/pyKVFinder/utils.html b/docs/_modules/pyKVFinder/utils.html
index 9017ee03..ba1624ed 100644
--- a/docs/_modules/pyKVFinder/utils.html
+++ b/docs/_modules/pyKVFinder/utils.html
@@ -3,7 +3,7 @@
 
   
   
-  pyKVFinder.utils — pyKVFinder 0.6.14 documentation
+  pyKVFinder.utils — pyKVFinder 0.7.0 documentation
       
       
 
@@ -15,8 +15,8 @@
   
         
         
-        
-        
+        
+        
         
     
     
@@ -36,7 +36,7 @@
               
           
               

-                0.6
+                0.7
               

 

   

@@ -46,40 +46,25 @@
   

 

         

@@ -129,7 +114,7 @@ 
Source code for pyKVFinder.utils
 
 
 

-[docs]
+[docs]
 def read_vdw(
     fn: Optional[Union[str, pathlib.Path]] = None
 ) -> Dict[str, Dict[str, float]]:
@@ -285,7 +270,7 @@ 
Source code for pyKVFinder.utils
 
 
 

-[docs]
+[docs]
 def read_pdb(
     fn: Union[str, pathlib.Path],
     vdw: Optional[Dict[str, Dict[str, float]]] = None,
@@ -382,7 +367,7 @@ 
Source code for pyKVFinder.utils
 
 
 

-[docs]
+[docs]
 def read_xyz(
     fn: Union[str, pathlib.Path], vdw: Optional[Dict[str, Dict[str, float]]] = None
 ) -> numpy.ndarray:
@@ -516,7 +501,7 @@ 
Source code for pyKVFinder.utils
 
 
 

-[docs]
+[docs]
 def read_cavity(
     cavity: Union[str, pathlib.Path],
     receptor: Union[str, pathlib.Path],
@@ -899,7 +884,7 @@ 
Source code for pyKVFinder.utils
 
 
 

-[docs]
+[docs]
 def calculate_frequencies(
     residues: Dict[str, List[List[str]]]
 ) -> Dict[str, Dict[str, Dict[str, int]]]:
@@ -1014,7 +999,7 @@ 
Source code for pyKVFinder.utils
 
 
 

-[docs]
+[docs]
 def plot_frequencies(
     frequencies: Dict[str, Dict[str, Dict[str, int]]],
     fn: Union[str, pathlib.Path] = "barplots.pdf",
@@ -1071,7 +1056,7 @@ 
Source code for pyKVFinder.utils
     {'KAA': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'ASN': 1, 'ASP': 2, 'GLN': 1, 'GLU': 4, 'GLY': 4, 'HIS': 1, 'LEU': 3, 'LYS': 2, 'MET': 1, 'PHE': 3, 'SER': 1, 'THR': 4, 'TYR': 1, 'VAL': 3}, 'CLASS': {'R1': 11, 'R2': 4, 'R3': 8, 'R4': 6, 'R5': 4, 'RX': 0}}}
     >>> plot_frequencies(frequencies, fn='barplots.pdf')
 
-    .. image:: ../_images/barplots.png
+    .. image:: images/barplots.png
         :width: 600
         :align: center
     """
@@ -1221,7 +1206,7 @@ 
Source code for pyKVFinder.utils
 
 
 

-[docs]
+[docs]
 def write_results(
     fn: Union[str, pathlib.Path],
     input: Optional[Union[str, pathlib.Path]],
diff --git a/docs/_sources/_api_reference/index.rst.txt b/docs/_sources/_api_reference/index.rst.txt
deleted file mode 100644
index 9d9325cd..00000000
--- a/docs/_sources/_api_reference/index.rst.txt
+++ /dev/null
@@ -1,40 +0,0 @@
-.. raw:: html
-
-    
API Reference

-
-The API of all pyKVFinder functions and classes with expected types and all parameters available.
-
-Functions
-=========
-
-.. toctree::
-    :maxdepth: 1
-
-    run_workflow
-    read_vdw
-    read_pdb
-    read_xyz
-    read_cavity
-    get_vertices
-    get_vertices_from_file
-    detect
-    spatial
-    depth
-    openings
-    hydropathy
-    constitutional
-    calculate_frequencies
-    plot_frequencies
-    export
-    export_openings
-    write_results
-
-Classes
-=======
-
-.. toctree::
-    :maxdepth: 1
-
-    Molecule
-    pyKVFinderResults
-    
\ No newline at end of file
diff --git a/docs/_sources/_cfg_files/vdw_file_template.rst.txt b/docs/_sources/_cfg_files/vdw_file_template.rst.txt
deleted file mode 100644
index 84ac929f..00000000
--- a/docs/_sources/_cfg_files/vdw_file_template.rst.txt
+++ /dev/null
@@ -1,17 +0,0 @@
-Van der Waals radii file template
-#################################
-
-The van der Waals radii file define the radius values for each atom by residue and when not defined, it uses a generic value based on the atom type. The package contains a built-in van der Waals radii file: `vdw.dat `_. However, the user can define its own file with a mandatory format and pass it to pyKVFinder. The format is shown below:
-
-.. code-block:: none
-
-    >RES
-    C       1.66
-    CA      2.00
-    N       1.97
-    O       1.69
-    H       0.91
-
-.. warning::
-  
-    The residue name should be in the standard PDB format and each radius value is separated by two tab characters of the atom name.
diff --git a/docs/_sources/_installation/index.rst.txt b/docs/_sources/_installation/index.rst.txt
deleted file mode 100644
index d4e7388d..00000000
--- a/docs/_sources/_installation/index.rst.txt
+++ /dev/null
@@ -1,57 +0,0 @@
-Requirements
-============
-
-If you don’t have Python v3 and/or SWIG yet, the installation procedure differs depending on the operating system.
-
-Python and SWIG can be installed with conda, or with a package manager on Linux and macOS.
-
-Package managers
-----------------
-
-On Linux:
-
-.. code-block:: bash
-    
-  sudo apt install python3 swig
-
-On macOS:
-
-.. code-block:: bash
-    
-  brew install python3 swig
-
-.. note:: 
-
-  Users can use their preferred package manager to install SWIG and Python v3.
-
-Conda
------
-
-If you use conda, you can install Python v3 and SWIG from the defaults channel:
-
-.. code-block:: bash
-    
-  # Use an environment rather than install in base environement (recommended)
-  conda create -n myenv python=3
-  conda activate myenv
-  # The SWIG install command
-  conda install swig
-
-Installation
-============
-
-The prerequisites for installing pyKVFinder is Python v3 and SWIG. If you don’t have Python and/or SWIG yet, please refer to this `section `_.
-
-To install the latest release on `PyPI `_, 
-run:
-
-.. code-block:: bash
-
-  pip install pyKVFinder
-
-Or to install the latest developmental version, run:
-
-.. code-block:: bash
-
-  git clone https://github.com/LBC-LNBio/pyKVFinder.git
-  pip install pyKVFinder
diff --git a/docs/_sources/_about/index.rst.txt b/docs/_sources/about/index.rst.txt
similarity index 62%
rename from docs/_sources/_about/index.rst.txt
rename to docs/_sources/about/index.rst.txt
index 21113d3d..567861b0 100644
--- a/docs/_sources/_about/index.rst.txt
+++ b/docs/_sources/about/index.rst.txt
@@ -1,9 +1,6 @@
-.. raw:: html
-
-    
About

-
+******
 Issues
-======
+******
 
 pyKVFinder package uses GitHub for project management. Please help us by reporting any problems or requests.
 
@@ -11,33 +8,40 @@ On `Issues `_ page, you can file
 
 .. toctree::
     
-    Bug Report 
-    Request for a new feature 
+    Bug Report 
+    Documentation 
+    Feature Request 
+    Maintenance 
+
 
 Only make sure the bug or request has not already been reported. Click on “Search” and enter some keywords to search.
 
 Thank you for helping us improve pyKVFinder!
 
+***************
 Scientific team
-===============
+***************
 
-pyKVFinder was developed by:
+pyKVFinder and PyMOL pyKVFinder Tools were developed by:
 
-- João Victor da Silva Guerra
-- Helder Veras Ribeiro Filho
-- Gabriel Ernesto Jara
-- Leandro Oliveira Bortot
-- José Geraldo de Carvalho Pereira
-- Paulo Sergio Lopes de Oliveira
+* João V. S. Guerra
+* Helder V. Ribeiro-Filho
+* Luiz F. G. Alves
+* Pablo W. A. Silva
+* Gabriel E. Jara
+* Leandro O. Bortot
+* José G. C. Pereira
+* Paulo S. Lopes-de-Oliveira
 
 Computational Biology Laboratory (`LBC `_), Brazilian Biosciences National Laboratory (`LNBio `_), Brazilian Center for Research in Energy and Materials (`CNPEM `_)
 
 If you have any further questions, inquires or if you wish to contribute to KVFinder project, please contact us at joao.guerra@lnbio.cnpem.br or paulo.oliveira@lnbio.cnpem.br.
 
+*****************
 Citing pyKVFinder
-=================
+*****************
 
-If you use pyKVFinder package, please cite:
+If you use `pyKVFinder package`, please cite:
 
 Guerra, J. V. S., Ribeiro-Filho, H. V., Jara, G. E., Bortot, L. O., Pereira, J. G. C., & Lopes-de-Oliveira, P. S. (2021). pyKVFinder: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science. BMC bioinformatics, 22(1), 607. ``_.
 
@@ -45,12 +49,18 @@ If you use `pyKVFinder.Molecule`, please also cite:
 
 Guerra, J. V. S., Alves, L. F. G., Bourissou, D., Lopes-de-Oliveira, P. S., & Szalóki, G. (2023). Cavity Characterization in Supramolecular Cages. Journal of chemical information and modeling, 63(12), 3772-3785. ``_.
 
+If you use `PyMOL pyKVFinder Tools`, please also cite:
+
+Guerra, J. V. da S., Ribeiro Filho, H. V., Bortot, L. O., Honorato, R. V., Pereira, J. G. de C., & Lopes-de-Oliveira, P. S. (2020). ParKVFinder: A thread-level parallel approach in biomolecular cavity detection. In SoftwareX (Vol. 12, p. 100606). Elsevier BV. https://doi.org/10.1016/j.softx.2020.100606.
+
+*******
 Funding
-=======
+*******
 
 This work was supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) [Grant Number 2018/00629-0], Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) [Grant Number 350244/2020-0], and Brazilian Center for Research in Energy and Materials (CNPEM).
 
+*******
 License
-=======
+*******
 
 The software is licensed under the terms of the GNU General Public License version 3 (GPL3) and is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
diff --git a/docs/_sources/index.rst.txt b/docs/_sources/index.rst.txt
index 0a6c3acf..21252c9d 100644
--- a/docs/_sources/index.rst.txt
+++ b/docs/_sources/index.rst.txt
@@ -1,60 +1,35 @@
+######################################
 Welcome to pyKVFinder's documentation!
-======================================
+######################################
 
 Welcome to the **Python-C parallel KVFinder (pyKVFinder)** documentation, this page was built to help you get started with our cavity detection and characterization package.
 
-* `Installation <_installation/index.html>`_
-* `Tutorial <_tutorial/index.html>`_
-* `API reference <_api_reference/index.html>`_
-* `Command-line interface <_cli/index.html>`_
-* `GitHub repository `_
-* `About <_about/index.html>`_
+.. Headings:
+..  # with overline, for parts
+..  * with overline, for chapters
+..  = for sections
+..  - for subsections
+..  ^ for subsubsections
+..  " for paragraphs
 
 .. toctree::
    :maxdepth: 1
-   :caption: Installation
-   :hidden:
+   :caption: Python Package
 
-   _installation/index
- 
-.. toctree::
-   :maxdepth: 1
-   :caption: Tutorial
-   :hidden:
-   
-   _tutorial/index
-   
-.. toctree::
-   :maxdepth: 1
-   :caption: API Reference
-   :hidden:
-
-   _api_reference/index
+   Installation 
+   Tutorial 
+   API Reference 
+   Examples 
 
 .. toctree::
    :maxdepth: 1
-   :caption: Command-line interface
-   :hidden:
-
-   _cli/index
+   :caption: Plugins
 
-.. toctree::
-    :maxdepth: 1
-    :caption: Configuration files
-    :hidden:
-
-    vdW radii <_cfg_files/vdw_file_template>
-    Custom grid <_cfg_files/box_file_template>
-    Hydrophobicity scale <_cfg_files/hydrophobicity_scale_file_template>
-
-.. toctree::
-   :maxdepth: 1
-   :caption: Citing pyKVFinder
-   :hidden:
+   Command-line interface 
+   PyMOL pyKVFinder Tools 
 
 .. toctree::
    :maxdepth: 1
    :caption: About
-   :hidden:
 
-   _about/index
+   about/index
diff --git a/docs/_sources/_api_reference/Molecule.rst.txt b/docs/_sources/package/api_reference/Molecule.rst.txt
similarity index 100%
rename from docs/_sources/_api_reference/Molecule.rst.txt
rename to docs/_sources/package/api_reference/Molecule.rst.txt
diff --git a/docs/_sources/_cfg_files/box_file_template.rst.txt b/docs/_sources/package/api_reference/box_file_template.rst.txt
similarity index 97%
rename from docs/_sources/_cfg_files/box_file_template.rst.txt
rename to docs/_sources/package/api_reference/box_file_template.rst.txt
index c0d5d330..103467b7 100644
--- a/docs/_sources/_cfg_files/box_file_template.rst.txt
+++ b/docs/_sources/package/api_reference/box_file_template.rst.txt
@@ -1,5 +1,5 @@
 Box configuration file template
-###############################
+===============================
 
 There are three methods for defining a custom 3D grid in pyKVFinder.
 
diff --git a/docs/_sources/_api_reference/calculate_frequencies.rst.txt b/docs/_sources/package/api_reference/calculate_frequencies.rst.txt
similarity index 100%
rename from docs/_sources/_api_reference/calculate_frequencies.rst.txt
rename to docs/_sources/package/api_reference/calculate_frequencies.rst.txt
diff --git a/docs/_sources/_api_reference/constitutional.rst.txt b/docs/_sources/package/api_reference/constitutional.rst.txt
similarity index 100%
rename from docs/_sources/_api_reference/constitutional.rst.txt
rename to docs/_sources/package/api_reference/constitutional.rst.txt
diff --git a/docs/_sources/_api_reference/depth.rst.txt b/docs/_sources/package/api_reference/depth.rst.txt
similarity index 100%
rename from docs/_sources/_api_reference/depth.rst.txt
rename to docs/_sources/package/api_reference/depth.rst.txt
diff --git a/docs/_sources/_api_reference/detect.rst.txt b/docs/_sources/package/api_reference/detect.rst.txt
similarity index 100%
rename from docs/_sources/_api_reference/detect.rst.txt
rename to docs/_sources/package/api_reference/detect.rst.txt
diff --git a/docs/_sources/_api_reference/export.rst.txt b/docs/_sources/package/api_reference/export.rst.txt
similarity index 100%
rename from docs/_sources/_api_reference/export.rst.txt
rename to docs/_sources/package/api_reference/export.rst.txt
diff --git a/docs/_sources/_api_reference/export_openings.rst.txt b/docs/_sources/package/api_reference/export_openings.rst.txt
similarity index 100%
rename from docs/_sources/_api_reference/export_openings.rst.txt
rename to docs/_sources/package/api_reference/export_openings.rst.txt
diff --git a/docs/_sources/_api_reference/get_vertices.rst.txt b/docs/_sources/package/api_reference/get_vertices.rst.txt
similarity index 100%
rename from docs/_sources/_api_reference/get_vertices.rst.txt
rename to docs/_sources/package/api_reference/get_vertices.rst.txt
diff --git a/docs/_sources/_api_reference/get_vertices_from_file.rst.txt b/docs/_sources/package/api_reference/get_vertices_from_file.rst.txt
similarity index 100%
rename from docs/_sources/_api_reference/get_vertices_from_file.rst.txt
rename to docs/_sources/package/api_reference/get_vertices_from_file.rst.txt
diff --git a/docs/_sources/_api_reference/hydropathy.rst.txt b/docs/_sources/package/api_reference/hydropathy.rst.txt
similarity index 100%
rename from docs/_sources/_api_reference/hydropathy.rst.txt
rename to docs/_sources/package/api_reference/hydropathy.rst.txt
diff --git a/docs/_sources/_cfg_files/hydrophobicity_scale_file_template.rst.txt b/docs/_sources/package/api_reference/hydrophobicity_scale_file_template.rst.txt
similarity index 98%
rename from docs/_sources/_cfg_files/hydrophobicity_scale_file_template.rst.txt
rename to docs/_sources/package/api_reference/hydrophobicity_scale_file_template.rst.txt
index 76b3c36d..4c4be074 100644
--- a/docs/_sources/_cfg_files/hydrophobicity_scale_file_template.rst.txt
+++ b/docs/_sources/package/api_reference/hydrophobicity_scale_file_template.rst.txt
@@ -1,5 +1,5 @@
 Hydrophobicity scale file template
-##################################
+==================================
 
 The hydrophobicity scale file defines the name of the scale and the hydrophobicity value for each residue and when not defined, it assigns zero to the missing residues. The package contains six built-in hydrophobicity scales: `Eisenberg & Weiss `_ [1], `Hessa & Heijne `_ [2], `Kyte & Doolittle `_ [3], `Moon & Fleming `_ [4], `Radzicka & Wolfenden `_ [5], `Wimley & White `_ [6] and `Zhao & London `_ [7]. However, the user can define its own file with a mandatory format and pass it to pyKVFinder. The format is shown below:
 
diff --git a/docs/source/_build/html/_sources/_api_reference/index.rst.txt b/docs/_sources/package/api_reference/index.rst.txt
similarity index 57%
rename from docs/source/_build/html/_sources/_api_reference/index.rst.txt
rename to docs/_sources/package/api_reference/index.rst.txt
index 9d9325cd..5e390c36 100644
--- a/docs/source/_build/html/_sources/_api_reference/index.rst.txt
+++ b/docs/_sources/package/api_reference/index.rst.txt
@@ -1,8 +1,8 @@
-.. raw:: html
+*************
+API Reference
+*************
 
-    
API Reference

-
-The API of all pyKVFinder functions and classes with expected types and all parameters available.
+The API of all pyKVFinder functions, classes and configuration files with expected types and all parameters available.
 
 Functions
 =========
@@ -37,4 +37,13 @@ Classes
 
     Molecule
     pyKVFinderResults
-    
\ No newline at end of file
+
+Configuration Files
+===================
+
+.. toctree::
+    :maxdepth: 1
+
+    vdw_file_template
+    box_file_template
+    hydrophobicity_scale_file_template
diff --git a/docs/_sources/_api_reference/openings.rst.txt b/docs/_sources/package/api_reference/openings.rst.txt
similarity index 100%
rename from docs/_sources/_api_reference/openings.rst.txt
rename to docs/_sources/package/api_reference/openings.rst.txt
diff --git a/docs/_sources/_api_reference/plot_frequencies.rst.txt b/docs/_sources/package/api_reference/plot_frequencies.rst.txt
similarity index 100%
rename from docs/_sources/_api_reference/plot_frequencies.rst.txt
rename to docs/_sources/package/api_reference/plot_frequencies.rst.txt
diff --git a/docs/_sources/_api_reference/pyKVFinderResults.rst.txt b/docs/_sources/package/api_reference/pyKVFinderResults.rst.txt
similarity index 100%
rename from docs/_sources/_api_reference/pyKVFinderResults.rst.txt
rename to docs/_sources/package/api_reference/pyKVFinderResults.rst.txt
diff --git a/docs/_sources/_api_reference/read_cavity.rst.txt b/docs/_sources/package/api_reference/read_cavity.rst.txt
similarity index 100%
rename from docs/_sources/_api_reference/read_cavity.rst.txt
rename to docs/_sources/package/api_reference/read_cavity.rst.txt
diff --git a/docs/_sources/_api_reference/read_pdb.rst.txt b/docs/_sources/package/api_reference/read_pdb.rst.txt
similarity index 100%
rename from docs/_sources/_api_reference/read_pdb.rst.txt
rename to docs/_sources/package/api_reference/read_pdb.rst.txt
diff --git a/docs/_sources/_api_reference/read_vdw.rst.txt b/docs/_sources/package/api_reference/read_vdw.rst.txt
similarity index 100%
rename from docs/_sources/_api_reference/read_vdw.rst.txt
rename to docs/_sources/package/api_reference/read_vdw.rst.txt
diff --git a/docs/_sources/_api_reference/read_xyz.rst.txt b/docs/_sources/package/api_reference/read_xyz.rst.txt
similarity index 100%
rename from docs/_sources/_api_reference/read_xyz.rst.txt
rename to docs/_sources/package/api_reference/read_xyz.rst.txt
diff --git a/docs/_sources/_api_reference/run_workflow.rst.txt b/docs/_sources/package/api_reference/run_workflow.rst.txt
similarity index 100%
rename from docs/_sources/_api_reference/run_workflow.rst.txt
rename to docs/_sources/package/api_reference/run_workflow.rst.txt
diff --git a/docs/_sources/_api_reference/spatial.rst.txt b/docs/_sources/package/api_reference/spatial.rst.txt
similarity index 100%
rename from docs/_sources/_api_reference/spatial.rst.txt
rename to docs/_sources/package/api_reference/spatial.rst.txt
diff --git a/docs/source/_build/html/_sources/_cfg_files/vdw_file_template.rst.txt b/docs/_sources/package/api_reference/vdw_file_template.rst.txt
similarity index 95%
rename from docs/source/_build/html/_sources/_cfg_files/vdw_file_template.rst.txt
rename to docs/_sources/package/api_reference/vdw_file_template.rst.txt
index 84ac929f..45c7ad14 100644
--- a/docs/source/_build/html/_sources/_cfg_files/vdw_file_template.rst.txt
+++ b/docs/_sources/package/api_reference/vdw_file_template.rst.txt
@@ -1,5 +1,5 @@
 Van der Waals radii file template
-#################################
+=================================
 
 The van der Waals radii file define the radius values for each atom by residue and when not defined, it uses a generic value based on the atom type. The package contains a built-in van der Waals radii file: `vdw.dat `_. However, the user can define its own file with a mandatory format and pass it to pyKVFinder. The format is shown below:
 
diff --git a/docs/_sources/_api_reference/write_results.rst.txt b/docs/_sources/package/api_reference/write_results.rst.txt
similarity index 100%
rename from docs/_sources/_api_reference/write_results.rst.txt
rename to docs/_sources/package/api_reference/write_results.rst.txt
diff --git a/docs/_sources/package/examples/index.rst.txt b/docs/_sources/package/examples/index.rst.txt
new file mode 100644
index 00000000..a4e8d731
--- /dev/null
+++ b/docs/_sources/package/examples/index.rst.txt
@@ -0,0 +1,13 @@
+********
+Examples
+********
+
+Jupyter notebook `examples `_ are available for:
+
+.. toctree::
+  :maxdepth: 0
+
+  Conservation analysis 
+  Data visualization 
+  Molecular dynamics analysis 
+  Supramolecular cages analysis 
diff --git a/docs/_sources/package/installation/index.rst.txt b/docs/_sources/package/installation/index.rst.txt
new file mode 100644
index 00000000..94026957
--- /dev/null
+++ b/docs/_sources/package/installation/index.rst.txt
@@ -0,0 +1,20 @@
+Installation
+============
+
+To install the latest release from `PyPI `_, 
+run:
+
+.. code-block:: bash
+
+  pip install pyKVFinder
+
+Or to install the latest developmental version from source, run:
+
+.. code-block:: bash
+
+  git clone https://github.com/LBC-LNBio/pyKVFinder.git
+  pip install -e pyKVFinder
+
+.. note:: 
+
+  SWIG is required for installing pyKVFinder from source, the installation procedure differs depending on the operating system. SWIG can be installed with conda (``conda install swig``), or with a package manager on Linux (``sudo apt install swig``) and macOS (``brew install swig``).
diff --git a/docs/_sources/_tutorial/index.rst.txt b/docs/_sources/package/tutorial/index.rst.txt
similarity index 95%
rename from docs/_sources/_tutorial/index.rst.txt
rename to docs/_sources/package/tutorial/index.rst.txt
index 52efb1b1..b3d4c950 100644
--- a/docs/_sources/_tutorial/index.rst.txt
+++ b/docs/_sources/package/tutorial/index.rst.txt
@@ -1,19 +1,19 @@
-.. raw:: html
+********
+Tutorial
+********
 
-    
Tutorial

-
-This section is an introductory overview of pyKVFinder features. For detailed reference documentation of the functions and classes contained in the package, see the `API reference <../_api_reference/index.html>`_.
+This section is an introductory overview of pyKVFinder features. For detailed reference documentation of the functions and classes contained in the package, see the `API reference <../api_reference/index.html>`_.
 
 Before reading this section, you should know a bit of Python. If you would like to refresh your memory, refer to this `Python tutorial `_.
 
 First of all, import pyKVFinder package on Python:
 
 .. code-block:: python
-
+  
   >>> import pyKVFinder
 
 Cavity detection and characterization
-#####################################
+=====================================
 
 All files used on this tutorial can be found in our package and in our `GitHub repository `_:
 
@@ -25,7 +25,7 @@ In this tutorial, we will use pyKVFinder on a catalytic subunit of a cAMP-depend
 pyKVFinder can be imported as a Python package in Python environment and users can decide to run the full pyKVFinder `workflow `_ through the single pyKVFinder function or run pyKVFinder functions in a `stepwise `_ fashion.
 
 Standard workflow
-*****************
+-----------------
 
 The **standard workflow** for cavity detection with spatial and constitutional characterization (volume, area and interface residues) can be run at once with one command:
 
@@ -115,7 +115,7 @@ Inside the *pyKVFinderResults object*, cavity and surface points, number of cavi
 
 .. seealso::
 
-  * `pyKVFinder.run_workflow <../_api_reference/run_workflow>`_
+  * `pyKVFinder.run_workflow <../api_reference/run_workflow>`_
 
 With these attributes, we can write the detected cavities and the characterization to files. Further, we can set a flag to plot the bar charts of the frequencies in a PDF file. Below, we illustrate the usage:
 
@@ -129,10 +129,10 @@ With these attributes, we can write the detected cavities and the characterizati
 
 .. seealso::
 
-  * `pyKVFinder.pyKVFinderResults <../_api_reference/pyKVFinderResults.html>`_
+  * `pyKVFinder.pyKVFinderResults <../api_reference/pyKVFinderResults.html>`_
 
 Full workflow
-*************
+-------------
 
 However, users may opt to perform the **full workflow** for cavity detection with spatial (volume and area), constitutional (interface residues), hydropathy and depth characterization. This full workflow can be run with one command by setting some parameters of ``pyKVFinder.run_workflow`` function:
 
@@ -197,7 +197,7 @@ Inside the *pyKVFinderResults object*, in addition to cavity and surface points,
 
 .. seealso::
 
-  * `pyKVFinder.run_workflow <../_api_reference/run_workflow>`_
+  * `pyKVFinder.run_workflow <../api_reference/run_workflow>`_
 
 With these attributes, we can write the detected cavities with depth annotated on B-factor column (temperature factor) and hydropathy annotated on Q-factor (occupancy) column, and the characterization to files. Below, we illustrate the usage:
 
@@ -211,15 +211,15 @@ With these attributes, we can write the detected cavities with depth annotated o
 
 .. seealso::
 
-  * `pyKVFinder.pyKVFinderResults <../_api_reference/pyKVFinderResults.html>`_
+  * `pyKVFinder.pyKVFinderResults <../api_reference/pyKVFinderResults.html>`_
 
 Separated steps
-***************
+---------------
 
 If users prefer, instead of running ``pyKVFinder.run_workflow`` function, you can apply the cavity detection and characterization in a step-by-step fashion. Below we describe each step in detail.
 
 1. Loading van der Waals radii dictionary
-=========================================
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The `van der Waals radii file <../_cfg_files/vdw_file_template.html>`_ define the radius values for each residue and when not defined, it uses a generic value based on the atom type. ``pyKVFinder.read_vdw`` takes a vdW radii file (*.dat*) and returns a dictionary contaning radii values for each atom of each residue.
 
@@ -237,10 +237,10 @@ The `van der Waals radii file <../_cfg_files/vdw_file_template.html>`_ define th
 
 .. seealso::
 
-  * `pyKVFinder.read_vdw <../_api_reference/read_vdw.html>`_
+  * `pyKVFinder.read_vdw <../api_reference/read_vdw.html>`_
 
 2. Loading data from target structure
-=====================================
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 ``pyKVFinder.read_pdb`` takes a target *.pdb* file and returns a NumPy array (``atomic``) with residue number, chain identifier, residue name, atom name, xyz coordinates and radius, considering a van der Waals radii dictionary, for each atom.
 
@@ -269,11 +269,11 @@ The `van der Waals radii file <../_cfg_files/vdw_file_template.html>`_ define th
 
 .. seealso::
 
-  * `pyKVFinder.read_pdb <../_api_reference/read_pdb.html>`_
-  * `pyKVFinder.read_xyz <../_api_reference/read_xyz.html>`_
+  * `pyKVFinder.read_pdb <../api_reference/read_pdb.html>`_
+  * `pyKVFinder.read_xyz <../api_reference/read_xyz.html>`_
 
 3. Dimensioning the 3D grid
-===========================
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The pyKVFinder 3D grid must be calculated based on the target *.pdb* or *.xyz* file, the Probe Out diameter and the grid spacing. 
 
@@ -298,10 +298,10 @@ The pyKVFinder 3D grid must be calculated based on the target *.pdb* or *.xyz* f
 
 .. seealso::
 
-  * `pyKVFinder.get_vertices <../_api_reference/get_vertices.html>`_
+  * `pyKVFinder.get_vertices <../api_reference/get_vertices.html>`_
 
 4. Detecting biomolecular cavities
-==================================
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 ``pyKVFinder.detect`` takes the NumPy array with residue number, chain identifier, residue name, atom name, xyz coordinates and radius for each atom, a NumPy array with vertices and a collection of detection parameters (``step``, ``probe_in``, ``probe_out``, ``removal_distance``, ``volume_cutoff``, ``surface``), and returns a tuple with the number of detected cavities and a NumPy array with the cavity points in the 3D grid.
 
@@ -356,10 +356,10 @@ The pyKVFinder 3D grid must be calculated based on the target *.pdb* or *.xyz* f
 
 .. seealso::
 
-  * `pyKVFinder.detect <../_api_reference/detect.html>`_
+  * `pyKVFinder.detect <../api_reference/detect.html>`_
 
 4.1 Detecting biomolecular cavities with ligand adjustment
-----------------------------------------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The cavity detection can be limited around the target ligand(s), which will be passed to pyKVFinder through a *.pdb* or *.xyz* file. Thus, the detected cavities are limited within a radius (``ligand_cutoff``) of the target ligand(s).
 
@@ -432,12 +432,12 @@ Afterwards, ``parKVFinder.detect`` takes the mandatory parameters (``atomic`` an
 
 .. seealso::
 
-  * `pyKVFinder.read_pdb <../_api_reference/read_pdb.html>`_
-  * `pyKVFinder.read_xyz <../_api_reference/read_xyz.html>`_
-  * `pyKVFinder.detect <../_api_reference/detect.html>`_
+  * `pyKVFinder.read_pdb <../api_reference/read_pdb.html>`_
+  * `pyKVFinder.read_xyz <../api_reference/read_xyz.html>`_
+  * `pyKVFinder.detect <../api_reference/detect.html>`_
 
 5. Performing spatial characterization
-======================================
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 A spatial characterization, that includes volume, area and defining surface points, is performed on the detected cavities. 
 
@@ -487,10 +487,10 @@ A spatial characterization, that includes volume, area and defining surface poin
 
 .. seealso::
 
-  * `pyKVFinder.spatial <../_api_reference/spatial.html>`_  
+  * `pyKVFinder.spatial <../api_reference/spatial.html>`_
 
 6. Performing constitutional characterization
-=============================================
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 A constitutional characterization, that identifies the interface residues, is performed on the detected cavities.
 
@@ -522,10 +522,10 @@ If you wish to ignore backbones contacts (C, CA, N, O) with the cavity when defi
 
 .. seealso::
 
-  * `pyKVFinder.constitutional <../_api_reference/constitutional.html>`_  
+  * `pyKVFinder.constitutional <../api_reference/constitutional.html>`_  
 
 6.1 Calculating and plotting frequencies
-----------------------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 With the interface residues defined, you can also calculate the frequencies of residues and classes of residues. The classes of residues are:
 
@@ -561,19 +561,19 @@ Afterwards, ``pyKVFinder.plot_frequencies`` takes the dictionary with the freque
 
 .. seealso::
 
-  * `pyKVFinder.calculate_frequencies <../_api_reference/calculate_frequencies.html>`_  
-  * `pyKVFinder.plot_frequencies <../_api_reference/plot_frequencies.html>`_  
+  * `pyKVFinder.calculate_frequencies <../api_reference/calculate_frequencies.html>`_  
+  * `pyKVFinder.plot_frequencies <../api_reference/plot_frequencies.html>`_  
 
 A sample barplot of ``pyKVFinder.plot_frequencies`` is shown below.
 
-.. image:: ../_images/plot-frequencies.png
+.. image:: images/plot-frequencies.png
     :width: 600
     :align: center
 
 |
 
 7. Performing hydropathy characterization
-=========================================
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 A hydropathy characterization, that maps a target hydrophobicity scale on surface points and calculate the average hydropathy, is performed on the surface points of the detected cavities.
 
@@ -628,10 +628,10 @@ A hydropathy characterization, that maps a target hydrophobicity scale on surfac
 
 .. seealso::
 
-  * `pyKVFinder.hydropathy <../_api_reference/hydropathy.html>`_    
+  * `pyKVFinder.hydropathy <../api_reference/hydropathy.html>`_    
 
 8. Performing depth characterization
-====================================
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 A depth characterization identifies the degree of burial of the binding site. First, it identifies the cavity volume boundary. Subsequently, the depth of each cavity point is heuristically estimated by the shortest Euclidean distance between the cavity point and its respective boundary points. With this, the maximum and average depths for the detected cavities are calculated.
 
@@ -673,15 +673,15 @@ A depth characterization identifies the degree of burial of the binding site. Fi
 
 .. seealso::
 
-  * `pyKVFinder.depth <../_api_reference/depth.html>`_  
+  * `pyKVFinder.depth <../api_reference/depth.html>`_  
 
 9. Exporting cavities
-=====================
+^^^^^^^^^^^^^^^^^^^^^
 
 There are four different ways to export the detected cavities to PDB-formatted files. 
 
 9.1 Exporting only cavity points
---------------------------------
+""""""""""""""""""""""""""""""""
 
 .. code-block:: python
 
@@ -689,7 +689,7 @@ There are four different ways to export the detected cavities to PDB-formatted f
   >>> pyKVFinder.export(output_cavity, cavities, None, vertices, step=step)
 
 9.2 Exporting cavity and surface points
----------------------------------------
+"""""""""""""""""""""""""""""""""""""""
 
 .. code-block:: python
 
@@ -697,7 +697,7 @@ There are four different ways to export the detected cavities to PDB-formatted f
   >>> pyKVFinder.export(output_cavity, cavities, surface, vertices, step=step)
 
 9.3 Exporting cavity and surface points with depth mapped on B-factor
----------------------------------------------------------------------
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 .. code-block:: python
 
@@ -705,7 +705,7 @@ There are four different ways to export the detected cavities to PDB-formatted f
   >>> pyKVFinder.export(output_cavity, cavities, surface, vertices, step=step, B=depths)
 
 9.4 Exporting cavity and surface points with depth mapped on B-factor and hydrophobicity scale mapped on Q-factor
------------------------------------------------------------------------------------------------------------------
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 .. code-block:: python
 
@@ -722,15 +722,15 @@ There are four different ways to export the detected cavities to PDB-formatted f
 
 .. seealso::
 
-  * `pyKVFinder.export <../_api_reference/export.html>`_  
+  * `pyKVFinder.export <../api_reference/export.html>`_  
 
-10.  Writing results
-====================
+10.   Writing results
+^^^^^^^^^^^^^^^^^^^^^
 
 The function call depends on the characterizations performed on the detected cavities.
 
 10.1 Cavity detection only
---------------------------
+""""""""""""""""""""""""""
 
 .. code-block:: python
 
@@ -738,7 +738,7 @@ The function call depends on the characterizations performed on the detected cav
   >>> pyKVFinder.write_results(output_results, input=pdb, ligand=None, output=output_cavity, step=step)
 
 10.2 Spatial characterization
------------------------------
+"""""""""""""""""""""""""""""
 
 .. code-block:: python
 
@@ -746,7 +746,7 @@ The function call depends on the characterizations performed on the detected cav
   >>> pyKVFinder.write_results(output_results, input=pdb, ligand=None, output=output_cavity, volume=volume, area=area, step=step)
 
 10.3 Spatial and constitutional characterization
-------------------------------------------------
+""""""""""""""""""""""""""""""""""""""""""""""""
 
 .. code-block:: python
 
@@ -754,7 +754,7 @@ The function call depends on the characterizations performed on the detected cav
   >>> pyKVFinder.write_results(output_results, input=pdb, ligand=None, output=output_cavity, volume=volume, area=area, residues=residues, frequencies=frequencies, step=step)
 
 10.4 Spatial, constitutional and depth characterization
--------------------------------------------------------
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 .. code-block:: python
 
@@ -762,7 +762,7 @@ The function call depends on the characterizations performed on the detected cav
   >>> pyKVFinder.write_results(output_results, input=pdb, ligand=None, output=output_cavity, volume=volume, area=area, max_depth=max_depth, avg_depth=avg_depth, residues=residues, frequencies=frequencies, step=step)
 
 10.5 Spatial, constitutional, depth and hydropathy characterization
--------------------------------------------------------------------
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 .. code-block:: python
 
@@ -775,10 +775,10 @@ The function call depends on the characterizations performed on the detected cav
 
 .. seealso::
 
-  * `pyKVFinder.write_results <../_api_reference/write_results.html>`_ 
+  * `pyKVFinder.write_results <../api_reference/write_results.html>`_ 
 
 Steered detection
-*****************
+-----------------
 
 All these steps showed so far were performed the detection on the whole target biomolecule; however, we can perform them on a custom 3D grid, where we can explore closed regions with a custom box, which can be defined by a *.toml* file.
 
@@ -841,7 +841,7 @@ A third way is to define a custom 3D grid with `parKVFinder `_ 
+  * `pyKVFinder.run_workflow <../api_reference/run_workflow>`_ 
 
 Separated steps
-===============
+^^^^^^^^^^^^^^^
 
 If you are running pyKVFinder package in a step-by-step fashion (`Separated steps `_), the steps `3 `_ and `4 `_ are different than before.
 
@@ -916,11 +916,11 @@ Users can define the ``box`` parameter as the filepath of one box configuration
 
 .. seealso::
 
-  * `pyKVFinder.get_vertices_from_file <../_api_reference/get_vertices_from_file.html>`_
-  * `pyKVFinder.detect <../_api_reference/detect.html>`_ 
+  * `pyKVFinder.get_vertices_from_file <../api_reference/get_vertices_from_file.html>`_
+  * `pyKVFinder.detect <../api_reference/detect.html>`_ 
 
 Molecular volume
-################
+================
 
 All files used on this tutorial can be found in our package and in our `GitHub repository `_:
 
@@ -929,7 +929,7 @@ All files used on this tutorial can be found in our package and in our `GitHub r
 In this tutorial, we will use pyKVFinder on perchlorate (ClO\ :sub:`4` \) to estimate the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES) and solvent accessible surface (SAS) to represent the molecular surface (see Figure below).
 
 +-------------------------------+--------------------------------+--------------------------------+
-| .. image:: ../_images/vdw.png | .. image:: ../_images/ses.png  | .. image:: ../_images/sas.png  |
+| .. image:: images/vdw.png     | .. image:: images/ses.png      | .. image:: images/sas.png      |
 |                               |                                |                                |
 | .. centered:: (a) vdW         | .. centered:: (b) SES          | .. centered:: (c) SAS          |
 +-------------------------------+--------------------------------+--------------------------------+
@@ -948,7 +948,7 @@ First, we must load the target molecular structure (ClO\ :sub:`4` \)  into ``pyK
 With the atomic information and vdW radii dictionary loaded, the molecule is inserted into a regular 3D grid, considering the vdW radii of any of the atoms. Natively, the vdW radii are taken from the `built-in dictionary `_. In the 3D grid, each voxel corresponds to a molecule (0) or solvent (1) points. Here, we can model our molecule using the vdW surface, SES or SAS.
 
 1. vdW volume
-*************
+-------------
 
 ``Molecule.vdw()`` takes a grid spacing and returns a NumPy array with the molecule points representing the vdW surface in the 3D grid. 
 
@@ -986,7 +986,7 @@ We can preview our modelled molecule in the 3D grid by running:
   
   >>> molecule.export("vdw-model.pdb")
 
-.. image:: ../_images/vdw-grid.png
+.. image:: images/vdw-grid.png
   :width: 500
   :align: center
 
@@ -1004,7 +1004,7 @@ Now, we can estimate the vdW volume by running:
   83.64
 
 2. SES volume
-*************
+-------------
 
 ``Molecule.surface()`` takes the grid spacing, the spherical probe size to model the surface, the SES representation and returns a NumPy array with the molecule points representing the SES in the 3D grid. 
 
@@ -1046,7 +1046,7 @@ We can preview our modelled molecule in the 3D grid by running:
   
   >>> molecule.preview()
 
-.. image:: ../_images/ses-grid.png
+.. image:: images/ses-grid.png
   :width: 500
   :align: center
 
@@ -1058,7 +1058,7 @@ Now, we can estimate the vdW volume by running:
   90.8
 
 3. SAS volume
-*************
+-------------
 
 ``Molecule.surface()`` takes a grid spacing, a spherical probe to model the surface, a SAS representation and returns a NumPy array with the molecule points representing the SES in the 3D grid. 
 
@@ -1100,7 +1100,7 @@ We can preview our modelled molecule in the 3D grid by running:
   
   >>> molecule.preview()
 
-.. image:: ../_images/sas-grid.png
+.. image:: images/sas-grid.png
   :width: 500
   :align: center
 
@@ -1110,16 +1110,3 @@ Now, we can estimate the vdW volume by running:
   
   >>> molecule.volume()
   340.28
-
-Examples
-########
-
-Jupyter notebook `examples `_ are available for:
-
-.. toctree::
-  :maxdepth: 0
-
-  Conservation analysis 
-  Data visualization 
-  Molecular dynamics analysis 
-  Supramolecular cages analysis 
diff --git a/docs/_sources/_cli/index.rst.txt b/docs/_sources/plugins/cli/index.rst.txt
similarity index 69%
rename from docs/_sources/_cli/index.rst.txt
rename to docs/_sources/plugins/cli/index.rst.txt
index ac8ad7ee..45e394a2 100644
--- a/docs/_sources/_cli/index.rst.txt
+++ b/docs/_sources/plugins/cli/index.rst.txt
@@ -1,6 +1,7 @@
-.. raw:: html
 
-    
Command-line interface

+**********************
+Command-line interface
+**********************
 
 In addition to pyKVFinder package, a command-line interface (CLI) is available to ease cavity detection and characterization with the full set of customizable parameters.
 
@@ -17,7 +18,7 @@ In addition to pyKVFinder package, a command-line interface (CLI) is available t
                     (<.pdb> | <.xyz>)
 
 Positional arguments
---------------------
+====================
 
 The positional arguments are:
 
@@ -25,10 +26,10 @@ The positional arguments are:
   
   .. code-block:: bash
     
-    $ pyKVFinder <.pdb>
+    $ pyKVFinder (<.pdb> | <.xyz>)
 
 Optional arguments
-------------------
+==================
 
 The optional arguments are:
 
@@ -49,7 +50,7 @@ The optional arguments are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> --verbose
+    $ pyKVFinder (<.pdb> | <.xyz>) --verbose
 
   :Default: ``False``
 
@@ -57,17 +58,17 @@ The optional arguments are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -b 
-    $ pyKVFinder <.pdb> --base_name 
+    $ pyKVFinder (<.pdb> | <.xyz>) -b 
+    $ pyKVFinder (<.pdb> | <.xyz>) --base_name 
 
-  :Default: Prefix of target PDB file (<.pdb>)
+  :Default: Prefix of target PDB or XYZ file (<.pdb> | <.xyz>)
 
 * ``-O `` or ``--output_directory ``: A path to a directory for output files.
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -O 
-    $ pyKVFinder <.pdb> --output_directory 
+    $ pyKVFinder (<.pdb> | <.xyz>) -O 
+    $ pyKVFinder (<.pdb> | <.xyz>) --output_directory 
 
   :Default: Current working directory
 
@@ -75,12 +76,12 @@ The optional arguments are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> --nthreads 
+    $ pyKVFinder (<.pdb> | <.xyz>) --nthreads 
 
   :Default: ``os.cpu_count() - 1``
 
-Detection and characterization
-******************************
+Cavity detection
+----------------
 
 The arguments for adjusting biomolecular detection are:
 
@@ -88,8 +89,8 @@ The arguments for adjusting biomolecular detection are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -d 
-    $ pyKVFinder <.pdb> --dictionary 
+    $ pyKVFinder (<.pdb> | <.xyz>) -d 
+    $ pyKVFinder (<.pdb> | <.xyz>) --dictionary 
 
   :Default: ``vdw.dat``
 
@@ -97,8 +98,8 @@ The arguments for adjusting biomolecular detection are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -s 
-    $ pyKVFinder <.pdb> --step 
+    $ pyKVFinder (<.pdb> | <.xyz>) -s 
+    $ pyKVFinder (<.pdb> | <.xyz>) --step 
 
   :Default: ``0.6``
 
@@ -106,8 +107,8 @@ The arguments for adjusting biomolecular detection are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -i 
-    $ pyKVFinder <.pdb> --probe_in 
+    $ pyKVFinder (<.pdb> | <.xyz>) -i 
+    $ pyKVFinder (<.pdb> | <.xyz>) --probe_in 
 
   :Default: ``1.4``
 
@@ -115,8 +116,8 @@ The arguments for adjusting biomolecular detection are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -o 
-    $ pyKVFinder <.pdb> --probe_out 
+    $ pyKVFinder (<.pdb> | <.xyz>) -o 
+    $ pyKVFinder (<.pdb> | <.xyz>) --probe_out 
 
   :Default: ``4.0``
 
@@ -124,8 +125,8 @@ The arguments for adjusting biomolecular detection are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -V 
-    $ pyKVFinder <.pdb> --volume_cutoff 
+    $ pyKVFinder (<.pdb> | <.xyz>) -V 
+    $ pyKVFinder (<.pdb> | <.xyz>) --volume_cutoff 
 
   :Default: ``5.0``
 
@@ -133,8 +134,8 @@ The arguments for adjusting biomolecular detection are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -R 
-    $ pyKVFinder <.pdb> --removal_distance 
+    $ pyKVFinder (<.pdb> | <.xyz>) -R 
+    $ pyKVFinder (<.pdb> | <.xyz>) --removal_distance 
 
   :Default: ``2.4``
 
@@ -142,8 +143,8 @@ The arguments for adjusting biomolecular detection are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -S 
-    $ pyKVFinder <.pdb> --surface 
+    $ pyKVFinder (<.pdb> | <.xyz>) -S 
+    $ pyKVFinder (<.pdb> | <.xyz>) --surface 
 
   :Default: ``SES``
 
@@ -151,12 +152,12 @@ The arguments for adjusting biomolecular detection are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> --ignore_backbone
+    $ pyKVFinder (<.pdb> | <.xyz>) --ignore_backbone
 
   :Default: ``None``
 
-Extra characterization
-**********************
+Additional characterization
+---------------------------
 
 The parameters for additional characterization are:
 
@@ -164,8 +165,8 @@ The parameters for additional characterization are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -D
-    $ pyKVFinder <.pdb> --depth
+    $ pyKVFinder (<.pdb> | <.xyz>) -D
+    $ pyKVFinder (<.pdb> | <.xyz>) --depth
 
   :Default: ``None``
 
@@ -173,7 +174,7 @@ The parameters for additional characterization are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> --plot_frequencies
+    $ pyKVFinder (<.pdb> | <.xyz>) --plot_frequencies
 
   :Default: ``None``
 
@@ -181,31 +182,31 @@ The parameters for additional characterization are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> --hydropathy
+    $ pyKVFinder (<.pdb> | <.xyz>) --hydropathy
 
   In addition, the user can define one of the built-in hydrophobicity scale. The built-in hydrophobicity scales are: EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, RadzickaWolfenden, WimleyWhite and ZhaoLondon.
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> --hydropathy EisenbergWeiss
-    $ pyKVFinder <.pdb> --hydropathy HessaHeijne
-    $ pyKVFinder <.pdb> --hydropathy KyteDoolittle
-    $ pyKVFinder <.pdb> --hydropathy MoonFleming
-    $ pyKVFinder <.pdb> --hydropathy RadzickaWolfenden
-    $ pyKVFinder <.pdb> --hydropathy WimleyWhite
-    $ pyKVFinder <.pdb> --hydropathy ZhaoLondon
+    $ pyKVFinder (<.pdb> | <.xyz>) --hydropathy EisenbergWeiss
+    $ pyKVFinder (<.pdb> | <.xyz>) --hydropathy HessaHeijne
+    $ pyKVFinder (<.pdb> | <.xyz>) --hydropathy KyteDoolittle
+    $ pyKVFinder (<.pdb> | <.xyz>) --hydropathy MoonFleming
+    $ pyKVFinder (<.pdb> | <.xyz>) --hydropathy RadzickaWolfenden
+    $ pyKVFinder (<.pdb> | <.xyz>) --hydropathy WimleyWhite
+    $ pyKVFinder (<.pdb> | <.xyz>) --hydropathy ZhaoLondon
 
   Further, the user can also define a custom hydrophobicity scale file via a TOML-formatted file (see template).
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> --hydropathy <.toml>
+    $ pyKVFinder (<.pdb> | <.xyz>) --hydropathy <.toml>
 
   :Default: ``None``
   :Constant: ``EisenbergWeiss``
 
 Box adjusment
-*************
+-------------
 
 The box adjustment argument is:
 
@@ -213,13 +214,13 @@ The box adjustment argument is:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -B <.toml>
-    $ pyKVFinder <.pdb> --box <.toml>
+    $ pyKVFinder (<.pdb> | <.xyz>) -B <.toml>
+    $ pyKVFinder (<.pdb> | <.xyz>) --box <.toml>
 
   :Default: ``None``
 
 Ligand adjustment
-*****************
+-----------------
 
 The ligand adjustment arguments are:
 
@@ -227,8 +228,8 @@ The ligand adjustment arguments are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -L <.pdb>
-    $ pyKVFinder <.pdb> --ligand <.pdb>
+    $ pyKVFinder (<.pdb> | <.xyz>) -L (<.pdb> | <.xyz>)
+    $ pyKVFinder (<.pdb> | <.xyz>) --ligand (<.pdb> | <.xyz>)
 
   :Default: ``None``
 
@@ -236,6 +237,6 @@ The ligand adjustment arguments are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -L <.pdb> --ligand_cutoff 
+    $ pyKVFinder (<.pdb> | <.xyz>) -L (<.pdb> | <.xyz>) --ligand_cutoff 
 
   :Default: ``5.0``
diff --git a/docs/_sources/plugins/pymol/index.rst.txt b/docs/_sources/plugins/pymol/index.rst.txt
new file mode 100644
index 00000000..5fa6b87c
--- /dev/null
+++ b/docs/_sources/plugins/pymol/index.rst.txt
@@ -0,0 +1,237 @@
+**********************
+PyMOL pyKVFinder Tools
+**********************
+
+If you wish to use pyKVFinder with a graphical user interface on [PyMOL](https://pymol.org/), PyMOL pyKVFinder Tools is available to use with PyMOL and has been been developed using Qt interface and Python3.
+
+Installation
+============
+
+First, you need to install PyMOL v2.x or v3.x on your computer. If you do not have it installed, please refer to PyMOL `website `_.
+
+After installing PyMOL, plug-in requires the installation of `pyKVFinder `_, `toml `_, and `pyqt5 `_ modules and PyMOL's native Python does not have it installed. So you need to install it:
+
+.. code-block:: bash
+
+    pip install pyKVFinder toml pyqt5
+
+
+.. note::
+    
+    `pip `_ package management system installation is required.
+
+Then, to install the `PyMOL pyKVFinder Tools` on PyMOL, download the latest `PyMOL-pyKVFinder-Tools.zip` from `here `_ and follow these steps:
+
+1. Open PyMOL.
+2. Go to **Plugin** menu, click on **Plugin Manager**.
+3. The **Plugin Manager** window will open, go to the **Install New Plugin** tab.
+4. Under **Install from local file** panel, click on **Choose file...**.
+5. The **Install Plugin** window will open, select the `PyMOL-pyKVFinder-Tools.zip` that you downloaded earliar.
+6. The **Select plugin directory** window will open, select
+   **/home/\/.pymol/startup** and click **OK**.
+7. The **Confirm** window will open, click **OK**.
+8. The **Sucess** window will appear, confirming that the plug-in has
+   been installed.
+9. Restart PyMOL.
+10. `PyMOL pyKVFinder Tools` is ready to use.
+
+Or, instead of selecting `PyMOL-pyKVFinder-Tools.zip` (Step 5), you can select `__init__.py` file on `pyKVFinder/plugins/PyMOL-pyKVFinder-Tools` directory tree.
+
+Tutorial
+========
+
+This tutorial will guide you through the steps to use PyMOL pyKVFinder Tools. All files used in this tutorial can be found our `GitHub repository `_:
+
+* `1FMO.pdb `_
+* `ADN.pdb `_
+
+In this tutorial, we will use pyKVFinder on a catalytic subunit of a cAMP-dependent protein kinase (cADK) to identify and characterize its cavities. First, load the `1FMO.pdb` and `ADN.pdb` file into PyMOL:
+
+.. image:: images/pymol_viewer_1.png
+    :width: 800
+    :align: center
+
+Whole biomolecule detection
+---------------------------
+
+The default parameters are designed to make a simple and fast whole biomolecule detection. 
+
+On PyMOL, open PyMOL pyKVFinder Tools under Plugin tab. The objects on the scene will be listed on the **Input PDB** combo box, on the **Main** tab. If not, press the **Refresh** button.
+
+The **Input PDB** selection sets which object will be analyzed by pyKVFinder. Select **1FMO** on the list box.
+
+.. image:: images/main_tab_1.png
+    :width: 800
+    :align: center
+
+To run pyKVFinder with the default parameters, just click **Run pyKVFinder** button.
+
+.. image:: images/main_tab_2.png
+    :width: 800
+    :align: center
+
+After execution is complete, cavities PDB is loaded into PyMOL viewer as \.KVFinder.output object and the results file is loaded on the **Results** tab. In addition, the focus automatically shifts to **Results** tab.
+
+.. image:: images/results_tab_1.png
+    :width: 800
+    :align: center
+
+We can select cavities in the **Volume** or **Surface Area** lists to highlight them on a new object called **cavities**, identifying each cavity. Additionally, we can select cavity tags in the **Interface Residues** list to highlight residues around the cavities on a new object named **residues**.
+
+.. image:: images/results_tab_2.png
+    :width: 800
+
+.. note::
+    
+    The interface residues surrounding the cavity KAH are colored in green (sticks), the surface points are colored in red (nb_spheres) and the remaining cavity points are colored in blue (non_bounded).
+
+We can visualize depth of the cavity points by clicking on **Depth** option on **Show descriptors**. We can select cavities in the **Average Depth** or **Maximum Depth** lists to highlight them on a new object called **depths**, identifying each cavity. 
+
+.. image:: images/results_tab_3.png
+    :width: 800
+
+.. note::
+    
+    The cavity points are colored using a gradient from blue to red to represent the depth of each point. The blue points correspond to the shallowest points on the cavity-bulk boundary, while the red points correspond to the deepest points. The depth scale ranges from 0.0 to the maximum depth of all cavities
+
+We can visualize hydropathy of the surface points by clicking on **Hydropathy** options on **Show descriptors**. We can select cavities in the **Average Hydropathy** list to highlight them on a new object called **hydropathy**, identifying each cavity. 
+
+.. image:: images/results_tab_4.png
+    :width: 800
+
+.. note::
+
+    The surface points are colored based on the closest amino acid to it. The Eisenberg & Weiss hydrophobicity scale ranges from -1.42 (highly hydrophobic) to 2.6 (highly hydrophilic).
+
+Changing cavity boundary
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+pyKVFinder is all about parameter customization. One of pyKVFinder's most powerful assets is the ability to manually set the cavity boundary.
+
+pyKVFinder works with a double probe system to detect cavities. A smaller probe, called Probe In, and a bigger one, called Probe Out, that defines two molecular surfaces with different molecular accessibility. The space left between these surfaces is considered cavities.
+
+Let's show the effect of varying **Probe Out** and **Removal Distance** on the cavity boundary.
+
+First, we should copy the cavity KAH to a new object to compare cavity boundary from the previous execution.
+
+.. code-block:: bash
+
+    # Copy KAH
+    select resn KAH and output.KVFinder.output
+    create KAH, sele
+    delete sele
+    # Color KAH
+    color magenta, KAH
+
+Adjusting Probe Out
+"""""""""""""""""""
+
+As mentioned above, adjusting the Probe Out size changes the level of the cavity boundary. So let's go back on the **Main** tab and change the **Probe Out** size to 8.0 Å. Run pyKVFinder again.
+
+
+.. image:: images/pymol_viewer_2.png
+    :width: 800
+
+Again, copy the cavity KAF (same region of the previous detection) to a new object (KAF_PO).
+
+.. code-block:: bash
+
+    # Copy KAF
+    select resn KAF and output.KVFinder.output
+    create KAF_PO, sele
+    delete sele
+
+.. image:: images/pymol_viewer_3.png
+    :width: 800
+
+The cavity detected with the 4 Å Probe Out (magenta) has a lower boundary than that detected with the 8 Å probe (white). Therefore, by increasing the size of the Probe Out, the cavity boundary is also raised.
+
+Adjusting Removal Distance
+""""""""""""""""""""""""""
+
+Besides adjusting the Probe Out size, we can also adjust the Removal Distance to change the cavity boundary. So let's go back to the **Main** tab and change the **Removal Distance** to 1.2 Å and the size of Probe Out back to 4.0 Å. Run pyKVFinder again.
+
+.. image:: images/pymol_viewer_4.png
+    :width: 800
+
+Again, copy the cavity KAG (same region of the previous detections) to a new object (KAG_RD).
+
+.. code-block:: bash
+
+    # Copy KAG
+    select resn KAG and output.KVFinder.output
+    create KAG_RD, sele
+    delete sele
+
+.. image:: images/pymol_viewer_5.png
+    :width: 800
+
+|
+  
+The cavity KAH detected with the 2.4 Å Removal Distance (magenta) has a lower boundary than that detected with the 1.2 Å (KAG; white). Therefore, by decreasing the Removal Distance, the cavity boundary is also raised.
+
+Furthermore, changing the cavity boundary by varying Probe Out and Removal Distance also affects cavity segregation.
+
+.. note::
+
+    Usually the Removal Distance adjustment is less time-consuming than the Probe Out adjustment for similar effects.
+
+Steered detection
+-----------------
+
+An important feature of parKVFinder is the steered detection of cavities. We continue our tutorial illustrating two distinct methods of cavity segmentation.
+
+Box adjustment mode 
+^^^^^^^^^^^^^^^^^^^
+
+Box adjustment mode explores closed regions with a custom box, which can be drawn via the GUI.
+
+On the **Search Space** tab, select **Box Adjustment** check box. This will enable a **Box Adjustment** frame, which handles the custom box in PyMOL viewer
+
+.. image:: images/search_space_tab_1.png
+    :width: 800
+
+Then, select the adenosine ligand on ADN object. This can be made on the PyMOL viewer by clicking on the ligand structure or using ``select resn ADN`` PyMOL command.
+
+Click on **Draw Box** Button. This will create a custom box that limits the search space. It is fully customizable, but we will not change it for now.
+
+.. image:: images/pymol_viewer_6.png
+    :width: 800
+
+On the **Main** tab, change **Removal Distance** back to 2.4 Å. Run pyKVFinder again.
+
+.. image:: images/pymol_viewer_7.png
+    :width: 800
+
+Now, let's customize the box parameters to segment the binding site of our target protein.
+
+Each axis is associated with one color (red with X, green with Y and blue with Z). The adjustment is made by the arrows or directly setting the value in the entry on the **Search Space** tab in the **Box Adjustment** group. We can also adjust the box angles by the same procedure. After altering the values, just click on **Redraw** button to redraw the box object using the new values.
+
+Then, on the **Search Space** tab, reduce **Maximum X** to 1.0 Å and click **Redraw Box**. Run pyKVFinder again.
+
+.. image:: images/pymol_viewer_8.png
+    :width: 800
+
+Lastly, click on **Delete Box** button to delete the custom box.
+
+Ligand adjustment mode
+^^^^^^^^^^^^^^^^^^^^^^
+
+A last feature is to limit the search around a structure. In this last example, let's do a whole protein prospection again, but limiting the search space around ligands.
+
+First, on the **Search Space** tab, deselect **Box Adjustment** check box, which will disable the previous enabled **Box Adjustment** frame.
+
+Still on the **Search Space** tab, click on the check button **Ligand Adjustment**, which will enable the **Refresh** button, the **Ligand PDB** combo box and the **Ligand Cutoff** entry.
+
+.. image:: images/search_space_tab_2.png
+    :width: 800
+
+Click the **Refresh** button to display all objects in the scene in the Ligand PDB combo box. Select the **ADN** on the combo box and reduce Ligand Cutoff to 3.0 Å. Run pyKVFinder again.
+
+.. image:: images/pymol_viewer_9.png
+    :width: 800
+
+On the **Search Space** tab, increase **Ligand Cutoff** back to 5.0 Å. Back on the **Main** tab, increase **Probe Out** to 10.0 Å and reduce **Removal Distance** to 0.0 Å. Run pyKVFinder again.
+
+.. image:: images/pymol_viewer_10.png
+    :width: 800
diff --git a/docs/_static/basic.css b/docs/_static/basic.css
index 30fee9d0..f316efcb 100644
--- a/docs/_static/basic.css
+++ b/docs/_static/basic.css
@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
diff --git a/docs/_static/doctools.js b/docs/_static/doctools.js
index d06a71d7..4d67807d 100644
--- a/docs/_static/doctools.js
+++ b/docs/_static/doctools.js
@@ -4,7 +4,7 @@
  *
  * Base JavaScript utilities for all Sphinx HTML documentation.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
diff --git a/docs/_static/documentation_options.js b/docs/_static/documentation_options.js
index 63f3b821..3c89f433 100644
--- a/docs/_static/documentation_options.js
+++ b/docs/_static/documentation_options.js
@@ -1,5 +1,5 @@
 const DOCUMENTATION_OPTIONS = {
-    VERSION: '0.6.14',
+    VERSION: '0.7.0',
     LANGUAGE: 'en',
     COLLAPSE_INDEX: false,
     BUILDER: 'html',
diff --git a/docs/_static/language_data.js b/docs/_static/language_data.js
index 250f5665..367b8ed8 100644
--- a/docs/_static/language_data.js
+++ b/docs/_static/language_data.js
@@ -5,7 +5,7 @@
  * This script contains the language-specific data used by searchtools.js,
  * namely the list of stopwords, stemmer, scorer and splitter.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -13,7 +13,7 @@
 var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
 
 
-/* Non-minified version is copied as a separate JS file, is available */
+/* Non-minified version is copied as a separate JS file, if available */
 
 /**
  * Porter Stemmer
diff --git a/docs/_static/searchtools.js b/docs/_static/searchtools.js
index 09d64585..b08d58c9 100644
--- a/docs/_static/searchtools.js
+++ b/docs/_static/searchtools.js
@@ -4,7 +4,7 @@
  *
  * Sphinx JavaScript utilities for the full-text search.
  *
- * :copyright: Copyright 2007-2023 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -62,8 +62,7 @@ const _displayItem = (item, searchTerms, highlightTerms) => {
   const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
   const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
   const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
-  const contentRoot = document.documentElement.dataset.content_root
-    ?? DOCUMENTATION_OPTIONS.URL_ROOT;
+  const contentRoot = document.documentElement.dataset.content_root;
 
   const [docName, title, anchor, descr, score, _filename] = item;
 
@@ -100,7 +99,7 @@ const _displayItem = (item, searchTerms, highlightTerms) => {
       .then((data) => {
         if (data)
           listItem.appendChild(
-            Search.makeSearchSummary(data, searchTerms)
+            Search.makeSearchSummary(data, searchTerms, anchor)
           );
         // highlight search terms in the summary
         if (SPHINX_HIGHLIGHT_ENABLED)  // set in sphinx_highlight.js
@@ -117,8 +116,8 @@ const _finishSearch = (resultCount) => {
     );
   else
     Search.status.innerText = _(
-      `Search finished, found ${resultCount} page(s) matching the search query.`
-    );
+      "Search finished, found ${resultCount} page(s) matching the search query."
+    ).replace('${resultCount}', resultCount);
 };
 const _displayNextItem = (
   results,
@@ -138,6 +137,22 @@ const _displayNextItem = (
   // search finished, update title and status message
   else _finishSearch(resultCount);
 };
+// Helper function used by query() to order search results.
+// Each input is an array of [docname, title, anchor, descr, score, filename].
+// Order the results by score (in opposite order of appearance, since the
+// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically.
+const _orderResultsByScoreThenName = (a, b) => {
+  const leftScore = a[4];
+  const rightScore = b[4];
+  if (leftScore === rightScore) {
+    // same score: sort alphabetically
+    const leftTitle = a[1].toLowerCase();
+    const rightTitle = b[1].toLowerCase();
+    if (leftTitle === rightTitle) return 0;
+    return leftTitle > rightTitle ? -1 : 1; // inverted is intentional
+  }
+  return leftScore > rightScore ? 1 : -1;
+};
 
 /**
  * Default splitQuery function. Can be overridden in ``sphinx.search`` with a
@@ -161,13 +176,26 @@ const Search = {
   _queued_query: null,
   _pulse_status: -1,
 
-  htmlToText: (htmlString) => {
+  htmlToText: (htmlString, anchor) => {
     const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html');
-    htmlElement.querySelectorAll(".headerlink").forEach((el) => { el.remove() });
+    for (const removalQuery of [".headerlink", "script", "style"]) {
+      htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() });
+    }
+    if (anchor) {
+      const anchorContent = htmlElement.querySelector(`[role="main"] ${anchor}`);
+      if (anchorContent) return anchorContent.textContent;
+
+      console.warn(
+        `Anchored content block not found. Sphinx search tries to obtain it via DOM query '[role=main] ${anchor}'. Check your theme or template.`
+      );
+    }
+
+    // if anchor not specified or not found, fall back to main content
     const docContent = htmlElement.querySelector('[role="main"]');
-    if (docContent !== undefined) return docContent.textContent;
+    if (docContent) return docContent.textContent;
+
     console.warn(
-      "Content block not found. Sphinx search tries to obtain it via '[role=main]'. Could you check your theme or template."
+      "Content block not found. Sphinx search tries to obtain it via DOM query '[role=main]'. Check your theme or template."
     );
     return "";
   },
@@ -240,16 +268,7 @@ const Search = {
     else Search.deferQuery(query);
   },
 
-  /**
-   * execute search (requires search index to be loaded)
-   */
-  query: (query) => {
-    const filenames = Search._index.filenames;
-    const docNames = Search._index.docnames;
-    const titles = Search._index.titles;
-    const allTitles = Search._index.alltitles;
-    const indexEntries = Search._index.indexentries;
-
+  _parseQuery: (query) => {
     // stem the search terms and add them to the correct list
     const stemmer = new Stemmer();
     const searchTerms = new Set();
@@ -285,21 +304,38 @@ const Search = {
     // console.info("required: ", [...searchTerms]);
     // console.info("excluded: ", [...excludedTerms]);
 
-    // array of [docname, title, anchor, descr, score, filename]
-    let results = [];
+    return [query, searchTerms, excludedTerms, highlightTerms, objectTerms];
+  },
+
+  /**
+   * execute search (requires search index to be loaded)
+   */
+  _performSearch: (query, searchTerms, excludedTerms, highlightTerms, objectTerms) => {
+    const filenames = Search._index.filenames;
+    const docNames = Search._index.docnames;
+    const titles = Search._index.titles;
+    const allTitles = Search._index.alltitles;
+    const indexEntries = Search._index.indexentries;
+
+    // Collect multiple result groups to be sorted separately and then ordered.
+    // Each is an array of [docname, title, anchor, descr, score, filename].
+    const normalResults = [];
+    const nonMainIndexResults = [];
+
     _removeChildren(document.getElementById("search-progress"));
 
-    const queryLower = query.toLowerCase();
+    const queryLower = query.toLowerCase().trim();
     for (const [title, foundTitles] of Object.entries(allTitles)) {
-      if (title.toLowerCase().includes(queryLower) && (queryLower.length >= title.length/2)) {
+      if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) {
         for (const [file, id] of foundTitles) {
-          let score = Math.round(100 * queryLower.length / title.length)
-          results.push([
+          const score = Math.round(Scorer.title * queryLower.length / title.length);
+          const boost = titles[file] === title ? 1 : 0;  // add a boost for document titles
+          normalResults.push([
             docNames[file],
             titles[file] !== title ? `${titles[file]} > ${title}` : title,
             id !== null ? "#" + id : "",
             null,
-            score,
+            score + boost,
             filenames[file],
           ]);
         }
@@ -309,46 +345,47 @@ const Search = {
     // search for explicit entries in index directives
     for (const [entry, foundEntries] of Object.entries(indexEntries)) {
       if (entry.includes(queryLower) && (queryLower.length >= entry.length/2)) {
-        for (const [file, id] of foundEntries) {
-          let score = Math.round(100 * queryLower.length / entry.length)
-          results.push([
+        for (const [file, id, isMain] of foundEntries) {
+          const score = Math.round(100 * queryLower.length / entry.length);
+          const result = [
             docNames[file],
             titles[file],
             id ? "#" + id : "",
             null,
             score,
             filenames[file],
-          ]);
+          ];
+          if (isMain) {
+            normalResults.push(result);
+          } else {
+            nonMainIndexResults.push(result);
+          }
         }
       }
     }
 
     // lookup as object
     objectTerms.forEach((term) =>
-      results.push(...Search.performObjectSearch(term, objectTerms))
+      normalResults.push(...Search.performObjectSearch(term, objectTerms))
     );
 
     // lookup as search terms in fulltext
-    results.push(...Search.performTermsSearch(searchTerms, excludedTerms));
+    normalResults.push(...Search.performTermsSearch(searchTerms, excludedTerms));
 
     // let the scorer override scores with a custom scoring function
-    if (Scorer.score) results.forEach((item) => (item[4] = Scorer.score(item)));
-
-    // now sort the results by score (in opposite order of appearance, since the
-    // display function below uses pop() to retrieve items) and then
-    // alphabetically
-    results.sort((a, b) => {
-      const leftScore = a[4];
-      const rightScore = b[4];
-      if (leftScore === rightScore) {
-        // same score: sort alphabetically
-        const leftTitle = a[1].toLowerCase();
-        const rightTitle = b[1].toLowerCase();
-        if (leftTitle === rightTitle) return 0;
-        return leftTitle > rightTitle ? -1 : 1; // inverted is intentional
-      }
-      return leftScore > rightScore ? 1 : -1;
-    });
+    if (Scorer.score) {
+      normalResults.forEach((item) => (item[4] = Scorer.score(item)));
+      nonMainIndexResults.forEach((item) => (item[4] = Scorer.score(item)));
+    }
+
+    // Sort each group of results by score and then alphabetically by name.
+    normalResults.sort(_orderResultsByScoreThenName);
+    nonMainIndexResults.sort(_orderResultsByScoreThenName);
+
+    // Combine the result groups in (reverse) order.
+    // Non-main index entries are typically arbitrary cross-references,
+    // so display them after other results.
+    let results = [...nonMainIndexResults, ...normalResults];
 
     // remove duplicate search results
     // note the reversing of results, so that in the case of duplicates, the highest-scoring entry is kept
@@ -362,7 +399,12 @@ const Search = {
       return acc;
     }, []);
 
-    results = results.reverse();
+    return results.reverse();
+  },
+
+  query: (query) => {
+    const [searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms] = Search._parseQuery(query);
+    const results = Search._performSearch(searchQuery, searchTerms, excludedTerms, highlightTerms, objectTerms);
 
     // for debugging
     //Search.lastresults = results.slice();  // a copy
@@ -435,14 +477,11 @@ const Search = {
         filenames[match[0]],
       ]);
     };
-    Object.keys(objects).forEach((prefix) => {
-      if (!(objects[prefix] instanceof Array)) {
-        objects[prefix] = Object.entries(objects[prefix]).map(([name, match]) => [...match, name]);
-      }
+    Object.keys(objects).forEach((prefix) =>
       objects[prefix].forEach((array) =>
         objectSearchCallback(prefix, array)
-      );
-    });
+      )
+    );
     return results;
   },
 
@@ -470,14 +509,18 @@ const Search = {
       // add support for partial matches
       if (word.length > 2) {
         const escapedWord = _escapeRegExp(word);
-        Object.keys(terms).forEach((term) => {
-          if (term.match(escapedWord) && !terms[word])
-            arr.push({ files: terms[term], score: Scorer.partialTerm });
-        });
-        Object.keys(titleTerms).forEach((term) => {
-          if (term.match(escapedWord) && !titleTerms[word])
-            arr.push({ files: titleTerms[word], score: Scorer.partialTitle });
-        });
+        if (!terms.hasOwnProperty(word)) {
+          Object.keys(terms).forEach((term) => {
+            if (term.match(escapedWord))
+              arr.push({ files: terms[term], score: Scorer.partialTerm });
+          });
+        }
+        if (!titleTerms.hasOwnProperty(word)) {
+          Object.keys(titleTerms).forEach((term) => {
+            if (term.match(escapedWord))
+              arr.push({ files: titleTerms[term], score: Scorer.partialTitle });
+          });
+        }
       }
 
       // no match but word was a required one
@@ -500,9 +543,8 @@ const Search = {
 
       // create the mapping
       files.forEach((file) => {
-        if (fileMap.has(file) && fileMap.get(file).indexOf(word) === -1)
-          fileMap.get(file).push(word);
-        else fileMap.set(file, [word]);
+        if (!fileMap.has(file)) fileMap.set(file, [word]);
+        else if (fileMap.get(file).indexOf(word) === -1) fileMap.get(file).push(word);
       });
     });
 
@@ -553,8 +595,8 @@ const Search = {
    * search summary for a given text. keywords is a list
    * of stemmed words.
    */
-  makeSearchSummary: (htmlText, keywords) => {
-    const text = Search.htmlToText(htmlText);
+  makeSearchSummary: (htmlText, keywords, anchor) => {
+    const text = Search.htmlToText(htmlText, anchor);
     if (text === "") return null;
 
     const textLower = text.toLowerCase();
diff --git a/docs/_about/index.html b/docs/about/index.html
similarity index 68%
rename from docs/_about/index.html
rename to docs/about/index.html
index 28f7d9bb..3b057ce5 100644
--- a/docs/_about/index.html
+++ b/docs/about/index.html
@@ -4,7 +4,7 @@
   
 
   
-  Issues — pyKVFinder 0.6.14 documentation
+  Issues — pyKVFinder 0.7.0 documentation
       
       
 
@@ -16,13 +16,13 @@
   
         
         
-        
-        
+        
+        
         
     
     
     
-     
+     
 
 
  
@@ -38,7 +38,7 @@
               
           
               

-                0.6
+                0.7
               

 

   

@@ -48,38 +48,25 @@
   

 

         

@@ -131,40 +116,40 @@ 
Index

 
_

 
@@ -173,15 +158,15 @@ 
_
A

   
   
 
 

   
   
 

@@ -189,13 +174,13 @@ 
A

 
C

 

   
   
 

@@ -203,15 +188,15 @@ 
C

 
D

 

   
   
 

@@ -219,19 +204,19 @@ 
D

 
E

 

   
   
 

@@ -239,7 +224,7 @@ 
E

 
F

 

   
 

@@ -247,13 +232,13 @@ 
F

 
G

 

   
   
 

@@ -261,7 +246,7 @@ 
G

 
H

 

   
 

@@ -269,13 +254,13 @@ 
H

 
M

 

   
   
 

@@ -283,17 +268,17 @@ 
M

 
N

 

   
   
 

@@ -301,7 +286,7 @@ 
N

 
O

 

   
 

@@ -309,29 +294,29 @@ 
O

 
P

 

   
   
 

@@ -339,25 +324,25 @@ 
P

 
R

 

   
   
 

@@ -365,17 +350,17 @@ 
R

 
S

 

   
   
 

@@ -383,17 +368,17 @@ 
S

 
V

 

   
   
 

@@ -401,11 +386,11 @@ 
V

 
W

 

   
   
 

@@ -413,7 +398,7 @@ 
W

 
X

 

   
 

diff --git a/docs/index.html b/docs/index.html
index d6b2bbd8..d5bf9850 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -4,7 +4,7 @@
   
 
   
-  Welcome to pyKVFinder’s documentation! — pyKVFinder 0.6.14 documentation
+  Welcome to pyKVFinder’s documentation! — pyKVFinder 0.7.0 documentation
       
       
 
@@ -16,13 +16,13 @@
   
         
         
-        
-        
+        
+        
         
     
     
     
-     
+     
 
 
  
@@ -38,7 +38,7 @@
               
           
               

-                0.6
+                0.7
               

 

   

@@ -48,40 +48,25 @@
   

 

         

@@ -111,27 +96,31 @@
   

 
Welcome to pyKVFinder’s documentation!

 
Welcome to the Python-C parallel KVFinder (pyKVFinder) documentation, this page was built to help you get started with our cavity detection and characterization package.

-
-

-

-

-

-

-

-

-

 

+
Python Package

+
 

 

+
Plugins

+
 

 

+
About

+
 

 

 
@@ -139,7 +128,7 @@ 
Welcome to pyKVFinder’s documentation!
-        
+        
     

 
   

diff --git a/docs/objects.inv b/docs/objects.inv
index ebf6debf..41e6e2e1 100644
Binary files a/docs/objects.inv and b/docs/objects.inv differ
diff --git a/docs/_api_reference/Molecule.html b/docs/package/api_reference/Molecule.html
similarity index 79%
rename from docs/_api_reference/Molecule.html
rename to docs/package/api_reference/Molecule.html
index 0348a588..7de8490a 100644
--- a/docs/_api_reference/Molecule.html
+++ b/docs/package/api_reference/Molecule.html
@@ -1,27 +1,27 @@
 
-
+
 
   
 
   
-  pyKVFinder.Molecule — pyKVFinder 0.6.14 documentation
-      
-      
+  pyKVFinder.Molecule — pyKVFinder 0.7.0 documentation
+      
+      
 
   
-    
+    
   
   
-        
-        
-        
-        
-        
-    
-    
-    
+        
+        
+        
+        
+        
+    
+    
+    
     
      
 
@@ -34,101 +34,52 @@
 
           
           
-          
+          
             pyKVFinder
-              
+              
           
               

-                0.6
+                0.7
               

 

-  

+  
     
     
     
   

 

         

@@ -137,18 +88,18 @@
 
     

 
       

         

           

   
   

@@ -160,7 +111,7 @@
 
pyKVFinder.Molecule

 

 

-class pyKVFinder.Molecule(molecule: str | Path, radii: str | Path | Dict[str, Any] = None, model: int | None = None, nthreads: int | None = None, verbose: bool = False)[source]

+class pyKVFinder.Molecule(molecule: str | Path, radii: str | Path | Dict[str, Any] | None = None, model: int | None = None, nthreads: int | None = None, verbose: bool = False)[source]
 
A class for representing molecular structures.

 

 
Parameters:

@@ -381,7 +332,7 @@ 
pyKVFinder.Molecule
 

-export(fn: str | Path = 'molecule.pdb') → None[source]

+export(fn: str | Path = 'molecule.pdb') → None[source]
 
Export molecule points (H) to a PDB-formatted file.

 

 
Parameters:

@@ -460,7 +411,7 @@ 
pyKVFinder.Molecule
 

-preview(**kwargs) → None[source]

+preview(**kwargs) → None[source]
 
Preview the molecular surface in the 3D grid.

 
Example

 
With the molecular surface modelled by Molecule.vdw() or Molecule.surface(), the modelled molecule in the 3D grid can be previewed by running:

@@ -501,7 +452,7 @@ 
pyKVFinder.Molecule
 

-surface(step: float = 0.6, probe: float = 1.4, surface: str = 'SES', padding: float | None = None) → None[source]

+surface(step: float = 0.6, probe: float = 1.4, surface: str = 'SES', padding: float | None = None) → None[source]
 
Fill the 3D grid with the molecule as the van der Waals surface representation.

 

 
Parameters:

@@ -589,7 +540,7 @@ 
pyKVFinder.Molecule
 

-vdw(step: float = 0.6, padding: float | None = None) → None[source]

+vdw(step: float = 0.6, padding: float | None = None) → None[source]
 
Fill the 3D grid with the molecule as the van der Waals surface representation.

 

 
Parameters:

@@ -638,7 +589,7 @@ 
pyKVFinder.Molecule
 

-volume() → float[source]

+volume() → float[source]
 
Estimate the volume of the molecule based on the molecular surface representation, ie, vdW, SES or SAS representations.

 

 
Returns:

diff --git a/docs/_cfg_files/box_file_template.html b/docs/package/api_reference/box_file_template.html
similarity index 68%
rename from docs/_cfg_files/box_file_template.html
rename to docs/package/api_reference/box_file_template.html
index 221b838e..8f0fe179 100644
--- a/docs/_cfg_files/box_file_template.html
+++ b/docs/package/api_reference/box_file_template.html
@@ -1,27 +1,27 @@
 
-
+
 
   
 
   
-  Box configuration file template — pyKVFinder 0.6.14 documentation
-      
-      
+  Box configuration file template — pyKVFinder 0.7.0 documentation
+      
+      
 
   
-    
+    
   
   
-        
-        
-        
-        
-        
-    
-    
-    
+        
+        
+        
+        
+        
+    
+    
+    
     
      
 
@@ -34,55 +34,50 @@
 
           
           
-          
+          
             pyKVFinder
-              
+              
           
               

-                0.6
+                0.7
               

 

-  

+  
     
     
     
   

 

         

@@ -91,17 +86,18 @@
 
     

 
       

         

           

   
   

diff --git a/docs/_api_reference/calculate_frequencies.html b/docs/package/api_reference/calculate_frequencies.html
similarity index 71%
rename from docs/_api_reference/calculate_frequencies.html
rename to docs/package/api_reference/calculate_frequencies.html
index 636e3894..afdd4401 100644
--- a/docs/_api_reference/calculate_frequencies.html
+++ b/docs/package/api_reference/calculate_frequencies.html
@@ -1,27 +1,27 @@
 
-
+
 
   
 
   
-  pyKVFinder.calculate_frequencies — pyKVFinder 0.6.14 documentation
-      
-      
+  pyKVFinder.calculate_frequencies — pyKVFinder 0.7.0 documentation
+      
+      
 
   
-    
+    
   
   
-        
-        
-        
-        
-        
-    
-    
-    
+        
+        
+        
+        
+        
+    
+    
+    
     
      
 
@@ -34,78 +34,68 @@
 
           
           
-          
+          
             pyKVFinder
-              
+              
           
               

-                0.6
+                0.7
               

 

-  

+  
     
     
     
   

 

         

@@ -114,18 +104,18 @@
 
     

 
       

         

           

   
   

@@ -137,7 +127,7 @@
 
pyKVFinder.calculate_frequencies

 

 

-pyKVFinder.calculate_frequencies(residues: Dict[str, List[List[str]]]) → Dict[str, Dict[str, Dict[str, int]]][source]

+pyKVFinder.calculate_frequencies(residues: Dict[str, List[List[str]]]) → Dict[str, Dict[str, Dict[str, int]]][source]
 
Calculate frequencies of residues and class of residues
 (R1, R2, R3, R4 and R5) for detected cavities.

 

diff --git a/docs/_api_reference/constitutional.html b/docs/package/api_reference/constitutional.html
similarity index 88%
rename from docs/_api_reference/constitutional.html
rename to docs/package/api_reference/constitutional.html
index 01d310fe..db76033d 100644
--- a/docs/_api_reference/constitutional.html
+++ b/docs/package/api_reference/constitutional.html
@@ -1,27 +1,27 @@
 
-
+
 
   
 
   
-  pyKVFinder.constitutional — pyKVFinder 0.6.14 documentation
-      
-      
+  pyKVFinder.constitutional — pyKVFinder 0.7.0 documentation
+      
+      
 
   
-    
+    
   
   
-        
-        
-        
-        
-        
-    
-    
-    
+        
+        
+        
+        
+        
+    
+    
+    
     
      
 
@@ -34,78 +34,68 @@
 
           
           
-          
+          
             pyKVFinder
-              
+              
           
               

-                0.6
+                0.7
               

 

-  

+  
     
     
     
   

 

         

@@ -114,18 +104,18 @@
 
     

 
       

         

           

   
   

@@ -137,7 +127,7 @@
 
pyKVFinder.constitutional

 

 

-pyKVFinder.constitutional(cavities: ndarray, atomic: ndarray | List[List[str | float | int]], vertices: ndarray | List[List[float]], step: float | int = 0.6, probe_in: float | int = 1.4, ignore_backbone: bool = False, selection: List[int] | List[str] | None = None, nthreads: int | None = None, verbose: bool = False) → Dict[str, List[List[str]]][source]

+pyKVFinder.constitutional(cavities: ndarray, atomic: ndarray | List[List[str | float | int]], vertices: ndarray | List[List[float]], step: float | int = 0.6, probe_in: float | int = 1.4, ignore_backbone: bool = False, selection: List[int] | List[str] | None = None, nthreads: int | None = None, verbose: bool = False) → Dict[str, List[List[str]]][source]
 
Constitutional characterization (interface residues) of the detected
 cavities.

 

diff --git a/docs/_api_reference/depth.html b/docs/package/api_reference/depth.html
similarity index 78%
rename from docs/_api_reference/depth.html
rename to docs/package/api_reference/depth.html
index 34dffa8f..41321190 100644
--- a/docs/_api_reference/depth.html
+++ b/docs/package/api_reference/depth.html
@@ -1,27 +1,27 @@
 
-
+
 
   
 
   
-  pyKVFinder.depth — pyKVFinder 0.6.14 documentation
-      
-      
+  pyKVFinder.depth — pyKVFinder 0.7.0 documentation
+      
+      
 
   
-    
+    
   
   
-        
-        
-        
-        
-        
-    
-    
-    
+        
+        
+        
+        
+        
+    
+    
+    
     
      
 
@@ -34,78 +34,68 @@
 
           
           
-          
+          
             pyKVFinder
-              
+              
           
               

-                0.6
+                0.7
               

 

-  

+  
     
     
     
   

 

         

@@ -114,18 +104,18 @@
 
     

 
       

         

           

   
   

@@ -137,7 +127,7 @@
 
pyKVFinder.depth

 

 

-pyKVFinder.depth(cavities: ndarray, step: float | int = 0.6, selection: List[int] | List[str] | None = None, nthreads: int | None = None, verbose: bool = False) → Tuple[ndarray, Dict[str, float], Dict[str, float]][source]

+pyKVFinder.depth(cavities: ndarray, step: float | int = 0.6, selection: List[int] | List[str] | None = None, nthreads: int | None = None, verbose: bool = False) → Tuple[ndarray, Dict[str, float], Dict[str, float]][source]
 
Characterization of the depth of the detected cavities, including depth
 per cavity point and maximum and average depths of detected cavities.

 

diff --git a/docs/_api_reference/detect.html b/docs/package/api_reference/detect.html
similarity index 88%
rename from docs/_api_reference/detect.html
rename to docs/package/api_reference/detect.html
index 374badc0..876ebf73 100644
--- a/docs/_api_reference/detect.html
+++ b/docs/package/api_reference/detect.html
@@ -1,27 +1,27 @@
 
-
+
 
   
 
   
-  pyKVFinder.detect — pyKVFinder 0.6.14 documentation
-      
-      
+  pyKVFinder.detect — pyKVFinder 0.7.0 documentation
+      
+      
 
   
-    
+    
   
   
-        
-        
-        
-        
-        
-    
-    
-    
+        
+        
+        
+        
+        
+    
+    
+    
     
      
 
@@ -34,78 +34,68 @@
 
           
           
-          
+          
             pyKVFinder
-              
+              
           
               

-                0.6
+                0.7
               

 

-  

+  
     
     
     
   

 

         

@@ -114,18 +104,18 @@
 
     

 
       

         

           

   
   

@@ -137,7 +127,7 @@
 
pyKVFinder.detect

 

 

-pyKVFinder.detect(atomic: ndarray | List[List[str | float | int]], vertices: ndarray | List[List[float]], step: float | int = 0.6, probe_in: float | int = 1.4, probe_out: float | int = 4.0, removal_distance: float | int = 2.4, volume_cutoff: float | int = 5.0, latomic: ndarray | List[List[float]] | None = None, ligand_cutoff: float | int = 5.0, box_adjustment: bool = False, surface: str = 'SES', nthreads: int | None = None, verbose: bool = False) → Tuple[int, ndarray][source]

+pyKVFinder.detect(atomic: ndarray | List[List[str | float | int]], vertices: ndarray | List[List[float]], step: float | int = 0.6, probe_in: float | int = 1.4, probe_out: float | int = 4.0, removal_distance: float | int = 2.4, volume_cutoff: float | int = 5.0, latomic: ndarray | List[List[float]] | None = None, ligand_cutoff: float | int = 5.0, box_adjustment: bool = False, surface: str = 'SES', nthreads: int | None = None, verbose: bool = False) → Tuple[int, ndarray][source]
 
Detects biomolecular cavities.

 
Cavity points that belongs to the same cavity are assigned with an integer
 in the grid.

diff --git a/docs/_api_reference/export.html b/docs/package/api_reference/export.html
similarity index 84%
rename from docs/_api_reference/export.html
rename to docs/package/api_reference/export.html
index 5c24b464..b7fac88b 100644
--- a/docs/_api_reference/export.html
+++ b/docs/package/api_reference/export.html
@@ -1,27 +1,27 @@
 
-
+
 
   
 
   
-  pyKVFinder.export — pyKVFinder 0.6.14 documentation
-      
-      
+  pyKVFinder.export — pyKVFinder 0.7.0 documentation
+      
+      
 
   
-    
+    
   
   
-        
-        
-        
-        
-        
-    
-    
-    
+        
+        
+        
+        
+        
+    
+    
+    
     
      
 
@@ -34,78 +34,68 @@
 
           
           
-          
+          
             pyKVFinder
-              
+              
           
               

-                0.6
+                0.7
               

 

-  

+  
     
     
     
   

 

         

@@ -114,18 +104,18 @@
 
     

 
       

         

           

   
   

@@ -137,7 +127,7 @@
 
pyKVFinder.export

 

 

-pyKVFinder.export(fn: str | Path | None, cavities: ndarray, surface: ndarray | None, vertices: ndarray | List[List[float]], step: float | int = 0.6, B: ndarray | None = None, Q: ndarray | None = None, selection: List[int] | List[str] | None = None, nthreads: int | None = None, append: bool = False, model: int = 0) → str | None[source]

+pyKVFinder.export(fn: str | Path | None, cavities: ndarray, surface: ndarray | None, vertices: ndarray | List[List[float]], step: float | int = 0.6, B: ndarray | None = None, Q: ndarray | None = None, selection: List[int] | List[str] | None = None, nthreads: int | None = None, append: bool = False, model: int = 0) → str | None[source]
 
Export cavitiy (H) and surface (HA) points to PDB-formatted file with
 a variable (B; optional) in B-factor column, and hydropathy to
 PDB-formatted file in B-factor column at surface points (HA).

diff --git a/docs/_api_reference/export_openings.html b/docs/package/api_reference/export_openings.html
similarity index 78%
rename from docs/_api_reference/export_openings.html
rename to docs/package/api_reference/export_openings.html
index 3a321121..20b87272 100644
--- a/docs/_api_reference/export_openings.html
+++ b/docs/package/api_reference/export_openings.html
@@ -1,27 +1,27 @@
 
-
+
 
   
 
   
-  pyKVFinder.export_openings — pyKVFinder 0.6.14 documentation
-      
-      
+  pyKVFinder.export_openings — pyKVFinder 0.7.0 documentation
+      
+      
 
   
-    
+    
   
   
-        
-        
-        
-        
-        
-    
-    
-    
+        
+        
+        
+        
+        
+    
+    
+    
     
      
 
@@ -34,78 +34,68 @@
 
           
           
-          
+          
             pyKVFinder
-              
+              
           
               

-                0.6
+                0.7
               

 

-  

+  
     
     
     
   

 

         

@@ -114,18 +104,18 @@
 
     

 
       

         

           

   
   

@@ -137,7 +127,7 @@
 
pyKVFinder.export_openings

 

 

-pyKVFinder.export_openings(fn: str | Path, openings: ndarray, vertices: ndarray | List[List[float]], step: float | int = 0.6, selection: List[int] | List[str] | None = None, nthreads: int | None = None, append: bool = False, model: int = 0) → None[source]

+pyKVFinder.export_openings(fn: str | Path, openings: ndarray, vertices: ndarray | List[List[float]], step: float | int = 0.6, selection: List[int] | List[str] | None = None, nthreads: int | None = None, append: bool = False, model: int = 0) → None[source]
 
Export opening points (H) to a PDB-formatted file.

 

 
Parameters:

diff --git a/docs/_api_reference/get_vertices.html b/docs/package/api_reference/get_vertices.html
similarity index 72%
rename from docs/_api_reference/get_vertices.html
rename to docs/package/api_reference/get_vertices.html
index 7a242251..97d02fe9 100644
--- a/docs/_api_reference/get_vertices.html
+++ b/docs/package/api_reference/get_vertices.html
@@ -1,27 +1,27 @@
 
-
+
 
   
 
   
-  pyKVFinder.get_vertices — pyKVFinder 0.6.14 documentation
-      
-      
+  pyKVFinder.get_vertices — pyKVFinder 0.7.0 documentation
+      
+      
 
   
-    
+    
   
   
-        
-        
-        
-        
-        
-    
-    
-    
+        
+        
+        
+        
+        
+    
+    
+    
     
      
 
@@ -34,78 +34,68 @@
 
           
           
-          
+          
             pyKVFinder
-              
+              
           
               

-                0.6
+                0.7
               

 

-  

+  
     
     
     
   

 

         

@@ -114,18 +104,18 @@
 
     

 
       

         

           

   
   

@@ -137,7 +127,7 @@
 
pyKVFinder.get_vertices

 

 

-pyKVFinder.get_vertices(atomic: ndarray | List[List[str | float | int]], probe_out: float | int = 4.0, step: float | int = 0.6) → ndarray[source]

+pyKVFinder.get_vertices(atomic: ndarray | List[List[str | float | int]], probe_out: float | int = 4.0, step: float | int = 0.6) → ndarray[source]
 
Gets 3D grid vertices.

 

 
Parameters:

diff --git a/docs/_api_reference/get_vertices_from_file.html b/docs/package/api_reference/get_vertices_from_file.html
similarity index 80%
rename from docs/_api_reference/get_vertices_from_file.html
rename to docs/package/api_reference/get_vertices_from_file.html
index 4885101c..12cc4a69 100644
--- a/docs/_api_reference/get_vertices_from_file.html
+++ b/docs/package/api_reference/get_vertices_from_file.html
@@ -1,27 +1,27 @@
 
-
+
 
   
 
   
-  pyKVFinder.get_vertices_from_file — pyKVFinder 0.6.14 documentation
-      
-      
+  pyKVFinder.get_vertices_from_file — pyKVFinder 0.7.0 documentation
+      
+      
 
   
-    
+    
   
   
-        
-        
-        
-        
-        
-    
-    
-    
+        
+        
+        
+        
+        
+    
+    
+    
     
      
 
@@ -34,78 +34,68 @@
 
           
           
-          
+          
             pyKVFinder
-              
+              
           
               

-                0.6
+                0.7
               

 

-  

+  
     
     
     
   

 

         

@@ -114,18 +104,18 @@
 
     

 
       

         

           

   
   

@@ -137,7 +127,7 @@
 
pyKVFinder.get_vertices_from_file

 

 

-pyKVFinder.get_vertices_from_file(fn: str | Path, atomic: ndarray | List[List[str | float | int]], step: float | int = 0.6, probe_in: float | int = 1.4, probe_out: float | int = 4.0, nthreads: int | None = None) → Tuple[ndarray, ndarray, ndarray][source]

+pyKVFinder.get_vertices_from_file(fn: str | Path, atomic: ndarray | List[List[str | float | int]], step: float | int = 0.6, probe_in: float | int = 1.4, probe_out: float | int = 4.0, nthreads: int | None = None) → Tuple[ndarray, ndarray, ndarray][source]
 
Gets 3D grid vertices from box configuration file or parKVFinder
 parameters file, selects atoms inside custom 3D grid, define sine
 and cosine of 3D grid angles and define xyz grid units.

diff --git a/docs/_api_reference/hydropathy.html b/docs/package/api_reference/hydropathy.html
similarity index 86%
rename from docs/_api_reference/hydropathy.html
rename to docs/package/api_reference/hydropathy.html
index 36a4f572..5098be20 100644
--- a/docs/_api_reference/hydropathy.html
+++ b/docs/package/api_reference/hydropathy.html
@@ -1,27 +1,27 @@
 
-
+
 
   
 
   
-  pyKVFinder.hydropathy — pyKVFinder 0.6.14 documentation
-      
-      
+  pyKVFinder.hydropathy — pyKVFinder 0.7.0 documentation
+      
+      
 
   
-    
+    
   
   
-        
-        
-        
-        
-        
-    
-    
-    
+        
+        
+        
+        
+        
+    
+    
+    
     
      
 
@@ -34,78 +34,68 @@
 
           
           
-          
+          
             pyKVFinder
-              
+              
           
               

-                0.6
+                0.7
               

 

-  

+  
     
     
     
   

 

         

@@ -114,18 +104,18 @@
 
     

 
       

         

           

   
   

@@ -137,7 +127,7 @@
 
pyKVFinder.hydropathy

 

 

-pyKVFinder.hydropathy(surface: ndarray, atomic: ndarray | List[List[str | float | int]], vertices: ndarray | List[List[float]], step: float | int = 0.6, probe_in: float | int = 1.4, hydrophobicity_scale: str | Path = 'EisenbergWeiss', ignore_backbone: bool = False, selection: List[int] | List[str] | None = None, nthreads: int | None = None, verbose: bool = False) → Tuple[ndarray, Dict[str, float]][source]

+pyKVFinder.hydropathy(surface: ndarray, atomic: ndarray | List[List[str | float | int]], vertices: ndarray | List[List[float]], step: float | int = 0.6, probe_in: float | int = 1.4, hydrophobicity_scale: str | Path = 'EisenbergWeiss', ignore_backbone: bool = False, selection: List[int] | List[str] | None = None, nthreads: int | None = None, verbose: bool = False) → Tuple[ndarray, Dict[str, float]][source]
 
Hydropathy characterization of the detected cavities.

 
Map a target hydrophobicity scale per surface point and calculate average hydropathy of detected cavities.

 

diff --git a/docs/_cfg_files/hydrophobicity_scale_file_template.html b/docs/package/api_reference/hydrophobicity_scale_file_template.html
similarity index 68%
rename from docs/_cfg_files/hydrophobicity_scale_file_template.html
rename to docs/package/api_reference/hydrophobicity_scale_file_template.html
index b4928b29..e1bccec0 100644
--- a/docs/_cfg_files/hydrophobicity_scale_file_template.html
+++ b/docs/package/api_reference/hydrophobicity_scale_file_template.html
@@ -1,28 +1,28 @@
 
-
+
 
   
 
   
-  Hydrophobicity scale file template — pyKVFinder 0.6.14 documentation
-      
-      
+  Hydrophobicity scale file template — pyKVFinder 0.7.0 documentation
+      
+      
 
   
-    
+    
   
   
-        
-        
-        
-        
-        
-    
-    
-    
-    
+        
+        
+        
+        
+        
+    
+    
+    
+    
      
 
 
@@ -34,55 +34,50 @@
 
           
           
-          
+          
             pyKVFinder
-              
+              
           
               

-                0.6
+                0.7
               

 

-  

+  
     
     
     
   

 

         

@@ -91,17 +86,18 @@
 
     

 
       

         

           

   
   

@@ -151,7 +147,7 @@ 
References
    
           

           

@@ -114,18 +104,18 @@
 
     

 
       

         

           

   
   

@@ -137,7 +127,7 @@
 
pyKVFinder.openings

 

 

-pyKVFinder.openings(cavities: ndarray, depths: ndarray | None = None, step: float | int = 0.6, openings_cutoff: int = 1, selection: List[int] | List[str] | None = None, nthreads: int | None = None, verbose: bool = False) → Tuple[int, ndarray, Dict[str, Dict[str, float]]][source]

+pyKVFinder.openings(cavities: ndarray, depths: ndarray | None = None, step: float | int = 0.6, openings_cutoff: int = 1, selection: List[int] | List[str] | None = None, nthreads: int | None = None, verbose: bool = False) → Tuple[int, ndarray, Dict[str, Dict[str, float]]][source]
 
[WIP] Identify openings of the detected cavities and calculate their areas.

 

 
Parameters:

diff --git a/docs/_api_reference/plot_frequencies.html b/docs/package/api_reference/plot_frequencies.html
similarity index 68%
rename from docs/_api_reference/plot_frequencies.html
rename to docs/package/api_reference/plot_frequencies.html
index f23a1017..7271121d 100644
--- a/docs/_api_reference/plot_frequencies.html
+++ b/docs/package/api_reference/plot_frequencies.html
@@ -1,27 +1,27 @@
 
-
+
 
   
 
   
-  pyKVFinder.plot_frequencies — pyKVFinder 0.6.14 documentation
-      
-      
+  pyKVFinder.plot_frequencies — pyKVFinder 0.7.0 documentation
+      
+      
 
   
-    
+    
   
   
-        
-        
-        
-        
-        
-    
-    
-    
+        
+        
+        
+        
+        
+    
+    
+    
     
      
 
@@ -34,78 +34,68 @@
 
           
           
-          
+          
             pyKVFinder
-              
+              
           
               

-                0.6
+                0.7
               

 

-  

+  
     
     
     
   

 

         

@@ -114,18 +104,18 @@
 
     

 
       

         

           

   
   

@@ -137,7 +127,7 @@
 
pyKVFinder.plot_frequencies

 

 

-pyKVFinder.plot_frequencies(frequencies: Dict[str, Dict[str, Dict[str, int]]], fn: str | Path = 'barplots.pdf') → None[source]

+pyKVFinder.plot_frequencies(frequencies: Dict[str, Dict[str, Dict[str, int]]], fn: str | Path = 'barplots.pdf') → None[source]
 
Plot bar charts of calculated frequencies (residues and classes of
 residues) for each detected cavity in a target PDF file.

 

@@ -183,7 +173,7 @@ 
pyKVFinder.plot_frequencies>>> plot_frequencies(frequencies, fn='barplots.pdf')
 

 

-../_images/barplots.png
+../../_images/barplots.png
 
 
 
diff --git a/docs/_api_reference/pyKVFinderResults.html b/docs/package/api_reference/pyKVFinderResults.html
similarity index 85%
rename from docs/_api_reference/pyKVFinderResults.html
rename to docs/package/api_reference/pyKVFinderResults.html
index ccb11ceb..4ad97f7a 100644
--- a/docs/_api_reference/pyKVFinderResults.html
+++ b/docs/package/api_reference/pyKVFinderResults.html
@@ -1,28 +1,28 @@
 
-
+
 
   
 
   
-  pyKVFinder.pyKVFinderResults — pyKVFinder 0.6.14 documentation
-      
-      
+  pyKVFinder.pyKVFinderResults — pyKVFinder 0.7.0 documentation
+      
+      
 
   
-    
+    
   
   
-        
-        
-        
-        
-        
-    
-    
-    
-    
+        
+        
+        
+        
+        
+    
+    
+    
+    
      
 
 
@@ -34,84 +34,52 @@
 
           
           
-          
+          
             pyKVFinder
-              
+              
           
               

-                0.6
+                0.7
               

 

-  

+  
     
     
     
   

 

         

@@ -120,18 +88,18 @@
 
     

 
       

         

           

   
   

@@ -143,7 +111,7 @@
 
pyKVFinder.pyKVFinderResults

 

 

-class pyKVFinder.pyKVFinderResults(cavities: ndarray, surface: ndarray, depths: ndarray | None, scales: ndarray | None, volume: Dict[str, float], area: Dict[str, float], max_depth: Dict[str, float] | None, avg_depth: Dict[str, float] | None, avg_hydropathy: Dict[str, float] | None, residues: Dict[str, List[List[str]]], frequencies: Dict[str, Dict[str, Dict[str, int]]] | None, _vertices: ndarray, _step: float | int, _input: str | Path | None = None, _ligand: str | Path | None = None)[source]

+class pyKVFinder.pyKVFinderResults(cavities: ndarray, surface: ndarray, depths: ndarray | None, scales: ndarray | None, volume: Dict[str, float], area: Dict[str, float], max_depth: Dict[str, float] | None, avg_depth: Dict[str, float] | None, avg_hydropathy: Dict[str, float] | None, residues: Dict[str, List[List[str]]], frequencies: Dict[str, Dict[str, Dict[str, int]]] | None, _vertices: ndarray, _step: float | int, _input: str | Path | None = None, _ligand: str | Path | None = None)[source]
 
A class containing pyKVFinder detection and characterization results.

 

 
Parameters:

@@ -398,7 +366,7 @@ 
pyKVFinder.pyKVFinderResults
 

-export(output: str | Path = 'cavity.pdb', nthreads: int | None = None) → str | None[source]

+export(output: str | Path = 'cavity.pdb', nthreads: int | None = None) → str | None[source]
 
Exports cavitiy (H) and surface (HA) points to PDB-formatted file
 with a variable (B; optional) in B-factor column, and hydropathy to
 PDB-formatted file in B-factor column at surface points (HA).

@@ -436,7 +404,7 @@ 
pyKVFinder.pyKVFinderResults
 

-export_all(fn: str | Path = 'results.toml', output: str | Path = 'cavity.pdb', include_frequencies_pdf: bool = False, pdf: str | Path = 'barplots.pdf', nthreads: int | None = None) → None[source]

+export_all(fn: str | Path = 'results.toml', output: str | Path = 'cavity.pdb', include_frequencies_pdf: bool = False, pdf: str | Path = 'barplots.pdf', nthreads: int | None = None) → None[source]
 
Exports cavities and characterization to PDB-formatted files,
 writes file paths and characterization to a TOML-formatted file, and
 optionally plot bar charts of frequencies (residues and classes of
@@ -491,7 +459,7 @@ 
pyKVFinder.pyKVFinderResults
 

-plot_frequencies(pdf: str | Path = 'barplots.pdf')[source]

+plot_frequencies(pdf: str | Path = 'barplots.pdf')[source]
 
Plot bar charts of frequencies (residues and classes of residues) in
 a PDF file.

 

@@ -530,7 +498,7 @@ 
pyKVFinder.pyKVFinderResults
 

-write(fn: str | Path = 'results.toml', output: str | Path | None = None) → None[source]

+write(fn: str | Path = 'results.toml', output: str | Path | None = None) → None[source]
 
Writes file paths and cavity characterization to TOML-formatted file

 

 
Parameters:

@@ -568,7 +536,7 @@ 
pyKVFinder.pyKVFinderResults
         
-        
+        
     

 
   

diff --git a/docs/_api_reference/read_cavity.html b/docs/package/api_reference/read_cavity.html
similarity index 82%
rename from docs/_api_reference/read_cavity.html
rename to docs/package/api_reference/read_cavity.html
index a97e357a..ee06ba2e 100644
--- a/docs/_api_reference/read_cavity.html
+++ b/docs/package/api_reference/read_cavity.html
@@ -1,27 +1,27 @@
 
-
+
 
   
 
   
-  pyKVFinder.read_cavity — pyKVFinder 0.6.14 documentation
-      
-      
+  pyKVFinder.read_cavity — pyKVFinder 0.7.0 documentation
+      
+      
 
   
-    
+    
   
   
-        
-        
-        
-        
-        
-    
-    
-    
+        
+        
+        
+        
+        
+    
+    
+    
     
      
 
@@ -34,78 +34,68 @@
 
           
           
-          
+          
             pyKVFinder
-              
+              
           
               

-                0.6
+                0.7
               

 

-  

+  
     
     
     
   

 

         

@@ -114,18 +104,18 @@
 
     

 
       

         

           

   
   

@@ -137,7 +127,7 @@
 
pyKVFinder.read_cavity

 

 

-pyKVFinder.read_cavity(cavity: str | Path, receptor: str | Path, step: float | int = 0.6, probe_in: float | int = 1.4, probe_out: float | int = 4.0, surface: str = 'SES', vdw: Dict[str, Dict[str, float]] | None = None, nthreads: int | None = None, verbose: bool = False) → ndarray[source]

+pyKVFinder.read_cavity(cavity: str | Path, receptor: str | Path, step: float | int = 0.6, probe_in: float | int = 1.4, probe_out: float | int = 4.0, surface: str = 'SES', vdw: Dict[str, Dict[str, float]] | None = None, nthreads: int | None = None, verbose: bool = False) → ndarray[source]
 
Read cavities and receptor inside a 3D grid.

 

 
Parameters:

diff --git a/docs/_api_reference/read_pdb.html b/docs/package/api_reference/read_pdb.html
similarity index 74%
rename from docs/_api_reference/read_pdb.html
rename to docs/package/api_reference/read_pdb.html
index bf3d5937..35a9f431 100644
--- a/docs/_api_reference/read_pdb.html
+++ b/docs/package/api_reference/read_pdb.html
@@ -1,27 +1,27 @@
 
-
+
 
   
 
   
-  pyKVFinder.read_pdb — pyKVFinder 0.6.14 documentation
-      
-      
+  pyKVFinder.read_pdb — pyKVFinder 0.7.0 documentation
+      
+      
 
   
-    
+    
   
   
-        
-        
-        
-        
-        
-    
-    
-    
+        
+        
+        
+        
+        
+    
+    
+    
     
      
 
@@ -34,78 +34,68 @@
 
           
           
-          
+          
             pyKVFinder
-              
+              
           
               

-                0.6
+                0.7
               

 

-  

+  
     
     
     
   

 

         

@@ -114,18 +104,18 @@
 
     

 
       

         

           

   
   

@@ -137,7 +127,7 @@
 
pyKVFinder.read_pdb

 

 

-pyKVFinder.read_pdb(fn: str | Path, vdw: Dict[str, Dict[str, float]] | None = None, model: int | None = None) → ndarray[source]

+pyKVFinder.read_pdb(fn: str | Path, vdw: Dict[str, Dict[str, float]] | None = None, model: int | None = None) → ndarray[source]
 
Reads PDB file into numpy.ndarrays.

 

 
Parameters:

diff --git a/docs/_api_reference/read_vdw.html b/docs/package/api_reference/read_vdw.html
similarity index 85%
rename from docs/_api_reference/read_vdw.html
rename to docs/package/api_reference/read_vdw.html
index 4a89de8c..df25549e 100644
--- a/docs/_api_reference/read_vdw.html
+++ b/docs/package/api_reference/read_vdw.html
@@ -1,27 +1,27 @@
 
-
+
 
   
 
   
-  pyKVFinder.read_vdw — pyKVFinder 0.6.14 documentation
-      
-      
+  pyKVFinder.read_vdw — pyKVFinder 0.7.0 documentation
+      
+      
 
   
-    
+    
   
   
-        
-        
-        
-        
-        
-    
-    
-    
+        
+        
+        
+        
+        
+    
+    
+    
     
      
 
@@ -34,78 +34,68 @@
 
           
           
-          
+          
             pyKVFinder
-              
+              
           
               

-                0.6
+                0.7
               

 

-  

+  
     
     
     
   

 

         

@@ -114,18 +104,18 @@
 
     

 
       

         

           

   
   

@@ -137,7 +127,7 @@
 
pyKVFinder.read_vdw

 

 

-pyKVFinder.read_vdw(fn: str | Path | None = None) → Dict[str, Dict[str, float]][source]

+pyKVFinder.read_vdw(fn: str | Path | None = None) → Dict[str, Dict[str, float]][source]
 
Reads van der Waals radii from .dat file.

 

 
Parameters:

diff --git a/docs/_api_reference/read_xyz.html b/docs/package/api_reference/read_xyz.html
similarity index 72%
rename from docs/_api_reference/read_xyz.html
rename to docs/package/api_reference/read_xyz.html
index 796254de..ab983a28 100644
--- a/docs/_api_reference/read_xyz.html
+++ b/docs/package/api_reference/read_xyz.html
@@ -1,27 +1,27 @@
 
-
+
 
   
 
   
-  pyKVFinder.read_xyz — pyKVFinder 0.6.14 documentation
-      
-      
+  pyKVFinder.read_xyz — pyKVFinder 0.7.0 documentation
+      
+      
 
   
-    
+    
   
   
-        
-        
-        
-        
-        
-    
-    
-    
+        
+        
+        
+        
+        
+    
+    
+    
     
      
 
@@ -34,78 +34,68 @@
 
           
           
-          
+          
             pyKVFinder
-              
+              
           
               

-                0.6
+                0.7
               

 

-  

+  
     
     
     
   

 

         

@@ -114,18 +104,18 @@
 
     

 
       

         

           

   
   

@@ -137,7 +127,7 @@
 
pyKVFinder.read_xyz

 

 

-pyKVFinder.read_xyz(fn: str | Path, vdw: Dict[str, Dict[str, float]] | None = None) → ndarray[source]

+pyKVFinder.read_xyz(fn: str | Path, vdw: Dict[str, Dict[str, float]] | None = None) → ndarray[source]
 
Reads XYZ file into numpy.ndarrays.

 

 
Parameters:

diff --git a/docs/_api_reference/run_workflow.html b/docs/package/api_reference/run_workflow.html
similarity index 92%
rename from docs/_api_reference/run_workflow.html
rename to docs/package/api_reference/run_workflow.html
index 3af56cdb..2a26b5d8 100644
--- a/docs/_api_reference/run_workflow.html
+++ b/docs/package/api_reference/run_workflow.html
@@ -1,29 +1,29 @@
 
-
+
 
   
 
   
-  pyKVFinder.run_workflow — pyKVFinder 0.6.14 documentation
-      
-      
+  pyKVFinder.run_workflow — pyKVFinder 0.7.0 documentation
+      
+      
 
   
-    
+    
   
   
-        
-        
-        
-        
-        
-    
-    
-    
+        
+        
+        
+        
+        
+    
+    
+    
     
-     
+     
 
 
  
@@ -34,78 +34,68 @@
 
           
           
-          
+          
             pyKVFinder
-              
+              
           
               

-                0.6
+                0.7
               

 

-  

+  
     
     
     
   

 

         

@@ -114,18 +104,18 @@
 
     

 
       

         

           

   
   

@@ -137,7 +127,7 @@
 
pyKVFinder.run_workflow

 

 

-pyKVFinder.run_workflow(input: str | pathlib.Path, ligand: str | pathlib.Path | None = None, vdw: str | pathlib.Path | None = None, box: str | pathlib.Path | None = None, step: float | int = 0.6, probe_in: float | int = 1.4, probe_out: float | int = 4.0, removal_distance: float | int = 2.4, volume_cutoff: float | int = 5.0, ligand_cutoff: float | int = 5.0, include_depth: bool = False, include_hydropathy: bool = False, hydrophobicity_scale: str | pathlib.Path = 'EisenbergWeiss', surface: str = 'SES', ignore_backbone: bool = False, model: int | None = None, nthreads: int | None = None, verbose: bool = False) → pyKVFinder.pyKVFinderResults[source]

+pyKVFinder.run_workflow(input: str | pathlib.Path, ligand: str | pathlib.Path | None = None, vdw: str | pathlib.Path | None = None, box: str | pathlib.Path | None = None, step: float | int = 0.6, probe_in: float | int = 1.4, probe_out: float | int = 4.0, removal_distance: float | int = 2.4, volume_cutoff: float | int = 5.0, ligand_cutoff: float | int = 5.0, include_depth: bool = False, include_hydropathy: bool = False, hydrophobicity_scale: str | pathlib.Path = 'EisenbergWeiss', surface: str = 'SES', ignore_backbone: bool = False, model: int | None = None, nthreads: int | None = None, verbose: bool = False) → pyKVFinder.pyKVFinderResults[source]
 
Detects and characterizes cavities (volume, area, depth [optional],
 hydropathy [optional] and interface residues).

 

@@ -523,7 +513,7 @@ 
pyKVFinder.run_workflow
           

           

 
diff --git a/docs/_api_reference/spatial.html b/docs/package/api_reference/spatial.html
similarity index 78%
rename from docs/_api_reference/spatial.html
rename to docs/package/api_reference/spatial.html
index 26322c9f..b0366971 100644
--- a/docs/_api_reference/spatial.html
+++ b/docs/package/api_reference/spatial.html
@@ -1,27 +1,27 @@
 
-
+
 
   
 
   
-  pyKVFinder.spatial — pyKVFinder 0.6.14 documentation
-      
-      
+  pyKVFinder.spatial — pyKVFinder 0.7.0 documentation
+      
+      
 
   
-    
+    
   
   
-        
-        
-        
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+    
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@@ -34,78 +34,68 @@
 
           
           
-          
+          
             pyKVFinder
-              
+              
           
               

-                0.6
+                0.7
               

 

-  

+  
     
     
     
   

 

         

@@ -114,18 +104,18 @@
 
     

 
       

         

           

   
   

@@ -137,7 +127,7 @@
 
pyKVFinder.spatial

 

 

-pyKVFinder.spatial(cavities: ndarray, step: float | int = 0.6, selection: List[int] | List[str] | None = None, nthreads: int | None = None, verbose: bool = False) → Tuple[ndarray, Dict[str, float], Dict[str, float]][source]

+pyKVFinder.spatial(cavities: ndarray, step: float | int = 0.6, selection: List[int] | List[str] | None = None, nthreads: int | None = None, verbose: bool = False) → Tuple[ndarray, Dict[str, float], Dict[str, float]][source]
 
Spatial characterization (volume and area) of the detected cavities.

 

 
Parameters:

diff --git a/docs/package/api_reference/vdw_file_template.html b/docs/package/api_reference/vdw_file_template.html
new file mode 100644
index 00000000..fea5d56d
--- /dev/null
+++ b/docs/package/api_reference/vdw_file_template.html
@@ -0,0 +1,156 @@
+
+
+
+  
+
+  
+  Van der Waals radii file template — pyKVFinder 0.7.0 documentation
+      
+      
+
+  
+    
+  
+  
+        
+        
+        
+        
+        
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+    
+    
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+ 
+  

+    
+
+    

+
+      

+        

+          

+  
+  

+

+          

+           

+             
+  

+
Van der Waals radii file template

+
The van der Waals radii file define the radius values for each atom by residue and when not defined, it uses a generic value based on the atom type. The package contains a built-in van der Waals radii file: vdw.dat. However, the user can define its own file with a mandatory format and pass it to pyKVFinder. The format is shown below:

+
>RES
+C       1.66
+CA      2.00
+N       1.97
+O       1.69
+H       0.91
+

+

+

+
Warning

+
The residue name should be in the standard PDB format and each radius value is separated by two tab characters of the atom name.

+

+

+
+
+           

+          

+          
+        

+      

+    

+  

+   
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+
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diff --git a/docs/_api_reference/write_results.html b/docs/package/api_reference/write_results.html
similarity index 90%
rename from docs/_api_reference/write_results.html
rename to docs/package/api_reference/write_results.html
index 45b1e262..0b32c962 100644
--- a/docs/_api_reference/write_results.html
+++ b/docs/package/api_reference/write_results.html
@@ -1,27 +1,27 @@
 
-
+
 
   
 
   
-  pyKVFinder.write_results — pyKVFinder 0.6.14 documentation
-      
-      
+  pyKVFinder.write_results — pyKVFinder 0.7.0 documentation
+      
+      
 
   
-    
+    
   
   
-        
-        
-        
-        
-        
-    
-    
-    
+        
+        
+        
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+    
+    
     
      
 
@@ -34,78 +34,68 @@
 
           
           
-          
+          
             pyKVFinder
-              
+              
           
               

-                0.6
+                0.7
               

 

-  

+  
     
     
     
   

 

         

@@ -114,18 +104,18 @@
 
     

 
       

         

           

   
   

@@ -137,7 +127,7 @@
 
pyKVFinder.write_results

 

 

-pyKVFinder.write_results(fn: str | Path, input: str | Path | None, ligand: str | Path | None, output: str | Path | None, volume: Dict[str, float] | None = None, area: Dict[str, float] | None = None, max_depth: Dict[str, float] | None = None, avg_depth: Dict[str, float] | None = None, avg_hydropathy: Dict[str, float] | None = None, residues: Dict[str, List[List[str]]] | None = None, frequencies: Dict[str, Dict[str, Dict[str, int]]] | None = None, step: float | int = 0.6) → None[source]

+pyKVFinder.write_results(fn: str | Path, input: str | Path | None, ligand: str | Path | None, output: str | Path | None, volume: Dict[str, float] | None = None, area: Dict[str, float] | None = None, max_depth: Dict[str, float] | None = None, avg_depth: Dict[str, float] | None = None, avg_hydropathy: Dict[str, float] | None = None, residues: Dict[str, List[List[str]]] | None = None, frequencies: Dict[str, Dict[str, Dict[str, int]]] | None = None, step: float | int = 0.6) → None[source]
 
Writes file paths and cavity characterization to TOML-formatted file.

 

 
Parameters:

diff --git a/docs/package/examples/index.html b/docs/package/examples/index.html
new file mode 100644
index 00000000..6cc63316
--- /dev/null
+++ b/docs/package/examples/index.html
@@ -0,0 +1,147 @@
+
+
+
+  
+
+  
+  Examples — pyKVFinder 0.7.0 documentation
+      
+      
+
+  
+    
+  
+  
+        
+        
+        
+        
+        
+    
+    
+    
+    
+     
+
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+ 
+  

+    
+
+    

+
+      

+        

+          

+  
+  

+

+          

+           

+             
+  

+
Examples

+
Jupyter notebook examples are available for:

+

+
+

+

+
+
+           

+          

+          
+        

+      

+    

+  

+   
+
+
+
\ No newline at end of file
diff --git a/docs/package/installation/index.html b/docs/package/installation/index.html
new file mode 100644
index 00000000..beb6292e
--- /dev/null
+++ b/docs/package/installation/index.html
@@ -0,0 +1,146 @@
+
+
+
+  
+
+  
+  Installation — pyKVFinder 0.7.0 documentation
+      
+      
+
+  
+    
+  
+  
+        
+        
+        
+        
+        
+    
+    
+    
+    
+     
+
+
+ 
+  

+    
+
+    

+
+      

+        

+          

+  
+  

+

+          

+           

+             
+  

+
Installation

+
To install the latest release from PyPI,
+run:

+
pip install pyKVFinder
+

+

+
Or to install the latest developmental version from source, run:

+
git clone https://github.com/LBC-LNBio/pyKVFinder.git
+pip install -e pyKVFinder
+

+

+

+
Note

+
SWIG is required for installing pyKVFinder from source, the installation procedure differs depending on the operating system. SWIG can be installed with conda (conda install swig), or with a package manager on Linux (sudo apt install swig) and macOS (brew install swig).

+

+

+
+
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\ No newline at end of file
diff --git a/docs/_tutorial/index.html b/docs/package/tutorial/index.html
similarity index 90%
rename from docs/_tutorial/index.html
rename to docs/package/tutorial/index.html
index 2d5afe46..2dd4010c 100644
--- a/docs/_tutorial/index.html
+++ b/docs/package/tutorial/index.html
@@ -1,29 +1,29 @@
 
-
+
 
   
 
   
-  Cavity detection and characterization — pyKVFinder 0.6.14 documentation
-      
-      
+  Tutorial — pyKVFinder 0.7.0 documentation
+      
+      
 
   
-    
+    
   
   
-        
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+     
 
 
  
@@ -34,107 +34,73 @@
 
           
           
-          
+          
             pyKVFinder
-              
+              
           
               

-                0.6
+                0.7
               

 

-  

+  
     
     
     
   

 

         

@@ -143,17 +109,17 @@
 
     

 
       

         

           

   
   

@@ -161,14 +127,16 @@
           

            

              
-  
Tutorial
This section is an introductory overview of pyKVFinder features. For detailed reference documentation of the functions and classes contained in the package, see the API reference.

+  

+
Tutorial

+
This section is an introductory overview of pyKVFinder features. For detailed reference documentation of the functions and classes contained in the package, see the API reference.

 
Before reading this section, you should know a bit of Python. If you would like to refresh your memory, refer to this Python tutorial.

 
First of all, import pyKVFinder package on Python:

 
>>> import pyKVFinder
 

 

 

-
Cavity detection and characterization

+
Cavity detection and characterization

 
All files used on this tutorial can be found in our package and in our GitHub repository:

 
    
 
  • 1FMO.pdb
    • 
@@ -177,7 +145,7 @@ 
    Cavity detection and characterizationworkflow through the single pyKVFinder function or run pyKVFinder functions in a stepwise fashion.
    
 
    
-
    Standard workflow
    
+
    Standard workflow
    
 
    The standard workflow for cavity detection with spatial and constitutional characterization (volume, area and interface residues) can be run at once with one command:
    
 
    >>> import os
 >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
@@ -269,7 +237,7 @@ 
    Standard workflow
 
    See also
    
     
 
    
 
    With these attributes, we can write the detected cavities and the characterization to files. Further, we can set a flag to plot the bar charts of the frequencies in a PDF file. Below, we illustrate the usage:
    
@@ -283,12 +251,12 @@ 
    Standard workflow
 
    See also
    
     
 
    
 
    
 
    
-
    Full workflow
    
+
    Full workflow
    
 
    However, users may opt to perform the full workflow for cavity detection with spatial (volume and area), constitutional (interface residues), hydropathy and depth characterization. This full workflow can be run with one command by setting some parameters of pyKVFinder.run_workflow function:
    
 
    >>> results = pyKVFinder.run_workflow(pdb, include_depth=True, include_hydropathy=True, hydrophobicity_scale='EisenbergWeiss')
 
    
@@ -349,7 +317,7 @@ 
    Full workflow
 
    See also
    
     
 
    
 
    With these attributes, we can write the detected cavities with depth annotated on B-factor column (temperature factor) and hydropathy annotated on Q-factor (occupancy) column, and the characterization to files. Below, we illustrate the usage:
    
@@ -363,15 +331,15 @@ 
    Full workflow
 
    See also
    
     
 

 

 

-
Separated steps

+
Separated steps

 
If users prefer, instead of running pyKVFinder.run_workflow function, you can apply the cavity detection and characterization in a step-by-step fashion. Below we describe each step in detail.

 

-
1. Loading van der Waals radii dictionary

+
1. Loading van der Waals radii dictionary

 
The van der Waals radii file define the radius values for each residue and when not defined, it uses a generic value based on the atom type. pyKVFinder.read_vdw takes a vdW radii file (.dat) and returns a dictionary contaning radii values for each atom of each residue.

 
>>> vdw = pyKVFinder.read_vdw()
 >>> vdw
@@ -386,12 +354,12 @@ 
1. Loading van der Waals radii dictionary
 
See also

 
 

 

 

-
2. Loading data from target structure

+
2. Loading data from target structure

 
pyKVFinder.read_pdb takes a target .pdb file and returns a NumPy array (atomic) with residue number, chain identifier, residue name, atom name, xyz coordinates and radius, considering a van der Waals radii dictionary, for each atom.

 
>>> import os
 >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
@@ -418,13 +386,13 @@ 
2. Loading data from target structure
 
See also

 
 

 

 

-
3. Dimensioning the 3D grid

+
3. Dimensioning the 3D grid

 
The pyKVFinder 3D grid must be calculated based on the target .pdb or .xyz file, the Probe Out diameter and the grid spacing.

 
pyKVFinder.get_vertices takes the NumPy array with residue number, chain identifier, residue name, atom name, xyz coordinates and radius for each atom, and the Probe Out (probe_out) and grid spacing (step) that will be applied in the detection, and returns a NumPy array with vertice coordinates (origin, X-axis, Y-axis, Z-axis) of the 3D grid.

 
>>> # Default Probe Out (probe_out): 4.0
@@ -446,12 +414,12 @@ 
3. Dimensioning the 3D grid
 
See also

 
 

 

 

-
4. Detecting biomolecular cavities

+
4. Detecting biomolecular cavities

 
pyKVFinder.detect takes the NumPy array with residue number, chain identifier, residue name, atom name, xyz coordinates and radius for each atom, a NumPy array with vertices and a collection of detection parameters (step, probe_in, probe_out, removal_distance, volume_cutoff, surface), and returns a tuple with the number of detected cavities and a NumPy array with the cavity points in the 3D grid.

 
>>> # Default Grid Spacing (step): 0.6
 >>> step = 0.6
@@ -507,9 +475,10 @@ 
4. Detecting biomolecular cavities
 
See also

 
 

+

 

 
4.1 Detecting biomolecular cavities with ligand adjustment

 
The cavity detection can be limited around the target ligand(s), which will be passed to pyKVFinder through a .pdb or .xyz file. Thus, the detected cavities are limited within a radius (ligand_cutoff) of the target ligand(s).

@@ -581,15 +550,14 @@ 
4.1 Detecting biomolecular cavities with ligand adjustment
 
See also

 
 

 

-

 

-
5. Performing spatial characterization

+
5. Performing spatial characterization

 
A spatial characterization, that includes volume, area and defining surface points, is performed on the detected cavities.

 
pyKVFinder.spatial takes the detected cavities and the grid spacing (step) and and returns a tuple with a NumPy array with the surface points in the 3D grid, a dictionary with the volume of the detected cavities and a dictionary with the area of the detected cavities.

 
>>> surface, volume, area = pyKVFinder.spatial(cavities, step=step)
@@ -639,12 +607,12 @@ 
5. Performing spatial characterization
 
See also

 
 

 

 

-
6. Performing constitutional characterization

+
6. Performing constitutional characterization

 
A constitutional characterization, that identifies the interface residues, is performed on the detected cavities.

 
pyKVFinder.constitutional takes the detected cavities, the NumPy array with residue number, chain identifier, residue name, atom name, xyz coordinates and radius for each atom, the NumPy array with vertice coordinates (origin, X-axis, Y-axis, Z-axis) and a collection of detection parameters (step, probe_in, ignore_backbone), and returns a dictionary with interface residues of each cavity.

 
>>> # Default ignore backbone contacts flag (ignore_backbone): False
@@ -671,9 +639,10 @@ 
6. Performing constitutional characterization
 
See also

 
 

+

 

 
6.1 Calculating and plotting frequencies

 
With the interface residues defined, you can also calculate the frequencies of residues and classes of residues. The classes of residues are:

@@ -719,19 +688,18 @@ 
6.1 Calculating and plotting frequencies
 
See also

 
 

 
A sample barplot of pyKVFinder.plot_frequencies is shown below.

-../_images/plot-frequencies.png
+../../_images/plot-frequencies.png
 

 


 

 

-

 

-
7. Performing hydropathy characterization

+
7. Performing hydropathy characterization

 
A hydropathy characterization, that maps a target hydrophobicity scale on surface points and calculate the average hydropathy, is performed on the surface points of the detected cavities.

 
pyKVFinder.hydropathy takes the surface points of the detected cavities, the NumPy array with residue number, chain identifier, residue name, atom name, xyz coordinates and radius for each atom, the NumPy array with vertice coordinates (origin, X-axis, Y-axis, Z-axis), a collection of detection parameters (step, probe_in) and a target hydrophobicity scale to be mapped on the surface points, and returns a tuple with a NumPy array with the hydropobicity scale mapped to the surface points in the 3D grid and a dictionary with the average hydrophobicity scale of the detected cavities and the range of the chosen hydrophobicity scale.

 
>>> # Default Hydrophobicity Scale (hydropathy): 'EisenbergWeiss'
@@ -785,12 +753,12 @@ 
7. Performing hydropathy characterization
 
See also

 
 

 

 

-
8. Performing depth characterization

+
8. Performing depth characterization

 
A depth characterization identifies the degree of burial of the binding site. First, it identifies the cavity volume boundary. Subsequently, the depth of each cavity point is heuristically estimated by the shortest Euclidean distance between the cavity point and its respective boundary points. With this, the maximum and average depths for the detected cavities are calculated.

 
pyKVFinder.depth takes the detected cavities and the grid spacing (step) and returns a tuple with a NumPy array with the depth of the cavity points in the 3D grid, a dictionary with the maximum depth of the detected cavities and a dictionary with the average depth of the detected cavities.

 
>>> depths, max_depth, avg_depth = pyKVFinder.depth(cavities, step=step)
@@ -829,36 +797,36 @@ 
8. Performing depth characterization
 
See also

 
 

 

 

-
9. Exporting cavities

+
9. Exporting cavities

 
There are four different ways to export the detected cavities to PDB-formatted files.

 

-
9.1 Exporting only cavity points

+
9.1 Exporting only cavity points

 
>>> output_cavity = 'cavity_wo_surface.pdb'
 >>> pyKVFinder.export(output_cavity, cavities, None, vertices, step=step)
 

 

 

 

-
9.2 Exporting cavity and surface points

+
9.2 Exporting cavity and surface points

 
>>> output_cavity = 'cavity.pdb'
 >>> pyKVFinder.export(output_cavity, cavities, surface, vertices, step=step)
 

 

 

 

-
9.3 Exporting cavity and surface points with depth mapped on B-factor

+
9.3 Exporting cavity and surface points with depth mapped on B-factor

 
>>> output_cavity = 'cavity_with_depth.pdb'
 >>> pyKVFinder.export(output_cavity, cavities, surface, vertices, step=step, B=depths)
 

 

 

 

-
9.4 Exporting cavity and surface points with depth mapped on B-factor and hydrophobicity scale mapped on Q-factor

+
9.4 Exporting cavity and surface points with depth mapped on B-factor and hydrophobicity scale mapped on Q-factor

 
>>> output_cavity = 'cavity_with_depth.pdb'
 >>> pyKVFinder.export(output_cavity, cavities, surface, vertices, step=step, B=depths, Q=scales)
 

@@ -874,44 +842,44 @@ 
9.4 Exporting cavity and surface points with depth mapped on B-factor and hy
 

 
See also

 
 

 

 

 

-
10.  Writing results

+
10.   Writing results

 
The function call depends on the characterizations performed on the detected cavities.

 

-
10.1 Cavity detection only

+
10.1 Cavity detection only

 
>>> output_results = 'results.toml'
 >>> pyKVFinder.write_results(output_results, input=pdb, ligand=None, output=output_cavity, step=step)
 

 

 

 

-
10.2 Spatial characterization

+
10.2 Spatial characterization

 
>>> output_results = 'results.toml'
 >>> pyKVFinder.write_results(output_results, input=pdb, ligand=None, output=output_cavity, volume=volume, area=area, step=step)
 

 

 

 

-
10.3 Spatial and constitutional characterization

+
10.3 Spatial and constitutional characterization

 
>>> output_results = 'results.toml'
 >>> pyKVFinder.write_results(output_results, input=pdb, ligand=None, output=output_cavity, volume=volume, area=area, residues=residues, frequencies=frequencies, step=step)
 

 

 

 

-
10.4 Spatial, constitutional and depth characterization

+
10.4 Spatial, constitutional and depth characterization

 
>>> output_results = 'results.toml'
 >>> pyKVFinder.write_results(output_results, input=pdb, ligand=None, output=output_cavity, volume=volume, area=area, max_depth=max_depth, avg_depth=avg_depth, residues=residues, frequencies=frequencies, step=step)
 

 

 

 

-
10.5 Spatial, constitutional, depth and hydropathy characterization

+
10.5 Spatial, constitutional, depth and hydropathy characterization

 
>>> output_results = 'results.toml'
 >>> pyKVFinder.write_results(output_results, input=pdb, ligand=None, output=output_cavity, volume=volume, area=area, max_depth=max_depth, avg_depth=avg_depth, avg_hydropathy=avg_hydropathy, residues=residues, frequencies=frequencies, step=step)
 

@@ -923,14 +891,14 @@ 
10.5 Spatial, constitutional, depth and hydropathy characterization
 
See also

 
 

 

 

 

 

-
Steered detection

+
Steered detection

 
All these steps showed so far were performed the detection on the whole target biomolecule; however, we can perform them on a custom 3D grid, where we can explore closed regions with a custom box, which can be defined by a .toml file.

 
There are three methods to define a custom 3D grid as shown in Box configuration file template.

 
First, we will create a box .toml file with:

@@ -986,7 +954,7 @@ 
Steered detection
-
Workflows

+
Workflows

 
Then, you can explore the box adjustment mode with the standard and full workflows, defining the box parameter as the filepath of one box configuration file from above (custom-box.toml, residues-box.toml or box.toml).

 
For instance, with custom-box.toml:

 
>>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
@@ -1001,12 +969,12 @@ 
Workflows
 
See also

 
 

 

 

-
Separated steps

+
Separated steps

 
If you are running pyKVFinder package in a step-by-step fashion (Separated steps), the steps 3 and 4 are different than before.

 

 

 

 

 

-
Molecular volume

+
Molecular volume

 
All files used on this tutorial can be found in our package and in our GitHub repository:

 
    
 
  • ClO4.pdb
    • 
@@ -1073,13 +1041,13 @@ 
    Molecular volume
 
-../_images/vdw.png
+../../_images/vdw.png
 
    
 (a) vdW
    
-../_images/ses.png
+../../_images/ses.png
 
    
 (b) SES
    
-../_images/sas.png
+../../_images/sas.png
 
    
 (c) SAS
    
 
@@ -1097,7 +1065,7 @@ 
    Molecular volumebuilt-in dictionary. In the 3D grid, each voxel corresponds to a molecule (0) or solvent (1) points. Here, we can model our molecule using the vdW surface, SES or SAS.
    
 
    
-
    1. vdW volume
    
+
    1. vdW volume
    
 
    Molecule.vdw() takes a grid spacing and returns a NumPy array with the molecule points representing the vdW surface in the 3D grid.
    
 
    >>> # Grid Spacing (step): 0.1
 >>> step = 0.1
@@ -1130,7 +1098,7 @@ 
    1. vdW volume
    >>> molecule.export("vdw-model.pdb")
 
    
 
    
-../_images/vdw-grid.png
+../../_images/vdw-grid.png
 
    We can also export our modelled molecule int the 3D grid by running:
    
 
    >>> molecule.preview()
 
    
@@ -1142,7 +1110,7 @@ 
    1. vdW volume
-
    2. SES volume
    
+
    2. SES volume
    
 
    Molecule.surface() takes the grid spacing, the spherical probe size to model the surface, the SES representation and returns a NumPy array with the molecule points representing the SES in the 3D grid.
    
 
    >>> # Grid Spacing (step): 0.1
 >>> step = 0.1
@@ -1179,7 +1147,7 @@ 
    2. SES volume
    >>> molecule.preview()
 
    
 
    
-../_images/ses-grid.png
+../../_images/ses-grid.png
 
    Now, we can estimate the vdW volume by running:
    
 
    >>> molecule.volume()
 90.8
@@ -1187,7 +1155,7 @@ 
    2. SES volume
-
    3. SAS volume
    
+
    3. SAS volume
    
 
    Molecule.surface() takes a grid spacing, a spherical probe to model the surface, a SAS representation and returns a NumPy array with the molecule points representing the SES in the 3D grid.
    
 
    >>> # Grid Spacing (step): 0.1
 >>> step = 0.1
@@ -1224,7 +1192,7 @@ 
    3. SAS volume
    >>> molecule.preview()
 
    
 
    
-../_images/sas-grid.png
+../../_images/sas-grid.png
 
    Now, we can estimate the vdW volume by running:
    
 
    >>> molecule.volume()
 340.28
@@ -1232,25 +1200,14 @@ 
    3. SAS volume
-
    Examples
    
-
    Jupyter notebook examples are available for:
    
-
    
-
-
    
 
    
 
 
            

           

           

 
   

diff --git a/docs/_cli/index.html b/docs/plugins/cli/index.html
similarity index 57%
rename from docs/_cli/index.html
rename to docs/plugins/cli/index.html
index 4a198d49..2b14890f 100644
--- a/docs/_cli/index.html
+++ b/docs/plugins/cli/index.html
@@ -1,29 +1,29 @@
 
-
+
 
   
 
   
-  Positional arguments — pyKVFinder 0.6.14 documentation
-      
-      
+  Command-line interface — pyKVFinder 0.7.0 documentation
+      
+      
 
   
-    
+    
   
   
-        
-        
-        
-        
-        
-    
-    
-    
-    
-     
+        
+        
+        
+        
+        
+    
+    
+    
+    
+     
 
 
  
@@ -34,61 +34,50 @@
 
           
           
-          
+          
             pyKVFinder
-              
+              
           
               

-                0.6
+                0.7
               

 

-  

+  
     
     
     
   

 

         

@@ -97,17 +86,17 @@
 
     

 
       

         

           

   
   

@@ -115,7 +104,9 @@
           

            

              
-  
Command-line interface
In addition to pyKVFinder package, a command-line interface (CLI) is available to ease cavity detection and characterization with the full set of customizable parameters.

+  

+
Command-line interface

+
In addition to pyKVFinder package, a command-line interface (CLI) is available to ease cavity detection and characterization with the full set of customizable parameters.

 
$ pyKVFinder
 Usage: pyKVFinder [-h] [-v] [--version] [-b <str>] [-O <str>]
                   [--nthreads <int>] [-d <str>] [-s <float>] [-i <float>]
@@ -128,18 +119,18 @@ 
Command-line interface
In addition to pyKVFinder package, a command-l
 

 

 

-
Positional arguments

+
Positional arguments

 
The positional arguments are:

 
    
 
  • (<.pdb> | <.xyz>): A path to a target PDB or XYZ file.
    
-
    $ pyKVFinder <.pdb>
+
    $ pyKVFinder (<.pdb> | <.xyz>)
 
    
 
    
 
    • 
 

 

 

-
Optional arguments

+
Optional arguments

 
The optional arguments are:

 
    
 
  • -h or --help: Show help message.
    
@@ -154,7 +145,7 @@ 
    Optional arguments-v or --verbose: Print extra information to standard output.
    
-
    $ pyKVFinder <.pdb> --verbose
+
    $ pyKVFinder (<.pdb> | <.xyz>) --verbose
 
    
 
    
 
    
@@ -164,19 +155,19 @@ 
    Optional arguments-b <str> or --base_name <str>: A prefix for output files.
    
-
    $ pyKVFinder <.pdb> -b <str>
-$ pyKVFinder <.pdb> --base_name <str>
+
    $ pyKVFinder (<.pdb> | <.xyz>) -b <str>
+$ pyKVFinder (<.pdb> | <.xyz>) --base_name <str>
 
    
 
    
 
    
 
    Default:
    
-
    Prefix of target PDB file (<.pdb>)
    
+
    Prefix of target PDB or XYZ file (<.pdb> | <.xyz>)
    
 
    
 
    
 
    • 
 
  • -O <str> or --output_directory <str>: A path to a directory for output files.
    
-
    $ pyKVFinder <.pdb> -O <str>
-$ pyKVFinder <.pdb> --output_directory <str>
+
    $ pyKVFinder (<.pdb> | <.xyz>) -O <str>
+$ pyKVFinder (<.pdb> | <.xyz>) --output_directory <str>
 
    
 
    
 
    
@@ -186,7 +177,7 @@ 
    Optional arguments--nthreads <int>: Number of threads to apply in parallel routines.
    
-
    $ pyKVFinder <.pdb> --nthreads <int>
+
    $ pyKVFinder (<.pdb> | <.xyz>) --nthreads <int>
 
    
 
    
 
    
@@ -196,13 +187,13 @@ 
    Optional arguments
-
    Detection and characterization
    
+
    
+
    Cavity detection
    
 
    The arguments for adjusting biomolecular detection are:
    
 
      
 
    • -d <str> or --dictionary <str>: A path to a van der Waals radii file (see template).
      
-
      $ pyKVFinder <.pdb> -d <str>
-$ pyKVFinder <.pdb> --dictionary <str>
+
      $ pyKVFinder (<.pdb> | <.xyz>) -d <str>
+$ pyKVFinder (<.pdb> | <.xyz>) --dictionary <str>
 
      
 
      
 
      
@@ -212,8 +203,8 @@ 
      Detection and characterization-s <float> or --step <float>: Grid spacing (A).
      
-
      $ pyKVFinder <.pdb> -s <float>
-$ pyKVFinder <.pdb> --step <float>
+
      $ pyKVFinder (<.pdb> | <.xyz>) -s <float>
+$ pyKVFinder (<.pdb> | <.xyz>) --step <float>
 
      
 
      
 
      
@@ -223,8 +214,8 @@ 
      Detection and characterization-i <float> or --probe_in <float>: Probe In size (A).
      
-
      $ pyKVFinder <.pdb> -i <float>
-$ pyKVFinder <.pdb> --probe_in <float>
+
      $ pyKVFinder (<.pdb> | <.xyz>) -i <float>
+$ pyKVFinder (<.pdb> | <.xyz>) --probe_in <float>
 
      
 
      
 
      
@@ -234,8 +225,8 @@ 
      Detection and characterization-o <float> or --probe_out <float>: Probe Out size (A).
      
-
      $ pyKVFinder <.pdb> -o <float>
-$ pyKVFinder <.pdb> --probe_out <float>
+
      $ pyKVFinder (<.pdb> | <.xyz>) -o <float>
+$ pyKVFinder (<.pdb> | <.xyz>) --probe_out <float>
 
      
 
      
 
      
@@ -245,8 +236,8 @@ 
      Detection and characterization-V <float> or --volume_cutoff <float>: Cavities volume filter (A3).
      
-
      $ pyKVFinder <.pdb> -V <float>
-$ pyKVFinder <.pdb> --volume_cutoff <float>
+
      $ pyKVFinder (<.pdb> | <.xyz>) -V <float>
+$ pyKVFinder (<.pdb> | <.xyz>) --volume_cutoff <float>
 
      
 
      
 
      
@@ -256,8 +247,8 @@ 
      Detection and characterization-R <float> or --removal_distance <float>: Length to be removed from the cavity-bulk frontier (A).
      
-
      $ pyKVFinder <.pdb> -R <float>
-$ pyKVFinder <.pdb> --removal_distance <float>
+
      $ pyKVFinder (<.pdb> | <.xyz>) -R <float>
+$ pyKVFinder (<.pdb> | <.xyz>) --removal_distance <float>
 
      
 
      
 
      
@@ -267,8 +258,8 @@ 
      Detection and characterization-S <str> or --surface <str>: A surface representation. Options are: SES and SAS. SES specifies solvent excluded surface and SAS specifies solvent accessible surface.
      
-
      $ pyKVFinder <.pdb> -S <str>
-$ pyKVFinder <.pdb> --surface <str>
+
      $ pyKVFinder (<.pdb> | <.xyz>) -S <str>
+$ pyKVFinder (<.pdb> | <.xyz>) --surface <str>
 
      
 
      
 
      
@@ -278,7 +269,7 @@ 
      Detection and characterization--ignore_backbone: Ignore backbone contacts to cavity when defining interface residues.
      
-
      $ pyKVFinder <.pdb> --ignore_backbone
+
      $ pyKVFinder (<.pdb> | <.xyz>) --ignore_backbone
 
      
 
      
 
      
@@ -289,13 +280,13 @@ 
      Detection and characterization
-
      Extra characterization
      
+
      
+
      Additional characterization
      
 
      The parameters for additional characterization are:
      
 
      
 
      
-
      Box adjusment
      
+
      Box adjusment
      
 
      The box adjustment argument is:
      
 
        
 
      • -B <.toml> or --box <.toml>: A path to TOML-formatted file with box parameters (see template). Adjust the 3D grid based on a list of residues ([“resnum”, “chain”]) and a padding or a set of four vertices (p1: origin, p2: X-axis max, p3: Y-axis max, p4: Z-axis max) with xyz coordinates ([x, y, z]).
        
-
        $ pyKVFinder <.pdb> -B <.toml>
-$ pyKVFinder <.pdb> --box <.toml>
+
        $ pyKVFinder (<.pdb> | <.xyz>) -B <.toml>
+$ pyKVFinder (<.pdb> | <.xyz>) --box <.toml>
 
        
 
        
 
        
@@ -361,12 +352,12 @@ 
        Box adjusment
-
        Ligand adjustment
        
+
        Ligand adjustment
        
 
        The ligand adjustment arguments are:
        
 
          
 
        • -L (<.pdb> | <.xyz>) or --ligand (<.pdb> | <.xyz>): A path to a ligand PDB or XYZ file to limit the cavities within a radius (ligand_cutoff) around it.
          
-
          $ pyKVFinder <.pdb> -L <.pdb>
-$ pyKVFinder <.pdb> --ligand <.pdb>
+
          $ pyKVFinder (<.pdb> | <.xyz>) -L (<.pdb> | <.xyz>)
+$ pyKVFinder (<.pdb> | <.xyz>) --ligand (<.pdb> | <.xyz>)
 
          
 
          
 
          
@@ -376,7 +367,7 @@ 
          Ligand adjustment--ligand_cutoff <float>: A radius value to limit a space around the defined ligand.
          
-
          $ pyKVFinder <.pdb> -L <.pdb> --ligand_cutoff <float>
+
          $ pyKVFinder (<.pdb> | <.xyz>) -L (<.pdb> | <.xyz>) --ligand_cutoff <float>
 
          
 
          
 
          
@@ -387,14 +378,15 @@ 
          Ligand adjustment
-        
-        
+        
+        
     
          
 
   
          
diff --git a/docs/plugins/pymol/index.html b/docs/plugins/pymol/index.html
new file mode 100644
index 00000000..156a805d
--- /dev/null
+++ b/docs/plugins/pymol/index.html
@@ -0,0 +1,297 @@
+
+
+
+  
+
+  
+  PyMOL pyKVFinder Tools — pyKVFinder 0.7.0 documentation
+      
+      
+
+  
+    
+  
+  
+        
+        
+        
+        
+        
+    
+    
+    
+    
+     
+
+
+ 
+  
          
+    
+
+    
          
+
+      
          
+        
          
+          
          
+  
+  
          
+
          
+          
          
+           
          
+             
+  
          
+
          PyMOL pyKVFinder Tools
          
+
          If you wish to use pyKVFinder with a graphical user interface on [PyMOL](https://pymol.org/), PyMOL pyKVFinder Tools is available to use with PyMOL and has been been developed using Qt interface and Python3.
          
+
          
+
          Installation
          
+
          First, you need to install PyMOL v2.x or v3.x on your computer. If you do not have it installed, please refer to PyMOL website.
          
+
          After installing PyMOL, plug-in requires the installation of pyKVFinder, toml, and pyqt5 modules and PyMOL’s native Python does not have it installed. So you need to install it:
          
+
          pip install pyKVFinder toml pyqt5
+
          
+
          
+
          
+
          Note
          
+
          pip package management system installation is required.
          
+
          
+
          Then, to install the PyMOL pyKVFinder Tools on PyMOL, download the latest PyMOL-pyKVFinder-Tools.zip from here and follow these steps:
          
+
            
+
          1. Open PyMOL.
            2. 
+
          2. Go to Plugin menu, click on Plugin Manager.
            3. 
+
          3. The Plugin Manager window will open, go to the Install New Plugin tab.
            4. 
+
          4. Under Install from local file panel, click on Choose file….
            5. 
+
          5. The Install Plugin window will open, select the PyMOL-pyKVFinder-Tools.zip that you downloaded earliar.
            6. 
+
          6. The Select plugin directory window will open, select
+/home/<user>/.pymol/startup and click OK.
            7. 
+
          7. The Confirm window will open, click OK.
            8. 
+
          8. The Sucess window will appear, confirming that the plug-in has
+been installed.
            9. 
+
          9. Restart PyMOL.
            10. 
+
          10. PyMOL pyKVFinder Tools is ready to use.
            11. 
+
          
+
          Or, instead of selecting PyMOL-pyKVFinder-Tools.zip (Step 5), you can select __init__.py file on pyKVFinder/plugins/PyMOL-pyKVFinder-Tools directory tree.
          
+
          
+
          
+
          Tutorial
          
+
          This tutorial will guide you through the steps to use PyMOL pyKVFinder Tools. All files used in this tutorial can be found our GitHub repository:
          
+
+
          In this tutorial, we will use pyKVFinder on a catalytic subunit of a cAMP-dependent protein kinase (cADK) to identify and characterize its cavities. First, load the 1FMO.pdb and ADN.pdb file into PyMOL:
          
+../../_images/pymol_viewer_1.png
+
          
+
          Whole biomolecule detection
          
+
          The default parameters are designed to make a simple and fast whole biomolecule detection.
          
+
          On PyMOL, open PyMOL pyKVFinder Tools under Plugin tab. The objects on the scene will be listed on the Input PDB combo box, on the Main tab. If not, press the Refresh button.
          
+
          The Input PDB selection sets which object will be analyzed by pyKVFinder. Select 1FMO on the list box.
          
+../../_images/main_tab_1.png
+
          To run pyKVFinder with the default parameters, just click Run pyKVFinder button.
          
+../../_images/main_tab_2.png
+
          After execution is complete, cavities PDB is loaded into PyMOL viewer as <Output Base Name>.KVFinder.output object and the results file is loaded on the Results tab. In addition, the focus automatically shifts to Results tab.
          
+../../_images/results_tab_1.png
+
          We can select cavities in the Volume or Surface Area lists to highlight them on a new object called cavities, identifying each cavity. Additionally, we can select cavity tags in the Interface Residues list to highlight residues around the cavities on a new object named residues.
          
+../../_images/results_tab_2.png
+
          
+
          Note
          
+
          The interface residues surrounding the cavity KAH are colored in green (sticks), the surface points are colored in red (nb_spheres) and the remaining cavity points are colored in blue (non_bounded).
          
+
          
+
          We can visualize depth of the cavity points by clicking on Depth option on Show descriptors. We can select cavities in the Average Depth or Maximum Depth lists to highlight them on a new object called depths, identifying each cavity.
          
+../../_images/results_tab_3.png
+
          
+
          Note
          
+
          The cavity points are colored using a gradient from blue to red to represent the depth of each point. The blue points correspond to the shallowest points on the cavity-bulk boundary, while the red points correspond to the deepest points. The depth scale ranges from 0.0 to the maximum depth of all cavities
          
+
          
+
          We can visualize hydropathy of the surface points by clicking on Hydropathy options on Show descriptors. We can select cavities in the Average Hydropathy list to highlight them on a new object called hydropathy, identifying each cavity.
          
+../../_images/results_tab_4.png
+
          
+
          Note
          
+
          The surface points are colored based on the closest amino acid to it. The Eisenberg & Weiss hydrophobicity scale ranges from -1.42 (highly hydrophobic) to 2.6 (highly hydrophilic).
          
+
          
+
          
+
          Changing cavity boundary
          
+
          pyKVFinder is all about parameter customization. One of pyKVFinder’s most powerful assets is the ability to manually set the cavity boundary.
          
+
          pyKVFinder works with a double probe system to detect cavities. A smaller probe, called Probe In, and a bigger one, called Probe Out, that defines two molecular surfaces with different molecular accessibility. The space left between these surfaces is considered cavities.
          
+
          Let’s show the effect of varying Probe Out and Removal Distance on the cavity boundary.
          
+
          First, we should copy the cavity KAH to a new object to compare cavity boundary from the previous execution.
          
+
          # Copy KAH
+select resn KAH and output.KVFinder.output
+create KAH, sele
+delete sele
+# Color KAH
+color magenta, KAH
+
          
+
          
+
          
+
          Adjusting Probe Out
          
+
          As mentioned above, adjusting the Probe Out size changes the level of the cavity boundary. So let’s go back on the Main tab and change the Probe Out size to 8.0 Å. Run pyKVFinder again.
          
+../../_images/pymol_viewer_2.png
+
          Again, copy the cavity KAF (same region of the previous detection) to a new object (KAF_PO).
          
+
          # Copy KAF
+select resn KAF and output.KVFinder.output
+create KAF_PO, sele
+delete sele
+
          
+
          
+../../_images/pymol_viewer_3.png
+
          The cavity detected with the 4 Å Probe Out (magenta) has a lower boundary than that detected with the 8 Å probe (white). Therefore, by increasing the size of the Probe Out, the cavity boundary is also raised.
          
+
          
+
          
+
          Adjusting Removal Distance
          
+
          Besides adjusting the Probe Out size, we can also adjust the Removal Distance to change the cavity boundary. So let’s go back to the Main tab and change the Removal Distance to 1.2 Å and the size of Probe Out back to 4.0 Å. Run pyKVFinder again.
          
+../../_images/pymol_viewer_4.png
+
          Again, copy the cavity KAG (same region of the previous detections) to a new object (KAG_RD).
          
+
          # Copy KAG
+select resn KAG and output.KVFinder.output
+create KAG_RD, sele
+delete sele
+
          
+
          
+../../_images/pymol_viewer_5.png
+
          
+

          
+
          
+
          The cavity KAH detected with the 2.4 Å Removal Distance (magenta) has a lower boundary than that detected with the 1.2 Å (KAG; white). Therefore, by decreasing the Removal Distance, the cavity boundary is also raised.
          
+
          Furthermore, changing the cavity boundary by varying Probe Out and Removal Distance also affects cavity segregation.
          
+
          
+
          Note
          
+
          Usually the Removal Distance adjustment is less time-consuming than the Probe Out adjustment for similar effects.
          
+
          
+
          
+
          
+
          
+
          
+
          Steered detection
          
+
          An important feature of parKVFinder is the steered detection of cavities. We continue our tutorial illustrating two distinct methods of cavity segmentation.
          
+
          
+
          Box adjustment mode
          
+
          Box adjustment mode explores closed regions with a custom box, which can be drawn via the GUI.
          
+
          On the Search Space tab, select Box Adjustment check box. This will enable a Box Adjustment frame, which handles the custom box in PyMOL viewer
          
+../../_images/search_space_tab_1.png
+
          Then, select the adenosine ligand on ADN object. This can be made on the PyMOL viewer by clicking on the ligand structure or using select resn ADN PyMOL command.
          
+
          Click on Draw Box Button. This will create a custom box that limits the search space. It is fully customizable, but we will not change it for now.
          
+../../_images/pymol_viewer_6.png
+
          On the Main tab, change Removal Distance back to 2.4 Å. Run pyKVFinder again.
          
+../../_images/pymol_viewer_7.png
+
          Now, let’s customize the box parameters to segment the binding site of our target protein.
          
+
          Each axis is associated with one color (red with X, green with Y and blue with Z). The adjustment is made by the arrows or directly setting the value in the entry on the Search Space tab in the Box Adjustment group. We can also adjust the box angles by the same procedure. After altering the values, just click on Redraw button to redraw the box object using the new values.
          
+
          Then, on the Search Space tab, reduce Maximum X to 1.0 Å and click Redraw Box. Run pyKVFinder again.
          
+../../_images/pymol_viewer_8.png
+
          Lastly, click on Delete Box button to delete the custom box.
          
+
          
+
          
+
          Ligand adjustment mode
          
+
          A last feature is to limit the search around a structure. In this last example, let’s do a whole protein prospection again, but limiting the search space around ligands.
          
+
          First, on the Search Space tab, deselect Box Adjustment check box, which will disable the previous enabled Box Adjustment frame.
          
+
          Still on the Search Space tab, click on the check button Ligand Adjustment, which will enable the Refresh button, the Ligand PDB combo box and the Ligand Cutoff entry.
          
+../../_images/search_space_tab_2.png
+
          Click the Refresh button to display all objects in the scene in the Ligand PDB combo box. Select the ADN on the combo box and reduce Ligand Cutoff to 3.0 Å. Run pyKVFinder again.
          
+../../_images/pymol_viewer_9.png
+
          On the Search Space tab, increase Ligand Cutoff back to 5.0 Å. Back on the Main tab, increase Probe Out to 10.0 Å and reduce Removal Distance to 0.0 Å. Run pyKVFinder again.
          
+../../_images/pymol_viewer_10.png
+
          
+
          
+
          
+
          
+
+
+           
          
+          
          
+          
+        
          
+      
          
+    
          
+  
          
+   
+
+
+
\ No newline at end of file
diff --git a/docs/search.html b/docs/search.html
index 1ec88fd9..1558af1e 100644
--- a/docs/search.html
+++ b/docs/search.html
@@ -3,7 +3,7 @@
 
   
   
-  Search — pyKVFinder 0.6.14 documentation
+  Search — pyKVFinder 0.7.0 documentation
       
       
 
@@ -16,8 +16,8 @@
   
         
         
-        
-        
+        
+        
         
     
     
@@ -39,7 +39,7 @@
               
           
               
          
-                0.6
+                0.7
               
          
 
          
   
          
@@ -49,40 +49,25 @@
   
          
 
          
         
          
diff --git a/docs/searchindex.js b/docs/searchindex.js
index 2cacb6a1..d4447f10 100644
--- a/docs/searchindex.js
+++ b/docs/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["_about/index", "_api_reference/Molecule", "_api_reference/calculate_frequencies", "_api_reference/constitutional", "_api_reference/depth", "_api_reference/detect", "_api_reference/export", "_api_reference/export_openings", "_api_reference/get_vertices", "_api_reference/get_vertices_from_file", "_api_reference/hydropathy", "_api_reference/index", "_api_reference/openings", "_api_reference/plot_frequencies", "_api_reference/pyKVFinderResults", "_api_reference/read_cavity", "_api_reference/read_pdb", "_api_reference/read_vdw", "_api_reference/read_xyz", "_api_reference/run_workflow", "_api_reference/spatial", "_api_reference/write_results", "_cfg_files/box_file_template", "_cfg_files/hydrophobicity_scale_file_template", "_cfg_files/vdw_file_template", "_cli/index", "_installation/index", "_tutorial/index", "index"], "filenames": ["_about/index.rst", "_api_reference/Molecule.rst", "_api_reference/calculate_frequencies.rst", 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-# Sphinx build info version 1
-# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 232001389621d83de19e91efe63c5513
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-
-
-
-  
-
-  
-  Issues — pyKVFinder 0.5.0 documentation
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          About
          
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          Issues
          
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          pyKVFinder package uses GitHub for project management. Please help us by reporting any problems or requests.
          
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          On Issues page, you can file a:
          
-
          
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          Only make sure the bug or request has not already been reported. Click on “Search” and enter some keywords to search.
          
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          Thank you for helping us improve pyKVFinder!
          
-
          
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          Scientific team
          
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          pyKVFinder was developed by:
          
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          • João Victor da Silva Guerra
            • 
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          • Helder Veras Ribeiro Filho
            • 
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          • Gabriel Ernesto Jara
            • 
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          • Leandro Oliveira Bortot
            • 
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          • José Geraldo de Carvalho Pereira
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          • Paulo Sergio Lopes de Oliveira
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          Computational Biology Laboratory (LBC), Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM)
          
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          If you have any further questions, inquires or if you wish to contribute to KVFinder project, please contact us at joao.guerra@lnbio.cnpem.br or paulo.oliveira@lnbio.cnpem.br.
          
-
          
-
          
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          Citing pyKVFinder
          
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          Guerra, J.V.d., Ribeiro-Filho, H.V., Jara, G.E. et al. pyKVFinder: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science. BMC Bioinformatics 22, 607 (2021). https://doi.org/10.1186/s12859-021-04519-4.
          
-
          
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          Funding
          
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          This work was supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) [Grant Number 2018/00629-0], Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) [Grant Number 350244/2020-0], and Brazilian Center for Research in Energy and Materials (CNPEM).
          
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          License
          
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          The software is licensed under the terms of the GNU General Public License version 3 (GPL3) and is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
          
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diff --git a/docs/source/_build/html/_api_reference/Molecule.html b/docs/source/_build/html/_api_reference/Molecule.html
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-  pyKVFinder.Molecule — pyKVFinder 0.5.0 documentation
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          pyKVFinder.Molecule
          
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-class pyKVFinder.Molecule(molecule: Union[str, Path], radii: Optional[Union[str, Path, Dict[str, Any]]] = None, model: Optional[int] = None, nthreads: Optional[int] = None, verbose: bool = False)[source]
          
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          A class for representing molecular structures.
          
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          Parameters:
          
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          • molecule (Union[str, pathlib.Path]) – A file path to the molecule in either PDB or XYZ format
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          • radii (Union[str, pathlib.Path, Dict[str, Any]], optional) – A file path to a van der Waals radii file or a dictionary of VDW radii, by default None. If None, apply the built-in van der Waals radii file: vdw.dat.
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          • model (int, optional) – The model number of a multi-model PDB file, by default None. If None, keep atoms from all models.
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          • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is os.cpu_count() - 1.
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          • verbose (bool, optional) – Print extra information to standard output, by default False.
            • 
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-_atomic
          
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          A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates and radius) for each atom.
          
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          Type:
          
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          numpy.ndarray
          
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-_dim
          
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          Grid dimensions.
          
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          Type:
          
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          tuple
          
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-_grid
          
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          Molecule points in the 3D grid (grid[nx][ny][nz]).
-Grid array has integer labels in each position, that are:
          
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          • 0: molecule points;
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          • 1: solvent points.
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          Type:
          
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          numpy.ndarray
          
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-_molecule
          
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          A file path to the molecule in either PDB or XYZ format.
          
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          Type:
          
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          Union[str, pathlib.Path]
          
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-_padding
          
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          The length to add to each direction of the 3D grid.
          
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          Type:
          
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          Spherical probe size to define the molecular surface based on a molecular representation.
          
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          Type:
          
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          A dictionary containing radii values, by default None.
          
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          Type:
          
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          Molecular surface representation. Keywords options are vdW (van der Waals surface), SES (Solvent Excluded Surface) or SAS (Solvent Accessible Surface), by default SES.
          
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          Type:
          
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          str, optional
          
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          A numpy.ndarray with sine and cossine of the grid rotation angles (sina, cosa, sinb, cosb).
          
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          Type:
          
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          Grid spacing (A).
          
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          Type:
          
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          A numpy.ndarray or a list with xyz vertices coordinates (origin, X-axis, Y-axis, Z-axis).
          
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          Type:
          
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          Number of threads for parallel processing.
          
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          Type:
          
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          Whether to print extra information to standard output.
          
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          Type:
          
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          Note
          
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          The van der Waals radii file defines the radius values for each atom by residue and when not defined, it uses a generic value based on the atom type. The function by default loads the built-in van der Waals radii file: vdw.dat.
          
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          See also
          
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          read_vdw
          
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          Example
          
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          The Molecule class loads the target molecular structure (ClO4) into pyKVFinder. class.
          
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          >>> import os
->>> from pyKVFinder import Molecule
->>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'ClO4.pdb')
->>> molecule = Molecule(pdb)
->>> molecule
->>> <pyKVFinder.main.Molecule object at 0x7f5ddacf2230>
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          The van der Waals radii can be define by:
          
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          • creating a Python dictionary:
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          >>> # PyMOL (v2.5.0) vdW radii values
->>> vdw = {'GEN': {'CL': 1.75, 'O': 1.52}}
->>> molecule = Molecule(pdb, radii=vdw)
->>> molecule.radii
-{'GEN': {'CL': 1.75, 'O': 1.52}}
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          • specifying a .dat file following template of van der Waals radii file.
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          >>> from pyKVFinder import read_vdw
->>> # ChimeraX vdW radii values
->>> with open('vdw.dat', 'w') as f:
-...     f.write('>GEN\nCL\t\t1.98\nO\t\t1.46\n')
->>> vdw = read_vdw('vdw.dat')
->>> molecule = Molecule(pdb, radii=vdw)
->>> molecule.radii
-{'GEN': {'CL': 1.98, 'O': 1.46}}
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-property atomic: ndarray
          
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          Get _atomic attribute.
          
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          Get _dim attribute
          
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          Export molecule points (H) to a PDB-formatted file.
          
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          Parameters:
          
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          fn (Union[str, pathlib.Path], optional) – A file path to the molecular volume in the grid-based rerpesentation in PDB format, by default “molecule.pdb”.
          
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          Example
          
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          >>> molecule.export('model.pdb')
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          Get _grid attribute.
          
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          Get _molecule attribute.
          
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          Get grid units in X-axis.
          
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          Get grid units in Y-axis.
          
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          Get grid units in Z-axis.
          
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          Get origin of the 3D grid.
          
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          Get X-axis max of the 3D grid.
          
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          Get Y-axis max of the 3D grid.
          
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          Get Z-axis max of the 3D grid.
          
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          Get _padding attribute.
          
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-preview(**kwargs) → None[source]
          
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          Preview the molecular surface in the 3D grid.
          
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          Example
          
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          With the molecular surface modelled by Molecule.vdw() or Molecule.surface(), the modelled molecule in the 3D grid can be previewed by running:
          
-
          >>> molecule.preview()
-
          
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-property probe: float
          
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          Get _probe attribute.
          
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          Get _radii attribute.
          
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-property representation: str
          
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          Get _representation attribute.
          
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          Get _rotation attribute.
          
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          Get _step attribute.
          
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-surface(step: float = 0.6, probe: float = 1.4, surface: str = 'SES', padding: Optional[float] = None) → None[source]
          
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          Fill the 3D grid with the molecule as the van der Waals surface representation.
          
-
          
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          Parameters:
          
-
            
-
          • step (float, optional) – Grid spacing (A), by default 0.6.
            • 
-
          • probe (float, optional) – Spherical probe size to define the molecular surface based on a molecular representation, by default 1.4.
            • 
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          • surface (str, optional) – Molecular surface representation. Keywords options are vdW (van der Waals surface), SES (Solvent Excluded Surface) or SAS (Solvent Accessible Surface), by default “SES”.
            • 
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          • padding (float, optional) – The length to add to each direction of the 3D grid, by default None. If None, automatically define the length based on molecule coordinates, probe size, grid spacing and atom radii.
            • 
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          Raises:
          
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          • TypeError – step must be a positive real number.
            • 
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          • ValueError – step must be a positive real number.
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          • TypeError – probe_out must be a positive real number.
            • 
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          • ValueError – probe_out must be a positive real number.
            • 
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-
          
-
          
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          Example
          
-
          The Molecule.surface() method takes the grid spacing, the spherical probe size to model the surface, the surface representation and returns a NumPy array with the molecule points representing the SES in the 3D grid.
          
-
          The molecular surface can be modelled as:
          
-
          
-
            
-
          • Solvent Excluded Surface (SES):
            • 
-
          
-
          >>> # Surface Representation: SES
->>> surface = 'SES'
->>> # Grid Spacing (step): 0.1
->>> step = 0.1
->>> # Spherical Probe (probe): 1.4
->>> probe = 1.4
->>> molecule.surface(step=step, probe=probe, surface=surface)
->>> molecule.grid
-array([[[1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        ...,
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1]],
-       ...,
-       [[1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        ...,
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1]]], dtype=int32)
-
          
-
          
-
          
-
          The molecular surface can be modelled as:
          
-
          
-
            
-
          • Solvent Accessible Surface (SAS):
            • 
-
          
-
          >>> # Surface Representation: SAS
->>> surface = 'SAS'
->>> # Grid Spacing (step): 0.1
->>> step = 0.1
->>> # Spherical Probe (probe): 1.4
->>> probe = 1.4
->>> molecule.surface(step=step, probe=probe, surface=surface)
->>> molecule.grid
-array([[[1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        ...,
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1]],
-       ...,
-       [[1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        ...,
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1]]], dtype=int32)
-
          
-
          
-
          
-
          
-
-
          
-
          
-vdw(step: float = 0.6, padding: Optional[float] = None) → None[source]
          
-
          Fill the 3D grid with the molecule as the van der Waals surface representation.
          
-
          
-
          Parameters:
          
-
            
-
          • step (float, optional) – Grid spacing (A), by default 0.6.
            • 
-
          • padding (float, optional) – The length to add to each direction of the 3D grid, by default None. If None, automatically define the length based on molecule coordinates, probe size, grid spacing and atom radii.
            • 
-
          
-
          
-
          Raises:
          
-
            
-
          • TypeError – step must be a positive real number.
            • 
-
          • ValueError – step must be a positive real number.
            • 
-
          
-
          
-
          
-
          Example
          
-
          The Molecule.vdw() method takes a grid spacing and returns a NumPy array with the molecule points representing the vdW surface in the 3D grid.
          
-
          >>> # Grid Spacing (step): 0.1
->>> step = 0.1
->>> molecule.vdw(step=step)
->>> molecule.grid
-array([[[1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        ...,
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1]],
-       ...,
-       [[1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        ...,
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1]]], dtype=int32)
-
          
-
          
-
          
-
-
          
-
          
-property vertices: ndarray
          
-
          Get _vertices attribute.
          
-
          
-
-
          
-
          
-volume() → float[source]
          
-
          Estimate the volume of the molecule based on the molecular surface representation, ie, vdW, SES or SAS representations.
          
-
          
-
          Returns:
          
-
          volume – Molecular volume (A³).
          
-
          
-
          Return type:
          
-
          float
          
-
          
-
          
-
          Example
          
-
          With the molecular surface modelled by Molecule.vdw() or Molecule.surface(), the volume can be estimated by running:
          
-
          >>> molecule.volume()
-90.8
-
          
-
          
-
          
-
-
          
-
          
-property xyzr: ndarray
          
-
          Get xyz coordinates and radius of molecule atoms.
          
-
          
-
-
          
-
-
          
-
-
-           
          
-          
          
-          
-        
          
-      
          
-    
          
-  
          
-   
-
-
-
\ No newline at end of file
diff --git a/docs/source/_build/html/_api_reference/calculate_frequencies.html b/docs/source/_build/html/_api_reference/calculate_frequencies.html
deleted file mode 100644
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+++ /dev/null
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-
-
-
-  
-
-  
-  pyKVFinder.calculate_frequencies — pyKVFinder 0.5.0 documentation
-      
-      
-    
-  
-  
-        
-        
-        
-        
-        
-    
-    
-    
-    
-     
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-  
          
-    
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-      
          
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-          
          
-  
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-
          
-          
          
-           
          
-             
-  
          
-
          pyKVFinder.calculate_frequencies
          
-
          
-
          
-pyKVFinder.calculate_frequencies(residues: Dict[str, List[List[str]]]) → Dict[str, Dict[str, Dict[str, int]]][source]
          
-
          Calculate frequencies of residues and class of residues
-(R1, R2, R3, R4 and R5) for detected cavities.
          
-
          
-
          Parameters:
          
-
          residues (Dict[str, List[List[str]]]) – A dictionary with a list of interface residues for each detected
-cavity.
          
-
          
-
          Returns:
          
-
          frequencies – A dictionary with frequencies of residues and class for
-residues of each detected cavity.
          
-
          
-
          Return type:
          
-
          Dict[str, Dict[str, Dict[str, int]]]
          
-
          
-
          
-
          
-
          Note
          
-
          The cavity nomenclature is based on the integer label. The cavity
-marked with 2, the first integer corresponding to a cavity, is KAA, the
-cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
          
-
          
-
          
-
          Note
          
-
          The classes of residues are:
          
-
            
-
          • Aliphatic apolar (R1): Alanine, Glycine, Isoleucine, Leucine, Methionine, Valine.
            • 
-
          • Aromatic (R2): Phenylalanine, Tryptophan, Tyrosine.
            • 
-
          • Polar Uncharged (R3): Asparagine, Cysteine, Glutamine, Proline, Serine, Threonine.
            • 
-
          • Negatively charged (R4): Aspartate, Glutamate.
            • 
-
          • Positively charged (R5): Arginine, Histidine, Lysine.
            • 
-
          • Non-standard (RX): Non-standard residues.
            • 
-
          
-
          
-
          
-
          See also
          
-
          constitutional, plot_frequencies, write_results
          
-
          
-
          Example
          
-
          With the interface residues identified with constitutional, we can calculate residues and classes of residues frequencies:
          
-
          >>> from pyKVFinder import calculate_frequencies
->>> residues
-{'KAA': [['49', 'E', 'LEU'], ['50', 'E', 'GLY'], ['51', 'E', 'THR'], ['52', 'E', 'GLY'], ['53', 'E', 'SER'], ['54', 'E', 'PHE'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['72', 'E', 'LYS'], ['74', 'E', 'LEU'], ['84', 'E', 'GLN'], ['87', 'E', 'HIS'], ['88', 'E', 'THR'], ['91', 'E', 'GLU'], ['104', 'E', 'VAL'], ['120', 'E', 'MET'], ['121', 'E', 'GLU'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['166', 'E', 'ASP'], ['168', 'E', 'LYS'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['184', 'E', 'ASP'], ['186', 'E', 'GLY'], ['187', 'E', 'PHE'], ['201', 'E', 'THR'], ['327', 'E', 'PHE']]}
->>> frequencies = calculate_frequencies(residues)
->>> frequencies
-{'KAA': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'ASN': 1, 'ASP': 2, 'GLN': 1, 'GLU': 4, 'GLY': 4, 'HIS': 1, 'LEU': 3, 'LYS': 2, 'MET': 1, 'PHE': 3, 'SER': 1, 'THR': 4, 'TYR': 1, 'VAL': 3}, 'CLASS': {'R1': 11, 'R2': 4, 'R3': 8, 'R4': 6, 'R5': 4, 'RX': 0}}}
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diff --git a/docs/source/_build/html/_api_reference/constitutional.html b/docs/source/_build/html/_api_reference/constitutional.html
deleted file mode 100644
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+++ /dev/null
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-
-
-
-  
-
-  
-  pyKVFinder.constitutional — pyKVFinder 0.5.0 documentation
-      
-      
-    
-  
-  
-        
-        
-        
-        
-        
-    
-    
-    
-    
-     
-
-
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-  
          
-    
-
-    
          
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-      
          
-        
          
-          
          
-  
-  
          
-
          
-          
          
-           
          
-             
-  
          
-
          pyKVFinder.constitutional
          
-
          
-
          
-pyKVFinder.constitutional(cavities: ndarray, atomic: Union[ndarray, List[List[Union[str, float, int]]]], vertices: Union[ndarray, List[List[float]]], step: Union[float, int] = 0.6, probe_in: Union[float, int] = 1.4, ignore_backbone: bool = False, selection: Optional[Union[List[int], List[str]]] = None, nthreads: Optional[int] = None, verbose: bool = False) → Dict[str, List[List[str]]][source]
          
-
          Constitutional characterization (interface residues) of the detected
-cavities.
          
-
          
-
          Parameters:
          
-
            
-
          • cavities (numpy.ndarray) – 
            Cavity points in the 3D grid (cavities[nx][ny][nz]).
-Cavities array has integer labels in each position, that are:
            
-
            
-
              
-
            • -1: bulk points;
              • 
-
            • 0: biomolecule points;
              • 
-
            • 1: empty space points;
              • 
-
            • >=2: cavity points.
              • 
-
            
-
            
-
            The empty space points are regions that do not meet the chosen
-volume cutoff to be considered a cavity.
            
-
            • 
-
          • atomic (Union[numpy.ndarray, List[List[Union[str, float, int]]]]) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
-and radius) for each atom.
            • 
-
          • vertices (Union[numpy.ndarray, List[List[float]]]) – A numpy.ndarray or a list with xyz vertices coordinates (origin,
-X-axis, Y-axis, Z-axis).
            • 
-
          • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.
            • 
-
          • probe_in (Union[float, int], optional) – Probe In size (A), by default 1.4.
            • 
-
          • ignore_backbone (bool, optional) – Whether to ignore backbone atoms (C, CA, N, O) when defining interface
-residues, by default False.
            • 
-
          • selection (Union[List[int], List[str]], optional) – A list of integer labels or a list of cavity names to be selectedA list of integer labels of each cavity to be selected, by default None.
            • 
-
          • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is
-os.cpu_count() - 1.
            • 
-
          • verbose (bool, optional) – Print extra information to standard output, by default False.
            • 
-
          
-
          
-
          Returns:
          
-
          residues – A dictionary with a list of interface residues for each detected
-cavity.
          
-
          
-
          Return type:
          
-
          Dict[str, List[List[str]]]
          
-
          
-
          Raises:
          
-
            
-
          • TypeError – cavities must be a numpy.ndarray.
            • 
-
          • ValueError – cavities has the incorrect shape. It must be (nx, ny, nz).
            • 
-
          • TypeError – atomic must be a list or a numpy.ndarray.
            • 
-
          • ValueError – atomic has incorrect shape. It must be (n, 8).
            • 
-
          • TypeError – vertices must be a list or a numpy.ndarray.
            • 
-
          • ValueError – vertices has incorrect shape. It must be (4, 3).
            • 
-
          • TypeError – step must be a positive real number.
            • 
-
          • ValueError – step must be a positive real number.
            • 
-
          • TypeError – probe_in must be a non-negative real number.
            • 
-
          • ValueError – probe_in must be a non-negative real number.
            • 
-
          • TypeError – ignore_backbone must be a boolean.
            • 
-
          • TypeError – selection must be a list of strings (cavity names) or integers (cavity labels).
            • 
-
          • ValueError – Invalid selection: {selection}.
            • 
-
          • TypeError – nthreads must be a positive integer.
            • 
-
          • ValueError – nthreads must be a positive integer.
            • 
-
          • TypeError – verbose must be a boolean.
            • 
-
          
-
          
-
          
-
          
-
          Note
          
-
          The cavity nomenclature is based on the integer label. The cavity marked
-with 2, the first integer corresponding to a cavity, is KAA, the cavity
-marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
          
-
          
-
          
-
          Note
          
-
          The classes of residues are:
          
-
            
-
          • Aliphatic apolar (R1): Alanine, Glycine, Isoleucine, Leucine, Methionine, Valine.
            • 
-
          • Aromatic (R2): Phenylalanine, Tryptophan, Tyrosine.
            • 
-
          • Polar Uncharged (R3): Asparagine, Cysteine, Glutamine, Proline, Serine, Threonine.
            • 
-
          • Negatively charged (R4): Aspartate, Glutamate.
            • 
-
          • Positively charged (R5): Arginine, Histidine, Lysine.
            • 
-
          • Non-standard (RX): Non-standard residues.
            • 
-
          
-
          
-
          
-
          See also
          
-
          read_pdb, read_xyz, detect, calculate_frequencies, write_results
          
-
          
-
          Example
          
-
          With the cavity points identified with detect, atomic data read with read_pdb or read_xyz, we can perform a constitutional characterization, that identifies the interface residues surrounding the cavities:
          
-
          >>> from pyKVFinder import constitutional
->>> residues = constitutional(cavities, atomic, vertices)
->>> residues
-{'KAA': [['14', 'E', 'SER'], ['15', 'E', 'VAL'], ['18', 'E', 'PHE'], ['19', 'E', 'LEU'], ['100', 'E', 'PHE'], ['152', 'E', 'LEU'], ['155', 'E', 'GLU'], ['156', 'E', 'TYR'], ['292', 'E', 'LYS'], ['302', 'E', 'TRP'], ['303', 'E', 'ILE'], ['306', 'E', 'TYR']], 'KAB': [['18', 'E', 'PHE'], ['22', 'E', 'ALA'], ['25', 'E', 'ASP'], ['26', 'E', 'PHE'], ['29', 'E', 'LYS'], ['97', 'E', 'ALA'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['156', 'E', 'TYR']], 'KAC': [['141', 'E', 'PRO'], ['142', 'E', 'HIS'], ['144', 'E', 'ARG'], ['145', 'E', 'PHE'], ['148', 'E', 'ALA'], ['299', 'E', 'THR'], ['300', 'E', 'THR'], ['305', 'E', 'ILE'], ['310', 'E', 'VAL'], ['311', 'E', 'GLU'], ['313', 'E', 'PRO']], 'KAD': [['122', 'E', 'TYR'], ['124', 'E', 'ALA'], ['176', 'E', 'GLN'], ['318', 'E', 'PHE'], ['320', 'E', 'GLY'], ['321', 'E', 'PRO'], ['322', 'E', 'GLY'], ['323', 'E', 'ASP']], 'KAE': [['95', 'E', 'LEU'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['100', 'E', 'PHE'], ['103', 'E', 'LEU'], ['104', 'E', 'VAL'], ['105', 'E', 'LYS'], ['106', 'E', 'LEU']], 'KAF': [['123', 'E', 'VAL'], ['124', 'E', 'ALA'], ['175', 'E', 'ASP'], ['176', 'E', 'GLN'], ['181', 'E', 'GLN']], 'KAG': [['34', 'E', 'SER'], ['37', 'E', 'THR'], ['96', 'E', 'GLN'], ['106', 'E', 'LEU'], ['107', 'E', 'GLU'], ['108', 'E', 'PHE'], ['109', 'E', 'SER']], 'KAH': [['49', 'E', 'LEU'], ['50', 'E', 'GLY'], ['51', 'E', 'THR'], ['52', 'E', 'GLY'], ['53', 'E', 'SER'], ['54', 'E', 'PHE'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['72', 'E', 'LYS'], ['74', 'E', 'LEU'], ['84', 'E', 'GLN'], ['87', 'E', 'HIS'], ['88', 'E', 'THR'], ['91', 'E', 'GLU'], ['104', 'E', 'VAL'], ['120', 'E', 'MET'], ['121', 'E', 'GLU'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['166', 'E', 'ASP'], ['168', 'E', 'LYS'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['184', 'E', 'ASP'], ['186', 'E', 'GLY'], ['187', 'E', 'PHE'], ['201', 'E', 'THR'], ['327', 'E', 'PHE']], 'KAI': [['131', 'E', 'HIS'], ['138', 'E', 'PHE'], ['142', 'E', 'HIS'], ['146', 'E', 'TYR'], ['174', 'E', 'ILE'], ['314', 'E', 'PHE']], 'KAJ': [['33', 'E', 'PRO'], ['89', 'E', 'LEU'], ['92', 'E', 'LYS'], ['93', 'E', 'ARG'], ['96', 'E', 'GLN'], ['349', 'E', 'GLU'], ['350', 'E', 'PHE']], 'KAK': [['157', 'E', 'LEU'], ['162', 'E', 'LEU'], ['163', 'E', 'ILE'], ['164', 'E', 'TYR'], ['185', 'E', 'PHE'], ['188', 'E', 'ALA']], 'KAL': [['49', 'E', 'LEU'], ['127', 'E', 'GLU'], ['129', 'E', 'PHE'], ['130', 'E', 'SER'], ['326', 'E', 'ASN'], ['327', 'E', 'PHE'], ['328', 'E', 'ASP'], ['330', 'E', 'TYR']], 'KAM': [['51', 'E', 'THR'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['73', 'E', 'ILE'], ['74', 'E', 'LEU'], ['75', 'E', 'ASP'], ['115', 'E', 'ASN'], ['335', 'E', 'ILE'], ['336', 'E', 'ARG']], 'KAN': [['165', 'E', 'ARG'], ['166', 'E', 'ASP'], ['167', 'E', 'LEU'], ['199', 'E', 'CYS'], ['200', 'E', 'GLY'], ['201', 'E', 'THR'], ['204', 'E', 'TYR'], ['205', 'E', 'LEU'], ['206', 'E', 'ALA'], ['209', 'E', 'ILE'], ['219', 'E', 'VAL'], ['220', 'E', 'ASP'], ['223', 'E', 'ALA']], 'KAO': [['48', 'E', 'THR'], ['51', 'E', 'THR'], ['56', 'E', 'ARG'], ['330', 'E', 'TYR'], ['331', 'E', 'GLU']], 'KAP': [['222', 'E', 'TRP'], ['238', 'E', 'PHE'], ['253', 'E', 'GLY'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['273', 'E', 'LEU']], 'KAQ': [['207', 'E', 'PRO'], ['208', 'E', 'GLU'], ['211', 'E', 'LEU'], ['213', 'E', 'LYS'], ['275', 'E', 'VAL'], ['277', 'E', 'LEU']], 'KAR': [['237', 'E', 'PRO'], ['238', 'E', 'PHE'], ['249', 'E', 'LYS'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['256', 'E', 'ARG']]}
-
          
-
          
-
          However, users may opt to ignore backbones contacts (C, CA, N, O) with the cavity when defining interface residues. Then, users must set ignore_backbone flag to True.
          
-
          >>> residues = constitutional(cavities, atomic, vertices, ignore_backbone=True)
->>> residues
-{'KAA': [['15', 'E', 'VAL'], ['18', 'E', 'PHE'], ['19', 'E', 'LEU'], ['100', 'E', 'PHE'], ['152', 'E', 'LEU'], ['155', 'E', 'GLU'], ['156', 'E', 'TYR'], ['292', 'E', 'LYS'], ['302', 'E', 'TRP'], ['303', 'E', 'ILE'], ['306', 'E', 'TYR']], 'KAB': [['18', 'E', 'PHE'], ['22', 'E', 'ALA'], ['25', 'E', 'ASP'], ['26', 'E', 'PHE'], ['29', 'E', 'LYS'], ['99', 'E', 'ASN'], ['156', 'E', 'TYR']], 'KAC': [['144', 'E', 'ARG'], ['145', 'E', 'PHE'], ['148', 'E', 'ALA'], ['299', 'E', 'THR'], ['300', 'E', 'THR'], ['305', 'E', 'ILE'], ['310', 'E', 'VAL'], ['311', 'E', 'GLU'], ['313', 'E', 'PRO']], 'KAD': [['122', 'E', 'TYR'], ['124', 'E', 'ALA'], ['176', 'E', 'GLN'], ['318', 'E', 'PHE']], 'KAE': [['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['103', 'E', 'LEU'], ['105', 'E', 'LYS'], ['106', 'E', 'LEU']], 'KAF': [['123', 'E', 'VAL'], ['175', 'E', 'ASP'], ['181', 'E', 'GLN']], 'KAG': [['34', 'E', 'SER'], ['37', 'E', 'THR'], ['96', 'E', 'GLN'], ['106', 'E', 'LEU'], ['109', 'E', 'SER']], 'KAH': [['49', 'E', 'LEU'], ['53', 'E', 'SER'], ['54', 'E', 'PHE'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['72', 'E', 'LYS'], ['74', 'E', 'LEU'], ['84', 'E', 'GLN'], ['87', 'E', 'HIS'], ['88', 'E', 'THR'], ['91', 'E', 'GLU'], ['104', 'E', 'VAL'], ['120', 'E', 'MET'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['166', 'E', 'ASP'], ['168', 'E', 'LYS'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['184', 'E', 'ASP'], ['187', 'E', 'PHE'], ['201', 'E', 'THR'], ['327', 'E', 'PHE']], 'KAI': [['131', 'E', 'HIS'], ['138', 'E', 'PHE'], ['142', 'E', 'HIS'], ['146', 'E', 'TYR'], ['174', 'E', 'ILE'], ['314', 'E', 'PHE']], 'KAJ': [['33', 'E', 'PRO'], ['89', 'E', 'LEU'], ['92', 'E', 'LYS'], ['93', 'E', 'ARG'], ['96', 'E', 'GLN'], ['349', 'E', 'GLU'], ['350', 'E', 'PHE']], 'KAK': [['157', 'E', 'LEU'], ['162', 'E', 'LEU'], ['164', 'E', 'TYR'], ['185', 'E', 'PHE'], ['188', 'E', 'ALA']], 'KAL': [['127', 'E', 'GLU'], ['129', 'E', 'PHE'], ['130', 'E', 'SER'], ['327', 'E', 'PHE'], ['328', 'E', 'ASP'], ['330', 'E', 'TYR']], 'KAM': [['51', 'E', 'THR'], ['56', 'E', 'ARG'], ['73', 'E', 'ILE'], ['115', 'E', 'ASN'], ['335', 'E', 'ILE']], 'KAN': [['165', 'E', 'ARG'], ['166', 'E', 'ASP'], ['167', 'E', 'LEU'], ['201', 'E', 'THR'], ['204', 'E', 'TYR'], ['205', 'E', 'LEU'], ['206', 'E', 'ALA'], ['209', 'E', 'ILE'], ['219', 'E', 'VAL'], ['220', 'E', 'ASP'], ['223', 'E', 'ALA']], 'KAO': [['48', 'E', 'THR'], ['51', 'E', 'THR'], ['56', 'E', 'ARG'], ['330', 'E', 'TYR']], 'KAP': [['222', 'E', 'TRP'], ['238', 'E', 'PHE'], ['255', 'E', 'VAL'], ['273', 'E', 'LEU']], 'KAQ': [['207', 'E', 'PRO'], ['208', 'E', 'GLU'], ['211', 'E', 'LEU'], ['213', 'E', 'LYS'], ['277', 'E', 'LEU']], 'KAR': [['238', 'E', 'PHE'], ['249', 'E', 'LYS'], ['255', 'E', 'VAL'], ['256', 'E', 'ARG']]}
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-pyKVFinder.depth(cavities: ndarray, step: Union[float, int] = 0.6, selection: Optional[Union[List[int], List[str]]] = None, nthreads: Optional[int] = None, verbose: bool = False) → Tuple[ndarray, Dict[str, float], Dict[str, float]][source]
          
-
          Characterization of the depth of the detected cavities, including depth
-per cavity point and maximum and average depths of detected cavities.
          
-
          
-
          Parameters:
          
-
            
-
          • cavities (numpy.ndarray) – 
            Cavity points in the 3D grid (cavities[nx][ny][nz]).
-Cavities array has integer labels in each position, that are:
            
-
            
-
              
-
            • -1: bulk points;
              • 
-
            • 0: biomolecule points;
              • 
-
            • 1: empty space points;
              • 
-
            • >=2: cavity points.
              • 
-
            
-
            
-
            The empty space points are regions that do not meet the chosen
-volume cutoff to be considered a cavity.
            
-
            • 
-
          • step (Union[float, int], optional) – Grid spacing (A).
            • 
-
          • selection (Union[List[int], List[str]], optional) – A list of integer labels or a list of cavity names to be selected, by default None.
            • 
-
          • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is
-os.cpu_count() - 1.
            • 
-
          • verbose (bool, optional) – Print extra information to standard output, by default False.
            • 
-
          
-
          
-
          Returns:
          
-
            
-
          • depths (numpy.ndarray) – A numpy.ndarray with depth of cavity points (depth[nx][ny][nz]).
            • 
-
          • max_depth (Dict[str, float]) – A dictionary with maximum depth of each detected cavity.
            • 
-
          • avg_depth (Dict[str, float]) – A dictionary with average depth of each detected cavity.
            • 
-
          
-
          
-
          
-
          Raises:
          
-
            
-
          • TypeError – cavities must be a numpy.ndarray.
            • 
-
          • ValueError – cavities has the incorrect shape. It must be (nx, ny, nz).
            • 
-
          • TypeError – step must be a positive real number.
            • 
-
          • ValueError – step must be a positive real number.
            • 
-
          • TypeError – selection must be a list of strings (cavity names) or integers (cavity labels).
            • 
-
          • ValueError – Invalid selection: {selection}.
            • 
-
          • TypeError – nthreads must be a positive integer.
            • 
-
          • ValueError – nthreads must be a positive integer.
            • 
-
          • TypeError – verbose must be a boolean.
            • 
-
          
-
          
-
          
-
          
-
          Note
          
-
          The cavity nomenclature is based on the integer label. The cavity marked
-with 2, the first integer corresponding to a cavity, is KAA, the cavity
-marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
          
-
          
-
          
-
          See also
          
-
          detect, export, write_results
          
-
          
-
          Example
          
-
          With the cavity points identified with detect, we can perform a depth characterization, that includes maximum depth, average depth and defining depth of cavity points:
          
-
          >>> from pyKVFinder import depth
->>> depths, max_depth, avg_depth = depth(cavities)
->>> depths
-array([[[0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        ...,
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.]],
-      ...,
-      [[0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        ...,
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.]]])
->>> max_depth
-{'KAA': 3.79, 'KAB': 2.68, 'KAC': 2.62, 'KAD': 0.85, 'KAE': 3.0, 'KAF': 0.85, 'KAG': 0.6, 'KAH': 10.73, 'KAI': 0.0, 'KAJ': 2.24, 'KAK': 0.0, 'KAL': 3.0, 'KAM': 1.2, 'KAN': 0.0, 'KAO': 1.04, 'KAP': 2.08, 'KAQ': 0.85, 'KAR': 0.6}
->>> avg_depth
-{'KAA': 1.35, 'KAB': 0.91, 'KAC': 0.68, 'KAD': 0.32, 'KAE': 0.99, 'KAF': 0.24, 'KAG': 0.1, 'KAH': 3.91, 'KAI': 0.0, 'KAJ': 0.96, 'KAK': 0.0, 'KAL': 1.07, 'KAM': 0.24, 'KAN': 0.0, 'KAO': 0.29, 'KAP': 0.7, 'KAQ': 0.22, 'KAR': 0.12}
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diff --git a/docs/source/_build/html/_api_reference/detect.html b/docs/source/_build/html/_api_reference/detect.html
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-  pyKVFinder.detect — pyKVFinder 0.5.0 documentation
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-pyKVFinder.detect(atomic: Union[ndarray, List[List[Union[str, float, int]]]], vertices: Union[ndarray, List[List[float]]], step: Union[float, int] = 0.6, probe_in: Union[float, int] = 1.4, probe_out: Union[float, int] = 4.0, removal_distance: Union[float, int] = 2.4, volume_cutoff: Union[float, int] = 5.0, latomic: Optional[Union[ndarray, List[List[float]]]] = None, ligand_cutoff: Union[float, int] = 5.0, box_adjustment: bool = False, surface: str = 'SES', nthreads: Optional[int] = None, verbose: bool = False) → Tuple[int, ndarray][source]
          
-
          Detects biomolecular cavities.
          
-
          Cavity points that belongs to the same cavity are assigned with an integer
-in the grid.
          
-
          
-
          Parameters:
          
-
            
-
          • atomic (Union[numpy.ndarray, List[List[Union[str, float, int]]]]) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
-and radius) for each atom.
            • 
-
          • vertices (Union[numpy.ndarray, List[List[float]]]) – A numpy.ndarray or a list with xyz vertices coordinates (origin,
-X-axis, Y-axis, Z-axis).
            • 
-
          • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.
            • 
-
          • probe_in (Union[float, int], optional) – Probe In size (A), by default 1.4.
            • 
-
          • probe_out (Union[float, int], optional) – Probe Out size (A), by default 4.0.
            • 
-
          • removal_distance (Union[float, int], optional) – A length to be removed from the cavity-bulk frontier (A), by
-default 2.4.
            • 
-
          • volume_cutoff (Union[float, int], optional) – Volume filter for detected cavities (A3), by default 5.0.
            • 
-
          • latomic (Union[numpy.ndarray, List[List[Union[str, float, int]]]], optional) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
-and radius) for each atom of a target ligand, by default None.
            • 
-
          • ligand_cutoff (Union[float, int], optional) – A radius to limit a space around a ligand (A), by default 5.0.
            • 
-
          • box_adjustment (bool, optional) – Whether a custom 3D grid is applied, by default False.
            • 
-
          • surface (str, optional) – Surface representation. Keywords options are SES (Solvent Excluded Surface) or SAS (Solvent
-Accessible Surface), by default SES.
            • 
-
          • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is
-os.cpu_count() - 1.
            • 
-
          • verbose (bool, optional) – Print extra information to standard output, by default False.
            • 
-
          
-
          
-
          Returns:
          
-
            
-
          • ncav (int) – Number of cavities.
            • 
-
          • cavities (numpy.ndarray) – Cavity points in the 3D grid (cavities[nx][ny][nz]).
-Cavities array has integer labels in each position, that are:
            
-
            
-
              
-
            • -1: bulk points;
              • 
-
            • 0: biomolecule points;
              • 
-
            • 1: empty space points;
              • 
-
            • >=2: cavity points.
              • 
-
            
-
            
-
            The empty space points are regions that do not meet the chosen
-volume cutoff to be considered a cavity.
            
-
            • 
-
          
-
          
-
          
-
          Raises:
          
-
            
-
          • TypeError – atomic must be a list or a numpy.ndarray.
            • 
-
          • ValueError – atomic has incorrect shape. It must be (n, 8).
            • 
-
          • TypeError – vertices must be a list or a numpy.ndarray.
            • 
-
          • ValueError – vertices has incorrect shape. It must be (4, 3).
            • 
-
          • TypeError – step must be a positive real number.
            • 
-
          • ValueError – step must be a positive real number.
            • 
-
          • TypeError – probe_in must be a non-negative real number.
            • 
-
          • ValueError – probe_in must be a non-negative real number.
            • 
-
          • TypeError – probe_out must be a non-negative real number.
            • 
-
          • ValueError – probe_out must be a non-negative real number.
            • 
-
          • ValueError – probe_out must be greater than probe_in.
            • 
-
          • TypeError – removal_distance must be a non-negative real number.
            • 
-
          • ValueError – removal_distance must be a non-negative real number.
            • 
-
          • TypeError – volume_cutoff must be a non-negative real number.
            • 
-
          • ValueError – volume_cutoff must be a non-negative real number.
            • 
-
          • TypeError – latomic must be a list, a numpy.ndarray or None.
            • 
-
          • ValueError – latomic has incorrect shape. It must be (n, 8).
            • 
-
          • TypeError – ligand_cutoff must be a positive real number.
            • 
-
          • ValueError – ligand_cutoff must be a positive real number.
            • 
-
          • TypeError – box_adjustment must be a boolean.
            • 
-
          • TypeError – surface must be a string.
            • 
-
          • TypeError – nthreads must be a positive integer.
            • 
-
          • ValueError – nthreads must be a positive integer.
            • 
-
          • ValueError – surface must be SAS or SES, not surface.
            • 
-
          
-
          
-
          
-
          
-
          See also
          
-
          read_pdb, read_xyz, get_vertices, get_vertices_from_file, spatial, depth, constitutional, export
          
-
          
-
          
-
          Warning
          
-
          If you are using box adjustment mode, do not forget to set box_adjustment
-flag to True and read the box configuration file with ‘get_vertices_from_file’
-function.
          
-
          
-
          
-
          Warning
          
-
          If you are using ligand adjustment mode, do not forget to read ligand atom
-coordinates with ‘read_pdb’ or ‘read_xyz’ functions.
          
-
          
-
          Example
          
-
          With the grid vertices defined with get_vertices and atomic data loaded with read_pdb or read_xyz, we can detect cavities on the whole target biomolecule:
          
-
          >>> from pyKVFinder import detect
->>> ncav, cavities = detect(atomic, vertices)
->>> ncav
-18
->>> cavities
-array([[[-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    ...,
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1]],
-   ...,
-   [[-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    ...,
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
-
          
-
          
-
          However, users may opt to perform cavity detection in a segmented space through ligand adjustment and/or box adjustment modes.
          
-
          The cavity detection can be limited around the target ligand(s), which will be passed to pyKVFinder through a .pdb or a .xyz files. Thus, the detected cavities are limited within a radius (ligand_cutoff) of the target ligand(s).
          
-
          >>> import os
->>> ligand = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'ADN.pdb')
->>> from pyKVFinder import read_pdb
->>> latomic = read_pdb(ligand)
->>> ncav, cavities = detect(atomic, vertices, latomic=latomic, ligand_cutoff=5.0)
->>> ncav
-2
->>> cavities
-array([[[-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    ...,
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1]],
-   ...,
-   [[-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    ...,
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
-
          
-
          
-
          Further, we can also perform cavity detection on a custom 3D grid, where we can explore closed regions with a custom box, which can be defined by a .toml file (see Box configuration file template).
          
-
          >>> import os
->>> fn = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'custom-box.toml')
->>> with open(fn, 'r') as f:
-...     print(f.read())
-[box]
-p1 = [3.11, 7.34, 1.59]
-p2 = [11.51, 7.34, 1.59]
-p3 = [3.11, 10.74, 1.59]
-p4 = [3.11, 7.34, 6.19]
-
          
-
          
-
          With this box adjustment mode, we must defined the 3D grid with get_vertices_from_file.
          
-
          >>> from pyKVFinder import get_vertices_from_file
->>> vertices, atomic = get_vertices_from_file(fn, atomic)
-
          
-
          
-
          Then, we can perform cavity detection:
          
-
          >>> ncav, cavities = detect(atomic, vertices, box_adjustment=True)
->>> ncav
-1
->>> cavities
-array([[[-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    ...,
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1]],
-   ...,
-   [[-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    ...,
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
-
          
-
          
-
          
-
          Warning
          
-
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diff --git a/docs/source/_build/html/_api_reference/export.html b/docs/source/_build/html/_api_reference/export.html
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-pyKVFinder.export(fn: Union[str, Path], cavities: Optional[ndarray], surface: Optional[ndarray], vertices: Union[ndarray, List[List[float]]], step: Union[float, int] = 0.6, B: Optional[ndarray] = None, output_hydropathy: Union[str, Path] = 'hydropathy.pdb', scales: Optional[ndarray] = None, selection: Optional[Union[List[int], List[str]]] = None, nthreads: Optional[int] = None, append: bool = False, model: int = 0) → None[source]
          
-
          Export cavitiy (H) and surface (HA) points to PDB-formatted file with
-a variable (B; optional) in B-factor column, and hydropathy to
-PDB-formatted file in B-factor column at surface points (HA).
          
-
          
-
          Parameters:
          
-
            
-
          • fn (Union[str, pathlib.Path]) – A path to PDB file for writing cavities.
            • 
-
          • cavities (numpy.ndarray, optional) – 
            Cavity points in the 3D grid (cavities[nx][ny][nz]).
-Cavities array has integer labels in each position, that are:
            
-
            
-
              
-
            • -1: bulk points;
              • 
-
            • 0: biomolecule points;
              • 
-
            • 1: empty space points;
              • 
-
            • >=2: cavity points.
              • 
-
            
-
            
-
            The empty space points are regions that do not meet the chosen
-volume cutoff to be considered a cavity.
            
-
            • 
-
          • surface (numpy.ndarray, optional) – 
            Surface points in the 3D grid (surface[nx][ny][nz]). If None, surface
-is a numpy.zeros array with same shape of cavities.
-Surface array has integer labels in each position, that are:
            
-
            
-
              
-
            • -1: bulk points;
              • 
-
            • 0: biomolecule or empty space points;
              • 
-
            • >=2: surface points.
              • 
-
            
-
            
-
            The empty space points are regions that do not meet the chosen
-volume cutoff to be considered a cavity.
            
-
            • 
-
          • vertices (Union[numpy.ndarray, List[List[float]]]) – A numpy.ndarray or a list with xyz vertices coordinates (origin,
-X-axis, Y-axis, Z-axis).
            • 
-
          • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.
            • 
-
          • B (numpy.ndarray, optional) – A numpy.ndarray with values to be mapped on B-factor column in cavity
-points (B[nx][ny][nz]), by default None.
            • 
-
          • output_hydropathy (Union[str, pathlib.Path], optional) – A path to hydropathy PDB file (surface points mapped with a
-hydrophobicity scale), by default hydropathy.pdb.
            • 
-
          • scales (numpy.ndarray, optional) – A numpy.ndarray with hydrophobicity scale values to be mapped on
-B-factor column in surface points (scales[nx][ny][nz]), by default
-None.
            • 
-
          • selection (Union[List[int], List[str]], optional) – A list of integer labels or a list of cavity names to be selected, by default None.
            • 
-
          • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is
-os.cpu_count() - 1.
            • 
-
          • append (bool, optional) – Whether to append cavities to the PDB file, by default False.
            • 
-
          • model (int, optional) – Model number, by default 0.
            • 
-
          
-
          
-
          Raises:
          
-
            
-
          • TypeError – fn must be a string or pathlib.Path.
            • 
-
          • TypeError – cavities must be a numpy.ndarray.
            • 
-
          • ValueError – cavities has the incorrect shape. It must be (nx, ny, nz).
            • 
-
          • TypeError – surface must be a numpy.ndarray.
            • 
-
          • ValueError – surface has the incorrect shape. It must be (nx, ny, nz).
            • 
-
          • TypeError – vertices must be a list or a numpy.ndarray.
            • 
-
          • ValueError – vertices has incorrect shape. It must be (4, 3).
            • 
-
          • TypeError – step must be a positive real number.
            • 
-
          • ValueError – step must be a positive real number.
            • 
-
          • TypeError – B must be a numpy.ndarray.
            • 
-
          • ValueError – B has the incorrect shape. It must be (nx, ny, nz).
            • 
-
          • TypeError – output_hydropathy must be a string.
            • 
-
          • TypeError – scales must be a numpy.ndarray.
            • 
-
          • ValueError – scales has the incorrect shape. It must be (nx, ny, nz).
            • 
-
          • TypeError – selection must be a list of strings (cavity names) or integers (cavity labels).
            • 
-
          • ValueError – Invalid selection: {selection}.
            • 
-
          • TypeError – nthreads must be a positive integer.
            • 
-
          • ValueError – nthreads must be a positive integer.
            • 
-
          • TypeError – append must be a boolean.
            • 
-
          • TypeError – model must be a integer.
            • 
-
          • RuntimeError – User must define surface when not defining cavities.
            • 
-
          
-
          
-
          
-
          
-
          Note
          
-
          The cavity nomenclature is based on the integer label. The cavity marked
-with 2, the first integer corresponding to a cavity, is KAA, the cavity
-marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
          
-
          
-
          
-
          See also
          
-
          detect, spatial, depth, hydropathy, write_results
          
-
          
-
          Example
          
-
          With the cavity and surface points identified and depth and hydrophobicity scale mapped in the 3D grid, we can:
          
-
            
-
          • Export cavity points
            • 
-
          
-
          >>> from pyKVFinder import export
->>> export('cavity_wo_surface.pdb', cavities, None, vertices)
-
          
-
          
-
            
-
          • Export cavity and surface points
            • 
-
          
-
          >>> export('cavities.pdb', cavities, surface, vertices)
-
          
-
          
-
            
-
          • Export cavity and surface points with depth mapped on them
            • 
-
          
-
          >>> export('cavities_with_depth.pdb', cavities, surface, vertices, B=depths)
-
          
-
          
-
            
-
          • Export surface points with hydrophobicity_scale mapped on them
            • 
-
          
-
          >>> export(None, None, surface, vertices, output_hydropathy='hydropathy.pdb', scales=scales)
-
          
-
          
-
            
-
          • Export all
            • 
-
          
-
          >>> export('cavities.pdb', cavities, surface, vertices, B=depths, output_hydropathy='hydropathy.pdb', scales=scales)
-
          
-
          
-
          
-
-
          
-
-
-           
          
-          
          
-          
-        
          
-      
          
-    
          
-  
          
-   
-
-
-
\ No newline at end of file
diff --git a/docs/source/_build/html/_api_reference/export_openings.html b/docs/source/_build/html/_api_reference/export_openings.html
deleted file mode 100644
index 4d930044..00000000
--- a/docs/source/_build/html/_api_reference/export_openings.html
+++ /dev/null
@@ -1,229 +0,0 @@
-
-
-
-  
-
-  
-  pyKVFinder.export_openings — pyKVFinder 0.5.0 documentation
-      
-      
-    
-  
-  
-        
-        
-        
-        
-        
-    
-    
-    
-    
-     
-
-
- 
-  
          
-    
-
-    
          
-
-      
          
-        
          
-          
          
-  
-  
          
-
          
-          
          
-           
          
-             
-  
          
-
          pyKVFinder.export_openings
          
-
          
-
          
-pyKVFinder.export_openings(fn: Union[str, Path], openings: ndarray, vertices: Union[ndarray, List[List[float]]], step: Union[float, int] = 0.6, selection: Optional[Union[List[int], List[str]]] = None, nthreads: Optional[int] = None, append: bool = False, model: int = 0) → None[source]
          
-
          Export opening points (H) to a PDB-formatted file.
          
-
          
-
          Parameters:
          
-
            
-
          • fn (Union[str, pathlib.Path]) – A path to PDB file for writing openings.
            • 
-
          • openings (numpy.ndarray) – 
            Openings points in the 3D grid (openings[nx][ny][nz]).
-Openings array has integer labels in each position, that are:
            
-
            
-
              
-
            • -1: bulk points;
              • 
-
            • 0: cavity or biomolecule points;
              • 
-
            • 1: empty space points;
              • 
-
            • >=2: Opening points.
              • 
-
            
-
            
-
            The empty space points are regions that do not meet the chosen
-openings cutoff to be considered an opening.
            
-
            • 
-
          • vertices (Union[numpy.ndarray, List[List[float]]]) – A numpy.ndarray or a list with xyz vertices coordinates (origin,
-X-axis, Y-axis, Z-axis).
            • 
-
          • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.
            • 
-
          • selection (Union[List[int], List[str]], optional) – A list of integer labels or a list of opening names to be selected, by default None.
            • 
-
          • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is
-os.cpu_count() - 1.
            • 
-
          • append (bool, optional) – Whether to append openings to the PDB file, by default False.
            • 
-
          • model (int, optional) – Model number, by default 0.
            • 
-
          
-
          
-
          Raises:
          
-
            
-
          • TypeError – openings must be a numpy.ndarray.
            • 
-
          • ValueError – openings has the incorrect shape. It must be (nx, ny, nz).
            • 
-
          • TypeError – vertices must be a list or a numpy.ndarray.
            • 
-
          • ValueError – vertices has incorrect shape. It must be (4, 3).
            • 
-
          • TypeError – step must be a positive real number.
            • 
-
          • ValueError – step must be a positive real number.
            • 
-
          • TypeError – selection must be a list of strings (opening names) or integers (opening labels).
            • 
-
          • ValueError – Invalid selection: {selection}.
            • 
-
          • TypeError – nthreads must be a positive integer.
            • 
-
          • ValueError – nthreads must be a positive integer.
            • 
-
          • TypeError – append must be a boolean.
            • 
-
          • TypeError – model must be a integer.
            • 
-
          • TypeError – fn must be a string or pathlib.Path.
            • 
-
          
-
          
-
          
-
          
-
          Note
          
-
          The opening nomenclature is based on the integer label. The opening marked
-with 2, the first integer corresponding to a opening, is OAA, the opening
-marked with 3 is OAB, the opening marked with 4 is OAC and so on.
          
-
          
-
          
-
          See also
          
-
          export, detect, depths, openings
          
-
          
-
          Example
          
-
          With the opening points identified with openings, we can export them to a PDB-formatted file:
          
-
          >>> from pyKVFinder import export_openings
->>> export_openings('openings.pdb', openings, vertices)
-
          
-
          
-
          
-
-
          
-
-
-           
          
-          
          
-          
-        
          
-      
          
-    
          
-  
          
-   
-
-
-
\ No newline at end of file
diff --git a/docs/source/_build/html/_api_reference/get_vertices.html b/docs/source/_build/html/_api_reference/get_vertices.html
deleted file mode 100644
index 457c2107..00000000
--- a/docs/source/_build/html/_api_reference/get_vertices.html
+++ /dev/null
@@ -1,210 +0,0 @@
-
-
-
-  
-
-  
-  pyKVFinder.get_vertices — pyKVFinder 0.5.0 documentation
-      
-      
-    
-  
-  
-        
-        
-        
-        
-        
-    
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-    
-    
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-        
          
-          
          
-  
-  
          
-
          
-          
          
-           
          
-             
-  
          
-
          pyKVFinder.get_vertices
          
-
          
-
          
-pyKVFinder.get_vertices(atomic: Union[ndarray, List[List[Union[str, float, int]]]], probe_out: Union[float, int] = 4.0, step: Union[float, int] = 0.6) → ndarray[source]
          
-
          Gets 3D grid vertices.
          
-
          
-
          Parameters:
          
-
            
-
          • atomic (Union[numpy.ndarray, List[List[Union[str, float, int]]]]) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
-and radius) for each atom.
            • 
-
          • probe_out (Union[float, int], optional) – Probe Out size (A), by default 4.0.
            • 
-
          • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.
            • 
-
          
-
          
-
          Returns:
          
-
          vertices – A numpy.ndarray with xyz vertices coordinates
-(origin, X-axis, Y-axis, Z-axis).
          
-
          
-
          Return type:
          
-
          numpy.ndarray
          
-
          
-
          Raises:
          
-
            
-
          • TypeError – atomic must be a list or a numpy.ndarray.
            • 
-
          • ValueError – atomic has incorrect shape. It must be (n, 8).
            • 
-
          • TypeError – probe_out must be a non-negative real number.
            • 
-
          • ValueError – probe_out must be a non-negative real number.
            • 
-
          • TypeError – step must be a positive real number.
            • 
-
          • ValueError – step must be a positive real number.
            • 
-
          
-
          
-
          
-
          
-
          See also
          
-
          read_pdb, read_xyz, detect, constitutional, hydropathy, export
          
-
          
-
          Example
          
-
          With the atomic data read with read_pdb or read_xyz, we can get the coordinates of 3D grid vertices (origin, X-axis, Y-axis, Z-axis):
          
-
          >>> from pyKVFinder import get_vertices
->>> vertices = get_vertices(atomic)
->>> vertices
-array([[-19.911, -32.125, -30.806],
-    [ 40.188, -32.125, -30.806],
-    [-19.911,  43.446, -30.806],
-    [-19.911, -32.125,  27.352]])
-
          
-
          
-
          
-
-
          
-
-
-           
          
-          
          
-          
-        
          
-      
          
-    
          
-  
          
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-
-
-
\ No newline at end of file
diff --git a/docs/source/_build/html/_api_reference/get_vertices_from_file.html b/docs/source/_build/html/_api_reference/get_vertices_from_file.html
deleted file mode 100644
index fc86184d..00000000
--- a/docs/source/_build/html/_api_reference/get_vertices_from_file.html
+++ /dev/null
@@ -1,240 +0,0 @@
-
-
-
-  
-
-  
-  pyKVFinder.get_vertices_from_file — pyKVFinder 0.5.0 documentation
-      
-      
-    
-  
-  
-        
-        
-        
-        
-        
-    
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-    
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-
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-        
          
-          
          
-  
-  
          
-
          
-          
          
-           
          
-             
-  
          
-
          pyKVFinder.get_vertices_from_file
          
-
          
-
          
-pyKVFinder.get_vertices_from_file(fn: Union[str, Path], atomic: Union[ndarray, List[List[Union[str, float, int]]]], step: Union[float, int] = 0.6, probe_in: Union[float, int] = 1.4, probe_out: Union[float, int] = 4.0, nthreads: Optional[int] = None) → Tuple[ndarray, ndarray, ndarray][source]
          
-
          Gets 3D grid vertices from box configuration file or parKVFinder
-parameters file, selects atoms inside custom 3D grid, define sine
-and cosine of 3D grid angles and define xyz grid units.
          
-
          
-
          Parameters:
          
-
            
-
          • fn (Union[str, pathlib.Path]) – A path to box configuration file (TOML-formatted).
            • 
-
          • atomic (Union[numpy.ndarray, List[List[Union[str, float, int]]]]) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
-and radius) for each atom.
            • 
-
          • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.
            • 
-
          • probe_in (Union[float, int], optional) – Probe In size (A), by default 1.4.
            • 
-
          • probe_out (Union[float, int], optional) – Probe Out size (A), by default 4.0.
            • 
-
          • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is
-os.cpu_count() - 1.
            • 
-
          
-
          
-
          Returns:
          
-
            
-
          • vertices (numpy.ndarray) – A numpy.ndarray with xyz vertices coordinates (origin, X-axis, Y-axis,
-Z-axis) of the custom box.
            • 
-
          • atomic (Union[numpy.ndarray, List[List[Union[str, float, int]]]]) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
-and radius) for each atom inside the custom box.
            • 
-
          
-
          
-
          
-
          Raises:
          
-
            
-
          • TypeError – fn must be a string or a pathlib.Path.
            • 
-
          • TypeError – atomic must be a list or a numpy.ndarray.
            • 
-
          • ValueError – atomic has incorrect shape. It must be (n, 8).
            • 
-
          • TypeError – step must be a positive real number.
            • 
-
          • ValueError – step must be a positive real number.
            • 
-
          • TypeError – probe_in must be a non-negative real number.
            • 
-
          • ValueError – probe_in must be a non-negative real number.
            • 
-
          • TypeError – probe_out must be a non-negative real number.
            • 
-
          • ValueError – probe_out must be a non-negative real number.
            • 
-
          • ValueError – probe_out must be greater than probe_in.
            • 
-
          • TypeError – nthreads must be a positive integer.
            • 
-
          • ValueError – You must define (p1, p2, p3, p4) or (residues, padding) keys in fn.
            • 
-
          • ValueError – Box not properly defined in fn.
            • 
-
          
-
          
-
          
-
          
-
          Note
          
-
          The box configuration scale file defines the vertices of the 3D grid used by pyKVFinder to detect and characterize cavities. There are three methods for defining a custom 3D grid in pyKVFinder. The first directly defines four vertices of the 3D grid (origin, X-axis, Y-axis and Z-axis), the second defines a list of residues and a padding, and the the third uses parKVFinder parameters file created by its PyMOL plugin. For more details, see Box configuration file template.
          
-
          
-
          
-
          See also
          
-
          read_pdb, read_xyz, detect, constitutional, hydropathy, export
          
-
          
-
          Example
          
-
          First, define a box configuration file (see Box configuration file template).
          
-
          >>> import os
->>> fn = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'custom-box.toml')
->>> with open(fn, 'r') as f:
-...     print(f.read())
-[box]
-p1 = [3.11, 7.34, 1.59]
-p2 = [11.51, 7.34, 1.59]
-p3 = [3.11, 10.74, 1.59]
-p4 = [3.11, 7.34, 6.19]
-
          
-
          
-
          With the atomic information and coordinates read with pyKVFinder.read_pdb and a box configuration file, we can get the coordinates of grid vertices and select atoms inside custom 3D grid.
          
-
          >>> from pyKVFinder import get_vertices_from_file
->>> vertices, atomic = pyKVFinder.get_vertices_from_file(fn, atomic)
-
          
-
          
-
          
-
          Warning
          
-
          Custom box coordinates adds Probe Out size in each direction to create the coordinates of grid vertices.
          
-
          
-
          
-
-
          
-
-
-           
          
-          
          
-          
-        
          
-      
          
-    
          
-  
          
-   
-
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-
\ No newline at end of file
diff --git a/docs/source/_build/html/_api_reference/hydropathy.html b/docs/source/_build/html/_api_reference/hydropathy.html
deleted file mode 100644
index 5c0c3dad..00000000
--- a/docs/source/_build/html/_api_reference/hydropathy.html
+++ /dev/null
@@ -1,341 +0,0 @@
-
-
-
-  
-
-  
-  pyKVFinder.hydropathy — pyKVFinder 0.5.0 documentation
-      
-      
-    
-  
-  
-        
-        
-        
-        
-        
-    
-    
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-    
-     
-
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-  
          
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-        
          
-          
          
-  
-  
          
-
          
-          
          
-           
          
-             
-  
          
-
          pyKVFinder.hydropathy
          
-
          
-
          
-pyKVFinder.hydropathy(surface: ndarray, atomic: Union[ndarray, List[List[Union[str, float, int]]]], vertices: Union[ndarray, List[List[float]]], step: Union[float, int] = 0.6, probe_in: Union[float, int] = 1.4, hydrophobicity_scale: Union[str, Path] = 'EisenbergWeiss', ignore_backbone: bool = False, selection: Optional[Union[List[int], List[str]]] = None, nthreads: Optional[int] = None, verbose: bool = False) → Tuple[ndarray, Dict[str, float]][source]
          
-
          Hydropathy characterization of the detected cavities.
          
-
          Map a target hydrophobicity scale per surface point and calculate average hydropathy of detected cavities.
          
-
          
-
          Parameters:
          
-
            
-
          • surface (numpy.ndarray) – 
            Surface points in the 3D grid (surface[nx][ny][nz]).
-Surface array has integer labels in each position, that are:
            
-
            
-
              
-
            • -1: bulk points;
              • 
-
            • 0: biomolecule or empty space points;
              • 
-
            • >=2: surface points.
              • 
-
            
-
            
-
            The empty space points are regions that do not meet the chosen
-volume cutoff to be considered a cavity.
            
-
            • 
-
          • atomic (Union[numpy.ndarray, List[List[Union[str, float, int]]]]) – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
-and radius) for each atom.
            • 
-
          • vertices (Union[numpy.ndarray, List[List[float]]]) – A numpy.ndarray or a list with xyz vertices coordinates (origin,
-X-axis, Y-axis, Z-axis).
            • 
-
          • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.
            • 
-
          • probe_in (Union[float, int], optional) – Probe In size (A), by default 1.4.
            • 
-
          • hydrophobicity_scale (str, optional) – 
            Name of a built-in hydrophobicity scale or a path to a
-TOML-formatted file with a custom hydrophobicity scale, by default
-EisenbergWeiss.
-The hydrophobicity scale file defines the name of the scale and the
-hydrophobicity value for each residue and when not defined, it assigns
-zero to the missing residues (see Hydrophobicity scale file
-template). The package contains six built-in hydrophobicity scales:
            
-
            
-
              
-
            • EisenbergWeiss [1];
              • 
-
            • HessaHeijne [2];
              • 
-
            • KyteDoolittle [3];
              • 
-
            • MoonFleming [4];
              • 
-
            • WimleyWhite [5];
              • 
-
            • ZhaoLondon [6].
              • 
-
            
-
            
-
            • 
-
          • ignore_backbone (bool, optional) – Whether to ignore backbone atoms (C, CA, N, O) when defining interface
-residues, by default False.
            • 
-
          • selection (Union[List[int], List[str]], optional) – A list of integer labels or a list of cavity names to be selected, by default None.
            • 
-
          • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is
-os.cpu_count() - 1.
            • 
-
          • verbose (bool, optional) – Print extra information to standard output, by default False.
            • 
-
          
-
          
-
          Returns:
          
-
            
-
          • scales (numpy.ndarray) – A numpy.ndarray with hydrophobicity scale value mapped at surface
-points (scales[nx][ny][nz]).
            • 
-
          • avg_hydropathy (Dict[str, float]) – A dictionary with average hydropathy for each detected cavity and
-the range of the hydrophobicity scale (min, max).
            • 
-
          
-
          
-
          
-
          Raises:
          
-
            
-
          • TypeError – surface must be a numpy.ndarray.
            • 
-
          • ValueError – surface has the incorrect shape. It must be (nx, ny, nz).
            • 
-
          • TypeError – atomic must be a list or a numpy.ndarray.
            • 
-
          • ValueError – atomic has incorrect shape. It must be (n, 8).
            • 
-
          • TypeError – vertices must be a list or a numpy.ndarray.
            • 
-
          • ValueError – vertices has incorrect shape. It must be (4, 3).
            • 
-
          • TypeError – step must be a positive real number.
            • 
-
          • ValueError – step must be a positive real number.
            • 
-
          • TypeError – probe_in must be a non-negative real number.
            • 
-
          • ValueError – probe_in must be a non-negative real number.
            • 
-
          • TypeError – hydrophobicity_scale must be a string or a pathlib.Path.
            • 
-
          • TypeError – ignore_backbone must be a boolean.
            • 
-
          • TypeError – selection must be a list of strings (cavity names) or integers (cavity labels).
            • 
-
          • ValueError – Invalid selection: {selection}.
            • 
-
          • TypeError – nthreads must be a positive integer.
            • 
-
          • ValueError – nthreads must be a positive integer.
            • 
-
          • TypeError – verbose must be a boolean.
            • 
-
          
-
          
-
          
-
          
-
          Note
          
-
          The cavity nomenclature is based on the integer label. The cavity marked
-with 2, the first integer corresponding to a cavity, is KAA, the cavity
-marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
          
-
          
-
          
-
          See also
          
-
          read_pdb, read_xyz, spatial, export, write_results
          
-
          
-
          Example
          
-
          With the surface points identified with pyKVFinder.spatial and atomic coordinates and information read with pyKVFinder.read_pdb or pyKVFinder.read_xyz, we can perform a hydropathy characterization, that maps a target hydrophobicity scale on surface points and calculate the average hydropathy
          
-
          >>> from pyKVFinder import hydropathy
->>> scales, avg_hydropathy = hydropathy(surface, atomic, vertices)
->>> scales
-array([[[0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        ...,
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.]],
-      ...,
-      [[0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        ...,
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.]]])
->>> avg_hydropathy
-{'KAA': -0.73, 'KAB': -0.05, 'KAC': -0.07, 'KAD': -0.62, 'KAE': -0.81, 'KAF': -0.14, 'KAG': -0.33, 'KAH': -0.16, 'KAI': -0.4, 'KAJ': 0.62, 'KAK': -0.99, 'KAL': 0.36, 'KAM': -0.33, 'KAN': 0.18, 'KAO': 0.88, 'KAP': -0.96, 'KAQ': 0.48, 'KAR': 0.24, 'EisenbergWeiss': [-1.42, 2.6]}
-
          
-
          
-
          However, users may opt to ignore backbones contacts (C, CA, N, O) with the cavity when mapping hydrophobicity scales on surface points. Then, users must set ignore_backbone flag to True.
          
-
          >>> from pyKVFinder import hydropathy
->>> scales, avg_hydropathy = hydropathy(surface, atomic, vertices, ignore_backbone=True)
->>> scales
-array([[[0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        ...,
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.]],
-      ...,
-      [[0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        ...,
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.]]])
->>> avg_hydropathy
-{'KAA': -0.7, 'KAB': 0.12, 'KAC': -0.08, 'KAD': -0.56, 'KAE': -0.28, 'KAF': -0.25, 'KAG': -0.28, 'KAH': -0.09, 'KAI': -0.4, 'KAJ': 0.96, 'KAK': -0.87, 'KAL': 0.23, 'KAM': 0.06, 'KAN': -0.1, 'KAO': 0.99, 'KAP': -1.04, 'KAQ': 0.48, 'KAR': -0.84, 'EisenbergWeiss': [-1.42, 2.6]}
-
          
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diff --git a/docs/source/_build/html/_api_reference/index.html b/docs/source/_build/html/_api_reference/index.html
deleted file mode 100644
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+++ /dev/null
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-  
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-  Functions — pyKVFinder 0.5.0 documentation
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diff --git a/docs/source/_build/html/_api_reference/openings.html b/docs/source/_build/html/_api_reference/openings.html
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-
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-  
-
-  
-  pyKVFinder.openings — pyKVFinder 0.5.0 documentation
-      
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          pyKVFinder.openings
          
-
          
-
          
-pyKVFinder.openings(cavities: ndarray, depths: Optional[ndarray] = None, step: Union[float, int] = 0.6, openings_cutoff: int = 1, selection: Optional[Union[List[int], List[str]]] = None, nthreads: Optional[int] = None, verbose: bool = False) → Tuple[int, ndarray, Dict[str, Dict[str, float]]][source]
          
-
          [WIP] Identify openings of the detected cavities and calculate their areas.
          
-
          
-
          Parameters:
          
-
            
-
          • cavities (numpy.ndarray) – 
            Cavity points in the 3D grid (cavities[nx][ny][nz]).
-Cavities array has integer labels in each position, that are:
            
-
            
-
              
-
            • -1: bulk points;
              • 
-
            • 0: biomolecule points;
              • 
-
            • 1: empty space points;
              • 
-
            • >=2: cavity points.
              • 
-
            
-
            
-
            • 
-
          • depths (Optional[numpy.ndarray], optional) – A numpy.ndarray with depth of cavity points (depth[nx][ny][nz]), by default None. If None, depths is calculated from cavities.
            • 
-
          • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.
            • 
-
          • openings_cutoff (int, optional) – The minimum number of voxels an opening must have, by default 1.
            • 
-
          • selection (Union[List[int], List[str]], optional) – A list of integer labels or a list of cavity names to be selected, by default None.
            • 
-
          • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is
-os.cpu_count() - 1.
            • 
-
          • verbose (bool, optional) – Print extra information to standard output, by default False.
            • 
-
          
-
          
-
          Returns:
          
-
            
-
          • nopenings (int) – Total number of openings.
            • 
-
          • openings (numpy.ndarray) – Openings points in the 3D grid (openings[nx][ny][nz]).
-Openings array has integer labels in each position, that are:
            
-
            
-
              
-
            • -1: bulk points;
              • 
-
            • 0: cavity or biomolecule points;
              • 
-
            • 1: empty space points;
              • 
-
            • >=2: Opening points.
              • 
-
            
-
            
-
            The empty space points are regions that do not meet the chosen
-openings cutoff to be considered an opening.
            
-
            • 
-
          • aopenings (Dict[str, Dict[str,float]]) – A dictionary with area of each detected opening.
            • 
-
          
-
          
-
          
-
          Raises:
          
-
            
-
          • TypeError – cavities must be a numpy.ndarray.
            • 
-
          • ValueError – cavities has the incorrect shape. It must be (nx, ny, nz).
            • 
-
          • TypeError – depths must be a numpy.ndarray.
            • 
-
          • ValueError – depths has the incorrect shape. It must be (nx, ny, nz).
            • 
-
          • TypeError – step must be a positive real number.
            • 
-
          • ValueError – step must be a positive real number.
            • 
-
          • TypeError – openings_cutoff must be an integer.
            • 
-
          • ValueError – openings_cutoff must be a positive integer.
            • 
-
          • TypeError – selection must be a list of strings (cavity names) or integers (cavity labels).
            • 
-
          • ValueError – Invalid selection: selection.
            • 
-
          • TypeError – nthreads must be a positive integer.
            • 
-
          • ValueError – nthreads must be a positive integer.
            • 
-
          • TypeError – verbose must be a boolean
            • 
-
          
-
          
-
          
-
          Example
          
-
          With the cavity points identified with detect, we can characterize their openings, that includes number and area of openings and defining opening points:
          
-
          >>> from pyKVFinder import openings
->>> nopenings, openings, aopenings = openings(cavities)
->>> nopenings
-16
->>> openings
-array([[[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]],
-      ...,
-      [[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]]])
->>> aopenings
-{'KAA': {'OAA': 47.41, 'OAG': 3.6}, 'KAB': {'OAB': 25.84}, 'KAC': {'OAC': 53.62}, 'KAD': {'OAD': 12.59}, 'KAE': {'OAE': 26.3}, 'KAF': {'OAF': 18.46}, 'KAG': {'OAH': 12.83}, 'KAH': {'OAK': 59.96}, 'KAJ': {'OAI': 16.11}, 'KAL': {'OAJ': 17.3}, 'KAM': {'OAL': 35.27}, 'KAO': {'OAM': 8.49}, 'KAP': {'OAN': 13.71}, 'KAQ': {'OAO': 13.16}, 'KAR': {'OAP': 15.36}}
-
          
-
          
-
          With the cavity and opening points identified, we can:
          
-
            
-
          • Export cavity points with opening points mapped on them:
            • 
-
          
-
          >>> from pyKVFinder import export
->>> export("cavities_with_openings.pdb", cavities, None, vertices, B=openings)
-
          
-
          
-
            
-
          • Export opening points with same nomenclature from aopenings:
            • 
-
          
-
          >>> from pyKVFinder import export_openings
->>> export_openings("openings.pdb", openings, vertices)
-
          
-
          
-
          
-
          See also
          
-
          detect, depth, export, export_openings
          
-
          
-
          
-
-
          
-
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diff --git a/docs/source/_build/html/_api_reference/plot_frequencies.html b/docs/source/_build/html/_api_reference/plot_frequencies.html
deleted file mode 100644
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-
-  
-  pyKVFinder.plot_frequencies — pyKVFinder 0.5.0 documentation
-      
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          pyKVFinder.plot_frequencies
          
-
          
-
          
-pyKVFinder.plot_frequencies(frequencies: Dict[str, Dict[str, Dict[str, int]]], fn: Union[str, Path] = 'barplots.pdf') → None[source]
          
-
          Plot bar charts of calculated frequencies (residues and classes of
-residues) for each detected cavity in a target PDF file.
          
-
          
-
          Parameters:
          
-
            
-
          • frequencies (Dict[str, Dict[str, Dict[str, int]]]) – A dictionary with frequencies of residues and class for
-residues of each detected cavity.
            • 
-
          • fn (Union[str, pathlib.Path], optional) – A path to PDF file for plotting bar charts of frequencies, by
-default barplots.pdf.
            • 
-
          
-
          
-
          Raises:
          
-
          TypeError – fn must be a string or a pathlib.Path.
          
-
          
-
          
-
          
-
          Note
          
-
          The cavity nomenclature is based on the integer label. The cavity
-marked with 2, the first integer corresponding to a cavity, is KAA, the
-cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
          
-
          
-
          
-
          Note
          
-
          The classes of residues are:
          
-
            
-
          • Aliphatic apolar (R1): Alanine, Glycine, Isoleucine, Leucine, Methionine, Valine.
            • 
-
          • Aromatic (R2): Phenylalanine, Tryptophan, Tyrosine.
            • 
-
          • Polar Uncharged (R3): Asparagine, Cysteine, Glutamine, Proline, Serine, Threonine.
            • 
-
          • Negatively charged (R4): Aspartate, Glutamate.
            • 
-
          • Positively charged (R5): Arginine, Histidine, Lysine.
            • 
-
          • Non-standard (RX): Non-standard residues.
            • 
-
          
-
          
-
          
-
          See also
          
-
          calculate_frequencies
          
-
          
-
          Example
          
-
          With the residues and classes of residues frequencies calculated with calculate_frequencies, we can plot the bar charts of these frequencies in a PDF file.
          
-
          >>> from pyKVFinder import plot_frequencies
->>> frequencies
-{'KAA': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'ASN': 1, 'ASP': 2, 'GLN': 1, 'GLU': 4, 'GLY': 4, 'HIS': 1, 'LEU': 3, 'LYS': 2, 'MET': 1, 'PHE': 3, 'SER': 1, 'THR': 4, 'TYR': 1, 'VAL': 3}, 'CLASS': {'R1': 11, 'R2': 4, 'R3': 8, 'R4': 6, 'R5': 4, 'RX': 0}}}
->>> plot_frequencies(frequencies, fn='barplots.pdf')
-
          
-
          
-../_images/barplots.png
-
          
-
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diff --git a/docs/source/_build/html/_api_reference/pyKVFinderResults.html b/docs/source/_build/html/_api_reference/pyKVFinderResults.html
deleted file mode 100644
index fcb141db..00000000
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+++ /dev/null
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-
-
-
-  
-
-  
-  pyKVFinder.pyKVFinderResults — pyKVFinder 0.5.0 documentation
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          pyKVFinder.pyKVFinderResults
          
-
          
-
          
-class pyKVFinder.pyKVFinderResults(cavities: ndarray, surface: ndarray, depths: Optional[ndarray], scales: Optional[ndarray], volume: Dict[str, float], area: Dict[str, float], max_depth: Optional[Dict[str, float]], avg_depth: Optional[Dict[str, float]], avg_hydropathy: Optional[Dict[str, float]], residues: Dict[str, List[List[str]]], frequencies: Optional[Dict[str, Dict[str, Dict[str, int]]]], _vertices: ndarray, _step: Union[float, int], _input: Optional[Union[str, Path]] = None, _ligand: Optional[Union[str, Path]] = None)[source]
          
-
          A class containing pyKVFinder detection and characterization results.
          
-
          
-
          Parameters:
          
-
            
-
          • cavities (numpy.ndarray) – 
            Cavity points in the 3D grid (cavities[nx][ny][nz]).
-Cavities array has integer labels in each position, that are:
            
-
            
-
              
-
            • -1: bulk points;
              • 
-
            • 0: biomolecule points;
              • 
-
            • 1: empty space points;
              • 
-
            • >=2: cavity points.
              • 
-
            
-
            
-
            The empty space points are regions that do not meet the chosen
-volume cutoff to be considered a cavity.
            
-
            • 
-
          • surface (numpy.ndarray) – 
            Surface points in the 3D grid (surface[nx][ny][nz]).
-Surface array has integer labels in each position, that are:
            
-
            
-
              
-
            • -1: bulk points;
              • 
-
            • 0: biomolecule or empty space points;
              • 
-
            • >=2: surface points.
              • 
-
            
-
            
-
            The empty space points are regions that do not meet the chosen
-volume cutoff to be considered a cavity.
            
-
            • 
-
          • depths (numpy.ndarray, optional) – A numpy.ndarray with depth of cavity points (depth[nx][ny][nz]).
            • 
-
          • scales (numpy.ndarray, optional) – A numpy.ndarray with hydrophobicity scale value mapped at surface
-points (scales[nx][ny][nz]).
            • 
-
          • volume (Dict[str, float]) – A dictionary with volume of each detected cavity.
            • 
-
          • area (Dict[str, float]) – A dictionary with area of each detected cavity.
            • 
-
          • max_depth (Dict[str, float], optional) – A dictionary with maximum depth of each detected cavity.
            • 
-
          • avg_depth (Dict[str, float], optional) – A dictionary with average depth of each detected cavity.
            • 
-
          • avg_hydropathy (Dict[str, float], optional) – A dictionary with average hydropathy for each detected cavity and
-the range of the hydrophobicity scale (min, max).
            • 
-
          • residues (Dict[str, List[List[str]]]) – A dictionary with a list of interface residues for each detected
-cavity.
            • 
-
          • frequencies (Dict[str, Dict[str, Dict[str, int]]], optional) – A dictionary with frequencies of residues and class for
-residues of each detected cavity.
            • 
-
          • _vertices (numpy.ndarray) – A numpy.ndarray or a list with xyz vertices coordinates (origin,
-X-axis, Y-axis, Z-axis).
            • 
-
          • _step (float) – Grid spacing (A).
            • 
-
          • _input (Union[str, pathlib.Path], optional) – A path to input PDB or XYZ file, by default None.
            • 
-
          • _ligand (Union[str, pathlib.Path], optional) – A path to ligand PDB or XYZ file, by default None.
            • 
-
          
-
          
-
          
-
          
-
          
-cavities
          
-
          Cavity points in the 3D grid (cavities[nx][ny][nz]).
-Cavities array has integer labels in each position, that are:
          
-
          
-
            
-
          • -1: bulk points;
            • 
-
          • 0: biomolecule points;
            • 
-
          • 1: empty space points;
            • 
-
          • >=2: cavity points.
            • 
-
          
-
          
-
          The empty space points are regions that do not meet the chosen
-volume cutoff to be considered a cavity.
          
-
          
-
          Type:
          
-
          numpy.ndarray
          
-
          
-
          
-
          
-
-
          
-
          
-surface
          
-
          Surface points in the 3D grid (surface[nx][ny][nz]).
-Surface array has integer labels in each position, that are:
          
-
          
-
            
-
          • -1: bulk points;
            • 
-
          • 0: biomolecule or empty space points;
            • 
-
          • >=2: surface points.
            • 
-
          
-
          
-
          The empty space points are regions that do not meet the chosen
-volume cutoff to be considered a cavity.
          
-
          
-
          Type:
          
-
          numpy.ndarray
          
-
          
-
          
-
          
-
-
          
-
          
-depths
          
-
          A numpy.ndarray with depth of cavity points (depth[nx][ny][nz]).
          
-
          
-
          Type:
          
-
          numpy.ndarray, optional
          
-
          
-
          
-
          
-
-
          
-
          
-scales
          
-
          A numpy.ndarray with hydrophobicity scale value mapped at surface
-points (scales[nx][ny][nz]).
          
-
          
-
          Type:
          
-
          numpy.ndarray, optional
          
-
          
-
          
-
          
-
-
          
-
          
-ncav
          
-
          Number of cavities.
          
-
          
-
          Type:
          
-
          int
          
-
          
-
          
-
          
-
-
          
-
          
-volume
          
-
          A dictionary with volume of each detected cavity.
          
-
          
-
          Type:
          
-
          Dict[str, float]
          
-
          
-
          
-
          
-
-
          
-
          
-area
          
-
          A dictionary with area of each detected cavity.
          
-
          
-
          Type:
          
-
          Dict[str, float]
          
-
          
-
          
-
          
-
-
          
-
          
-max_depth
          
-
          A dictionary with maximum depth of each detected cavity.
          
-
          
-
          Type:
          
-
          Dict[str, float], optional
          
-
          
-
          
-
          
-
-
          
-
          
-avg_depth
          
-
          A dictionary with average depth of each detected cavity.
          
-
          
-
          Type:
          
-
          Dict[str, float], optional
          
-
          
-
          
-
          
-
-
          
-
          
-avg_hydropathy
          
-
          A dictionary with average hydropathy for each detected cavity and
-the range of the hydrophobicity scale (min, max).
          
-
          
-
          Type:
          
-
          Dict[str, float], optional
          
-
          
-
          
-
          
-
-
          
-
          
-residues
          
-
          A dictionary with a list of interface residues for each detected
-cavity.
          
-
          
-
          Type:
          
-
          Dict[str, List[List[str]]]
          
-
          
-
          
-
          
-
-
          
-
          
-frequencies
          
-
          A dictionary with frequencies of residues and class for
-residues of each detected cavity.
          
-
          
-
          Type:
          
-
          Dict[str, Dict[str, Dict[str, int]]], optional
          
-
          
-
          
-
          
-
-
          
-
          
-_vertices
          
-
          A numpy.ndarray or a list with xyz vertices coordinates (origin,
-X-axis, Y-axis, Z-axis).
          
-
          
-
          Type:
          
-
          numpy.ndarray
          
-
          
-
          
-
          
-
-
          
-
          
-_step
          
-
          Grid spacing (A).
          
-
          
-
          Type:
          
-
          float
          
-
          
-
          
-
          
-
-
          
-
          
-_input
          
-
          A path to input PDB or XYZ file, by default None.
          
-
          
-
          Type:
          
-
          Union[str, pathlib.Path], optional
          
-
          
-
          
-
          
-
-
          
-
          
-_ligand
          
-
          A path to ligand PDB or XYZ file, by default None.
          
-
          
-
          Type:
          
-
          Union[str, pathlib.Path], optional
          
-
          
-
          
-
          
-
-
          
-
          
-export(output: Union[str, Path] = 'cavity.pdb', output_hydropathy: Union[str, Path] = 'hydropathy.pdb', nthreads: Optional[int] = None) → None[source]
          
-
          Exports cavitiy (H) and surface (HA) points to PDB-formatted file
-with a variable (B; optional) in B-factor column, and hydropathy to
-PDB-formatted file in B-factor column at surface points (HA).
          
-
          
-
          Parameters:
          
-
            
-
          • output (Union[str, pathlib.Path]), optional) – A path to PDB file for writing cavities, by default cavity.pdb.
            • 
-
          • output_hydropathy (Union[str, pathlib.Path], optional) – A path to PDB file for writing hydropathy at surface points, by
-default hydropathy.pdb.
            • 
-
          • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is
-os.cpu_count() - 1.
            • 
-
          
-
          
-
          
-
          
-
          Note
          
-
          The cavity nomenclature is based on the integer label. The cavity
-marked with 2, the first integer corresponding to a cavity, is KAA,
-the cavity marked with 3 is KAB, the cavity marked with 4 is KAC
-and so on.
          
-
          
-
          Example
          
-
          >>> from pyKVFinder import pyKVFinder
->>> import os
->>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
->>> results = pyKVFinder(pdb)
->>> results.export()
-
          
-
          
-
          
-
-
          
-
          
-export_all(fn: Union[str, Path] = 'results.toml', output: Union[str, Path] = 'cavity.pdb', output_hydropathy: Union[str, Path] = 'hydropathy.pdb', include_frequencies_pdf: bool = False, pdf: Union[str, Path] = 'barplots.pdf', nthreads: Optional[int] = None) → None[source]
          
-
          Exports cavities and characterization to PDB-formatted files,
-writes file paths and characterization to a TOML-formatted file, and
-optionally plot bar charts of frequencies (residues and classes of
-residues) in a PDF file.
          
-
          
-
          Parameters:
          
-
            
-
          • fn (Union[str, pathlib.Path], optional) – A path to TOML-formatted file for writing file paths and
-cavity characterization (volume, area and interface residues)
-per cavity detected, by default results.toml.
            • 
-
          • output (Union[str, pathlib.Path], optional) – A path to PDB file for writing cavities, by default cavity.pdb.
            • 
-
          • output_hydropathy (Union[str, pathlib.Path], optional) – A path to PDB file for writing hydropathy at surface points,
-by default hydropathy.pdb.
            • 
-
          • include_frequencies_pdf (bool, optional) – Whether to plot frequencies (residues and classes of residues)
-to PDF file, by default False.
            • 
-
          • pdf (Union[str, pathlib.Path], optional) – A path to a PDF file, by default barplots.pdf.
            • 
-
          • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is
-os.cpu_count() - 1.
            • 
-
          
-
          
-
          
-
          
-
          Note
          
-
          The cavity nomenclature is based on the integer label. The cavity
-marked with 2, the first integer corresponding to a cavity, is KAA,
-the cavity marked with 3 is KAB, the cavity marked with 4 is KAC
-and so on.
          
-
          
-
          
-
          Note
          
-
          The classes of residues are:
          
-
            
-
          • Aliphatic apolar (R1): Alanine, Glycine, Isoleucine, Leucine, Methionine, Valine.
            • 
-
          • Aromatic (R2): Phenylalanine, Tryptophan, Tyrosine.
            • 
-
          • Polar Uncharged (R3): Asparagine, Cysteine, Glutamine, Proline, Serine, Threonine.
            • 
-
          • Negatively charged (R4): Aspartate, Glutamate.
            • 
-
          • Positively charged (R5): Arginine, Histidine, Lysine.
            • 
-
          • Non-standard (RX): Non-standard residues.
            • 
-
          
-
          
-
          Example
          
-
          >>> from pyKVFinder import pyKVFinder
->>> import os
->>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
->>> results = pyKVFinder(pdb)
->>> results.export_all()
-
          
-
          
-
          Yet, we can set a include_frequencies_pdf flag to True to plot the bar charts of the frequencies in a PDF file.
          
-
          >>> results.export_all(include_frequencies_pdf=True)
-
          
-
          
-
          
-
-
          
-
          
-plot_frequencies(pdf: Union[str, Path] = 'barplots.pdf')[source]
          
-
          Plot bar charts of frequencies (residues and classes of residues) in
-a PDF file.
          
-
          
-
          Parameters:
          
-
          pdf (Union[str, pathlib.Path], optional) – A path to a PDF file, by default barplots.pdf.
          
-
          
-
          
-
          
-
          Note
          
-
          The cavity nomenclature is based on the integer label. The cavity
-marked with 2, the first integer corresponding to a cavity, is KAA,
-the cavity marked with 3 is KAB, the cavity marked with 4 is KAC
-and so on.
          
-
          
-
          
-
          Note
          
-
          The classes of residues are:
          
-
            
-
          • Aliphatic apolar (R1): Alanine, Glycine, Isoleucine, Leucine, Methionine, Valine.
            • 
-
          • Aromatic (R2): Phenylalanine, Tryptophan, Tyrosine.
            • 
-
          • Polar Uncharged (R3): Asparagine, Cysteine, Glutamine, Proline, Serine, Threonine.
            • 
-
          • Negatively charged (R4): Aspartate, Glutamate.
            • 
-
          • Positively charged (R5): Arginine, Histidine, Lysine.
            • 
-
          • Non-standard (RX): Non-standard residues
            • 
-
          
-
          
-
          Example
          
-
          >>> from pyKVFinder import pyKVFinder
->>> import os
->>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
->>> results = pyKVFinder(pdb)
->>> results.plot_frequencies()
-
          
-
          
-
          
-
-
          
-
          
-write(fn: Union[str, Path] = 'results.toml', output: Optional[Union[str, Path]] = None, output_hydropathy: Optional[Union[str, Path]] = None) → None[source]
          
-
          Writes file paths and cavity characterization to TOML-formatted file
          
-
          
-
          Parameters:
          
-
            
-
          • fn (Union[str, pathlib.Path], optional) – A path to TOML-formatted file for writing file paths and cavity
-characterization (volume, area, depth and interface residues)
-per cavity detected, by default results.toml.
            • 
-
          • output (Union[str, pathlib.Path], optional) – A path to a cavity PDB file, by default None.
            • 
-
          • output_hydropathy (Union[str, pathlib.Path], optional) – A path to PDB file for writing hydropathy at surface points, by
-default None.
            • 
-
          
-
          
-
          
-
          
-
          Note
          
-
          The cavity nomenclature is based on the integer label. The cavity
-marked with 2, the first integer corresponding to a cavity, is KAA,
-the cavity marked with 3 is KAB, the cavity marked with 4 is KAC
-and so on.
          
-
          
-
          Example
          
-
          >>> from pyKVFinder import pyKVFinder
->>> import os
->>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
->>> results = pyKVFinder(pdb)
->>> results.write()
-
          
-
          
-
          
-
-
          
-
-
          
-
-
-           
          
-          
          
-          
-        
          
-      
          
-    
          
-  
          
-   
-
-
-
\ No newline at end of file
diff --git a/docs/source/_build/html/_api_reference/read_cavity.html b/docs/source/_build/html/_api_reference/read_cavity.html
deleted file mode 100644
index 5ac28772..00000000
--- a/docs/source/_build/html/_api_reference/read_cavity.html
+++ /dev/null
@@ -1,253 +0,0 @@
-
-
-
-  
-
-  
-  pyKVFinder.read_cavity — pyKVFinder 0.5.0 documentation
-      
-      
-    
-  
-  
-        
-        
-        
-        
-        
-    
-    
-    
-    
-     
-
-
- 
-  
          
-    
-
-    
          
-
-      
          
-        
          
-          
          
-  
-  
          
-
          
-          
          
-           
          
-             
-  
          
-
          pyKVFinder.read_cavity
          
-
          
-
          
-pyKVFinder.read_cavity(cavity: Union[str, Path], receptor: Union[str, Path], step: Union[float, int] = 0.6, probe_in: Union[float, int] = 1.4, probe_out: Union[float, int] = 4.0, surface: str = 'SES', vdw: Optional[Dict[str, Dict[str, float]]] = None, nthreads: Optional[int] = None, verbose: bool = False) → ndarray[source]
          
-
          Read cavities and receptor inside a 3D grid.
          
-
          
-
          Parameters:
          
-
            
-
          • cavity (Union[str, pathlib.Path]) – A path to a PDB file of cavities.
            • 
-
          • receptor (Union[str, pathlib.Path]) – A path to a PDB or XYZ file of the receptor.
            • 
-
          • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.
            • 
-
          • probe_in (Union[float, int], optional) – Probe In size (A), by default 1.4.
            • 
-
          • probe_out (Union[float, int], optional) – Probe Out size (A), by default 4.0.
            • 
-
          • surface (str, optional) – Surface representation. Keywords options are SES (Solvent Excluded Surface) or SAS (Solvent
-Accessible Surface), by default “SES”.
            • 
-
          • vdw (Dict[str, Dict[str, float]], optional) – A dictionary containing radii values, by default None. If None, use output of read_vdw().
            • 
-
          • nthreads (Optional[int], optional) – Number of threads, by default None. If None, the number of threads is
-os.cpu_count() - 1.
            • 
-
          • verbose (bool, optional) – Print extra information to standard output, by default False.
            • 
-
          
-
          
-
          Returns:
          
-
          grid – Cavity and receptor points in the 3D grid (grid[nx][ny][nz]).
-Grid array has integer labels in each position, that are:
          
-
          
-
            
-
          • -1: bulk points or empty space points;
            • 
-
          • 0: biomolecule points;
            • 
-
          • >=2: cavity points.
            • 
-
          
-
          
-
          
-
          
-
          Return type:
          
-
          numpy.ndarray
          
-
          
-
          Raises:
          
-
            
-
          • TypeError – cavity must be a string or a pathlib.Path.
            • 
-
          • TypeError – receptor must be a string or a pathlib.Path.
            • 
-
          • TypeError – target must have .pdb or .xyz extension.
            • 
-
          • TypeError – step must be a positive real number.
            • 
-
          • ValueError – step must be a positive real number.
            • 
-
          • TypeError – probe_in must be a non-negative real number.
            • 
-
          • ValueError – probe_in must be a non-negative real number.
            • 
-
          • TypeError – probe_out must be a non-negative real number.
            • 
-
          • ValueError – probe_out must be a non-negative real number.
            • 
-
          • ValueError – probe_out must be greater than probe_in.
            • 
-
          • TypeError – surface must be a str.
            • 
-
          • TypeError – nthreads must be a positive integer.
            • 
-
          • ValueError – nthreads must be a positive integer.
            • 
-
          • TypeError – verbose must be a boolean.
            • 
-
          • ValueError – surface must be SAS or SES, not {surface}.
            • 
-
          
-
          
-
          
-
          
-
          Note
          
-
          The function takes the built-in dictionary when the vdw argument is not specified. If you wish to use a custom van der Waals radii file, you must read it with read_vdw as shown earlier and pass it as read_cavity(cavity, receptor, vdw=vdw).
          
-
          
-
          
-
          See also
          
-
          read_pdb, read_xyz, get_vertices, get_vertices_from_file, spatial, depth, constitutional, hydropathy, export
          
-
          
-
          Example
          
-
          With a previously calculated cavity, that can be manually curated in a molecular visualization software, such as PyMOL, we can read it with its respective receptor back to pyKVFinder:
          
-
          >>> import os
->>> import pyKVFinder
->>> from pyKVFinder import read_cavity
->>> cavity = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.KVFinder.output.pdb')
->>> receptor = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
->>> grid = read_cavity(cavity, receptor)
->>> grid
-array([[[-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    ...,
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1]],
-   ...,
-   [[-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    ...,
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
-
          
-
          
-
          
-
-
          
-
-
-           
          
-          
          
-          
-        
          
-      
          
-    
          
-  
          
-   
-
-
-
\ No newline at end of file
diff --git a/docs/source/_build/html/_api_reference/read_pdb.html b/docs/source/_build/html/_api_reference/read_pdb.html
deleted file mode 100644
index 6b1ad6a3..00000000
--- a/docs/source/_build/html/_api_reference/read_pdb.html
+++ /dev/null
@@ -1,217 +0,0 @@
-
-
-
-  
-
-  
-  pyKVFinder.read_pdb — pyKVFinder 0.5.0 documentation
-      
-      
-    
-  
-  
-        
-        
-        
-        
-        
-    
-    
-    
-    
-     
-
-
- 
-  
          
-    
-
-    
          
-
-      
          
-        
          
-          
          
-  
-  
          
-
          
-          
          
-           
          
-             
-  
          
-
          pyKVFinder.read_pdb
          
-
          
-
          
-pyKVFinder.read_pdb(fn: Union[str, Path], vdw: Optional[Dict[str, Dict[str, float]]] = None, model: Optional[int] = None) → ndarray[source]
          
-
          Reads PDB file into numpy.ndarrays.
          
-
          
-
          Parameters:
          
-
            
-
          • fn (Union[str, pathlib.Path]) – A path to PDB file.
            • 
-
          • vdw (Dict[str, Dict[str, float]], optional) – A dictionary containing radii values, by default None. If None, use output of read_vdw().
            • 
-
          • model (int, optional) – The model number of a multi-model PDB file, by default None. If None, keep atoms from all models.
            • 
-
          
-
          
-
          Returns:
          
-
          atomic – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
-and radius) for each atom.
          
-
          
-
          Return type:
          
-
          numpy.ndarray
          
-
          
-
          Raises:
          
-
          TypeError – fn must be a string or a pathlib.Path.
          
-
          
-
          
-
          
-
          Note
          
-
          The van der Waals radii file defines the radius values for each atom by residue and when not defined, it uses a generic value based on the atom type. The function by default loads the built-in van der Waals radii file: vdw.dat.
          
-
          
-
          
-
          See also
          
-
          read_vdw, read_xyz, get_vertices, get_vertices_from_file, detect, constitutional, hydropathy
          
-
          
-
          Example
          
-
          With the vdW radii dictionary loaded with read_vdw, we can read a target PDB file into Numpy array (atomic data):
          
-
          >>> import os
->>> import pyKVFinder
->>> from pyKVFinder import read_pdb
->>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
->>> atomic = read_pdb(pdb)
->>> atomic
-array([['13', 'E', 'GLU', ..., '-15.642', '-14.858', '1.824'],
-   ['13', 'E', 'GLU', ..., '-14.62', '-15.897', '1.908'],
-   ['13', 'E', 'GLU', ..., '-13.357', '-15.508', '1.908'],
-   ...,
-   ['350', 'E', 'PHE', ..., '18.878', '-9.885', '1.908'],
-   ['350', 'E', 'PHE', ..., '17.624', '-9.558', '1.908'],
-   ['350', 'E', 'PHE', ..., '19.234', '-13.442', '1.69']],
-  dtype='<U32')
-
          
-
          
-
          
-
          Warning
          
-
          The function takes the built-in dictionary when the vdw argument is not specified. If you wish to use a custom van der Waals radii file, you must read it with read_vdw as shown earlier and pass it as read_pdb(pdb, vdw=vdw).
          
-
          
-
          
-
-
          
-
-
-           
          
-          
          
-          
-        
          
-      
          
-    
          
-  
          
-   
-
-
-
\ No newline at end of file
diff --git a/docs/source/_build/html/_api_reference/read_vdw.html b/docs/source/_build/html/_api_reference/read_vdw.html
deleted file mode 100644
index 1a8cec15..00000000
--- a/docs/source/_build/html/_api_reference/read_vdw.html
+++ /dev/null
@@ -1,226 +0,0 @@
-
-
-
-  
-
-  
-  pyKVFinder.read_vdw — pyKVFinder 0.5.0 documentation
-      
-      
-    
-  
-  
-        
-        
-        
-        
-        
-    
-    
-    
-    
-     
-
-
- 
-  
          
-    
-
-    
          
-
-      
          
-        
          
-          
          
-  
-  
          
-
          
-          
          
-           
          
-             
-  
          
-
          pyKVFinder.read_vdw
          
-
          
-
          
-pyKVFinder.read_vdw(fn: Optional[Union[str, Path]] = None) → Dict[str, Dict[str, float]][source]
          
-
          Reads van der Waals radii from .dat file.
          
-
          
-
          Parameters:
          
-
          fn (Optional[Union[str, pathlib.Path]], optional) – A path to a van der Waals radii file, by default None. If None, apply the built-in van der
-Waals radii file: vdw.dat.
          
-
          
-
          Returns:
          
-
          vdw – A dictionary containing radii values.
          
-
          
-
          Return type:
          
-
          Dict[str, Dict[str, float]]
          
-
          
-
          Raises:
          
-
            
-
          • TypeError – fn must be a string or a pathlib.Path.
            • 
-
          • ValueError – A line in vdw has incorrect format. The values must be double
-    tab-separated.
            • 
-
          • ValueError – A line in vdw has an incorrect radius type for an atom.
            • 
-
          
-
          
-
          
-
          
-
          Note
          
-
          The van der Waals radii file defines the radius values for each
-atom by residue and when not defined, it uses a generic value
-based on the atom type (see van der Waals file template).
-The package contains a built-in van der Waals radii file: vdw.dat.
          
-
          
-
          
-
          See also
          
-
          read_pdb, read_xyz, Molecule
          
-
          
-
          Example
          
-
          The read_vdw function takes the built-in dictionary when a .dat file is not specified.
          
-
          >>> from pyKVFinder import read_vdw
->>> vdw = read_vdw()
->>> vdw
-{'ALA': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB1': 1.487, '1HB': 1.487, 'HB2': 1.487, '2HB': 1.487, 'HB3': 1.487, '3HB': 1.487, 'C': 1.908, 'O': 1.6612}, 'ARG': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG2': 1.487, '2HG': 1.487, 'HG3': 1.487, 'HG1': 1.487, '1HG': 1.487, 'CD': 1.908, 'HD2': 1.387, '1HD': 1.387, '2HD': 1.387, 'HD3': 1.387, 'HD1': 1.387, 'NE': 1.75, 'HE': 0.6, 'CZ': 1.908, 'NH1': 1.75, 'HH11': 0.6, '1HH1': 0.6, 'HH12': 0.6, '2HH1': 0.6, 'NH2': 1.75, 'HH21': 0.6, '2HH2': 0.6, 'HH22': 0.6, '1HH2': 0.6, 'C': 1.908, 'O': 1.6612}, 'ASH': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.908, 'OD1': 1.6612, 'OD2': 1.721, 'HD2': 0.0001, 'C': 1.908, 'O': 1.6612}, 'ASN': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'OD1': 1.6612, 'ND2': 1.824, 'HD21': 0.6, '1HD2': 0.6, 'HD22': 0.6, '2HD2': 0.6, 'C': 1.908, 'O': 1.6612}, 'ASP': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'OD1': 1.6612, 'OD2': 1.6612, 'C': 1.908, 'O': 1.6612}, 'CYM': {'N': 1.824, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB3': 1.387, 'HB2': 1.387, 'SG': 2.0, 'C': 1.908, 'O': 1.6612}, 'CYS': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.387, '2HB': 1.387, '1HB': 1.387, 'HB3': 1.387, 'HB1': 1.387, 'SG': 2.0, 'HG': 0.6, 'C': 1.908, 'O': 1.6612}, 'CYX': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.387, 'HB3': 1.387, 'SG': 2.0, 'C': 1.908, 'O': 1.6612}, 'GLH': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.908, 'HG2': 1.487, 'HG3': 1.487, 'CD': 1.908, 'OE1': 1.6612, 'OE2': 1.721, 'HE2': 0.0001, 'C': 1.908, 'O': 1.6612}, 'GLN': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG2': 1.487, '2HG': 1.487, 'HG3': 1.487, 'HG1': 1.487, '1HG': 1.487, 'CD': 1.908, 'OE1': 1.6612, 'NE2': 1.824, 'HE21': 0.6, '1HE2': 0.6, 'HE22': 0.6, '2HE2': 0.6, 'C': 1.908, 'O': 1.6612}, 'GLU': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG2': 1.487, '2HG': 1.487, 'HG3': 1.487, 'HG1': 1.487, '1HG': 1.487, 'CD': 1.908, 'OE1': 1.6612, 'OE2': 1.6612, 'C': 1.908, 'O': 1.6612}, 'GLY': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA2': 1.387, 'HA1': 1.387, '1HA': 1.387, '2HA': 1.387, 'HA3': 1.387, 'C': 1.908, 'O': 1.6612}, 'HID': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.85, 'ND1': 1.75, 'HD1': 0.6, 'CE1': 1.85, 'HE1': 1.359, 'NE2': 1.75, 'CD2': 2.0, 'HD2': 1.409, 'C': 1.908, 'O': 1.6612}, 'HIE': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.85, 'ND1': 1.75, 'CE1': 1.85, 'HE1': 1.359, 'NE2': 1.75, 'HE2': 0.6, 'CD2': 2.0, 'HD2': 1.409, 'C': 1.908, 'O': 1.6612}, 'HIP': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.85, 'ND1': 1.75, 'HD1': 0.6, 'CE1': 1.85, 'HE1': 1.359, 'NE2': 1.75, 'HE2': 0.6, 'CD2': 2.0, 'HD2': 1.409, 'C': 1.908, 'O': 1.6612}, 'ILE': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB': 1.487, 'CG2': 1.908, 'HG21': 1.487, '1HG2': 1.487, 'HG22': 1.487, '2HG2': 1.487, 'HG23': 1.487, '3HG2': 1.487, 'CG1': 1.908, 'HG12': 1.487, '2HG1': 1.487, 'HG13': 1.487, 'HG11': 1.487, '1HG1': 1.487, 'CD1': 1.908, 'HD11': 1.487, '1HD1': 1.487, 'HD12': 1.487, '2HD1': 1.487, 'HD13': 1.487, '3HD1': 1.487, 'C': 1.908, 'O': 1.6612}, 'LEU': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG': 1.487, 'CD1': 1.908, 'HD11': 1.487, '1HD1': 1.487, 'HD12': 1.487, '2HD1': 1.487, 'HD13': 1.487, '3HD1': 1.487, 'CD2': 1.908, 'HD21': 1.487, '1HD2': 1.487, 'HD22': 1.487, '2HD2': 1.487, 'HD23': 1.487, '3HD2': 1.487, 'C': 1.908, 'O': 1.6612}, 'LYN': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.908, 'HG2': 1.487, 'HG3': 1.487, 'CD': 1.908, 'HD2': 1.487, 'HD3': 1.487, 'CE': 1.908, 'HE2': 1.1, 'HE3': 1.1, 'NZ': 1.824, 'HZ2': 0.6, 'HZ3': 0.6, 'C': 1.908, 'O': 1.6612}, 'LYS': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG2': 1.487, '2HG': 1.487, 'HG3': 1.487, 'HG1': 1.487, '1HG': 1.487, 'CD': 1.908, 'HD2': 1.487, '1HD': 1.487, '2HD': 1.487, 'HD3': 1.487, 'HD1': 1.487, 'CE': 1.908, 'HE2': 1.1, '2HE': 1.1, 'HE3': 1.1, '1HE': 1.1, 'HE1': 1.1, 'NZ': 1.824, 'HZ1': 0.6, '1HZ': 0.6, 'HZ2': 0.6, '2HZ': 0.6, 'HZ3': 0.6, '3HZ': 0.6, 'C': 1.908, 'O': 1.6612}, 'MET': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG2': 1.387, '2HG': 1.387, 'HG3': 1.387, 'HG1': 1.387, '1HG': 1.387, 'SD': 2.0, 'CE': 1.908, 'HE1': 1.387, '1HE': 1.387, 'HE2': 1.387, '2HE': 1.387, 'HE3': 1.387, '3HE': 1.387, 'C': 1.908, 'O': 1.6612}, 'PHE': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'CD1': 1.908, 'HD1': 1.459, 'CE1': 1.908, 'HE1': 1.459, 'CZ': 1.908, 'HZ': 1.459, 'CE2': 1.908, 'HE2': 1.459, 'CD2': 1.908, 'HD2': 1.459, 'C': 1.908, 'O': 1.6612}, 'PRO': {'N': 1.824, 'CD': 1.908, 'HD2': 1.387, '1HD': 1.387, '2HD': 1.387, 'HD3': 1.387, 'HD1': 1.387, 'CG': 1.908, 'HG2': 1.487, '2HG': 1.487, 'HG3': 1.487, 'HG1': 1.487, '1HG': 1.487, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CA': 1.908, 'HA': 1.387, 'C': 1.908, 'O': 1.6612}, 'SER': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.387, '2HB': 1.387, '1HB': 1.387, 'HB3': 1.387, 'HB1': 1.387, 'OG': 1.721, 'HG': 0.0001, 'C': 1.908, 'O': 1.6612}, 'THR': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB': 1.387, 'CG2': 1.908, 'HG21': 1.487, '1HG2': 1.487, 'HG22': 1.487, '2HG2': 1.487, 'HG23': 1.487, '3HG2': 1.487, 'OG1': 1.721, 'HG1': 0.0001, 'C': 1.908, 'O': 1.6612}, 'TRP': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.85, 'CD1': 2.0, 'HD1': 1.409, 'NE1': 1.75, 'HE1': 0.6, 'CE2': 1.85, 'CZ2': 1.908, 'HZ2': 1.459, 'CH2': 1.908, 'HH2': 1.459, 'CZ3': 1.908, 'HZ3': 1.459, 'CE3': 1.908, 'HE3': 1.459, 'CD2': 1.85, 'C': 1.908, 'O': 1.6612}, 'TYR': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'CD1': 1.908, 'HD1': 1.459, 'CE1': 1.908, 'HE1': 1.459, 'CZ': 1.908, 'OH': 1.721, 'HH': 0.0001, 'CE2': 1.908, 'HE2': 1.459, 'CD2': 1.908, 'HD2': 1.459, 'C': 1.908, 'O': 1.6612}, 'VAL': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB': 1.487, 'CG1': 1.908, 'CG2': 1.908, 'HG11': 1.487, '1HG2': 1.487, '1HG1': 1.487, 'HG21': 1.487, 'HG12': 1.487, '2HG1': 1.487, 'HG22': 1.487, '2HG2': 1.487, 'HG13': 1.487, '3HG2': 1.487, '3HG1': 1.487, 'HG23': 1.487, 'C': 1.908, 'O': 1.6612}, 'HIS': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.85, 'ND1': 1.75, 'HD1': 0.6, 'CE1': 1.85, 'HE1': 1.359, 'NE2': 1.75, 'CD2': 2.0, 'HD2': 1.409, 'C': 1.908, 'O': 1.6612}, 'PTR': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.908, 'CD1': 1.908, 'HD1': 1.459, 'CE1': 1.908, 'HE1': 1.459, 'CZ': 1.908, 'CE2': 1.908, 'HE2': 1.459, 'CD2': 1.908, 'HD2': 1.459, 'OH': 1.6837, 'P': 2.1, 'O1P': 1.85, 'O2P': 1.85, 'O3P': 1.85, 'C': 1.908, 'O': 1.6612}, 'SEP': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.387, 'HB3': 1.387, '1HB': 1.387, '2HB': 1.387, 'OG': 1.6837, 'P': 2.1, 'O1P': 1.85, 'O2P': 1.85, 'O3P': 1.85, 'C': 1.908, 'O': 1.6612}, 'TPO': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB': 1.387, 'CG2': 1.908, 'HG21': 1.487, 'HG22': 1.487, 'HG23': 1.487, '1HG2': 1.487, '2HG2': 1.487, '3HG2': 1.487, 'OG1': 1.6837, 'P': 2.1, 'O1P': 1.85, 'O2P': 1.85, 'O3P': 1.85, 'C': 1.908, 'O': 1.6612}, 'H2D': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.85, 'ND1': 1.75, 'CE1': 1.85, 'HE1': 1.359, 'NE2': 1.75, 'HE2': 0.6, 'CD2': 2.0, 'HD2': 1.409, 'P': 2.1, 'O1P': 1.85, 'O2P': 1.85, 'O3P': 1.85, 'C': 1.908, 'O': 1.6612}, 'Y1P': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.908, 'CD1': 1.908, 'HD1': 1.459, 'CE1': 1.908, 'HE1': 1.459, 'CZ': 1.908, 'CE2': 1.908, 'HE2': 1.459, 'CD2': 1.908, 'HD2': 1.459, 'OG': 1.6837, 'P': 2.1, 'O1P': 1.721, 'O2P': 1.6612, 'O3P': 1.6612, 'H1P': 0.0001, 'C': 1.908, 'O': 1.6612}, 'T1P': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB': 1.387, 'CG2': 1.908, 'HG21': 1.487, 'HG22': 1.487, 'HG23': 1.487, 'OG': 1.6837, 'P': 2.1, 'O1P': 1.721, 'O2P': 1.6612, 'O3P': 1.6612, 'H1P': 0.0001, 'C': 1.908, 'O': 1.6612}, 'S1P': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.387, 'HB3': 1.387, 'OG': 1.6837, 'P': 2.1, 'O1P': 1.721, 'O2P': 1.6612, 'O3P': 1.6612, 'H1P': 0.0001, 'C': 1.908, 'O': 1.6612}, 'GEN': {'AC': 2.0, 'AG': 1.72, 'AL': 2.0, 'AM': 2.0, 'AR': 1.88, 'AS': 1.85, 'AT': 2.0, 'AU': 1.66, 'B': 2.0, 'BA': 2.0, 'BE': 2.0, 'BH': 2.0, 'BI': 2.0, 'BK': 2.0, 'BR': 1.85, 'C': 1.66, 'CA': 2.0, 'CD': 1.58, 'CE': 2.0, 'CF': 2.0, 'CL': 1.75, 'CM': 2.0, 'CO': 2.0, 'CR': 2.0, 'CS': 2.0, 'CU': 1.4, 'DB': 2.0, 'DS': 2.0, 'DY': 2.0, 'ER': 2.0, 'ES': 2.0, 'EU': 2.0, 'F': 1.47, 'FE': 2.0, 'FM': 2.0, 'FR': 2.0, 'GA': 1.87, 'GD': 2.0, 'GE': 2.0, 'H': 0.91, 'HE': 1.4, 'HF': 2.0, 'HG': 1.55, 'HO': 2.0, 'HS': 2.0, 'I': 1.98, 'IN': 1.93, 'IR': 2.0, 'K': 2.75, 'KR': 2.02, 'LA': 2.0, 'LI': 1.82, 'LR': 2.0, 'LU': 2.0, 'MD': 2.0, 'MG': 1.73, 'MN': 2.0, 'MO': 2.0, 'MT': 2.0, 'N': 1.97, 'NA': 2.27, 'NB': 2.0, 'ND': 2.0, 'NE': 1.54, 'NI': 1.63, 'NO': 2.0, 'NP': 2.0, 'O': 1.69, 'OS': 2.0, 'P': 2.1, 'PA': 2.0, 'PB': 2.02, 'PD': 1.63, 'PM': 2.0, 'PO': 2.0, 'PR': 2.0, 'PT': 1.72, 'PU': 2.0, 'RA': 2.0, 'RB': 2.0, 'RE': 2.0, 'RF': 2.0, 'RH': 2.0, 'RN': 2.0, 'RU': 2.0, 'S': 2.09, 'SB': 2.0, 'SC': 2.0, 'SE': 1.9, 'SG': 2.0, 'SI': 2.1, 'SM': 2.0, 'SN': 2.17, 'SR': 2.0, 'TA': 2.0, 'TB': 2.0, 'TC': 2.0, 'TE': 2.06, 'TH': 2.0, 'TI': 2.0, 'TL': 1.96, 'TM': 2.0, 'U': 1.86, 'V': 2.0, 'W': 2.0, 'XE': 2.16, 'Y': 2.0, 'YB': 2.0, 'ZN': 1.39, 'ZR': 2.0}}
-
          
-
          
-
          The van der Waals radii can be define by:
          
-
          
-
            
-
          • creating a Python dictionary:
            • 
-
          
-
          >>> vdw = {'GEN': {'C': 1.66, 'CA': 2.0, 'N': 1.97, 'O': 1.69, 'H': 0.91}}
-
          
-
          
-
            
-
          • specifying a .dat file following template of van der Waals radii file.
            • 
-
          
-
          >>> with open('vdw.dat', 'w') as f:
-...     f.write('>GEN\nC\t\t1.66\nCA\t\t2.00\nN\t\t1.97\nO\t\t1.69\nH\t\t0.91\n')
->>> vdw = read_vdw('vdw.dat')
->>> vdw
-{'GEN': {'C': 1.66, 'CA': 2.0, 'N': 1.97, 'O': 1.69, 'H': 0.91}}
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diff --git a/docs/source/_build/html/_api_reference/read_xyz.html b/docs/source/_build/html/_api_reference/read_xyz.html
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-
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-  
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-  
-  pyKVFinder.read_xyz — pyKVFinder 0.5.0 documentation
-      
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          pyKVFinder.read_xyz
          
-
          
-
          
-pyKVFinder.read_xyz(fn: Union[str, Path], vdw: Optional[Dict[str, Dict[str, float]]] = None) → ndarray[source]
          
-
          Reads XYZ file into numpy.ndarrays.
          
-
          
-
          Parameters:
          
-
            
-
          • fn (Union[str, pathlib.Path]) – A path to XYZ file.
            • 
-
          • vdw (Dict[str, Dict[str, float]], optional) – A dictionary containing radii values, by default None. If None, use output of read_vdw().
            • 
-
          
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-
          Returns:
          
-
          atomic – A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
-and radius) for each atom.
          
-
          
-
          Return type:
          
-
          numpy.ndarray
          
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          Raises:
          
-
          TypeError – fn must be a string or a pathlib.Path.
          
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-
          Note
          
-
          The van der Waals radii file defines the radius values for each atom
-by residue and when not defined, it uses a generic value based on the
-atom type. The function by default loads the built-in van der Waals radii
-file: vdw.dat.
          
-
          
-
          
-
          See also
          
-
          read_vdw, read_pdb, get_vertices, get_vertices_from_file, detect, constitutional, hydropathy
          
-
          
-
          Example
          
-
          With the vdW radii dictionary loaded with pyKVFinder.read_vdw, we can read a target XYZ file into Numpy arrays (atomic information and atomic coordinates):
          
-
          >>> import os
->>> import pyKVFinder
->>> from pyKVFinder import read_xyz
->>> xyz = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.xyz')
->>> atomic = read_xyz(xyz)
->>> atominfo
-array([['1', 'A', 'UNK', ..., '-15.642', '-14.858', '1.97'],
-   ['2', 'A', 'UNK', ..., '-14.62', '-15.897', '1.66'],
-   ['3', 'A', 'UNK', ..., '-13.357', '-15.508', '1.66'],
-   ...,
-   ['2790', 'A', 'UNK', ..., '18.878', '-9.885', '1.66'],
-   ['2791', 'A', 'UNK', ..., '17.624001', '-9.558', '1.66'],
-   ['2792', 'A', 'UNK', ..., '19.233999', '-13.442', '1.69']],
-  dtype='<U32')
-
          
-
          
-
          
-
          Warning
          
-
          The function takes the built-in dictionary when the vdw argument is not specified. If you wish to use a custom van der Waals radii file, you must read it with read_vdw as shown earlier and pass it as read_xyz(xyz, vdw=vdw).
          
-
          
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-
-
-
-  
-
-  
-  pyKVFinder.run_workflow — pyKVFinder 0.5.0 documentation
-      
-      
-    
-  
-  
-        
-        
-        
-        
-        
-    
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-      
          
-        
          
-          
          
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-          
          
-           
          
-             
-  
          
-
          pyKVFinder.run_workflow
          
-
          
-
          
-pyKVFinder.run_workflow(input: Union[str, pathlib.Path], ligand: Optional[Union[str, pathlib.Path]] = None, vdw: Optional[Union[str, pathlib.Path]] = None, box: Optional[Union[str, pathlib.Path]] = None, step: Union[float, int] = 0.6, probe_in: Union[float, int] = 1.4, probe_out: Union[float, int] = 4.0, removal_distance: Union[float, int] = 2.4, volume_cutoff: Union[float, int] = 5.0, ligand_cutoff: Union[float, int] = 5.0, include_depth: bool = False, include_hydropathy: bool = False, hydrophobicity_scale: Union[str, pathlib.Path] = 'EisenbergWeiss', surface: str = 'SES', ignore_backbone: bool = False, model: Optional[int] = None, nthreads: Optional[int] = None, verbose: bool = False) → pyKVFinder.pyKVFinderResults[source]
          
-
          Detects and characterizes cavities (volume, area, depth [optional],
-hydropathy [optional] and interface residues).
          
-
          
-
          Parameters:
          
-
            
-
          • input (Union[str, pathlib.Path]) – A path to a target structure file, in PDB or XYZ format, to detect and characterize cavities.
            • 
-
          • ligand (Union[str, pathlib.Path], optional) – A path to ligand file, in PDB or XYZ format, by default None.
            • 
-
          • vdw (Union[str, pathlib.Path], optional) – A path to a van der Waals radii file, by default None. If None, apply the built-in van der
-Waals radii file: vdw.dat.
            • 
-
          • box (Union[str, pathlib.Path], optional) – A path to box configuration file (TOML-formatted), by default None.
            • 
-
          • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.
            • 
-
          • probe_in (Union[float, int], optional) – Probe In size (A), by default 1.4.
            • 
-
          • probe_out (Union[float, int], optional) – Probe Out size (A), by default 4.0.
            • 
-
          • removal_distance (Union[float, int], optional) – Length to be removed from the cavity-bulk frontier (A), by default 2.4.
            • 
-
          • volume_cutoff (Union[float, int], optional) – Cavities volume filter (A3), by default 5.0.
            • 
-
          • ligand_cutoff (Union[float, int], optional) – Radius value to limit a space around a ligand (A), by default 5.0.
            • 
-
          • include_depth (bool, optional) – Whether to characterize the depth of the detected cavities, by
-default False.
            • 
-
          • include_hydropathy (bool, optional) – Whether to characterize the hydropathy of the detected cavities, by
-default False.
            • 
-
          • hydrophobicity_scale (Union[str, pathlib.Path], optional) – Name of a built-in hydrophobicity scale (EisenbergWeiss, HessaHeijne,
-KyteDoolitte, MoonFleming, WimleyWhite, ZhaoLondon) or a path to a
-TOML-formatted file with a custom hydrophobicity scale, by default
-EisenbergWeiss.
            • 
-
          • surface (str, optional) – Keywords options are SES (Solvent Excluded Surface) or SAS (Solvent
-Accessible Surface), by default SES.
            • 
-
          • ignore_backbone (bool, optional) – Whether to ignore backbone atoms (C, CA, N, O) when defining interface
-residues, by default False.
            • 
-
          • model (int, optional) – Model number, by default None. If None, keep atoms from all models.
            • 
-
          • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is
-os.cpu_count() - 1.
            • 
-
          • verbose (bool, optional) – Print extra information to standard output, by default False.
            • 
-
          
-
          
-
          Returns:
          
-
          results –
          
-
          A class with the following attributes defined:
          
-
          
-
            
-
          • cavities : numpy.ndarray
            
-
            
-
            Cavity points in the 3D grid (cavities[nx][ny][nz]).
-Cavities array has integer labels in each position, that are:
            
-
              
-
            • -1: bulk points;
              • 
-
            • 0: biomolecule points;
              • 
-
            • 1: empty space points;
              • 
-
            • >=2: cavity points.
              • 
-
            
-
            The empty space points are regions that do not meet the chosen
-volume cutoff to be considered a cavity.
            
-
            
-
            • 
-
          • surface : numpy.ndarray
            
-
            
-
            Surface points in the 3D grid (surface[nx][ny][nz]).
-Surface array has integer labels in each position, that are:
            
-
              
-
            • -1: bulk points;
              • 
-
            • 0: biomolecule or empty space points;
              • 
-
            • >=2: surface points.
              • 
-
            
-
            The empty space points are regions that do not meet the chosen
-volume cutoff to be considered a cavity.
            
-
            
-
            • 
-
          • depths : numpy.ndarray, optional
            
-
            
-
            A numpy.ndarray with depth of cavity points (depth[nx][ny][nz]).
            
-
            
-
            • 
-
          • scales : numpy.ndarray, optional
            
-
            
-
            A numpy.ndarray with hydrophobicity scale value mapped at surface
-points (scales[nx][ny][nz]).
            
-
            
-
            • 
-
          • ncav : int
            
-
            
-
            Number of cavities.
            
-
            
-
            • 
-
          • volume : Dict[str, float]
            
-
            
-
            A dictionary with volume of each detected cavity.
            
-
            
-
            • 
-
          • area : Dict[str, float]
            
-
            
-
            A dictionary with area of each detected cavity.
            
-
            
-
            • 
-
          • max_depth : Dict[str, float], optional
            
-
            
-
            A dictionary with maximum depth of each detected cavity.
            
-
            
-
            • 
-
          • avg_depth : Dict[str, float], optional
            
-
            
-
            A dictionary with average depth of each detected cavity.
            
-
            
-
            • 
-
          • avg_hydropathy : Dict[str, float], optional
            
-
            
-
            A dictionary with average hydropathy for each detected cavity and
-the range of the hydrophobicity scale (min, max).
            
-
            
-
            • 
-
          • residues: Dict[str, List[List[str]]]
            
-
            
-
            A dictionary with a list of interface residues for each detected
-cavity.
            
-
            
-
            • 
-
          • frequencies : Dict[str, Dict[str, Dict[str, int]]], optional
            
-
            
-
            A dictionary with frequencies of residues and class for
-residues of each detected cavity.
            
-
            
-
            • 
-
          • _vertices : numpy.ndarray
            
-
            
-
            A numpy.ndarray or a list with xyz vertices coordinates (origin,
-X-axis, Y-axis, Z-axis).
            
-
            
-
            • 
-
          • _step : float
            
-
            
-
            Grid spacing (A).
            
-
            
-
            • 
-
          • _input : Union[str, pathlib.Path], optional
            
-
            
-
            A path to input PDB or XYZ file.
            
-
            
-
            • 
-
          • _ligand : Union[str, pathlib.Path], optional
            
-
            
-
            A path to ligand PDB or XYZ file.
            
-
            
-
            • 
-
          
-
          
-
          
-
          
-
          Return type:
          
-
          pyKVFinderResults
          
-
          
-
          Raises:
          
-
            
-
          • TypeError – input must have .pdb or .xyz extension.
            • 
-
          • TypeError – ligand must have .pdb or .xyz extension.
            • 
-
          
-
          
-
          
-
          
-
          Note
          
-
          The cavity nomenclature is based on the integer label. The cavity marked
-with 2, the first integer corresponding to a cavity, is KAA, the cavity
-marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
          
-
          
-
          
-
          Note
          
-
          The classes of residues are:
          
-
            
-
          • Aliphatic apolar (R1): Alanine, Glycine, Isoleucine, Leucine, Methionine, Valine.
            • 
-
          • Aromatic (R2): Phenylalanine, Tryptophan, Tyrosine.
            • 
-
          • Polar Uncharged (R3): Asparagine, Cysteine, Glutamine, Proline, Serine, Threonine.
            • 
-
          • Negatively charged (R4): Aspartate, Glutamate.
            • 
-
          • Positively charged (R5): Arginine, Histidine, Lysine.
            • 
-
          • Non-standard (RX): Non-standard residues.
            • 
-
          
-
          
-
          
-
          See also
          
-
          pyKVFinderResults
          
-
          
-
          Example
          
-
          The standard workflow for cavity detection with spatial (surface points, volume, area) and constitutional (interface residues and their frequencies) characterization  can be run at once with one command:
          
-
          >>> import os
->>> import pyKVFinder
->>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
->>> results = pyKVFinder.run_workflow(pdb)
->>> results
-<pyKVFinderResults object>
->>> results.cavities
-array([[[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]],
-       ...,
-       [[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
->>> results.surface
-array([[[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]],
-       ...,
-       [[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
->>> results.ncav
->>> 18
->>> results.volume
-{'KAA': 137.16, 'KAB': 47.52, 'KAC': 66.96, 'KAD': 8.21, 'KAE': 43.63, 'KAF': 12.53, 'KAG': 6.26, 'KAH': 520.13, 'KAI': 12.31, 'KAJ': 26.57, 'KAK': 12.31, 'KAL': 33.91, 'KAM': 23.11, 'KAN': 102.82, 'KAO': 6.05, 'KAP': 15.55, 'KAQ': 7.99, 'KAR': 7.78}
->>> results.area
-{'KAA': 126.41, 'KAB': 62.37, 'KAC': 74.57, 'KAD': 19.06, 'KAE': 57.08, 'KAF': 22.77, 'KAG': 15.38, 'KAH': 496.97, 'KAI': 30.58, 'KAJ': 45.64, 'KAK': 30.58, 'KAL': 45.58, 'KAM': 45.25, 'KAN': 129.77, 'KAO': 12.28, 'KAP': 25.04, 'KAQ': 13.46, 'KAR': 16.6}
->>> results.residues
-{'KAA': [['14', 'E', 'SER'], ['15', 'E', 'VAL'], ['18', 'E', 'PHE'], ['19', 'E', 'LEU'], ['100', 'E', 'PHE'], ['152', 'E', 'LEU'], ['155', 'E', 'GLU'], ['156', 'E', 'TYR'], ['292', 'E', 'LYS'], ['302', 'E', 'TRP'], ['303', 'E', 'ILE'], ['306', 'E', 'TYR']], 'KAB': [['18', 'E', 'PHE'], ['22', 'E', 'ALA'], ['25', 'E', 'ASP'], ['26', 'E', 'PHE'], ['29', 'E', 'LYS'], ['97', 'E', 'ALA'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['156', 'E', 'TYR']], 'KAC': [['141', 'E', 'PRO'], ['142', 'E', 'HIS'], ['144', 'E', 'ARG'], ['145', 'E', 'PHE'], ['148', 'E', 'ALA'], ['299', 'E', 'THR'], ['300', 'E', 'THR'], ['305', 'E', 'ILE'], ['310', 'E', 'VAL'], ['311', 'E', 'GLU'], ['313', 'E', 'PRO']], 'KAD': [['122', 'E', 'TYR'], ['124', 'E', 'ALA'], ['176', 'E', 'GLN'], ['318', 'E', 'PHE'], ['320', 'E', 'GLY'], ['321', 'E', 'PRO'], ['322', 'E', 'GLY'], ['323', 'E', 'ASP']], 'KAE': [['95', 'E', 'LEU'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['100', 'E', 'PHE'], ['103', 'E', 'LEU'], ['104', 'E', 'VAL'], ['105', 'E', 'LYS'], ['106', 'E', 'LEU']], 'KAF': [['123', 'E', 'VAL'], ['124', 'E', 'ALA'], ['175', 'E', 'ASP'], ['176', 'E', 'GLN'], ['181', 'E', 'GLN']], 'KAG': [['34', 'E', 'SER'], ['37', 'E', 'THR'], ['96', 'E', 'GLN'], ['106', 'E', 'LEU'], ['107', 'E', 'GLU'], ['108', 'E', 'PHE'], ['109', 'E', 'SER']], 'KAH': [['49', 'E', 'LEU'], ['50', 'E', 'GLY'], ['51', 'E', 'THR'], ['52', 'E', 'GLY'], ['53', 'E', 'SER'], ['54', 'E', 'PHE'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['72', 'E', 'LYS'], ['74', 'E', 'LEU'], ['84', 'E', 'GLN'], ['87', 'E', 'HIS'], ['88', 'E', 'THR'], ['91', 'E', 'GLU'], ['104', 'E', 'VAL'], ['120', 'E', 'MET'], ['121', 'E', 'GLU'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['166', 'E', 'ASP'], ['168', 'E', 'LYS'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['184', 'E', 'ASP'], ['186', 'E', 'GLY'], ['187', 'E', 'PHE'], ['201', 'E', 'THR'], ['327', 'E', 'PHE']], 'KAI': [['131', 'E', 'HIS'], ['138', 'E', 'PHE'], ['142', 'E', 'HIS'], ['146', 'E', 'TYR'], ['174', 'E', 'ILE'], ['314', 'E', 'PHE']], 'KAJ': [['33', 'E', 'PRO'], ['89', 'E', 'LEU'], ['92', 'E', 'LYS'], ['93', 'E', 'ARG'], ['96', 'E', 'GLN'], ['349', 'E', 'GLU'], ['350', 'E', 'PHE']], 'KAK': [['157', 'E', 'LEU'], ['162', 'E', 'LEU'], ['163', 'E', 'ILE'], ['164', 'E', 'TYR'], ['185', 'E', 'PHE'], ['188', 'E', 'ALA']], 'KAL': [['49', 'E', 'LEU'], ['127', 'E', 'GLU'], ['129', 'E', 'PHE'], ['130', 'E', 'SER'], ['326', 'E', 'ASN'], ['327', 'E', 'PHE'], ['328', 'E', 'ASP'], ['330', 'E', 'TYR']], 'KAM': [['51', 'E', 'THR'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['73', 'E', 'ILE'], ['74', 'E', 'LEU'], ['75', 'E', 'ASP'], ['115', 'E', 'ASN'], ['335', 'E', 'ILE'], ['336', 'E', 'ARG']], 'KAN': [['165', 'E', 'ARG'], ['166', 'E', 'ASP'], ['167', 'E', 'LEU'], ['199', 'E', 'CYS'], ['200', 'E', 'GLY'], ['201', 'E', 'THR'], ['204', 'E', 'TYR'], ['205', 'E', 'LEU'], ['206', 'E', 'ALA'], ['209', 'E', 'ILE'], ['219', 'E', 'VAL'], ['220', 'E', 'ASP'], ['223', 'E', 'ALA']], 'KAO': [['48', 'E', 'THR'], ['51', 'E', 'THR'], ['56', 'E', 'ARG'], ['330', 'E', 'TYR'], ['331', 'E', 'GLU']], 'KAP': [['222', 'E', 'TRP'], ['238', 'E', 'PHE'], ['253', 'E', 'GLY'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['273', 'E', 'LEU']], 'KAQ': [['207', 'E', 'PRO'], ['208', 'E', 'GLU'], ['211', 'E', 'LEU'], ['213', 'E', 'LYS'], ['275', 'E', 'VAL'], ['277', 'E', 'LEU']], 'KAR': [['237', 'E', 'PRO'], ['238', 'E', 'PHE'], ['249', 'E', 'LYS'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['256', 'E', 'ARG']]}
->>> results.frequencies
-{'KAA': {'RESIDUES': {'GLU': 1, 'ILE': 1, 'LEU': 2, 'LYS': 1, 'PHE': 2, 'SER': 1, 'TRP': 1, 'TYR': 2, 'VAL': 1}, 'CLASS': {'R1': 4, 'R2': 5, 'R3': 1, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAB': {'RESIDUES': {'ALA': 2, 'ASN': 1, 'ASP': 1, 'LYS': 1, 'PHE': 2, 'TYR': 1, 'VAL': 1}, 'CLASS': {'R1': 3, 'R2': 3, 'R3': 1, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAC': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'GLU': 1, 'HIS': 1, 'ILE': 1, 'PHE': 1, 'PRO': 2, 'THR': 2, 'VAL': 1}, 'CLASS': {'R1': 5, 'R2': 1, 'R3': 2, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAD': {'RESIDUES': {'ALA': 1, 'ASP': 1, 'GLN': 1, 'GLY': 2, 'PHE': 1, 'PRO': 1, 'TYR': 1}, 'CLASS': {'R1': 4, 'R2': 2, 'R3': 1, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAE': {'RESIDUES': {'ASN': 1, 'LEU': 3, 'LYS': 1, 'PHE': 1, 'VAL': 2}, 'CLASS': {'R1': 5, 'R2': 1, 'R3': 1, 'R4': 0, 'R5': 1, 'RX': 0}}, 'KAF': {'RESIDUES': {'ALA': 1, 'ASP': 1, 'GLN': 2, 'VAL': 1}, 'CLASS': {'R1': 2, 'R2': 0, 'R3': 2, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAG': {'RESIDUES': {'GLN': 1, 'GLU': 1, 'LEU': 1, 'PHE': 1, 'SER': 2, 'THR': 1}, 'CLASS': {'R1': 1, 'R2': 1, 'R3': 4, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAH': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'ASN': 1, 'ASP': 2, 'GLN': 1, 'GLU': 4, 'GLY': 4, 'HIS': 1, 'LEU': 3, 'LYS': 2, 'MET': 1, 'PHE': 3, 'SER': 1, 'THR': 4, 'TYR': 1, 'VAL': 3}, 'CLASS': {'R1': 11, 'R2': 4, 'R3': 8, 'R4': 6, 'R5': 4, 'RX': 0}}, 'KAI': {'RESIDUES': {'HIS': 2, 'ILE': 1, 'PHE': 2, 'TYR': 1}, 'CLASS': {'R1': 1, 'R2': 3, 'R3': 0, 'R4': 0, 'R5': 2, 'RX': 0}}, 'KAJ': {'RESIDUES': {'ARG': 1, 'GLN': 1, 'GLU': 1, 'LEU': 1, 'LYS': 1, 'PHE': 1, 'PRO': 1}, 'CLASS': {'R1': 2, 'R2': 1, 'R3': 1, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAK': {'RESIDUES': {'ALA': 1, 'ILE': 1, 'LEU': 2, 'PHE': 1, 'TYR': 1}, 'CLASS': {'R1': 4, 'R2': 2, 'R3': 0, 'R4': 0, 'R5': 0, 'RX': 0}}, 'KAL': {'RESIDUES': {'ASN': 1, 'ASP': 1, 'GLU': 1, 'LEU': 1, 'PHE': 2, 'SER': 1, 'TYR': 1}, 'CLASS': {'R1': 1, 'R2': 3, 'R3': 2, 'R4': 2, 'R5': 0, 'RX': 0}}, 'KAM': {'RESIDUES': {'ARG': 2, 'ASN': 1, 'ASP': 1, 'GLY': 1, 'ILE': 2, 'LEU': 1, 'THR': 1}, 'CLASS': {'R1': 4, 'R2': 0, 'R3': 2, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAN': {'RESIDUES': {'ALA': 2, 'ARG': 1, 'ASP': 2, 'CYS': 1, 'GLY': 1, 'ILE': 1, 'LEU': 2, 'THR': 1, 'TYR': 1, 'VAL': 1}, 'CLASS': {'R1': 7, 'R2': 1, 'R3': 2, 'R4': 2, 'R5': 1, 'RX': 0}}, 'KAO': {'RESIDUES': {'ARG': 1, 'GLU': 1, 'THR': 2, 'TYR': 1}, 'CLASS': {'R1': 0, 'R2': 1, 'R3': 2, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAP': {'RESIDUES': {'GLY': 1, 'LEU': 1, 'LYS': 1, 'PHE': 1, 'TRP': 1, 'VAL': 1}, 'CLASS': {'R1': 3, 'R2': 2, 'R3': 0, 'R4': 0, 'R5': 1, 'RX': 0}}, 'KAQ': {'RESIDUES': {'GLU': 1, 'LEU': 2, 'LYS': 1, 'PRO': 1, 'VAL': 1}, 'CLASS': {'R1': 4, 'R2': 0, 'R3': 0, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAR': {'RESIDUES': {'ARG': 1, 'LYS': 2, 'PHE': 1, 'PRO': 1, 'VAL': 1}, 'CLASS': {'R1': 2, 'R2': 1, 'R3': 0, 'R4': 0, 'R5': 3, 'RX': 0}}}
-
          
-
          
-
          However, users may opt to perform cavity detection in a segmented space through ligand adjustment and/or box adjustment modes.
          
-
          The cavity detection can be limited around the target ligand(s), which will be passed to pyKVFinder through a .pdb or a .xyz files. Thus, the detected cavities are limited within a radius (ligand_cutoff) of the target ligand(s).
          
-
          >>> ligand = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'ADN.pdb')
->>> results = pyKVFinder.run_workflow(pdb, ligand)
->>> results
-<pyKVFinderResults object>
->>> results.cavities
-array([[[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]],
-       ...,
-       [[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
->>> results.surface
-array([[[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]],
-       ...,
-       [[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
->>> results.ncav
->>> 18
->>> results.volume
-{'KAA': 365.04, 'KAB': 16.85}
->>> results.area
-{'KAA': 328.79, 'KAB': 23.15}
->>> results.residues
-{'KAA': [['49', 'E', 'LEU'], ['50', 'E', 'GLY'], ['51', 'E', 'THR'], ['52', 'E', 'GLY'], ['53', 'E', 'SER'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['72', 'E', 'LYS'], ['104', 'E', 'VAL'], ['120', 'E', 'MET'], ['121', 'E', 'GLU'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['166', 'E', 'ASP'], ['168', 'E', 'LYS'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['184', 'E', 'ASP'], ['327', 'E', 'PHE']], 'KAB': [['49', 'E', 'LEU'], ['127', 'E', 'GLU'], ['130', 'E', 'SER'], ['326', 'E', 'ASN'], ['327', 'E', 'PHE'], ['328', 'E', 'ASP'], ['330', 'E', 'TYR']]}
->>> results.frequencies
-{'KAA': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'ASN': 1, 'ASP': 2, 'GLU': 3, 'GLY': 3, 'LEU': 2, 'LYS': 2, 'MET': 1, 'PHE': 1, 'SER': 1, 'THR': 2, 'TYR': 1, 'VAL': 3}, 'CLASS': {'R1': 9, 'R2': 2, 'R3': 5, 'R4': 5, 'R5': 3, 'RX': 0}}, 'KAB': {'RESIDUES': {'ASN': 1, 'ASP': 1, 'GLU': 1, 'LEU': 1, 'PHE': 1, 'SER': 1, 'TYR': 1}, 'CLASS': {'R1': 1, 'R2': 2, 'R3': 2, 'R4': 2, 'R5': 0, 'RX': 0}}}
-
          
-
          
-
          Further, we can also perform cavity detection on a custom 3D grid, where we can explore closed regions with a custom box, which can be defined by a .toml file (see Box configuration file template).
          
-
          >>> fn = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'custom-box.toml')
->>> with open(fn, 'r') as f:
-...     print(f.read())
-[box]
-p1 = [3.11, 7.34, 1.59]
-p2 = [11.51, 7.34, 1.59]
-p3 = [3.11, 10.74, 1.59]
-p4 = [3.11, 7.34, 6.19]
->>> results = pyKVFinder.run_workflow(pdb, box=fn)
->>> results
-<pyKVFinderResults object>
->>> results.cavities
-array([[[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]],
-       ...,
-       [[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
->>> results.surface
-array([[[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]],
-       ...,
-       [[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
->>> results.ncav
->>> 1
->>> results.volume
-{'KAA': 115.78}
->>> results.area
-{'KAA': 33.91}
->>> results.residues
-{'KAA': [['49', 'E', 'LEU'], ['50', 'E', 'GLY'], ['51', 'E', 'THR'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['104', 'E', 'VAL'], ['121', 'E', 'GLU'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['327', 'E', 'PHE']]}
->>> results.frequencies
-{'KAA': {'RESIDUES': {'ALA': 1, 'ASN': 1, 'GLU': 3, 'GLY': 1, 'LEU': 2, 'PHE': 1, 'THR': 2, 'TYR': 1, 'VAL': 3}, 'CLASS': {'R1': 7, 'R2': 2, 'R3': 3, 'R4': 3, 'R5': 0, 'RX': 0}}}
-
          
-
          
-
          However, users may opt to perform the full workflow for cavity detection with spatial (surface points, volume and area), constitutional (interface residues and their frequencies), hydropathy and depth characterization. This full workflow can be run with one command by setting some parameters of run_workflow function:
          
-
          >>> results = pyKVFinder.run_workflow(pdb, include_depth=True, include_hydropathy=True, hydrophobicity_scale='EisenbergWeiss')
->>> results.depths
-array([[[0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        ...,
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.]],
-       ...,
-       [[0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        ...,
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.]]])
->>> results.scales
-array([[[0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        ...,
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.]],
-       ...,
-       [[0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        ...,
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.]]])
->>> results.avg_depth
-{'KAA': 1.35, 'KAB': 0.91, 'KAC': 0.68, 'KAD': 0.32, 'KAE': 0.99, 'KAF': 0.24, 'KAG': 0.1, 'KAH': 3.91, 'KAI': 0.0, 'KAJ': 0.96, 'KAK': 0.0, 'KAL': 1.07, 'KAM': 0.24, 'KAN': 0.0, 'KAO': 0.29, 'KAP': 0.7, 'KAQ': 0.22, 'KAR': 0.12}
->>> results.max_depth
-{'KAA': 3.79, 'KAB': 2.68, 'KAC': 2.62, 'KAD': 0.85, 'KAE': 3.0, 'KAF': 0.85, 'KAG': 0.6, 'KAH': 10.73, 'KAI': 0.0, 'KAJ': 2.24, 'KAK': 0.0, 'KAL': 3.0, 'KAM': 1.2, 'KAN': 0.0, 'KAO': 1.04, 'KAP': 2.08, 'KAQ': 0.85, 'KAR': 0.6}
->>> results.avg_hydropathy
-{'KAA': -0.73, 'KAB': -0.05, 'KAC': -0.07, 'KAD': -0.62, 'KAE': -0.81, 'KAF': -0.14, 'KAG': -0.33, 'KAH': -0.17, 'KAI': -0.4, 'KAJ': 0.62, 'KAK': -0.99, 'KAL': 0.36, 'KAM': -0.33, 'KAN': 0.18, 'KAO': 0.88, 'KAP': -0.96, 'KAQ': 0.48, 'KAR': 0.24, 'EisenbergWeiss': [-1.42, 2.6]}
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diff --git a/docs/source/_build/html/_api_reference/spatial.html b/docs/source/_build/html/_api_reference/spatial.html
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-pyKVFinder.spatial(cavities: ndarray, step: Union[float, int] = 0.6, selection: Optional[Union[List[int], List[str]]] = None, nthreads: Optional[int] = None, verbose: bool = False) → Tuple[ndarray, Dict[str, float], Dict[str, float]][source]
          
-
          Spatial characterization (volume and area) of the detected cavities.
          
-
          
-
          Parameters:
          
-
            
-
          • cavities (numpy.ndarray) – 
            Cavity points in the 3D grid (cavities[nx][ny][nz]).
-Cavities array has integer labels in each position, that are:
            
-
            
-
              
-
            • -1: bulk points;
              • 
-
            • 0: biomolecule points;
              • 
-
            • 1: empty space points;
              • 
-
            • >=2: cavity points.
              • 
-
            
-
            
-
            The empty space points are regions that do not meet the chosen
-volume cutoff to be considered a cavity.
            
-
            • 
-
          • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.
            • 
-
          • selection (Union[List[int], List[str]], optional) – A list of integer labels or a list of cavity names to be selected, by default None.
            • 
-
          • nthreads (int, optional) – Number of threads, by default None. If None, the number of threads is
-os.cpu_count() - 1.
            • 
-
          • verbose (bool, optional) – Print extra information to standard output, by default False.
            • 
-
          
-
          
-
          Returns:
          
-
            
-
          • surface (numpy.ndarray) – Surface points in the 3D grid (surface[nx][ny][nz]).
-Surface array has integer labels in each position, that are:
            
-
            
-
              
-
            • -1: bulk points;
              • 
-
            • 0: biomolecule or empty space points;
              • 
-
            • >=2: surface points.
              • 
-
            
-
            
-
            The empty space points are regions that do not meet the chosen
-volume cutoff to be considered a cavity.
            
-
            • 
-
          • volume (Dict[str, float]) – A dictionary with volume of each detected cavity.
            • 
-
          • area (Dict[str, float]) – A dictionary with area of each detected cavity.
            • 
-
          
-
          
-
          
-
          
-
          
-
          Note
          
-
          The cavity nomenclature is based on the integer label. The cavity marked
-with 2, the first integer corresponding to a cavity, is KAA, the cavity
-marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
          
-
          
-
          
-
          Raises:
          
-
            
-
          • TypeError – cavities must be a numpy.ndarray.
            • 
-
          • ValueError – cavities has the incorrect shape. It must be (nx, ny, nz).
            • 
-
          • TypeError – step must be a positive real number.
            • 
-
          • ValueError – step must be a positive real number.
            • 
-
          • TypeError – selection must be a list of strings (cavity names) or integers (cavity labels).
            • 
-
          • ValueError – Invalid selection: {selection}.
            • 
-
          • TypeError – nthreads must be a positive integer.
            • 
-
          • ValueError – nthreads must be a positive integer.
            • 
-
          • TypeError – verbose must be a boolean.
            • 
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-
          
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          See also
          
-
          detect, hydropathy, export
          
-
          
-
          Example
          
-
          With the cavity points identified with detect, we can perform a spatial characterization, that includes volume, area and defining surface points:
          
-
          >>> from pyKVFinder import spatial
->>> surface, volume, area = spatial(cavities)
->>> surface
-array([[[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]],
-       ...,
-       [[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
->>> volume
-{'KAA': 137.16, 'KAB': 47.52, 'KAC': 66.96, 'KAD': 8.21, 'KAE': 43.63, 'KAF': 12.53, 'KAG': 6.26, 'KAH': 520.13, 'KAI': 12.31, 'KAJ': 26.57, 'KAK': 12.31, 'KAL': 33.91, 'KAM': 23.11, 'KAN': 102.82, 'KAO': 6.05, 'KAP': 15.55, 'KAQ': 7.99, 'KAR': 7.78}
->>> area
-{'KAA': 126.41, 'KAB': 62.37, 'KAC': 74.57, 'KAD': 19.06, 'KAE': 57.08, 'KAF': 22.77, 'KAG': 15.38, 'KAH': 496.97, 'KAI': 30.58, 'KAJ': 45.64, 'KAK': 30.58, 'KAL': 45.58, 'KAM': 45.25, 'KAN': 129.77, 'KAO': 12.28, 'KAP': 25.04, 'KAQ': 13.46, 'KAR': 16.6}
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diff --git a/docs/source/_build/html/_api_reference/write_results.html b/docs/source/_build/html/_api_reference/write_results.html
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-pyKVFinder.write_results(fn: Union[str, Path], input: Optional[Union[str, Path]], ligand: Optional[Union[str, Path]], output: Optional[Union[str, Path]], output_hydropathy: Optional[Union[str, Path]] = None, volume: Optional[Dict[str, float]] = None, area: Optional[Dict[str, float]] = None, max_depth: Optional[Dict[str, float]] = None, avg_depth: Optional[Dict[str, float]] = None, avg_hydropathy: Optional[Dict[str, float]] = None, residues: Optional[Dict[str, List[List[str]]]] = None, frequencies: Optional[Dict[str, Dict[str, Dict[str, int]]]] = None, step: Union[float, int] = 0.6) → None[source]
          
-
          Writes file paths and cavity characterization to TOML-formatted file.
          
-
          
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          Parameters:
          
-
            
-
          • fn (Union[str, pathlib.Path]) – A path to TOML-formatted file for writing file paths and
-cavity characterization (volume, area, depth [optional] and interface
-residues) per cavity detected.
            • 
-
          • input (Union[str, pathlib.Path], optional) – A path to input PDB or XYZ file.
            • 
-
          • ligand (Union[str, pathlib.Path], optional) – A path to ligand PDB or XYZ file.
            • 
-
          • output (Union[str, pathlib.Path], optional) – A path to cavity PDB file.
            • 
-
          • output_hydropathy (Union[str, pathlib.Path], optional) – A path to hydropathy PDB file (surface points mapped with a
-hydrophobicity scale), by default None.
            • 
-
          • volume (Dict[str, float], optional) – A dictionary with volume of each detected cavity, by default None.
            • 
-
          • area (Dict[str, float], optional) – A dictionary with area of each detected cavity, by default None.
            • 
-
          • max_depth (Dict[str, float], optional) – A dictionary with maximum depth of each detected cavity, by default
-None.
            • 
-
          • avg_depth (Dict[str, float], optional) – A dictionary with average depth of each detected cavity, by default
-None.
            • 
-
          • avg_hydropapthy (Dict[str, float], optional) – A dictionary with average hydropathy of each detected cavity and range
-of the hydrophobicity scale mapped, by default None.
            • 
-
          • residues (Dict[str, List[List[str]]], optional) – A dictionary with interface residues of each detected cavity, by
-default None.
            • 
-
          • frequencies (Dict[str, Dict[str, Dict[str, int]]], optional) – A dictionary with frequencies of interface residues and classes of
-residues of each detected cavity, by default None.
            • 
-
          • step (Union[float, int], optional) – Grid spacing (A), by default 0.6.
            • 
-
          
-
          
-
          Raises:
          
-
            
-
          • TypeError – fn must be a string or a pathlib.Path.
            • 
-
          • TypeError – input must be a string or a pathlib.Path.
            • 
-
          • TypeError – ligand must be a string or a pathlib.Path.
            • 
-
          • TypeError – output must be a string or a pathlib.Path.
            • 
-
          • TypeError – output_hydropathy must be a string or a pathlib.Path.
            • 
-
          • TypeError – volume must be a dictionary.
            • 
-
          • TypeError – area must be a dictionary.
            • 
-
          • TypeError – max_depth must be a dictionary.
            • 
-
          • TypeError – avg_depth must be a dictionary.
            • 
-
          • TypeError – avg_hydropathy must be a dictionary.
            • 
-
          • TypeError – residues must be a dictionary.
            • 
-
          • TypeError – frequencies must be a dictionary.
            • 
-
          • TypeError – step must be a positive real number.
            • 
-
          • ValueError – step must be a positive real number.
            • 
-
          
-
          
-
          
-
          
-
          Note
          
-
          The cavity nomenclature is based on the integer label. The cavity
-marked with 2, the first integer corresponding to a cavity, is KAA, the
-cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
          
-
          
-
          
-
          See also
          
-
          detect, spatial, depth, constitutional, hydropathy, export
          
-
          
-
          Example
          
-
          With the cavity and surface points identified and depth and hydrophobicity scale mapped in the 3D grid, we can:
          
-
            
-
          • Write cavity detection:
            • 
-
          
-
          >>> from pyKVFinder import write_results
->>> import os
->>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
->>> write_results('results.toml', input=pdb, ligand=None, output='cavities.pdb')
-
          
-
          
-
            
-
          • Write spatial characterization
            • 
-
          
-
          >>> volume
-{'KAA': 137.16, 'KAB': 47.52, 'KAC': 66.96, 'KAD': 8.21, 'KAE': 43.63, 'KAF': 12.53, 'KAG': 6.26, 'KAH': 520.13, 'KAI': 12.31, 'KAJ': 26.57, 'KAK': 12.31, 'KAL': 33.91, 'KAM': 23.11, 'KAN': 102.82, 'KAO': 6.05, 'KAP': 15.55, 'KAQ': 7.99, 'KAR': 7.78}
->>> area
-{'KAA': 120.52, 'KAB': 58.76, 'KAC': 72.06, 'KAD': 17.62, 'KAE': 56.44, 'KAF': 22.53, 'KAG': 15.38, 'KAH': 489.25, 'KAI': 29.87, 'KAJ': 44.85, 'KAK': 30.58, 'KAL': 43.59, 'KAM': 45.25, 'KAN': 129.77, 'KAO': 11.57, 'KAP': 24.8, 'KAQ': 12.59, 'KAR': 15.97}
->>> write_results('results.toml', input=pdb, ligand=None, output=None, volume=volume, area=area)
-
          
-
          
-
            
-
          • Write constitutional characterization
            • 
-
          
-
          >>> residues
-{'KAA': [['14', 'E', 'SER'], ['15', 'E', 'VAL'], ['18', 'E', 'PHE'], ['19', 'E', 'LEU'], ['100', 'E', 'PHE'], ['152', 'E', 'LEU'], ['155', 'E', 'GLU'], ['156', 'E', 'TYR'], ['292', 'E', 'LYS'], ['302', 'E', 'TRP'], ['303', 'E', 'ILE'], ['306', 'E', 'TYR']], 'KAB': [['18', 'E', 'PHE'], ['22', 'E', 'ALA'], ['25', 'E', 'ASP'], ['26', 'E', 'PHE'], ['29', 'E', 'LYS'], ['97', 'E', 'ALA'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['156', 'E', 'TYR']], 'KAC': [['141', 'E', 'PRO'], ['142', 'E', 'HIS'], ['144', 'E', 'ARG'], ['145', 'E', 'PHE'], ['148', 'E', 'ALA'], ['299', 'E', 'THR'], ['300', 'E', 'THR'], ['305', 'E', 'ILE'], ['310', 'E', 'VAL'], ['311', 'E', 'GLU'], ['313', 'E', 'PRO']], 'KAD': [['122', 'E', 'TYR'], ['124', 'E', 'ALA'], ['176', 'E', 'GLN'], ['318', 'E', 'PHE'], ['320', 'E', 'GLY'], ['321', 'E', 'PRO'], ['322', 'E', 'GLY'], ['323', 'E', 'ASP']], 'KAE': [['95', 'E', 'LEU'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['100', 'E', 'PHE'], ['103', 'E', 'LEU'], ['104', 'E', 'VAL'], ['105', 'E', 'LYS'], ['106', 'E', 'LEU']], 'KAF': [['123', 'E', 'VAL'], ['124', 'E', 'ALA'], ['175', 'E', 'ASP'], ['176', 'E', 'GLN'], ['181', 'E', 'GLN']], 'KAG': [['34', 'E', 'SER'], ['37', 'E', 'THR'], ['96', 'E', 'GLN'], ['106', 'E', 'LEU'], ['107', 'E', 'GLU'], ['108', 'E', 'PHE'], ['109', 'E', 'SER']], 'KAH': [['49', 'E', 'LEU'], ['50', 'E', 'GLY'], ['51', 'E', 'THR'], ['52', 'E', 'GLY'], ['53', 'E', 'SER'], ['54', 'E', 'PHE'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['72', 'E', 'LYS'], ['74', 'E', 'LEU'], ['84', 'E', 'GLN'], ['87', 'E', 'HIS'], ['88', 'E', 'THR'], ['91', 'E', 'GLU'], ['104', 'E', 'VAL'], ['120', 'E', 'MET'], ['121', 'E', 'GLU'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['166', 'E', 'ASP'], ['168', 'E', 'LYS'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['184', 'E', 'ASP'], ['186', 'E', 'GLY'], ['187', 'E', 'PHE'], ['201', 'E', 'THR'], ['327', 'E', 'PHE']], 'KAI': [['131', 'E', 'HIS'], ['138', 'E', 'PHE'], ['142', 'E', 'HIS'], ['146', 'E', 'TYR'], ['174', 'E', 'ILE'], ['314', 'E', 'PHE']], 'KAJ': [['33', 'E', 'PRO'], ['89', 'E', 'LEU'], ['92', 'E', 'LYS'], ['93', 'E', 'ARG'], ['96', 'E', 'GLN'], ['349', 'E', 'GLU'], ['350', 'E', 'PHE']], 'KAK': [['157', 'E', 'LEU'], ['162', 'E', 'LEU'], ['163', 'E', 'ILE'], ['164', 'E', 'TYR'], ['185', 'E', 'PHE'], ['188', 'E', 'ALA']], 'KAL': [['49', 'E', 'LEU'], ['127', 'E', 'GLU'], ['129', 'E', 'PHE'], ['130', 'E', 'SER'], ['326', 'E', 'ASN'], ['327', 'E', 'PHE'], ['328', 'E', 'ASP'], ['330', 'E', 'TYR']], 'KAM': [['51', 'E', 'THR'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['73', 'E', 'ILE'], ['74', 'E', 'LEU'], ['75', 'E', 'ASP'], ['115', 'E', 'ASN'], ['335', 'E', 'ILE'], ['336', 'E', 'ARG']], 'KAN': [['165', 'E', 'ARG'], ['166', 'E', 'ASP'], ['167', 'E', 'LEU'], ['199', 'E', 'CYS'], ['200', 'E', 'GLY'], ['201', 'E', 'THR'], ['204', 'E', 'TYR'], ['205', 'E', 'LEU'], ['206', 'E', 'ALA'], ['209', 'E', 'ILE'], ['219', 'E', 'VAL'], ['220', 'E', 'ASP'], ['223', 'E', 'ALA']], 'KAO': [['48', 'E', 'THR'], ['51', 'E', 'THR'], ['56', 'E', 'ARG'], ['330', 'E', 'TYR'], ['331', 'E', 'GLU']], 'KAP': [['222', 'E', 'TRP'], ['238', 'E', 'PHE'], ['253', 'E', 'GLY'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['273', 'E', 'LEU']], 'KAQ': [['207', 'E', 'PRO'], ['208', 'E', 'GLU'], ['211', 'E', 'LEU'], ['213', 'E', 'LYS'], ['275', 'E', 'VAL'], ['277', 'E', 'LEU']], 'KAR': [['237', 'E', 'PRO'], ['238', 'E', 'PHE'], ['249', 'E', 'LYS'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['256', 'E', 'ARG']]}
->>> frequencies
-{'KAA': {'RESIDUES': {'GLU': 1, 'ILE': 1, 'LEU': 2, 'LYS': 1, 'PHE': 2, 'SER': 1, 'TRP': 1, 'TYR': 2, 'VAL': 1}, 'CLASS': {'R1': 4, 'R2': 5, 'R3': 1, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAB': {'RESIDUES': {'ALA': 2, 'ASN': 1, 'ASP': 1, 'LYS': 1, 'PHE': 2, 'TYR': 1, 'VAL': 1}, 'CLASS': {'R1': 3, 'R2': 3, 'R3': 1, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAC': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'GLU': 1, 'HIS': 1, 'ILE': 1, 'PHE': 1, 'PRO': 2, 'THR': 2, 'VAL': 1}, 'CLASS': {'R1': 5, 'R2': 1, 'R3': 2, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAD': {'RESIDUES': {'ALA': 1, 'ASP': 1, 'GLN': 1, 'GLY': 2, 'PHE': 1, 'PRO': 1, 'TYR': 1}, 'CLASS': {'R1': 4, 'R2': 2, 'R3': 1, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAE': {'RESIDUES': {'ASN': 1, 'LEU': 3, 'LYS': 1, 'PHE': 1, 'VAL': 2}, 'CLASS': {'R1': 5, 'R2': 1, 'R3': 1, 'R4': 0, 'R5': 1, 'RX': 0}}, 'KAF': {'RESIDUES': {'ALA': 1, 'ASP': 1, 'GLN': 2, 'VAL': 1}, 'CLASS': {'R1': 2, 'R2': 0, 'R3': 2, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAG': {'RESIDUES': {'GLN': 1, 'GLU': 1, 'LEU': 1, 'PHE': 1, 'SER': 2, 'THR': 1}, 'CLASS': {'R1': 1, 'R2': 1, 'R3': 4, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAH': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'ASN': 1, 'ASP': 2, 'GLN': 1, 'GLU': 4, 'GLY': 4, 'HIS': 1, 'LEU': 3, 'LYS': 2, 'MET': 1, 'PHE': 3, 'SER': 1, 'THR': 4, 'TYR': 1, 'VAL': 3}, 'CLASS': {'R1': 11, 'R2': 4, 'R3': 8, 'R4': 6, 'R5': 4, 'RX': 0}}, 'KAI': {'RESIDUES': {'HIS': 2, 'ILE': 1, 'PHE': 2, 'TYR': 1}, 'CLASS': {'R1': 1, 'R2': 3, 'R3': 0, 'R4': 0, 'R5': 2, 'RX': 0}}, 'KAJ': {'RESIDUES': {'ARG': 1, 'GLN': 1, 'GLU': 1, 'LEU': 1, 'LYS': 1, 'PHE': 1, 'PRO': 1}, 'CLASS': {'R1': 2, 'R2': 1, 'R3': 1, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAK': {'RESIDUES': {'ALA': 1, 'ILE': 1, 'LEU': 2, 'PHE': 1, 'TYR': 1}, 'CLASS': {'R1': 4, 'R2': 2, 'R3': 0, 'R4': 0, 'R5': 0, 'RX': 0}}, 'KAL': {'RESIDUES': {'ASN': 1, 'ASP': 1, 'GLU': 1, 'LEU': 1, 'PHE': 2, 'SER': 1, 'TYR': 1}, 'CLASS': {'R1': 1, 'R2': 3, 'R3': 2, 'R4': 2, 'R5': 0, 'RX': 0}}, 'KAM': {'RESIDUES': {'ARG': 2, 'ASN': 1, 'ASP': 1, 'GLY': 1, 'ILE': 2, 'LEU': 1, 'THR': 1}, 'CLASS': {'R1': 4, 'R2': 0, 'R3': 2, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAN': {'RESIDUES': {'ALA': 2, 'ARG': 1, 'ASP': 2, 'CYS': 1, 'GLY': 1, 'ILE': 1, 'LEU': 2, 'THR': 1, 'TYR': 1, 'VAL': 1}, 'CLASS': {'R1': 7, 'R2': 1, 'R3': 2, 'R4': 2, 'R5': 1, 'RX': 0}}, 'KAO': {'RESIDUES': {'ARG': 1, 'GLU': 1, 'THR': 2, 'TYR': 1}, 'CLASS': {'R1': 0, 'R2': 1, 'R3': 2, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAP': {'RESIDUES': {'GLY': 1, 'LEU': 1, 'LYS': 1, 'PHE': 1, 'TRP': 1, 'VAL': 1}, 'CLASS': {'R1': 3, 'R2': 2, 'R3': 0, 'R4': 0, 'R5': 1, 'RX': 0}}, 'KAQ': {'RESIDUES': {'GLU': 1, 'LEU': 2, 'LYS': 1, 'PRO': 1, 'VAL': 1}, 'CLASS': {'R1': 4, 'R2': 0, 'R3': 0, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAR': {'RESIDUES': {'ARG': 1, 'LYS': 2, 'PHE': 1, 'PRO': 1, 'VAL': 1}, 'CLASS': {'R1': 2, 'R2': 1, 'R3': 0, 'R4': 0, 'R5': 3, 'RX': 0}}}
->>> write_results('results.toml', input=pdb, ligand=None, output=output_cavity, volume=volume, area=area, residues=residues, frequencies=frequencies)
-
          
-
          
-
            
-
          • Write depth characterization
            • 
-
          
-
          >>> max_depth
-{'KAA': 3.79, 'KAB': 2.68, 'KAC': 2.62, 'KAD': 0.85, 'KAE': 3.0, 'KAF': 0.85, 'KAG': 0.6, 'KAH': 10.73, 'KAI': 2.55, 'KAJ': 2.24, 'KAK': 0.0, 'KAL': 3.0, 'KAM': 1.2, 'KAN': 0.0, 'KAO': 1.04, 'KAP': 2.08, 'KAQ': 0.85, 'KAR': 0.6}
->>> avg_depth
-{'KAA': 1.28, 'KAB': 0.86, 'KAC': 0.67, 'KAD': 0.29, 'KAE': 0.98, 'KAF': 0.24, 'KAG': 0.1, 'KAH': 3.75, 'KAI': 1.5, 'KAJ': 0.96, 'KAK': 0.0, 'KAL': 1.0, 'KAM': 0.24, 'KAN': 0.0, 'KAO': 0.29, 'KAP': 0.7, 'KAQ': 0.22, 'KAR': 0.12}
->>> write_results('results.toml', input=pdb, ligand=None, output=None, max_depth=max_depth, avg_depth=avg_depth)
-
          
-
          
-
            
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          • Write hydropathy characterization
            • 
-
          
-
          >>> avg_hydropathy
-{'KAA': -0.73, 'KAB': -0.06, 'KAC': -0.07, 'KAD': -0.62, 'KAE': -0.81, 'KAF': -0.14, 'KAG': -0.33, 'KAH': -0.16, 'KAI': -0.4, 'KAJ': 0.62, 'KAK': -0.99, 'KAL': 0.35, 'KAM': -0.33, 'KAN': 0.18, 'KAO': 0.88, 'KAP': -0.96, 'KAQ': 0.48, 'KAR': 0.24, 'EisenbergWeiss': [-1.42, 2.6]}
->>> write_results('results.toml', input=pdb, ligand=None, output=None, output_hydropathy='hydropathy.pdb', avg_hydropathy=avg_hydropathy)
-
          
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          • Write all
            • 
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          >>> write_results('results.toml', input=pdb, ligand=None, output='cavities.pdb', output_hydropathy='hydropathy.pdb', volume=volume, area=area, max_depth=max_depth, avg_depth=avg_depth, avg_hydropathy=avg_hydropathy, residues=residues, frequencies=frequencies)
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diff --git a/docs/source/_build/html/_cfg_files/box_file_template.html b/docs/source/_build/html/_cfg_files/box_file_template.html
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          The first directly defines four vertices of the 3D grid (origin, X-axis, Y-axis and Z-axis), an example is shown below:
          
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          [box]
-# px = [x, y, z]
-p1 = [0.0, 0.0, 0.0]
-p2 = [1.0, 0.0, 0.0]
-p3 = [0.0, 1.0, 0.0]
-p4 = [0.0, 0.0, 1.0]
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-residues = [ ["resnum", "chain", "resname",], ["resnum", "chain", "resname",], ]
-padding =  3.5
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          Example: residues-box.toml.
          
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          The third uses parKVFinder’s TOML-formatted parameters file created by its PyMOL plugin.
          
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-x = 0.0
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-ALA = -0.64
-ARG = 2.6
-ASN = 0.8
-ASP = 0.92
-CYS = -0.3
-GLN = 0.87
-GLU = 0.76
-GLY = -0.49
-HIS = 0.41
-ILE = -1.42
-LEU = -1.09
-LYS = 1.54
-MET = -0.66
-PHE = -1.22
-PRO = -0.12
-SER = 0.18
-THR = 0.05
-TRP = -0.83
-TYR = -0.27
-VAL = -1.11
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          1. Eisenberg D, Weiss RM, Terwilliger TC. The hydrophobic moment detects periodicity in protein hydrophobicity. Proceedings of the National Academy of Sciences. 1984;81.
            2. 
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          2. Hessa T, Kim H, Bihlmaier K, Lundin C, Boekel J, Andersson H, et al. Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature. 2005;433.
            3. 
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          3. Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology. 1982;157.
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          4. Moon CP, Fleming KG. Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers. Proceedings of the National Academy of Sciences. 2011;108.
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          5. Wimley WC, White SH. Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nature Structural & Molecular Biology. 1996;3.
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          6. Zhao G, London E. An amino acid “transmembrane tendency” scale that approaches the theoretical limit to accuracy for prediction of transmembrane helices: Relationship to biological hydrophobicity. Protein Science. 2006;15.
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          >RES
-C       1.66
-CA      2.00
-N       1.97
-O       1.69
-H       0.91
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          Command-line interface
          In addition to pyKVFinder package, a command-line interface (CLI) is available to ease cavity detection and characterization with the full set of customizable parameters.
          
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-Usage: pyKVFinder [-h] [-v] [--version] [-b <str>] [-O <str>]
-                  [--nthreads <int>] [-d <str>] [-s <float>] [-i <float>]
-                  [-o <float>] [-V <float>] [-R <float>] [-S <str>]
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-$ pyKVFinder --help
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-$ pyKVFinder <.pdb> --base_name <str>
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            Prefix of target PDB file (<.pdb>)
            
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-$ pyKVFinder <.pdb> --output_directory <str>
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          Detection and characterization
          
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-$ pyKVFinder <.pdb> --dictionary <str>
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            vdw.dat
            
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-
            $ pyKVFinder <.pdb> -s <float>
-$ pyKVFinder <.pdb> --step <float>
-
            
-
            
-
            
-
            Default:
            
-
            0.6
            
-
            
-
            
-
            • 
-
          • -i <float> or --probe_in <float>: Probe In size (A).
            
-
            $ pyKVFinder <.pdb> -i <float>
-$ pyKVFinder <.pdb> --probe_in <float>
-
            
-
            
-
            
-
            Default:
            
-
            1.4
            
-
            
-
            
-
            • 
-
          • -o <float> or --probe_out <float>: Probe Out size (A).
            
-
            $ pyKVFinder <.pdb> -o <float>
-$ pyKVFinder <.pdb> --probe_out <float>
-
            
-
            
-
            
-
            Default:
            
-
            4.0
            
-
            
-
            
-
            • 
-
          • -V <float> or --volume_cutoff <float>: Cavities volume filter (A3).
            
-
            $ pyKVFinder <.pdb> -V <float>
-$ pyKVFinder <.pdb> --volume_cutoff <float>
-
            
-
            
-
            
-
            Default:
            
-
            5.0
            
-
            
-
            
-
            • 
-
          • -R <float> or --removal_distance <float>: Length to be removed from the cavity-bulk frontier (A).
            
-
            $ pyKVFinder <.pdb> -R <float>
-$ pyKVFinder <.pdb> --removal_distance <float>
-
            
-
            
-
            
-
            Default:
            
-
            2.4
            
-
            
-
            
-
            • 
-
          • -S <str> or --surface <str>: A surface representation. Options are: SES and SAS. SES specifies solvent excluded surface and SAS specifies solvent accessible surface.
            
-
            $ pyKVFinder <.pdb> -S <str>
-$ pyKVFinder <.pdb> --surface <str>
-
            
-
            
-
            
-
            Default:
            
-
            SES
            
-
            
-
            
-
            • 
-
          • --ignore_backbone: Ignore backbone contacts to cavity when defining interface residues.
            
-
            $ pyKVFinder <.pdb> --ignore_backbone
-
            
-
            
-
            
-
            Default:
            
-
            None
            
-
            
-
            
-
            • 
-
          
-
          
-
          
-
          Extra characterization
          
-
          The parameters for additional characterization are:
          
-
            
-
          • --D or --depth: Characterize the depth of the detected cavities. This mode includes depth of each cavity point as the B-factor in the cavity PDB file and maximum and average depth of the detected cavities in the results file.
            
-
            $ pyKVFinder <.pdb> -D
-$ pyKVFinder <.pdb> --depth
-
            
-
            
-
            
-
            Default:
            
-
            None
            
-
            
-
            
-
            • 
-
          • --plot_frequencies: Plot bar charts of calculated frequencies (residues and classes of residues) of the detected cavities in a PDF file. The classes of residues are aliphatic apolar (R1), aromatic (R2), polar uncharged (R3), negatively charged (R4), positively charged (R5) and non-standard (RX) residues.
            
-
            $ pyKVFinder <.pdb> --plot_frequencies
-
            
-
            
-
            
-
            Default:
            
-
            None
            
-
            
-
            
-
            • 
-
          • --hydropathy [{EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, WimleyWhite, ZhaoLondon, <.toml>}]: Characterize the hydropathy of the detected cavities. This mode maps a target hydrophobicity scale as B-factor at surface points of the detected cavities. Also, it calculates the average hydropathy of each detected cavity. The constant hydrophobicity scale is EisenbergWeiss.
            
-
            $ pyKVFinder <.pdb> --hydropathy
-
            
-
            
-
            In addition, the user can define one of the built-in hydrophobicity scale. The built-in hydrophobicity scales are: EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, WimleyWhite and ZhaoLondon.
            
-
            $ pyKVFinder <.pdb> --hydropathy EisenbergWeiss
-$ pyKVFinder <.pdb> --hydropathy HessaHeijne
-$ pyKVFinder <.pdb> --hydropathy KyteDoolittle
-$ pyKVFinder <.pdb> --hydropathy MoonFleming
-$ pyKVFinder <.pdb> --hydropathy WimleyWhite
-$ pyKVFinder <.pdb> --hydropathy ZhaoLondon
-
            
-
            
-
            Further, the user can also define a custom hydrophobicity scale file via a TOML-formatted file (see template).
            
-
            $ pyKVFinder <.pdb> --hydropathy <.toml>
-
            
-
            
-
            
-
            Default:
            
-
            None
            
-
            
-
            Constant:
            
-
            EisenbergWeiss
            
-
            
-
            
-
            • 
-
          
-
          
-
          
-
          Box adjusment
          
-
          The box adjustment argument is:
          
-
            
-
          • -B <.toml> or --box <.toml>: A path to TOML-formatted file with box parameters (see template). Adjust the 3D grid based on a list of residues ([“resnum”, “chain”]) and a padding or a set of four vertices (p1: origin, p2: X-axis max, p3: Y-axis max, p4: Z-axis max) with xyz coordinates ([x, y, z]).
            
-
            $ pyKVFinder <.pdb> -B <.toml>
-$ pyKVFinder <.pdb> --box <.toml>
-
            
-
            
-
            
-
            Default:
            
-
            None
            
-
            
-
            
-
            • 
-
          
-
          
-
          
-
          Ligand adjustment
          
-
          The ligand adjustment arguments are:
          
-
            
-
          • -L (<.pdb> | <.xyz>) or --ligand (<.pdb> | <.xyz>): A path to a ligand PDB or XYZ file to limit the cavities within a radius (ligand_cutoff) around it.
            
-
            $ pyKVFinder <.pdb> -L <.pdb>
-$ pyKVFinder <.pdb> --ligand <.pdb>
-
            
-
            
-
            
-
            Default:
            
-
            None
            
-
            
-
            
-
            • 
-
          • --ligand_cutoff <float>: A radius value to limit a space around the defined ligand.
            
-
            $ pyKVFinder <.pdb> -L <.pdb> --ligand_cutoff <float>
-
            
-
            
-
            
-
            Default:
            
-
            5.0
            
-
            
-
            
-
            • 
-
          
-
          
-
          
-
-
-           
          
-          
          
-          
-        
          
-      
          
-    
          
-  
          
-   
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diff --git a/docs/source/_build/html/_installation/index.html b/docs/source/_build/html/_installation/index.html
deleted file mode 100644
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--- a/docs/source/_build/html/_installation/index.html
+++ /dev/null
@@ -1,187 +0,0 @@
-
-
-
-  
-
-  
-  Requirements — pyKVFinder 0.5.0 documentation
-      
-      
-    
-  
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-        
          
-          
          
-  
-  
          
-
          
-          
          
-           
          
-             
-  
          
-
          Requirements
          
-
          If you don’t have Python v3 and/or SWIG yet, the installation procedure differs depending on the operating system.
          
-
          Python and SWIG can be installed with conda, or with a package manager on Linux and macOS.
          
-
          
-
          Package managers
          
-
          On Linux:
          
-
          sudo apt install python3 swig
-
          
-
          
-
          On macOS:
          
-
          brew install python3 swig
-
          
-
          
-
          
-
          Note
          
-
          Users can use their preferred package manager to install SWIG and Python v3.
          
-
          
-
          
-
          
-
          Conda
          
-
          If you use conda, you can install Python v3 and SWIG from the defaults channel:
          
-
          # Use an environment rather than install in base environement (recommended)
-conda create -n myenv python=3
-conda activate myenv
-# The SWIG install command
-conda install swig
-
          
-
          
-
          
-
          
-
          
-
          Installation
          
-
          The prerequisites for installing pyKVFinder is Python v3 and SWIG. If you don’t have Python and/or SWIG yet, please refer to this section.
          
-
          To install the latest release on PyPI,
-run:
          
-
          pip install pyKVFinder
-
          
-
          
-
          Or to install the latest developmental version, run:
          
-
          git clone https://github.com/LBC-LNBio/pyKVFinder.git
-pip install pyKVFinder
-
          
-
          
-
          
-
-
-           
          
-          
          
-          
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-      
          
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-  
          
-   
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diff --git a/docs/source/_build/html/_modules/index.html b/docs/source/_build/html/_modules/index.html
deleted file mode 100644
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--- a/docs/source/_build/html/_modules/index.html
+++ /dev/null
@@ -1,135 +0,0 @@
-
-
-
-  
-  
-  Overview: module code — pyKVFinder 0.5.0 documentation
-      
-      
-    
-  
-  
-        
-        
-        
-        
-        
-    
-    
-     
-
-
- 
-  
          
-    
-
-    
          
-
-      
          
-        
          
-          
          
-  
            
-      
          •  »
            • 
-      
          • Overview: module code
            • 
-      
          • 
-      
            • 
-  
          
-  
          
-
          
-          
          
-           
          
-             
-  
          All modules for which code is available
          
-
-
-           
          
-          
          
-          
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-      
          
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-  
          
-   
-
-
-
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diff --git a/docs/source/_build/html/_modules/pyKVFinder/grid.html b/docs/source/_build/html/_modules/pyKVFinder/grid.html
deleted file mode 100644
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--- a/docs/source/_build/html/_modules/pyKVFinder/grid.html
+++ /dev/null
@@ -1,3106 +0,0 @@
-
-
-
-  
-  
-  pyKVFinder.grid — pyKVFinder 0.5.0 documentation
-      
-      
-    
-  
-  
-        
-        
-        
-        
-        
-    
-    
-     
-
-
- 
-  
          
-    
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-        
          
-          
          
-  
-  
          
-
          
-          
          
-           
          
-             
-  
          Source code for pyKVFinder.grid
          -import os
-import pathlib
-from typing import Dict, List, Optional, Tuple, Union
-
-import numpy
-
-__all__ = [
-    "get_vertices",
-    "get_vertices_from_file",
-    "detect",
-    "spatial",
-    "depth",
-    "constitutional",
-    "hydropathy",
-    "openings",
-    "export",
-    "export_openings",
-]
-
-
-
          [docs]def get_vertices(
-    atomic: Union[numpy.ndarray, List[List[Union[str, float, int]]]],
-    probe_out: Union[float, int] = 4.0,
-    step: Union[float, int] = 0.6,
-) -> numpy.ndarray:
-    """Gets 3D grid vertices.
-
-    Parameters
-    ----------
-    atomic : Union[numpy.ndarray, List[List[Union[str, float, int]]]]
-        A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
-        and radius) for each atom.
-    probe_out : Union[float, int], optional
-        Probe Out size (A), by default 4.0.
-    step : Union[float, int], optional
-        Grid spacing (A), by default 0.6.
-
-    Returns
-    -------
-    vertices : numpy.ndarray
-        A numpy.ndarray with xyz vertices coordinates
-        (origin, X-axis, Y-axis, Z-axis).
-
-    Raises
-    ------
-    TypeError
-        `atomic` must be a list or a numpy.ndarray.
-    ValueError
-        `atomic` has incorrect shape. It must be (n, 8).
-    TypeError
-        `probe_out` must be a non-negative real number.
-    ValueError
-        `probe_out` must be a non-negative real number.
-    TypeError
-        `step` must be a positive real number.
-    ValueError
-        `step` must be a positive real number.
-
-    See Also
-    --------
-    read_pdb
-    read_xyz
-    detect
-    constitutional
-    hydropathy
-    export
-
-    Example
-    -------
-    With the atomic data read with ``read_pdb`` or ``read_xyz``, we can get the coordinates of 3D grid vertices (origin, X-axis, Y-axis, Z-axis):
-
-    >>> from pyKVFinder import get_vertices
-    >>> vertices = get_vertices(atomic)
-    >>> vertices
-    array([[-19.911, -32.125, -30.806],
-        [ 40.188, -32.125, -30.806],
-        [-19.911,  43.446, -30.806],
-        [-19.911, -32.125,  27.352]])
-    """
-    # Check arguments types
-    if type(atomic) not in [numpy.ndarray, list]:
-        raise TypeError("`atomic` must be a list or a numpy.ndarray.")
-    elif len(numpy.asarray(atomic).shape) != 2:
-        raise ValueError("`atomic` has incorrect shape. It must be (n, 8).")
-    elif numpy.asarray(atomic).shape[1] != 8:
-        raise ValueError("`atomic` has incorrect shape. It must be (n, 8).")
-    if type(probe_out) not in [int, float, numpy.float64]:
-        raise TypeError("`probe_out` must be a non-negative real number.")
-    elif probe_out < 0.0:
-        raise ValueError("`probe_out` must be a non-negative real number.")
-    if type(step) not in [int, float, numpy.float64]:
-        raise TypeError("`step` must be a positive real number.")
-    elif step <= 0.0:
-        raise ValueError("`step` must be a positive real number.")
-
-    # Convert atomic type
-    if type(atomic) == list:
-        atomic = numpy.asarray(atomic)
-
-    # Extract xyzr from atomic
-    xyzr = atomic[:, 4:].astype(numpy.float64)
-
-    # Prepare vertices
-    P1 = numpy.min(xyzr[:, 0:3], axis=0) - probe_out - step
-    xmax, ymax, zmax = numpy.max(xyzr[:, 0:3], axis=0) + probe_out + step
-    P2 = numpy.array([xmax, P1[1], P1[2]])
-    P3 = numpy.array([P1[0], ymax, P1[2]])
-    P4 = numpy.array([P1[0], P1[1], zmax])
-
-    # Pack vertices
-    vertices = numpy.array([P1, P2, P3, P4])
-
-    return vertices
          
-
-
-
          [docs]def get_vertices_from_file(
-    fn: Union[str, pathlib.Path],
-    atomic: Union[numpy.ndarray, List[List[Union[str, float, int]]]],
-    step: Union[float, int] = 0.6,
-    probe_in: Union[float, int] = 1.4,
-    probe_out: Union[float, int] = 4.0,
-    nthreads: Optional[int] = None,
-) -> Tuple[numpy.ndarray, numpy.ndarray, numpy.ndarray]:
-    """Gets 3D grid vertices from box configuration file or parKVFinder
-    parameters file, selects atoms inside custom 3D grid, define sine
-    and cosine of 3D grid angles and define xyz grid units.
-
-    Parameters
-    ----------
-    fn : Union[str, pathlib.Path]
-        A path to box configuration file (TOML-formatted).
-    atomic : Union[numpy.ndarray, List[List[Union[str, float, int]]]]
-        A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
-        and radius) for each atom.
-    step : Union[float, int], optional
-        Grid spacing (A), by default 0.6.
-    probe_in : Union[float, int], optional
-        Probe In size (A), by default 1.4.
-    probe_out : Union[float, int], optional
-        Probe Out size (A), by default 4.0.
-    nthreads : int, optional
-        Number of threads, by default None. If None, the number of threads is
-        `os.cpu_count() - 1`.
-
-    Returns
-    -------
-    vertices : numpy.ndarray
-        A numpy.ndarray with xyz vertices coordinates (origin, X-axis, Y-axis,
-        Z-axis) of the custom box.
-    atomic : Union[numpy.ndarray, List[List[Union[str, float, int]]]]
-        A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
-        and radius) for each atom inside the custom box.
-
-    Raises
-    ------
-    TypeError
-        `fn` must be a string or a pathlib.Path.
-    TypeError
-        `atomic` must be a list or a numpy.ndarray.
-    ValueError
-        `atomic` has incorrect shape. It must be (n, 8).
-    TypeError
-        `step` must be a positive real number.
-    ValueError
-        `step` must be a positive real number.
-    TypeError
-        `probe_in` must be a non-negative real number.
-    ValueError
-        `probe_in` must be a non-negative real number.
-    TypeError
-        `probe_out` must be a non-negative real number.
-    ValueError
-        `probe_out` must be a non-negative real number.
-    ValueError
-        `probe_out` must be greater than `probe_in`.
-    TypeError
-        `nthreads` must be a positive integer.
-    ValueError
-        You must define (p1, p2, p3, p4) or (residues, padding) keys in `fn`.
-    ValueError
-        Box not properly defined in `fn`.
-
-    Note
-    ----
-    The box configuration scale file defines the vertices of the 3D grid used by pyKVFinder to detect and characterize cavities. There are three methods for defining a custom 3D grid in pyKVFinder. The first directly defines four vertices of the 3D grid (origin, X-axis, Y-axis and Z-axis), the second defines a list of residues and a padding, and the the third uses parKVFinder parameters file created by its PyMOL plugin. For more details, see `Box configuration file template`.
-
-    See Also
-    --------
-    read_pdb
-    read_xyz
-    detect
-    constitutional
-    hydropathy
-    export
-
-    Example
-    -------
-    First, define a box configuration file (see ``Box configuration file template``).
-
-    >>> import os
-    >>> fn = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'custom-box.toml')
-    >>> with open(fn, 'r') as f:
-    ...     print(f.read())
-    [box]
-    p1 = [3.11, 7.34, 1.59]
-    p2 = [11.51, 7.34, 1.59]
-    p3 = [3.11, 10.74, 1.59]
-    p4 = [3.11, 7.34, 6.19]
-
-    With the atomic information and coordinates read with ``pyKVFinder.read_pdb`` and a box configuration file, we can get the coordinates of grid vertices and select atoms inside custom 3D grid.
-
-    >>> from pyKVFinder import get_vertices_from_file
-    >>> vertices, atomic = pyKVFinder.get_vertices_from_file(fn, atomic)
-
-    .. warning::
-        Custom box coordinates adds Probe Out size in each direction to create the coordinates of grid vertices.
-    """
-    from _pyKVFinder import _filter_pdb
-    from toml import load
-
-    # Check arguments types
-    if type(fn) not in [str, pathlib.Path]:
-        raise TypeError("`fn` must be a string or a pathlib.Path.")
-    if type(atomic) not in [numpy.ndarray, list]:
-        raise TypeError("`atomic` must be a list or a numpy.ndarray.")
-    elif len(numpy.asarray(atomic).shape) != 2:
-        raise ValueError("`atomic` has incorrect shape. It must be (n, 8).")
-    elif numpy.asarray(atomic).shape[1] != 8:
-        raise ValueError("`atomic` has incorrect shape. It must be (n, 8).")
-    if type(step) not in [float, int]:
-        raise TypeError("`step` must be a positive real number.")
-    elif step <= 0.0:
-        raise ValueError("`step` must be a positive real number.")
-    if type(probe_in) not in [float, int]:
-        raise TypeError("`probe_in` must be a non-negative real number.")
-    elif probe_in < 0.0:
-        raise ValueError("`probe_in` must be a non-negative real number.")
-    if type(probe_out) not in [float, int]:
-        raise TypeError("`probe_out` must be a non-negative real number.")
-    elif probe_out < 0.0:
-        raise ValueError("`probe_out` must be a non-negative real number.")
-    elif probe_out < probe_in:
-        raise ValueError("`probe_out` must be greater than `probe_in`.")
-    if nthreads is None:
-        nthreads = os.cpu_count() - 1
-    else:
-        if type(nthreads) not in [int]:
-            raise TypeError("`nthreads` must be a positive integer.")
-        elif nthreads <= 0:
-            raise ValueError("`nthreads` must be a positive integer.")
-
-    # Convert type
-    if type(atomic) == list:
-        atomic = numpy.asarray(atomic)
-
-    # Extract atominfo from atomic
-    atominfo = numpy.asarray(
-        ([[f"{atom[0]}_{atom[1]}_{atom[2]}", atom[3]] for atom in atomic[:, :4]])
-    )
-
-    # Extract xyzr from atomic
-    xyzr = atomic[:, 4:].astype(numpy.float64)
-
-    # Read box file
-    tmp = load(fn)
-    if "SETTINGS" in tmp.keys():
-        if "visiblebox" in tmp["SETTINGS"].keys():
-            box = tmp["SETTINGS"]["visiblebox"]
-            box = {key: list(box[key].values()) for key in box.keys()}
-            vertices = _get_vertices_from_box(box, probe_out)
-    else:
-        box = tmp["box"] if "box" in tmp.keys() else tmp
-
-        # Check conditions
-        if all([key in box.keys() for key in ["p1", "p2", "p3", "p4"]]):
-            if any([key in box.keys() for key in ["padding", "residues"]]):
-                raise ValueError(
-                    f"You must define (p1, p2, p3, p4) or (residues, padding) keys in {fn}."
-                )
-            vertices = _get_vertices_from_box(box, probe_out)
-        elif "residues" in box.keys():
-            if any([key in box.keys() for key in ["p1", "p2", "p3", "p4"]]):
-                raise ValueError(
-                    f"You must define (p1, p2, p3, p4) or (residues, padding) keys in {fn}."
-                )
-            if "padding" not in box.keys():
-                box["padding"] = 3.5
-            vertices = _get_vertices_from_residues(box, atominfo, xyzr, probe_out)
-        else:
-            raise ValueError(f"Box not properly defined in {fn}.")
-
-    # Get sincos
-    sincos = numpy.round(_get_sincos(vertices), 4)
-
-    # Get dimensions
-    nx, ny, nz = _get_dimensions(vertices, step)
-
-    # Get atoms inside box only
-    _filter_pdb(nx, ny, nz, xyzr, vertices[0], sincos, step, probe_in, nthreads)
-
-    # Get indexes of the atoms inside the box
-    indexes = xyzr[:, 3] != 0
-
-    # Slice atominfo and xyzr
-    atomic = atomic[indexes, :]
-
-    return vertices, atomic
          
-
-
-def _get_vertices_from_box(
-    box: Dict[str, List[float]], probe_out: float = 4.0
-) -> numpy.ndarray:
-    """Gets 3D grid vertices from box coordinates.
-
-    Parameters
-    ----------
-    box : Dict[str, List[float]]
-        A dictionary with xyz coordinates of p1, p2, p3 and p4.
-    probe_out : float, optional
-        Probe Out size (A), by default 4.0.
-
-    Returns
-    -------
-    vertices : numpy.ndarray
-        A numpy.ndarray of vertices coordinates (origin, Xmax, Ymax, Zmax).
-
-    Example
-    -------
-    >>> [box]
-    >>> p1 = [x1, y1, z1]
-    >>> p2 = [x2, y2, z2]
-    >>> p3 = [x3, y3, z3]
-    >>> p4 = [x4, y4, z4]
-    """
-    # Get vertices
-    P1 = numpy.asarray(box["p1"])
-    P2 = numpy.asarray(box["p2"])
-    P3 = numpy.asarray(box["p3"])
-    P4 = numpy.asarray(box["p4"])
-
-    # Get sincos
-    sincos = numpy.round(_get_sincos(numpy.asarray([P1, P2, P3, P4])), 4)
-
-    # Get probe out additions
-    # p1 = (x1, y1, z1)
-    x1 = (
-        -(probe_out * sincos[3])
-        - (probe_out * sincos[0] * sincos[2])
-        + (probe_out * sincos[1] * sincos[2])
-    )
-    y1 = -(probe_out * sincos[1]) - (probe_out * sincos[0])
-    z1 = (
-        -(probe_out * sincos[2])
-        + (probe_out * sincos[0] * sincos[3])
-        - (probe_out * sincos[1] * sincos[3])
-    )
-    # p2 = (x2, y2, z2)
-    x2 = (
-        (probe_out * sincos[3])
-        - (probe_out * sincos[0] * sincos[2])
-        + (probe_out * sincos[1] * sincos[2])
-    )
-    y2 = -(probe_out * sincos[1]) - (probe_out * sincos[0])
-    z2 = (
-        (probe_out * sincos[2])
-        + (probe_out * sincos[0] * sincos[3])
-        - (probe_out * sincos[1] * sincos[3])
-    )
-    # p3 = (x3, y3, z3)
-    x3 = (
-        -(probe_out * sincos[3])
-        + (probe_out * sincos[0] * sincos[2])
-        + (probe_out * sincos[1] * sincos[2])
-    )
-    y3 = (probe_out * sincos[1]) - (probe_out * sincos[0])
-    z3 = (
-        -(probe_out * sincos[2])
-        - (probe_out * sincos[0] * sincos[3])
-        - (probe_out * sincos[1] * sincos[3])
-    )
-    # p4 = (x4, y4, z4)
-    x4 = (
-        -(probe_out * sincos[3])
-        - (probe_out * sincos[0] * sincos[2])
-        - (probe_out * sincos[1] * sincos[2])
-    )
-    y4 = -(probe_out * sincos[1]) + (probe_out * sincos[0])
-    z4 = (
-        -(probe_out * sincos[2])
-        + (probe_out * sincos[0] * sincos[3])
-        + (probe_out * sincos[1] * sincos[3])
-    )
-
-    # Adjust vertices
-    P1 += numpy.asarray([x1, y1, z1])
-    P2 += numpy.asarray([x2, y2, z2])
-    P3 += numpy.asarray([x3, y3, z3])
-    P4 += numpy.asarray([x4, y4, z4])
-
-    vertices = numpy.round([P1, P2, P3, P4], 3)
-
-    return vertices
-
-
-def _get_vertices_from_residues(
-    box: Dict[str, List[float]],
-    atominfo: numpy.ndarray,
-    xyzr: numpy.ndarray,
-    probe_out: float = 4.0,
-) -> numpy.ndarray:
-    """Gets 3D grid vertices based on a list of residues (name and chain)
-    and a padding value.
-
-    Parameters
-    ----------
-    box : Dict[str, List[float]]
-        A dictionary with a list of residues (name and chain) and a
-        padding value.
-    atominfo : numpy.ndarray
-        A numpy.ndarray with residue number, chain, residue name and
-        atom name.
-    xyzr : numpy.ndarray
-        A numpy.ndarray with xyz coordinates and radius of input atoms.
-    probe_out : float, optional
-        Probe Out size (A), by default 4.0.
-
-    Returns
-    -------
-    vertices : numpy.ndarray
-        A numpy.ndarray of vertices coordinates (origin, Xmax, Ymax, Zmax).
-
-    Box File
-    --------
-    >>> [box]
-    >>> residues = [ ["resnum", "chain", "resname",], ["resnum", "chain",
-    ... "resname"], ]
-    >>> padding =  3.5
-    """
-    # Prepare residues list
-    box["residues"] = numpy.array(["_".join(item[0:3]) for item in box["residues"]])
-
-    # Get coordinates of residues
-    indexes = numpy.in1d(atominfo[:, 0], box["residues"])
-    xyzr = xyzr[indexes, 0:3]
-
-    # Calculate vertices
-    P1 = numpy.min(xyzr[:, 0:3], axis=0) - probe_out - box["padding"]
-    xmax, ymax, zmax = numpy.max(xyzr[:, 0:3], axis=0) + probe_out + box["padding"]
-    P2 = numpy.array([xmax, P1[1], P1[2]])
-    P3 = numpy.array([P1[0], ymax, P1[2]])
-    P4 = numpy.array([P1[0], P1[1], zmax])
-
-    vertices = numpy.round([P1, P2, P3, P4], 3)
-
-    return vertices
-
-
-def _get_dimensions(
-    vertices: Union[numpy.ndarray, List[List[float]]], step: Union[float, int] = 0.6
-) -> Tuple[int, int, int]:
-    """Gets dimensions of 3D grid from vertices.
-
-    Parameters
-    ----------
-    vertices : Union[numpy.ndarray, List[List[float]]]
-        A numpy.ndarray or a list with xyz vertices coordinates
-        (origin, X-axis, Y-axis, Z-axis).
-    step : Union[float, int], optional
-        Grid spacing (A), by default 0.6.
-
-    Returns
-    -------
-    nx : int
-        x grid units.
-    ny : int
-        y grid units.
-    nz : int
-        z grid units.
-
-    Raises
-    ------
-    TypeError
-        `vertices` must be a list or a numpy.ndarray.
-    ValueError
-        `vertices` has incorrect shape.
-    TypeError
-        `step` must be a positive real number.
-    ValueError
-        `step` must be a positive real number.
-    """
-    # Check arguments
-    if type(vertices) not in [numpy.ndarray, list]:
-        raise TypeError("`vertices` must be a list or a numpy.ndarray.")
-    if numpy.asarray(vertices).shape != (4, 3):
-        raise ValueError("`vertices` has incorrect shape. It must be (4, 3).")
-    if type(step) not in [float, int]:
-        raise TypeError("`step` must be a positive real number.")
-    elif step <= 0.0:
-        raise ValueError("`step` must be a positive real number.")
-
-    # Convert type
-    if type(vertices) == list:
-        vertices = numpy.asarray(vertices)
-    if type(step) == int:
-        step = float(step)
-
-    # Unpack vertices
-    P1, P2, P3, P4 = vertices
-
-    # Calculate distance between points
-    norm1 = numpy.linalg.norm(P2 - P1)
-    norm2 = numpy.linalg.norm(P3 - P1)
-    norm3 = numpy.linalg.norm(P4 - P1)
-
-    # Calculate grid dimensions
-    nx = int(norm1 / step) + 1 if norm1 % step != 0 else int(norm1 / step)
-    ny = int(norm2 / step) + 1 if norm1 % step != 0 else int(norm1 / step)
-    nz = int(norm3 / step) + 1 if norm1 % step != 0 else int(norm1 / step)
-
-    return nx, ny, nz
-
-
-def _get_sincos(vertices: Union[numpy.ndarray, List[List[float]]]) -> numpy.ndarray:
-    """Gets sine and cossine of the grid rotation angles from a list of vertices
-    coordinates.
-
-    Parameters
-    ----------
-    vertices : Union[numpy.ndarray, List[List[float]]]
-        A numpy.ndarray or a list of xyz vertices coordinates (origin, X-axis,
-        Y-axis, Z-axis).
-
-    Returns
-    -------
-    sincos : numpy.ndarray
-        A numpy.ndarray with sine and cossine of the grid rotation
-        angles (sina, cosa, sinb, cosb).
-
-    Raises
-    ------
-    TypeError
-        `vertices` must be a list or a numpy.ndarray.
-    ValueError
-        `vertices` has incorrect shape. It must be (4, 3).
-    """
-    # Check arguments
-    if type(vertices) not in [numpy.ndarray, list]:
-        raise TypeError("`vertices` must be a list or a numpy.ndarray.")
-    if numpy.asarray(vertices).shape != (4, 3):
-        raise ValueError("`vertices` has incorrect shape. It must be (4, 3).")
-
-    # Convert type
-    if type(vertices) == list:
-        vertices = numpy.asarray(vertices)
-
-    # Unpack vertices
-    P1, P2, P3, P4 = vertices
-
-    # Calculate distance between points
-    norm1 = numpy.linalg.norm(P2 - P1)
-    norm2 = numpy.linalg.norm(P3 - P1)
-    norm3 = numpy.linalg.norm(P4 - P1)
-
-    # Calculate sin and cos of angles a and b
-    sincos = numpy.array(
-        [
-            (P4[1] - P1[1]) / norm3,  # sin a
-            (P3[1] - P1[1]) / norm2,  # cos a
-            (P2[2] - P1[2]) / norm1,  # sin b
-            (P2[0] - P1[0]) / norm1,  # cos b
-        ]
-    )
-
-    return sincos
-
-
-
          [docs]def detect(
-    atomic: Union[numpy.ndarray, List[List[Union[str, float, int]]]],
-    vertices: Union[numpy.ndarray, List[List[float]]],
-    step: Union[float, int] = 0.6,
-    probe_in: Union[float, int] = 1.4,
-    probe_out: Union[float, int] = 4.0,
-    removal_distance: Union[float, int] = 2.4,
-    volume_cutoff: Union[float, int] = 5.0,
-    latomic: Optional[Union[numpy.ndarray, List[List[float]]]] = None,
-    ligand_cutoff: Union[float, int] = 5.0,
-    box_adjustment: bool = False,
-    surface: str = "SES",
-    nthreads: Optional[int] = None,
-    verbose: bool = False,
-) -> Tuple[int, numpy.ndarray]:
-    """Detects biomolecular cavities.
-
-    Cavity points that belongs to the same cavity are assigned with an integer
-    in the grid.
-
-    Parameters
-    ----------
-    atomic : Union[numpy.ndarray, List[List[Union[str, float, int]]]]
-        A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
-        and radius) for each atom.
-    vertices : Union[numpy.ndarray, List[List[float]]]
-        A numpy.ndarray or a list with xyz vertices coordinates (origin,
-        X-axis, Y-axis, Z-axis).
-    step : Union[float, int], optional
-        Grid spacing (A), by default 0.6.
-    probe_in : Union[float, int], optional
-        Probe In size (A), by default 1.4.
-    probe_out : Union[float, int], optional
-        Probe Out size (A), by default 4.0.
-    removal_distance : Union[float, int], optional
-        A length to be removed from the cavity-bulk frontier (A), by
-        default 2.4.
-    volume_cutoff : Union[float, int], optional
-        Volume filter for detected cavities (A3), by default 5.0.
-    latomic : Union[numpy.ndarray, List[List[Union[str, float, int]]]], optional
-        A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
-        and radius) for each atom of a target ligand, by default None.
-    ligand_cutoff : Union[float, int], optional
-        A radius to limit a space around a ligand (A), by default 5.0.
-    box_adjustment : bool, optional
-        Whether a custom 3D grid is applied, by default False.
-    surface : str, optional
-        Surface representation. Keywords options are SES (Solvent Excluded Surface) or SAS (Solvent
-        Accessible Surface), by default SES.
-    nthreads : int, optional
-        Number of threads, by default None. If None, the number of threads is
-        `os.cpu_count() - 1`.
-    verbose : bool, optional
-        Print extra information to standard output, by default False.
-
-    Returns
-    -------
-    ncav : int
-        Number of cavities.
-    cavities : numpy.ndarray
-        Cavity points in the 3D grid (cavities[nx][ny][nz]).
-        Cavities array has integer labels in each position, that are:
-
-            * -1: bulk points;
-
-            * 0: biomolecule points;
-
-            * 1: empty space points;
-
-            * >=2: cavity points.
-
-        The empty space points are regions that do not meet the chosen
-        volume cutoff to be considered a cavity.
-
-    Raises
-    ------
-    TypeError
-        `atomic` must be a list or a numpy.ndarray.
-    ValueError
-        `atomic` has incorrect shape. It must be (n, 8).
-    TypeError
-        `vertices` must be a list or a numpy.ndarray.
-    ValueError
-        `vertices` has incorrect shape. It must be (4, 3).
-    TypeError
-        `step` must be a positive real number.
-    ValueError
-        `step` must be a positive real number.
-    TypeError
-        `probe_in` must be a non-negative real number.
-    ValueError
-        `probe_in` must be a non-negative real number.
-    TypeError
-        `probe_out` must be a non-negative real number.
-    ValueError
-        `probe_out` must be a non-negative real number.
-    ValueError
-        `probe_out` must be greater than `probe_in`.
-    TypeError
-        `removal_distance` must be a non-negative real number.
-    ValueError
-        `removal_distance` must be a non-negative real number.
-    TypeError
-        `volume_cutoff` must be a non-negative real number.
-    ValueError
-        `volume_cutoff` must be a non-negative real number.
-    TypeError
-        `latomic` must be a list, a numpy.ndarray or None.
-    ValueError
-        `latomic` has incorrect shape. It must be (n, 8).
-    TypeError
-        `ligand_cutoff` must be a positive real number.
-    ValueError
-        `ligand_cutoff` must be a positive real number.
-    TypeError
-        `box_adjustment` must be a boolean.
-    TypeError
-        `surface` must be a string.
-    TypeError
-        `nthreads` must be a positive integer.
-    ValueError
-        `nthreads` must be a positive integer.
-    ValueError
-        `surface` must be SAS or SES, not `surface`.
-
-    See also
-    --------
-    read_pdb
-    read_xyz
-    get_vertices
-    get_vertices_from_file
-    spatial
-    depth
-    constitutional
-    export
-
-    Warning
-    -------
-    If you are using box adjustment mode, do not forget to set box_adjustment
-    flag to True and read the box configuration file with 'get_vertices_from_file'
-    function.
-
-    Warning
-    -------
-    If you are using ligand adjustment mode, do not forget to read ligand atom
-    coordinates with 'read_pdb' or 'read_xyz' functions.
-
-    Example
-    -------
-    With the grid vertices defined with ``get_vertices`` and atomic data loaded with ``read_pdb`` or ``read_xyz``, we can detect cavities on the whole target biomolecule:
-
-    >>> from pyKVFinder import detect
-    >>> ncav, cavities = detect(atomic, vertices)
-    >>> ncav
-    18
-    >>> cavities
-    array([[[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]],
-       ...,
-       [[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
-
-    However, users may opt to perform cavity detection in a segmented space through ligand adjustment and/or box adjustment modes.
-
-    The cavity detection can be limited around the target ligand(s), which will be passed to pyKVFinder through a *.pdb* or a *.xyz* files. Thus, the detected cavities are limited within a radius (``ligand_cutoff``) of the target ligand(s).
-
-    >>> import os
-    >>> ligand = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'ADN.pdb')
-    >>> from pyKVFinder import read_pdb
-    >>> latomic = read_pdb(ligand)
-    >>> ncav, cavities = detect(atomic, vertices, latomic=latomic, ligand_cutoff=5.0)
-    >>> ncav
-    2
-    >>> cavities
-    array([[[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]],
-       ...,
-       [[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
-
-    Further, we can also perform cavity detection on a custom 3D grid, where we can explore closed regions with a custom box, which can be defined by a *.toml* file (see `Box configuration file template`).
-
-    >>> import os
-    >>> fn = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'custom-box.toml')
-    >>> with open(fn, 'r') as f:
-    ...     print(f.read())
-    [box]
-    p1 = [3.11, 7.34, 1.59]
-    p2 = [11.51, 7.34, 1.59]
-    p3 = [3.11, 10.74, 1.59]
-    p4 = [3.11, 7.34, 6.19]
-
-    With this box adjustment mode, we must defined the 3D grid with ``get_vertices_from_file``. 
-
-    >>> from pyKVFinder import get_vertices_from_file
-    >>> vertices, atomic = get_vertices_from_file(fn, atomic)
-
-    Then, we can perform cavity detection:
-
-    >>> ncav, cavities = detect(atomic, vertices, box_adjustment=True)
-    >>> ncav
-    1
-    >>> cavities
-    array([[[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]],
-       ...,
-       [[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
-
-    .. warning::
-        If you are using box adjusment mode, do not forget to set ``box_adjustment`` flag to ``True``.
-    """
-    from _pyKVFinder import _detect, _detect_ladj
-
-    # Check arguments
-    if type(atomic) not in [numpy.ndarray, list]:
-        raise TypeError("`atomic` must be a list or a numpy.ndarray.")
-    elif len(numpy.asarray(atomic).shape) != 2:
-        raise ValueError("`atomic` has incorrect shape. It must be (n, 8).")
-    elif numpy.asarray(atomic).shape[1] != 8:
-        raise ValueError("`atomic` has incorrect shape. It must be (n, 8).")
-    if type(vertices) not in [numpy.ndarray, list]:
-        raise TypeError("`vertices` must be a list or a numpy.ndarray.")
-    elif numpy.asarray(vertices).shape != (4, 3):
-        raise ValueError("`vertices` has incorrect shape. It must be (4, 3).")
-    if type(step) not in [float, int]:
-        raise TypeError("`step` must be a positive real number.")
-    elif step <= 0.0:
-        raise ValueError("`step` must be a positive real number.")
-    if type(probe_in) not in [float, int]:
-        raise TypeError("`probe_in` must be a non-negative real number.")
-    elif probe_in < 0.0:
-        raise ValueError("`probe_in` must be a non-negative real number.")
-    if type(probe_out) not in [float, int]:
-        raise TypeError("`probe_out` must be a non-negative real number.")
-    elif probe_out < 0.0:
-        raise ValueError("`probe_out` must be a non-negative real number.")
-    elif probe_out < probe_in:
-        raise ValueError("`probe_out` must be greater than `probe_in`.")
-    if type(removal_distance) not in [float, int]:
-        raise TypeError("`removal_distance` must be a non-negative real number.")
-    elif removal_distance < 0.0:
-        raise ValueError("`removal_distance` must be a non-negative real number.")
-    if type(volume_cutoff) not in [float, int]:
-        raise TypeError("`volume_cutoff` must be a non-negative real number.")
-    elif volume_cutoff < 0.0:
-        raise ValueError("`volume_cutoff` must be a non-negative real number.")
-    if latomic is not None:
-        if type(latomic) not in [numpy.ndarray, list]:
-            raise TypeError("`latomic` must be a list, a numpy.ndarray or None.")
-        if len(numpy.asarray(latomic).shape) != 2:
-            raise ValueError("`latomic` has incorrect shape. It must be (n, 8).")
-        elif numpy.asarray(latomic).shape[1] != 8:
-            raise ValueError("`latomic` has incorrect shape. It must be (n, 8).")
-    if type(ligand_cutoff) not in [float, int]:
-        raise TypeError("`ligand_cutoff` must be a positive real number.")
-    elif ligand_cutoff <= 0.0:
-        raise ValueError("`ligand_cutoff` must be a positive real number.")
-    if type(box_adjustment) not in [bool]:
-        raise TypeError("`box_adjustment` must be a boolean.")
-    if type(surface) not in [str]:
-        raise TypeError("`surface` must be a string.")
-    if nthreads is None:
-        nthreads = os.cpu_count() - 1
-    else:
-        if type(nthreads) not in [int]:
-            raise TypeError("`nthreads` must be a positive integer.")
-        elif nthreads <= 0:
-            raise ValueError("`nthreads` must be a positive integer.")
-    if type(verbose) not in [bool]:
-        raise TypeError("`verbose` must be a boolean.")
-
-    # Convert types
-    if type(atomic) == list:
-        atomic = numpy.asarray(atomic)
-    if type(vertices) == list:
-        vertices = numpy.asarray(vertices)
-    if type(step) == int:
-        step = float(step)
-    if type(probe_in) == int:
-        probe_in = float(probe_in)
-    if type(probe_out) == int:
-        probe_out = float(probe_out)
-    if type(removal_distance) == int:
-        removal_distance = float(removal_distance)
-    if type(volume_cutoff) == int:
-        volume_cutoff = float(volume_cutoff)
-    if type(ligand_cutoff) == int:
-        ligand_cutoff = float(ligand_cutoff)
-    if type(latomic) == list:
-        latomic = numpy.asarray(latomic)
-
-    # Convert numpy.ndarray data types
-    vertices = vertices.astype("float64") if vertices.dtype != "float64" else vertices
-
-    # Extract xyzr from atomic
-    xyzr = atomic[:, 4:].astype(numpy.float64)
-
-    # Extract lxyzr from latomic
-    if latomic is not None:
-        lxyzr = latomic[:, 4:].astype(numpy.float64)
-
-    # Define ligand adjustment mode
-    ligand_adjustment = True if latomic is not None else False
-
-    # Unpack vertices
-    P1, P2, P3, P4 = vertices
-
-    if surface == "SES":
-        if verbose:
-            print("> Surface representation: Solvent Excluded Surface (SES)")
-        surface = True
-    elif surface == "SAS":
-        if verbose:
-            print("> Surface representation: Solvent Accessible Surface (SAS)")
-        surface = False
-    else:
-        raise ValueError(f"`surface` must be SAS or SES, not {surface}.")
-
-    # Get sincos: sine and cossine of the grid rotation angles (sina, cosa, sinb, cosb)
-    sincos = _get_sincos(vertices)
-
-    # Get dimensions
-    nx, ny, nz = _get_dimensions(vertices, step)
-
-    # Calculate number of voxels
-    nvoxels = nx * ny * nz
-
-    # Detect cavities
-    if ligand_adjustment:
-        ncav, cavities = _detect_ladj(
-            nvoxels,
-            nx,
-            ny,
-            nz,
-            xyzr,
-            lxyzr,
-            P1,
-            sincos,
-            step,
-            probe_in,
-            probe_out,
-            removal_distance,
-            volume_cutoff,
-            ligand_adjustment,
-            ligand_cutoff,
-            box_adjustment,
-            P2,
-            surface,
-            nthreads,
-            verbose,
-        )
-    else:
-        ncav, cavities = _detect(
-            nvoxels,
-            nx,
-            ny,
-            nz,
-            xyzr,
-            P1,
-            sincos,
-            step,
-            probe_in,
-            probe_out,
-            removal_distance,
-            volume_cutoff,
-            box_adjustment,
-            P2,
-            surface,
-            nthreads,
-            verbose,
-        )
-
-    return ncav, cavities.reshape(nx, ny, nz)
          
-
-
-def _select_cavities(cavities: numpy.ndarray, selection: List[int]) -> numpy.ndarray:
-    """Select cavities in the 3D grid by cavity labels.
-
-    Parameters
-    ----------
-    cavities : numpy.ndarray
-        Cavity points in the 3D grid (cavities[nx][ny][nz]).
-        Cavities array has integer labels in each position, that are:
-
-            * -1: bulk points;
-
-            * 0: biomolecule points;
-
-            * 1: empty space points;
-
-            * >=2: cavity points.
-    selection : List[int]
-        A list of integer labels of each cavity to be selected.
-
-    Returns
-    -------
-    selected : numpy.ndarray
-        Selected cavity points in the 3D grid.
-        Selected cavities array has integer labels in each position, that are:
-
-            * -1: bulk points;
-
-            * 0: biomolecule points;
-
-            * 1: empty space points or unselected cavity points;
-
-            * >=2: selected cavity points.
-    """
-    # Copy cavities
-    selected = numpy.copy(cavities)
-
-    # When outside selection, change cavities tags to 1
-    for cav in range(2, cavities.max() + 1):
-        if cav not in selection:
-            selected[cavities == cav] = 1
-
-    return selected
-
-
-def _get_cavity_name(index: int) -> str:
-    """Get cavity name, eg KAA, KAB, and so on, based on the index.
-
-    Parameters
-    ----------
-    index : int
-        Index in the dictionary.
-
-    Returns
-    -------
-    cavity_name : str
-        Cavity name
-    """
-    cavity_name = f"K{chr(65 + int(index / 26) % 26)}{chr(65 + (index % 26))}"
-    return cavity_name
-
-
-def _get_cavity_label(cavity_name: str) -> int:
-    """Get cavity label, eg 2, 3, and so on, based on the cavity name.
-
-    Parameters
-    ----------
-    cavity_name : str
-        Cavity name
-
-    Returns
-    -------
-    cavity_label : int
-        Integer label of each cavity.
-
-    Raises
-    ------
-    ValueError
-        Invalid cavity name: `cavity_name`.
-    """
-    # Check cavity name
-    if cavity_name[0] != "K":
-        raise ValueError(f"Invalid cavity name: {cavity_name}.")
-
-    # Get cavity label
-    cavity_label = (ord(cavity_name[1]) - 65) * 26 + (ord(cavity_name[2]) - 65) + 2
-
-    return cavity_label
-
-
-def _process_spatial(
-    raw_volume: numpy.ndarray,
-    raw_area: numpy.ndarray,
-    ncav: int,
-    selection: Optional[List[int]] = None,
-) -> Tuple[Dict[str, float], Dict[str, float]]:
-    """Processes arrays of volumes and areas.
-
-    Parameters
-    ----------
-    raw_volume : numpy.ndarray
-        A numpy.ndarray of volumes.
-    raw_area : numpy.ndarray
-        A numpy.ndarray of areas.
-    ncav : int
-        Number of cavities.
-    selection : List[int], optional
-        A list of integer labels of each cavity to be selected, by default None.
-
-    Returns
-    -------
-    volume : Dict[str, float]
-        A dictionary with volume of each detected cavity.
-    area : Dict[str, float]
-        A dictionary with area of each detected cavity.
-    """
-    volume, area = {}, {}
-
-    # Prepare volume and area dictionary
-    for index in range(ncav):
-        key = _get_cavity_name(index)
-        volume[key] = float(round(raw_volume[index], 2))
-        area[key] = float(round(raw_area[index], 2))
-
-    if selection is not None:
-        # Get keys from selection
-        all_keys = list(volume.keys())
-        keys = [all_keys[sele - 2] for sele in selection]
-
-        # Get volume and area of selection
-        volume = {key: volume[key] for key in keys}
-        area = {key: area[key] for key in keys}
-
-    return volume, area
-
-
-
          [docs]def spatial(
-    cavities: numpy.ndarray,
-    step: Union[float, int] = 0.6,
-    selection: Optional[Union[List[int], List[str]]] = None,
-    nthreads: Optional[int] = None,
-    verbose: bool = False,
-) -> Tuple[numpy.ndarray, Dict[str, float], Dict[str, float]]:
-    """Spatial characterization (volume and area) of the detected cavities.
-
-    Parameters
-    ----------
-    cavities : numpy.ndarray
-        Cavity points in the 3D grid (cavities[nx][ny][nz]).
-        Cavities array has integer labels in each position, that are:
-
-            * -1: bulk points;
-
-            * 0: biomolecule points;
-
-            * 1: empty space points;
-
-            * >=2: cavity points.
-
-        The empty space points are regions that do not meet the chosen
-        volume cutoff to be considered a cavity.
-    step : Union[float, int], optional
-        Grid spacing (A), by default 0.6.
-    selection : Union[List[int], List[str]], optional
-        A list of integer labels or a list of cavity names to be selected, by default None.
-    nthreads : int, optional
-        Number of threads, by default None. If None, the number of threads is
-        `os.cpu_count() - 1`.
-    verbose : bool, optional
-        Print extra information to standard output, by default False.
-
-    Returns
-    -------
-    surface : numpy.ndarray
-        Surface points in the 3D grid (surface[nx][ny][nz]).
-        Surface array has integer labels in each position, that are:
-
-            * -1: bulk points;
-
-            * 0: biomolecule or empty space points;
-
-            * >=2: surface points.
-
-        The empty space points are regions that do not meet the chosen
-        volume cutoff to be considered a cavity.
-    volume : Dict[str, float]
-        A dictionary with volume of each detected cavity.
-    area : Dict[str, float]
-        A dictionary with area of each detected cavity.
-
-    Note
-    ----
-    The cavity nomenclature is based on the integer label. The cavity marked
-    with 2, the first integer corresponding to a cavity, is KAA, the cavity
-    marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
-
-    Raises
-    ------
-    TypeError
-        `cavities` must be a numpy.ndarray.
-    ValueError
-        `cavities` has the incorrect shape. It must be (nx, ny, nz).
-    TypeError
-        `step` must be a positive real number.
-    ValueError
-        `step` must be a positive real number.
-    TypeError
-        `selection` must be a list of strings (cavity names) or integers (cavity labels).
-    ValueError
-        Invalid `selection`: {selection}.
-    TypeError
-        `nthreads` must be a positive integer.
-    ValueError
-        `nthreads` must be a positive integer.
-    TypeError
-        `verbose` must be a boolean.
-
-    See Also
-    --------
-    detect
-    hydropathy
-    export
-
-    Example
-    -------
-    With the cavity points identified with ``detect``, we can perform a spatial characterization, that includes volume, area and defining surface points:
-
-    >>> from pyKVFinder import spatial
-    >>> surface, volume, area = spatial(cavities)
-    >>> surface
-    array([[[-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            ...,
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1]],
-           ...,
-           [[-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            ...,
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
-    >>> volume
-    {'KAA': 137.16, 'KAB': 47.52, 'KAC': 66.96, 'KAD': 8.21, 'KAE': 43.63, 'KAF': 12.53, 'KAG': 6.26, 'KAH': 520.13, 'KAI': 12.31, 'KAJ': 26.57, 'KAK': 12.31, 'KAL': 33.91, 'KAM': 23.11, 'KAN': 102.82, 'KAO': 6.05, 'KAP': 15.55, 'KAQ': 7.99, 'KAR': 7.78}
-    >>> area
-    {'KAA': 126.41, 'KAB': 62.37, 'KAC': 74.57, 'KAD': 19.06, 'KAE': 57.08, 'KAF': 22.77, 'KAG': 15.38, 'KAH': 496.97, 'KAI': 30.58, 'KAJ': 45.64, 'KAK': 30.58, 'KAL': 45.58, 'KAM': 45.25, 'KAN': 129.77, 'KAO': 12.28, 'KAP': 25.04, 'KAQ': 13.46, 'KAR': 16.6}
-    """
-    from _pyKVFinder import _spatial
-
-    # Check arguments
-    if type(cavities) not in [numpy.ndarray]:
-        raise TypeError("`cavities` must be a numpy.ndarray.")
-    elif len(cavities.shape) != 3:
-        raise ValueError("`cavities` has the incorrect shape. It must be (nx, ny, nz).")
-    if type(step) not in [float, int]:
-        raise TypeError("`step` must be a positive real number.")
-    elif step <= 0.0:
-        raise ValueError("`step` must be a positive real number.")
-    if selection is not None:
-        # Check selection types
-        if all(isinstance(x, int) for x in selection):
-            pass
-        elif all(isinstance(x, str) for x in selection):
-            selection = [_get_cavity_label(sele) for sele in selection]
-        else:
-            raise TypeError(
-                "`selection` must be a list of strings (cavity names) or integers (cavity labels)."
-            )
-        # Check if selection includes valid cavity labels
-        if any(x < 2 for x in selection):
-            raise ValueError(f"Invalid `selection`: {selection}.")
-    if nthreads is None:
-        nthreads = os.cpu_count() - 1
-    else:
-        if type(nthreads) not in [int]:
-            raise TypeError("`nthreads` must be a positive integer.")
-        elif nthreads <= 0:
-            raise ValueError("`nthreads` must be a positive integer.")
-    if type(verbose) not in [bool]:
-        raise TypeError("`verbose` must be a boolean.")
-
-    # Convert types
-    if type(step) == int:
-        step = float(step)
-
-    # Convert numpy.ndarray data types
-    cavities = cavities.astype("int32") if cavities.dtype != "int32" else cavities
-
-    # Get number of cavities
-    ncav = int(cavities.max() - 1)
-
-    # Select cavities
-    if selection is not None:
-        cavities = _select_cavities(cavities, selection)
-
-    # Get cavities shape
-    nx, ny, nz = cavities.shape
-
-    # Get surface points, volume and area
-    surface, volume, area = _spatial(
-        cavities, nx * ny * nz, ncav, ncav, step, nthreads, verbose
-    )
-    volume, area = _process_spatial(volume, area, ncav)
-
-    return surface.reshape(nx, ny, nz), volume, area
          
-
-
-def _process_depth(
-    raw_max_depth: numpy.ndarray,
-    raw_avg_depth: numpy.ndarray,
-    ncav: int,
-    selection: Optional[List[int]] = None,
-) -> Tuple[Dict[str, float], Dict[str, float]]:
-    """Processes arrays of maximum and average depths.
-
-    Parameters
-    ----------
-    raw_max_depth : numpy.ndarray
-        A numpy.ndarray of maximum depth.
-    raw_avg_depth : numpy.ndarray
-        A numpy.ndarray of average depth.
-    ncav : int
-        Number of cavities.
-    selection : List[int], optional
-        A list of integer labels of each cavity to be selected, by default None.
-
-    Returns
-    -------
-    max_depth : Dict[str, float]
-        A dictionary with maximum depth of each detected cavity.
-    avg_depth : Dict[str, float]
-        A dictionary with average depth of each detected cavity.
-    """
-    max_depth, avg_depth = {}, {}
-
-    # Prepare maximum and average depth dictionary
-    for index in range(ncav):
-        key = _get_cavity_name(index)
-        max_depth[key] = float(round(raw_max_depth[index], 2))
-        avg_depth[key] = float(round(raw_avg_depth[index], 2))
-
-    if selection is not None:
-        # Get keys from selection
-        all_keys = list(max_depth.keys())
-        keys = [all_keys[sele - 2] for sele in selection]
-
-        # Get volume and area of selection
-        max_depth = {key: max_depth[key] for key in keys}
-        avg_depth = {key: avg_depth[key] for key in keys}
-
-    return max_depth, avg_depth
-
-
-
          [docs]def depth(
-    cavities: numpy.ndarray,
-    step: Union[float, int] = 0.6,
-    selection: Optional[Union[List[int], List[str]]] = None,
-    nthreads: Optional[int] = None,
-    verbose: bool = False,
-) -> Tuple[numpy.ndarray, Dict[str, float], Dict[str, float]]:
-    """Characterization of the depth of the detected cavities, including depth
-    per cavity point and maximum and average depths of detected cavities.
-
-    Parameters
-    ----------
-    cavities : numpy.ndarray
-        Cavity points in the 3D grid (cavities[nx][ny][nz]).
-        Cavities array has integer labels in each position, that are:
-
-            * -1: bulk points;
-
-            * 0: biomolecule points;
-
-            * 1: empty space points;
-
-            * >=2: cavity points.
-
-        The empty space points are regions that do not meet the chosen
-        volume cutoff to be considered a cavity.
-    step : Union[float, int], optional
-        Grid spacing (A).
-    selection : Union[List[int], List[str]], optional
-        A list of integer labels or a list of cavity names to be selected, by default None.
-    nthreads : int, optional
-        Number of threads, by default None. If None, the number of threads is
-        `os.cpu_count() - 1`.
-    verbose : bool, optional
-        Print extra information to standard output, by default False.
-
-    Returns
-    -------
-    depths : numpy.ndarray
-        A numpy.ndarray with depth of cavity points (depth[nx][ny][nz]).
-    max_depth : Dict[str, float]
-        A dictionary with maximum depth of each detected cavity.
-    avg_depth : Dict[str, float]
-        A dictionary with average depth of each detected cavity.
-
-    Raises
-    ------
-    TypeError
-        `cavities` must be a numpy.ndarray.
-    ValueError
-        `cavities` has the incorrect shape. It must be (nx, ny, nz).
-    TypeError
-        `step` must be a positive real number.
-    ValueError
-        `step` must be a positive real number.
-    TypeError
-        `selection` must be a list of strings (cavity names) or integers (cavity labels).
-    ValueError
-        Invalid `selection`: {selection}.
-    TypeError
-        `nthreads` must be a positive integer.
-    ValueError
-        `nthreads` must be a positive integer.
-    TypeError
-        `verbose` must be a boolean.
-
-    Note
-    ----
-    The cavity nomenclature is based on the integer label. The cavity marked
-    with 2, the first integer corresponding to a cavity, is KAA, the cavity
-    marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
-
-    See Also
-    --------
-    detect
-    export
-    write_results
-
-    Example
-    -------
-    With the cavity points identified with ``detect``, we can perform a depth characterization, that includes maximum depth, average depth and defining depth of cavity points:
-
-    >>> from pyKVFinder import depth
-    >>> depths, max_depth, avg_depth = depth(cavities)
-    >>> depths
-    array([[[0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            ...,
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.]],
-          ...,
-          [[0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            ...,
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.]]])
-    >>> max_depth
-    {'KAA': 3.79, 'KAB': 2.68, 'KAC': 2.62, 'KAD': 0.85, 'KAE': 3.0, 'KAF': 0.85, 'KAG': 0.6, 'KAH': 10.73, 'KAI': 0.0, 'KAJ': 2.24, 'KAK': 0.0, 'KAL': 3.0, 'KAM': 1.2, 'KAN': 0.0, 'KAO': 1.04, 'KAP': 2.08, 'KAQ': 0.85, 'KAR': 0.6}
-    >>> avg_depth
-    {'KAA': 1.35, 'KAB': 0.91, 'KAC': 0.68, 'KAD': 0.32, 'KAE': 0.99, 'KAF': 0.24, 'KAG': 0.1, 'KAH': 3.91, 'KAI': 0.0, 'KAJ': 0.96, 'KAK': 0.0, 'KAL': 1.07, 'KAM': 0.24, 'KAN': 0.0, 'KAO': 0.29, 'KAP': 0.7, 'KAQ': 0.22, 'KAR': 0.12}
-    """
-    from _pyKVFinder import _depth
-
-    # Check arguments
-    if type(cavities) not in [numpy.ndarray]:
-        raise TypeError("`cavities` must be a numpy.ndarray.")
-    elif len(cavities.shape) != 3:
-        raise ValueError("`cavities` has the incorrect shape. It must be (nx, ny, nz).")
-    if type(step) not in [float, int]:
-        raise TypeError("`step` must be a positive real number.")
-    elif step <= 0.0:
-        raise ValueError("`step` must be a positive real number.")
-    if selection is not None:
-        # Check selection types
-        if all(isinstance(x, int) for x in selection):
-            pass
-        elif all(isinstance(x, str) for x in selection):
-            selection = [_get_cavity_label(sele) for sele in selection]
-        else:
-            raise TypeError(
-                "`selection` must be a list of strings (cavity names) or integers (cavity labels)."
-            )
-        # Check if selection includes valid cavity labels
-        if any(x < 2 for x in selection):
-            raise ValueError(f"Invalid `selection`: {selection}.")
-    if nthreads is None:
-        nthreads = os.cpu_count() - 1
-    else:
-        if type(nthreads) not in [int]:
-            raise TypeError("`nthreads` must be a positive integer.")
-        elif nthreads <= 0:
-            raise ValueError("`nthreads` must be a positive integer.")
-    if type(verbose) not in [bool]:
-        raise TypeError("`verbose` must be a boolean.")
-
-    # Convert types
-    if type(step) == int:
-        step = float(step)
-
-    # Check numpy.ndarray data types
-    cavities = cavities.astype("int32") if cavities.dtype != "int32" else cavities
-
-    # Get number of cavities
-    ncav = int(cavities.max() - 1)
-
-    # Select cavities
-    if selection is not None:
-        cavities = _select_cavities(cavities, selection)
-
-    # Get cavities shape
-    nx, ny, nz = cavities.shape
-
-    # Get depth of cavity points, maximum depth and average depth
-    depths, max_depth, avg_depth = _depth(
-        cavities, nx * ny * nz, ncav, ncav, step, nthreads, verbose
-    )
-    max_depth, avg_depth = _process_depth(max_depth, avg_depth, ncav, selection)
-
-    return depths.reshape(nx, ny, nz), max_depth, avg_depth
          
-
-
-def _process_residues(
-    raw: List[str], ncav: int, selection: Optional[List[int]] = None
-) -> Dict[str, List[List[str]]]:
-    """Processes raw list of residues from _constitutional to a list of
-    residue information per cavity name.
-
-    Parameters
-    ----------
-    raw : List[str]
-        A list of residues with cavities separated by '-1'.
-    ncav : int
-        Number of cavities.
-    selection : List[int], optional
-        A list of integer labels of each cavity to be selected, by default None.
-
-    Returns
-    -------
-    residues : Dict[str, List[List[str]]]
-        A dictionary with a list of interface residues for each detected
-        cavity.
-    """
-    from itertools import groupby
-
-    residues = {}
-
-    if selection is None:
-        selection = list(range(ncav + 1))
-    else:
-        selection = [sele - 2 for sele in selection]
-
-    index = 0
-    for flag, cavity_residues in groupby(raw, lambda res: res == "-1"):
-        if not flag:
-            key = _get_cavity_name(selection[index])
-            residues[key] = [
-                item.split("_") for item in list(dict.fromkeys(cavity_residues))
-            ]
-            index += 1
-
-    return residues
-
-
-
          [docs]def constitutional(
-    cavities: numpy.ndarray,
-    atomic: Union[numpy.ndarray, List[List[Union[str, float, int]]]],
-    vertices: Union[numpy.ndarray, List[List[float]]],
-    step: Union[float, int] = 0.6,
-    probe_in: Union[float, int] = 1.4,
-    ignore_backbone: bool = False,
-    selection: Optional[Union[List[int], List[str]]] = None,
-    nthreads: Optional[int] = None,
-    verbose: bool = False,
-) -> Dict[str, List[List[str]]]:
-    """Constitutional characterization (interface residues) of the detected
-    cavities.
-
-    Parameters
-    ----------
-    cavities : numpy.ndarray
-        Cavity points in the 3D grid (cavities[nx][ny][nz]).
-        Cavities array has integer labels in each position, that are:
-
-            * -1: bulk points;
-
-            * 0: biomolecule points;
-
-            * 1: empty space points;
-
-            * >=2: cavity points.
-
-        The empty space points are regions that do not meet the chosen
-        volume cutoff to be considered a cavity.
-    atomic : Union[numpy.ndarray, List[List[Union[str, float, int]]]]
-        A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
-        and radius) for each atom.
-    vertices : Union[numpy.ndarray, List[List[float]]]
-        A numpy.ndarray or a list with xyz vertices coordinates (origin,
-        X-axis, Y-axis, Z-axis).
-    step : Union[float, int], optional
-        Grid spacing (A), by default 0.6.
-    probe_in : Union[float, int], optional
-        Probe In size (A), by default 1.4.
-    ignore_backbone : bool, optional
-        Whether to ignore backbone atoms (C, CA, N, O) when defining interface
-        residues, by default False.
-    selection : Union[List[int], List[str]], optional
-        A list of integer labels or a list of cavity names to be selectedA list of integer labels of each cavity to be selected, by default None.
-    nthreads : int, optional
-        Number of threads, by default None. If None, the number of threads is
-        `os.cpu_count() - 1`.
-    verbose : bool, optional
-        Print extra information to standard output, by default False.
-
-    Returns
-    -------
-    residues: Dict[str, List[List[str]]]
-        A dictionary with a list of interface residues for each detected
-        cavity.
-
-    Raises
-    ------
-    TypeError
-        `cavities` must be a numpy.ndarray.
-    ValueError
-        `cavities` has the incorrect shape. It must be (nx, ny, nz).
-    TypeError
-        `atomic` must be a list or a numpy.ndarray.
-    ValueError
-        `atomic` has incorrect shape. It must be (n, 8).
-    TypeError
-        `vertices` must be a list or a numpy.ndarray.
-    ValueError
-        `vertices` has incorrect shape. It must be (4, 3).
-    TypeError
-        `step` must be a positive real number.
-    ValueError
-        `step` must be a positive real number.
-    TypeError
-        `probe_in` must be a non-negative real number.
-    ValueError
-        `probe_in` must be a non-negative real number.
-    TypeError
-        `ignore_backbone` must be a boolean.
-    TypeError
-        `selection` must be a list of strings (cavity names) or integers (cavity labels).
-    ValueError
-        Invalid `selection`: {selection}.
-    TypeError
-        `nthreads` must be a positive integer.
-    ValueError
-        `nthreads` must be a positive integer.
-    TypeError
-        `verbose` must be a boolean.
-
-    Note
-    ----
-    The cavity nomenclature is based on the integer label. The cavity marked
-    with 2, the first integer corresponding to a cavity, is KAA, the cavity
-    marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
-
-    Note
-    ----
-    The classes of residues are:
-
-    * Aliphatic apolar (R1): Alanine, Glycine, Isoleucine, Leucine, Methionine, Valine.
-
-    * Aromatic (R2): Phenylalanine, Tryptophan, Tyrosine.
-
-    * Polar Uncharged (R3): Asparagine, Cysteine, Glutamine, Proline, Serine, Threonine.
-
-    * Negatively charged (R4): Aspartate, Glutamate.
-
-    * Positively charged (R5): Arginine, Histidine, Lysine.
-
-    * Non-standard (RX): Non-standard residues.
-
-    See Also
-    --------
-    read_pdb
-    read_xyz
-    detect 
-    calculate_frequencies
-    write_results
-
-    Example
-    -------
-    With the cavity points identified with ``detect``, atomic data read with ``read_pdb`` or ``read_xyz``, we can perform a constitutional characterization, that identifies the interface residues surrounding the cavities:
-
-    >>> from pyKVFinder import constitutional
-    >>> residues = constitutional(cavities, atomic, vertices)
-    >>> residues
-    {'KAA': [['14', 'E', 'SER'], ['15', 'E', 'VAL'], ['18', 'E', 'PHE'], ['19', 'E', 'LEU'], ['100', 'E', 'PHE'], ['152', 'E', 'LEU'], ['155', 'E', 'GLU'], ['156', 'E', 'TYR'], ['292', 'E', 'LYS'], ['302', 'E', 'TRP'], ['303', 'E', 'ILE'], ['306', 'E', 'TYR']], 'KAB': [['18', 'E', 'PHE'], ['22', 'E', 'ALA'], ['25', 'E', 'ASP'], ['26', 'E', 'PHE'], ['29', 'E', 'LYS'], ['97', 'E', 'ALA'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['156', 'E', 'TYR']], 'KAC': [['141', 'E', 'PRO'], ['142', 'E', 'HIS'], ['144', 'E', 'ARG'], ['145', 'E', 'PHE'], ['148', 'E', 'ALA'], ['299', 'E', 'THR'], ['300', 'E', 'THR'], ['305', 'E', 'ILE'], ['310', 'E', 'VAL'], ['311', 'E', 'GLU'], ['313', 'E', 'PRO']], 'KAD': [['122', 'E', 'TYR'], ['124', 'E', 'ALA'], ['176', 'E', 'GLN'], ['318', 'E', 'PHE'], ['320', 'E', 'GLY'], ['321', 'E', 'PRO'], ['322', 'E', 'GLY'], ['323', 'E', 'ASP']], 'KAE': [['95', 'E', 'LEU'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['100', 'E', 'PHE'], ['103', 'E', 'LEU'], ['104', 'E', 'VAL'], ['105', 'E', 'LYS'], ['106', 'E', 'LEU']], 'KAF': [['123', 'E', 'VAL'], ['124', 'E', 'ALA'], ['175', 'E', 'ASP'], ['176', 'E', 'GLN'], ['181', 'E', 'GLN']], 'KAG': [['34', 'E', 'SER'], ['37', 'E', 'THR'], ['96', 'E', 'GLN'], ['106', 'E', 'LEU'], ['107', 'E', 'GLU'], ['108', 'E', 'PHE'], ['109', 'E', 'SER']], 'KAH': [['49', 'E', 'LEU'], ['50', 'E', 'GLY'], ['51', 'E', 'THR'], ['52', 'E', 'GLY'], ['53', 'E', 'SER'], ['54', 'E', 'PHE'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['72', 'E', 'LYS'], ['74', 'E', 'LEU'], ['84', 'E', 'GLN'], ['87', 'E', 'HIS'], ['88', 'E', 'THR'], ['91', 'E', 'GLU'], ['104', 'E', 'VAL'], ['120', 'E', 'MET'], ['121', 'E', 'GLU'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['166', 'E', 'ASP'], ['168', 'E', 'LYS'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['184', 'E', 'ASP'], ['186', 'E', 'GLY'], ['187', 'E', 'PHE'], ['201', 'E', 'THR'], ['327', 'E', 'PHE']], 'KAI': [['131', 'E', 'HIS'], ['138', 'E', 'PHE'], ['142', 'E', 'HIS'], ['146', 'E', 'TYR'], ['174', 'E', 'ILE'], ['314', 'E', 'PHE']], 'KAJ': [['33', 'E', 'PRO'], ['89', 'E', 'LEU'], ['92', 'E', 'LYS'], ['93', 'E', 'ARG'], ['96', 'E', 'GLN'], ['349', 'E', 'GLU'], ['350', 'E', 'PHE']], 'KAK': [['157', 'E', 'LEU'], ['162', 'E', 'LEU'], ['163', 'E', 'ILE'], ['164', 'E', 'TYR'], ['185', 'E', 'PHE'], ['188', 'E', 'ALA']], 'KAL': [['49', 'E', 'LEU'], ['127', 'E', 'GLU'], ['129', 'E', 'PHE'], ['130', 'E', 'SER'], ['326', 'E', 'ASN'], ['327', 'E', 'PHE'], ['328', 'E', 'ASP'], ['330', 'E', 'TYR']], 'KAM': [['51', 'E', 'THR'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['73', 'E', 'ILE'], ['74', 'E', 'LEU'], ['75', 'E', 'ASP'], ['115', 'E', 'ASN'], ['335', 'E', 'ILE'], ['336', 'E', 'ARG']], 'KAN': [['165', 'E', 'ARG'], ['166', 'E', 'ASP'], ['167', 'E', 'LEU'], ['199', 'E', 'CYS'], ['200', 'E', 'GLY'], ['201', 'E', 'THR'], ['204', 'E', 'TYR'], ['205', 'E', 'LEU'], ['206', 'E', 'ALA'], ['209', 'E', 'ILE'], ['219', 'E', 'VAL'], ['220', 'E', 'ASP'], ['223', 'E', 'ALA']], 'KAO': [['48', 'E', 'THR'], ['51', 'E', 'THR'], ['56', 'E', 'ARG'], ['330', 'E', 'TYR'], ['331', 'E', 'GLU']], 'KAP': [['222', 'E', 'TRP'], ['238', 'E', 'PHE'], ['253', 'E', 'GLY'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['273', 'E', 'LEU']], 'KAQ': [['207', 'E', 'PRO'], ['208', 'E', 'GLU'], ['211', 'E', 'LEU'], ['213', 'E', 'LYS'], ['275', 'E', 'VAL'], ['277', 'E', 'LEU']], 'KAR': [['237', 'E', 'PRO'], ['238', 'E', 'PHE'], ['249', 'E', 'LYS'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['256', 'E', 'ARG']]}
-
-    However, users may opt to ignore backbones contacts (C, CA, N, O) with the cavity when defining interface residues. Then, users must set ``ignore_backbone`` flag to ``True``.
-
-    >>> residues = constitutional(cavities, atomic, vertices, ignore_backbone=True)
-    >>> residues
-    {'KAA': [['15', 'E', 'VAL'], ['18', 'E', 'PHE'], ['19', 'E', 'LEU'], ['100', 'E', 'PHE'], ['152', 'E', 'LEU'], ['155', 'E', 'GLU'], ['156', 'E', 'TYR'], ['292', 'E', 'LYS'], ['302', 'E', 'TRP'], ['303', 'E', 'ILE'], ['306', 'E', 'TYR']], 'KAB': [['18', 'E', 'PHE'], ['22', 'E', 'ALA'], ['25', 'E', 'ASP'], ['26', 'E', 'PHE'], ['29', 'E', 'LYS'], ['99', 'E', 'ASN'], ['156', 'E', 'TYR']], 'KAC': [['144', 'E', 'ARG'], ['145', 'E', 'PHE'], ['148', 'E', 'ALA'], ['299', 'E', 'THR'], ['300', 'E', 'THR'], ['305', 'E', 'ILE'], ['310', 'E', 'VAL'], ['311', 'E', 'GLU'], ['313', 'E', 'PRO']], 'KAD': [['122', 'E', 'TYR'], ['124', 'E', 'ALA'], ['176', 'E', 'GLN'], ['318', 'E', 'PHE']], 'KAE': [['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['103', 'E', 'LEU'], ['105', 'E', 'LYS'], ['106', 'E', 'LEU']], 'KAF': [['123', 'E', 'VAL'], ['175', 'E', 'ASP'], ['181', 'E', 'GLN']], 'KAG': [['34', 'E', 'SER'], ['37', 'E', 'THR'], ['96', 'E', 'GLN'], ['106', 'E', 'LEU'], ['109', 'E', 'SER']], 'KAH': [['49', 'E', 'LEU'], ['53', 'E', 'SER'], ['54', 'E', 'PHE'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['72', 'E', 'LYS'], ['74', 'E', 'LEU'], ['84', 'E', 'GLN'], ['87', 'E', 'HIS'], ['88', 'E', 'THR'], ['91', 'E', 'GLU'], ['104', 'E', 'VAL'], ['120', 'E', 'MET'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['166', 'E', 'ASP'], ['168', 'E', 'LYS'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['184', 'E', 'ASP'], ['187', 'E', 'PHE'], ['201', 'E', 'THR'], ['327', 'E', 'PHE']], 'KAI': [['131', 'E', 'HIS'], ['138', 'E', 'PHE'], ['142', 'E', 'HIS'], ['146', 'E', 'TYR'], ['174', 'E', 'ILE'], ['314', 'E', 'PHE']], 'KAJ': [['33', 'E', 'PRO'], ['89', 'E', 'LEU'], ['92', 'E', 'LYS'], ['93', 'E', 'ARG'], ['96', 'E', 'GLN'], ['349', 'E', 'GLU'], ['350', 'E', 'PHE']], 'KAK': [['157', 'E', 'LEU'], ['162', 'E', 'LEU'], ['164', 'E', 'TYR'], ['185', 'E', 'PHE'], ['188', 'E', 'ALA']], 'KAL': [['127', 'E', 'GLU'], ['129', 'E', 'PHE'], ['130', 'E', 'SER'], ['327', 'E', 'PHE'], ['328', 'E', 'ASP'], ['330', 'E', 'TYR']], 'KAM': [['51', 'E', 'THR'], ['56', 'E', 'ARG'], ['73', 'E', 'ILE'], ['115', 'E', 'ASN'], ['335', 'E', 'ILE']], 'KAN': [['165', 'E', 'ARG'], ['166', 'E', 'ASP'], ['167', 'E', 'LEU'], ['201', 'E', 'THR'], ['204', 'E', 'TYR'], ['205', 'E', 'LEU'], ['206', 'E', 'ALA'], ['209', 'E', 'ILE'], ['219', 'E', 'VAL'], ['220', 'E', 'ASP'], ['223', 'E', 'ALA']], 'KAO': [['48', 'E', 'THR'], ['51', 'E', 'THR'], ['56', 'E', 'ARG'], ['330', 'E', 'TYR']], 'KAP': [['222', 'E', 'TRP'], ['238', 'E', 'PHE'], ['255', 'E', 'VAL'], ['273', 'E', 'LEU']], 'KAQ': [['207', 'E', 'PRO'], ['208', 'E', 'GLU'], ['211', 'E', 'LEU'], ['213', 'E', 'LYS'], ['277', 'E', 'LEU']], 'KAR': [['238', 'E', 'PHE'], ['249', 'E', 'LYS'], ['255', 'E', 'VAL'], ['256', 'E', 'ARG']]}
-    """
-    from _pyKVFinder import _constitutional
-
-    # Check arguments
-    if type(cavities) not in [numpy.ndarray]:
-        raise TypeError("`cavities` must be a numpy.ndarray.")
-    elif len(cavities.shape) != 3:
-        raise ValueError("`cavities` has the incorrect shape. It must be (nx, ny, nz).")
-    if type(atomic) not in [numpy.ndarray, list]:
-        raise TypeError("`atomic` must be a list or a numpy.ndarray.")
-    elif len(numpy.asarray(atomic).shape) != 2:
-        raise ValueError("`atomic` has incorrect shape. It must be (n, 8).")
-    elif numpy.asarray(atomic).shape[1] != 8:
-        raise ValueError("`atomic` has incorrect shape. It must be (n, 8).")
-    if type(vertices) not in [numpy.ndarray, list]:
-        raise TypeError("`vertices` must be a list or a numpy.ndarray.")
-    elif numpy.asarray(vertices).shape != (4, 3):
-        raise ValueError("`vertices` has incorrect shape. It must be (4, 3).")
-    if type(step) not in [float, int]:
-        raise TypeError("`step` must be a positive real number.")
-    elif step <= 0.0:
-        raise ValueError("`step` must be a positive real number.")
-    if type(probe_in) not in [float, int]:
-        raise TypeError("`probe_in` must be a non-negative real number.")
-    elif probe_in < 0.0:
-        raise ValueError("`probe_in` must be a non-negative real number.")
-    if type(ignore_backbone) not in [bool]:
-        raise TypeError("`ignore_backbone` must be a boolean.")
-    if selection is not None:
-        # Check selection types
-        if all(isinstance(x, int) for x in selection):
-            pass
-        elif all(isinstance(x, str) for x in selection):
-            selection = [_get_cavity_label(sele) for sele in selection]
-        else:
-            raise TypeError(
-                "`selection` must be a list of strings (cavity names) or integers (cavity labels)."
-            )
-        # Check if selection includes valid cavity labels
-        if any(x < 2 for x in selection):
-            raise ValueError(f"Invalid `selection`: {selection}.")
-    if nthreads is None:
-        nthreads = os.cpu_count() - 1
-    else:
-        if type(nthreads) not in [int]:
-            raise TypeError("`nthreads` must be a positive integer.")
-        elif nthreads <= 0:
-            raise ValueError("`nthreads` must be a positive integer.")
-    if type(verbose) not in [bool]:
-        raise TypeError("`verbose` must be a boolean.")
-
-    # Convert types
-    if type(atomic) == list:
-        atomic = numpy.asarray(atomic)
-    if type(vertices) == list:
-        vertices = numpy.asarray(vertices)
-    if type(step) == int:
-        step = float(step)
-    if type(probe_in) == int:
-        probe_in = float(probe_in)
-
-    # Convert numpy.ndarray data types
-    cavities = cavities.astype("int32") if cavities.dtype != "int32" else cavities
-    vertices = vertices.astype("float64") if vertices.dtype != "float64" else vertices
-
-    # Extract atominfo from atomic
-    atominfo = numpy.asarray(
-        ([[f"{atom[0]}_{atom[1]}_{atom[2]}", atom[3]] for atom in atomic[:, :4]])
-    )
-
-    # Extract xyzr from atomic
-    xyzr = atomic[:, 4:].astype(numpy.float64)
-
-    # Get number of cavities
-    ncav = int(cavities.max() - 1)
-
-    # Get sincos: sine and cossine of the grid rotation angles (sina, cosa, sinb, cosb)
-    sincos = _get_sincos(vertices)
-
-    # Select cavities
-    if selection is not None:
-        cavities = _select_cavities(cavities, selection)
-
-    # Unpack vertices
-    P1, P2, P3, P4 = vertices
-
-    # Remove backbone from atominfo
-    if ignore_backbone:
-        mask = numpy.where(
-            (atominfo[:, 1] != "C")
-            & (atominfo[:, 1] != "CA")
-            & (atominfo[:, 1] != "N")
-            & (atominfo[:, 1] != "O")
-        )
-        atominfo = atominfo[
-            mask[0],
-        ]
-        xyzr = xyzr[
-            mask[0],
-        ]
-
-    # Prepare atominfo
-    atominfo = atominfo[:, 0].tolist()
-
-    # Get interface residues
-    # BUG: Segmentation Fault when running it after depth characterization
-    residues = _constitutional(
-        cavities, atominfo, xyzr, P1, sincos, step, probe_in, ncav, nthreads, verbose
-    )
-    residues = _process_residues(residues, ncav, selection)
-
-    return residues
          
-
-
-def _process_hydropathy(
-    raw_avg_hydropathy: numpy.ndarray, ncav: int, selection: Optional[List[int]] = None
-) -> Dict[str, float]:
-    """Processes array of average hydropathy.
-
-    Parameters
-    ----------
-    raw_avg_hydropathy : numpy.ndarray
-        A numpy.ndarray of average hydropathy.
-    ncav : int
-        Number of cavities.
-    selection : List[int], optional
-        A list of integer labels of each cavity to be selected.
-
-    Returns
-    -------
-    avg_hydropathy : Dict[str, float]
-        A dictionary with average hydropathy per detected cavity.
-    """
-    avg_hydropathy = {}
-
-    for index in range(ncav):
-        key = _get_cavity_name(index)
-        avg_hydropathy[key] = float(round(raw_avg_hydropathy[index], 2))
-
-    if selection is not None:
-        # Get keys from selection
-        all_keys = list(avg_hydropathy.keys())
-        keys = [all_keys[sele - 2] for sele in selection]
-
-        # Get average hydropathy of selection
-        avg_hydropathy = {key: avg_hydropathy[key] for key in keys}
-
-    return avg_hydropathy
-
-
-
          [docs]def hydropathy(
-    surface: numpy.ndarray,
-    atomic: Union[numpy.ndarray, List[List[Union[str, float, int]]]],
-    vertices: Union[numpy.ndarray, List[List[float]]],
-    step: Union[float, int] = 0.6,
-    probe_in: Union[float, int] = 1.4,
-    hydrophobicity_scale: Union[str, pathlib.Path] = "EisenbergWeiss",
-    ignore_backbone: bool = False,
-    selection: Optional[Union[List[int], List[str]]] = None,
-    nthreads: Optional[int] = None,
-    verbose: bool = False,
-) -> Tuple[numpy.ndarray, Dict[str, float]]:
-    """Hydropathy characterization of the detected cavities.
-
-    Map a target hydrophobicity scale per surface point and calculate average hydropathy of detected cavities.
-
-    Parameters
-    ----------
-    surface : numpy.ndarray
-        Surface points in the 3D grid (surface[nx][ny][nz]).
-        Surface array has integer labels in each position, that are:
-
-            * -1: bulk points;
-
-            * 0: biomolecule or empty space points;
-
-            * >=2: surface points.
-
-        The empty space points are regions that do not meet the chosen
-        volume cutoff to be considered a cavity.
-    atomic : Union[numpy.ndarray, List[List[Union[str, float, int]]]]
-        A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
-        and radius) for each atom.
-    vertices : Union[numpy.ndarray, List[List[float]]]
-        A numpy.ndarray or a list with xyz vertices coordinates (origin,
-        X-axis, Y-axis, Z-axis).
-    step : Union[float, int], optional
-        Grid spacing (A), by default 0.6.
-    probe_in : Union[float, int], optional
-        Probe In size (A), by default 1.4.
-    hydrophobicity_scale : str, optional
-        Name of a built-in hydrophobicity scale or a path to a
-        TOML-formatted file with a custom hydrophobicity scale, by default
-        `EisenbergWeiss`.
-        The hydrophobicity scale file defines the name of the scale and the
-        hydrophobicity value for each residue and when not defined, it assigns
-        zero to the missing residues (see `Hydrophobicity scale file
-        template`). The package contains six built-in hydrophobicity scales:
-
-            * EisenbergWeiss [1]_;
-            * HessaHeijne [2]_;
-            * KyteDoolittle [3]_;
-            * MoonFleming [4]_; 
-            * WimleyWhite [5]_;
-            * ZhaoLondon [6]_.
-
-    ignore_backbone : bool, optional
-        Whether to ignore backbone atoms (C, CA, N, O) when defining interface
-        residues, by default False.
-    selection : Union[List[int], List[str]], optional
-        A list of integer labels or a list of cavity names to be selected, by default None.
-    nthreads : int, optional
-        Number of threads, by default None. If None, the number of threads is
-        `os.cpu_count() - 1`.
-    verbose : bool, optional
-        Print extra information to standard output, by default False.
-
-    Returns
-    -------
-    scales : numpy.ndarray
-        A numpy.ndarray with hydrophobicity scale value mapped at surface
-        points (scales[nx][ny][nz]).
-    avg_hydropathy : Dict[str, float]
-        A dictionary with average hydropathy for each detected cavity and
-        the range of the hydrophobicity scale (min, max).
-
-    Raises
-    ------
-    TypeError
-        `surface` must be a numpy.ndarray.
-    ValueError
-        `surface` has the incorrect shape. It must be (nx, ny, nz).
-    TypeError
-        `atomic` must be a list or a numpy.ndarray.
-    ValueError
-        `atomic` has incorrect shape. It must be (n, 8).
-    TypeError
-        `vertices` must be a list or a numpy.ndarray.
-    ValueError
-        `vertices` has incorrect shape. It must be (4, 3).
-    TypeError
-        `step` must be a positive real number.
-    ValueError
-        `step` must be a positive real number.
-    TypeError
-        `probe_in` must be a non-negative real number.
-    ValueError
-        `probe_in` must be a non-negative real number.
-    TypeError
-        `hydrophobicity_scale` must be a string or a pathlib.Path.
-    TypeError
-        `ignore_backbone` must be a boolean.
-    TypeError
-        `selection` must be a list of strings (cavity names) or integers (cavity labels).
-    ValueError
-        Invalid `selection`: {selection}.
-    TypeError
-        `nthreads` must be a positive integer.
-    ValueError
-        `nthreads` must be a positive integer.
-    TypeError
-        `verbose` must be a boolean.
-
-    Note
-    ----
-    The cavity nomenclature is based on the integer label. The cavity marked
-    with 2, the first integer corresponding to a cavity, is KAA, the cavity
-    marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
-
-    See Also
-    --------
-    read_pdb
-    read_xyz
-    spatial
-    export
-    write_results
-
-    Example
-    -------
-    With the surface points identified with ``pyKVFinder.spatial`` and atomic coordinates and information read with ``pyKVFinder.read_pdb`` or ``pyKVFinder.read_xyz``, we can perform a hydropathy characterization, that maps a target hydrophobicity scale on surface points and calculate the average hydropathy
-
-    >>> from pyKVFinder import hydropathy
-    >>> scales, avg_hydropathy = hydropathy(surface, atomic, vertices)
-    >>> scales
-    array([[[0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            ...,
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.]],
-          ...,
-          [[0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            ...,
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.]]])
-    >>> avg_hydropathy
-    {'KAA': -0.73, 'KAB': -0.05, 'KAC': -0.07, 'KAD': -0.62, 'KAE': -0.81, 'KAF': -0.14, 'KAG': -0.33, 'KAH': -0.16, 'KAI': -0.4, 'KAJ': 0.62, 'KAK': -0.99, 'KAL': 0.36, 'KAM': -0.33, 'KAN': 0.18, 'KAO': 0.88, 'KAP': -0.96, 'KAQ': 0.48, 'KAR': 0.24, 'EisenbergWeiss': [-1.42, 2.6]}
-
-    However, users may opt to ignore backbones contacts (C, CA, N, O) with the cavity when mapping hydrophobicity scales on surface points. Then, users must set ``ignore_backbone`` flag to ``True``.
-
-    >>> from pyKVFinder import hydropathy
-    >>> scales, avg_hydropathy = hydropathy(surface, atomic, vertices, ignore_backbone=True)
-    >>> scales
-    array([[[0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            ...,
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.]],
-          ...,
-          [[0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            ...,
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.]]])
-    >>> avg_hydropathy
-    {'KAA': -0.7, 'KAB': 0.12, 'KAC': -0.08, 'KAD': -0.56, 'KAE': -0.28, 'KAF': -0.25, 'KAG': -0.28, 'KAH': -0.09, 'KAI': -0.4, 'KAJ': 0.96, 'KAK': -0.87, 'KAL': 0.23, 'KAM': 0.06, 'KAN': -0.1, 'KAO': 0.99, 'KAP': -1.04, 'KAQ': 0.48, 'KAR': -0.84, 'EisenbergWeiss': [-1.42, 2.6]}
-
-    References
-    ----------
-    .. [1] Eisenberg D, Weiss RM, Terwilliger TC. The hydrophobic moment
-       detects periodicity in protein hydrophobicity. Proceedings of the
-       National Academy of Sciences. 1984;81.
-
-    .. [2] Hessa T, Kim H, Bihlmaier K, Lundin C, Boekel J, Andersson H, et al.
-       Recognition of transmembrane helices by the endoplasmic reticulum
-       translocon. Nature. 2005;433.
-
-    .. [3] Kyte J, Doolittle RF. A simple method for displaying the hydropathic
-       character of a protein. Journal of Molecular Biology. 1982;157.
-
-    .. [4] Moon CP, Fleming KG. Side-chain hydrophobicity scale derived from
-       transmembrane protein folding into lipid bilayers. Proceedings of the
-       National Academy of Sciences. 2011;108.
-
-    .. [5] Wimley WC, White SH. Experimentally determined hydrophobicity scale
-       for proteins at membrane interfaces. Nature Structural & Molecular
-       Biology. 1996;3.
-
-    .. [6] Zhao G, London E. An amino acid “transmembrane tendency” scale that
-       approaches the theoretical limit to accuracy for prediction of
-       transmembrane helices: Relationship to biological hydrophobicity.
-       Protein Science. 2006;15.
-    """
-    import toml
-    from _pyKVFinder import _hydropathy
-
-    # Check arguments
-    if type(surface) not in [numpy.ndarray]:
-        raise TypeError("`surface` must be a numpy.ndarray.")
-    elif len(surface.shape) != 3:
-        raise ValueError("`surface` has the incorrect shape. It must be (nx, ny, nz).")
-    if type(atomic) not in [numpy.ndarray, list]:
-        raise TypeError("`atomic` must be a list or a numpy.ndarray.")
-    elif len(numpy.asarray(atomic).shape) != 2:
-        raise ValueError("`atomic` has incorrect shape. It must be (n, 8).")
-    elif numpy.asarray(atomic).shape[1] != 8:
-        raise ValueError("`atomic` has incorrect shape. It must be (n, 8).")
-    if type(vertices) not in [numpy.ndarray, list]:
-        raise TypeError("`vertices` must be a list or a numpy.ndarray.")
-    elif numpy.asarray(vertices).shape != (4, 3):
-        raise ValueError("`vertices` has incorrect shape. It must be (4, 3).")
-    if type(step) not in [float, int]:
-        raise TypeError("`step` must be a positive real number.")
-    elif step <= 0.0:
-        raise ValueError("`step` must be a positive real number.")
-    if type(probe_in) not in [float, int]:
-        raise TypeError("`probe_in` must be a non-negative real number.")
-    elif probe_in < 0.0:
-        raise ValueError("`probe_in` must be a non-negative real number.")
-    if type(hydrophobicity_scale) not in [str, pathlib.Path]:
-        raise TypeError("`hydrophobicity_scale` must be a string or a pathlib.Path.")
-    if type(ignore_backbone) not in [bool]:
-        raise TypeError("`ignore_backbone` must be a boolean.")
-    if selection is not None:
-        # Check selection types
-        if all(isinstance(x, int) for x in selection):
-            pass
-        elif all(isinstance(x, str) for x in selection):
-            selection = [_get_cavity_label(sele) for sele in selection]
-        else:
-            raise TypeError(
-                "`selection` must be a list of strings (cavity names) or integers (cavity labels)."
-            )
-        # Check if selection includes valid cavity labels
-        if any(x < 2 for x in selection):
-            raise ValueError(f"Invalid `selection`: {selection}.")
-    if nthreads is None:
-        nthreads = os.cpu_count() - 1
-    else:
-        if type(nthreads) not in [int]:
-            raise TypeError("`nthreads` must be a positive integer.")
-        elif nthreads <= 0:
-            raise ValueError("`nthreads` must be a positive integer.")
-    if type(verbose) not in [bool]:
-        raise TypeError("`verbose` must be a boolean.")
-
-    # Convert types
-    if type(atomic) == list:
-        atomic = numpy.asarray(atomic)
-    if type(vertices) == list:
-        vertices = numpy.asarray(vertices)
-    if type(step) == int:
-        step = float(step)
-    if type(probe_in) == int:
-        probe_in = float(probe_in)
-
-    # Convert numpy.ndarray data types
-    surface = surface.astype("int32") if surface.dtype != "int32" else surface
-    vertices = vertices.astype("float64") if vertices.dtype != "float64" else vertices
-
-    # Extract atominfo from atomic
-    atominfo = numpy.asarray(
-        ([[f"{atom[0]}_{atom[1]}_{atom[2]}", atom[3]] for atom in atomic[:, :4]])
-    )
-
-    # Extract xyzr from atomic
-    xyzr = atomic[:, 4:].astype(numpy.float64)
-
-    # Get number of cavities
-    ncav = int(surface.max() - 1)
-
-    # Get sincos: sine and cossine of the grid rotation angles (sina, cosa, sinb, cosb)
-    sincos = _get_sincos(vertices)
-
-    # Select cavities
-    if selection is not None:
-        surface = _select_cavities(surface, selection)
-
-    # Get dimensions
-    nx, ny, nz = surface.shape
-    nvoxels = nx * ny * nz
-
-    # Load hydrophobicity scales
-    if hydrophobicity_scale in [
-        "EisenbergWeiss",
-        "HessaHeijne",
-        "KyteDoolittle",
-        "MoonFleming",
-        "WimleyWhite",
-        "ZhaoLondon",
-    ]:
-        hydrophobicity_scale = os.path.join(
-            os.path.abspath(os.path.dirname(__file__)),
-            f"data/{hydrophobicity_scale}.toml",
-        )
-    f = toml.load(hydrophobicity_scale)
-    data, name = list(f.values())[0], list(f.keys())[0]
-    resn, scale = list(data.keys()), numpy.asarray(list(data.values()))
-
-    # Unpack vertices
-    P1, P2, P3, P4 = vertices
-
-    # Remove backbone from atominfo
-    if ignore_backbone:
-        mask = numpy.where(
-            (atominfo[:, 1] != "C")
-            & (atominfo[:, 1] != "CA")
-            & (atominfo[:, 1] != "N")
-            & (atominfo[:, 1] != "O")
-        )
-        atominfo = atominfo[
-            mask[0],
-        ]
-        xyzr = xyzr[
-            mask[0],
-        ]
-
-    # Get residue name from atominfo
-    resname = list(map(lambda x: x.split("_")[2], atominfo[:, 0]))
-
-    # Get hydrophobicity scales in 3D grid and average hydropathy
-    scales, avg_hydropathy = _hydropathy(
-        nvoxels,
-        ncav,
-        surface,
-        xyzr,
-        P1,
-        sincos,
-        resname,
-        resn,
-        scale,
-        step,
-        probe_in,
-        nthreads,
-        verbose,
-    )
-    avg_hydropathy = _process_hydropathy(avg_hydropathy, ncav, selection)
-    avg_hydropathy[f"{name}"] = [float(scale.min()), float(scale.max())]
-
-    return scales.reshape(nx, ny, nz), avg_hydropathy
          
-
-
-def _get_opening_name(index: int) -> str:
-    """Get opening name, eg OAA, OAB, and so on, based on the index.
-
-    Parameters
-    ----------
-    index : int
-        Index in the dictionary.
-
-    Returns
-    -------
-    opening_name : str
-        Opening name
-    """
-    opening_name = f"O{chr(65 + int(index / 26) % 26)}{chr(65 + (index % 26))}"
-    return opening_name
-
-
-def _get_opening_label(opening_name: str) -> int:
-    """Get opening label, eg 2, 3, and so on, based on the opening name.
-
-    Parameters
-    ----------
-    opening_name : str
-        Opening name
-
-    Returns
-    -------
-    copening_label : int
-        Integer label of each opening.
-
-    Raises
-    ------
-    ValueError
-        Invalid opening name: `opening_name`.
-    """
-    # Check opening name
-    if opening_name[0] != "O":
-        raise ValueError(f"Invalid opening name: {opening_name}.")
-
-    # Get cavity label
-    cavity_label = (ord(opening_name[1]) - 65) * 26 + (ord(opening_name[2]) - 65) + 2
-
-    return cavity_label
-
-
-def _process_openings(
-    raw_openings: numpy.ndarray,
-    opening2cavity: numpy.ndarray,
-) -> Dict[str, Dict[str, float]]:
-    """Processes arrays of openings' areas.
-
-    Parameters
-    ----------
-    raw_openings : numpy.ndarray
-        A numpy.ndarray of openings' areas.
-    openings2cavity: numpy.ndarray
-        A numpy.ndarray of openings as indexes and cavities as values.
-
-    Returns
-    -------
-    area : Dict[str, Dict[str,float]]
-        A dictionary with area of each detected opening.
-    """
-    area = {}
-
-    # Get number of openings
-    nopenings = raw_openings.shape[0]
-
-    for index in range(nopenings):
-        # Get opening name
-        opening = _get_opening_name(index)
-
-        # Get cavity name
-        cavity = _get_cavity_name(opening2cavity[index])
-
-        # Save opening area
-        if cavity not in area.keys():
-            area[cavity] = {}
-        area[cavity][opening] = float(round(raw_openings[index], 2))
-
-    # Sort keys
-    area = dict(sorted(area.items()))
-
-    return area
-
-
-
          [docs]def openings(
-    cavities: numpy.ndarray,
-    depths: Optional[numpy.ndarray] = None,
-    step: Union[float, int] = 0.6,
-    openings_cutoff: int = 1,
-    selection: Optional[Union[List[int], List[str]]] = None,
-    nthreads: Optional[int] = None,
-    verbose: bool = False,
-) -> Tuple[int, numpy.ndarray, Dict[str, Dict[str, float]]]:
-    """[WIP] Identify openings of the detected cavities and calculate their areas.
-
-    Parameters
-    ----------
-    cavities : numpy.ndarray
-        Cavity points in the 3D grid (cavities[nx][ny][nz]).
-        Cavities array has integer labels in each position, that are:
-
-            * -1: bulk points;
-
-            * 0: biomolecule points;
-
-            * 1: empty space points;
-
-            * >=2: cavity points.
-    depths : Optional[numpy.ndarray], optional
-        A numpy.ndarray with depth of cavity points (depth[nx][ny][nz]), by default None. If None, depths is calculated from cavities.
-    step : Union[float, int], optional
-        Grid spacing (A), by default 0.6.
-    openings_cutoff : int, optional
-        The minimum number of voxels an opening must have, by default 1.
-    selection : Union[List[int], List[str]], optional
-        A list of integer labels or a list of cavity names to be selected, by default None.
-    nthreads : int, optional
-        Number of threads, by default None. If None, the number of threads is
-        `os.cpu_count() - 1`.
-    verbose : bool, optional
-        Print extra information to standard output, by default False.
-
-    Returns
-    -------
-    nopenings : int
-        Total number of openings.
-    openings : numpy.ndarray
-        Openings points in the 3D grid (openings[nx][ny][nz]).
-        Openings array has integer labels in each position, that are:
-
-            * -1: bulk points;
-
-            * 0: cavity or biomolecule points;
-
-            * 1: empty space points;
-
-            * >=2: Opening points.
-
-        The empty space points are regions that do not meet the chosen
-        openings cutoff to be considered an opening.
-    aopenings : Dict[str, Dict[str,float]]
-        A dictionary with area of each detected opening.
-
-    Raises
-    ------
-    TypeError
-        `cavities` must be a numpy.ndarray.
-    ValueError
-        `cavities` has the incorrect shape. It must be (nx, ny, nz).
-    TypeError
-        `depths` must be a numpy.ndarray.
-    ValueError
-        `depths` has the incorrect shape. It must be (nx, ny, nz).
-    TypeError
-        `step` must be a positive real number.
-    ValueError
-        `step` must be a positive real number.
-    TypeError
-        `openings_cutoff` must be an integer.
-    ValueError
-        `openings_cutoff` must be a positive integer.
-    TypeError
-        `selection` must be a list of strings (cavity names) or integers (cavity labels).
-    ValueError
-        Invalid `selection`: `selection`.
-    TypeError
-        `nthreads` must be a positive integer.
-    ValueError
-        `nthreads` must be a positive integer.
-    TypeError
-        `verbose` must be a boolean
-    
-    Example
-    -------
-    With the cavity points identified with ``detect``, we can characterize their openings, that includes number and area of openings and defining opening points:
-
-    >>> from pyKVFinder import openings
-    >>> nopenings, openings, aopenings = openings(cavities)
-    >>> nopenings
-    16
-    >>> openings
-    array([[[-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            ...,
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1]],
-          ...,
-          [[-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            ...,
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1]]])   
-    >>> aopenings
-    {'KAA': {'OAA': 47.41, 'OAG': 3.6}, 'KAB': {'OAB': 25.84}, 'KAC': {'OAC': 53.62}, 'KAD': {'OAD': 12.59}, 'KAE': {'OAE': 26.3}, 'KAF': {'OAF': 18.46}, 'KAG': {'OAH': 12.83}, 'KAH': {'OAK': 59.96}, 'KAJ': {'OAI': 16.11}, 'KAL': {'OAJ': 17.3}, 'KAM': {'OAL': 35.27}, 'KAO': {'OAM': 8.49}, 'KAP': {'OAN': 13.71}, 'KAQ': {'OAO': 13.16}, 'KAR': {'OAP': 15.36}}
-
-    With the cavity and opening points identified, we can:
-
-    * Export cavity points with opening points mapped on them:
-
-    >>> from pyKVFinder import export
-    >>> export("cavities_with_openings.pdb", cavities, None, vertices, B=openings)
-
-    * Export opening points with same nomenclature from ``aopenings``:
-    
-    >>> from pyKVFinder import export_openings
-    >>> export_openings("openings.pdb", openings, vertices)    
-
-    See Also
-    --------
-    detect
-    depth
-    export
-    export_openings
-    """
-    from _pyKVFinder import _area, _openings, _openings2cavities
-
-    # Check arguments
-    if type(cavities) not in [numpy.ndarray]:
-        raise TypeError("`cavities` must be a numpy.ndarray.")
-    elif len(cavities.shape) != 3:
-        raise ValueError("`cavities` has the incorrect shape. It must be (nx, ny, nz).")
-    if depths is None:
-        depths, _, _ = depth(cavities, step, selection, nthreads, verbose)
-    elif type(depths) not in [numpy.ndarray]:
-        raise TypeError("`depths` must be a numpy.ndarray.")
-    elif len(depths.shape) != 3:
-        raise ValueError("`depths` has the incorrect shape. It must be (nx, ny, nz).")
-    if type(step) not in [float, int]:
-        raise TypeError("`step` must be a positive real number.")
-    elif step <= 0.0:
-        raise ValueError("`step` must be a positive real number.")
-    if type(openings_cutoff) not in [int]:
-        raise TypeError("`openings_cutoff` must be an integer.")
-    elif openings_cutoff < 0:
-        raise ValueError("`openings_cutoff` must be a positive integer.")
-    if selection is not None:
-        # Check selection types
-        if all(isinstance(x, int) for x in selection):
-            pass
-        elif all(isinstance(x, str) for x in selection):
-            selection = [_get_cavity_label(sele) for sele in selection]
-        else:
-            raise TypeError(
-                "`selection` must be a list of strings (cavity names) or integers (cavity labels)."
-            )
-        # Check if selection includes valid cavity labels
-        if any(x < 2 for x in selection):
-            raise ValueError(f"Invalid `selection`: {selection}.")
-    if nthreads is None:
-        nthreads = os.cpu_count() - 1
-    else:
-        if type(nthreads) not in [int]:
-            raise TypeError("`nthreads` must be a positive integer.")
-        elif nthreads <= 0:
-            raise ValueError("`nthreads` must be a positive integer.")
-    if type(verbose) not in [bool]:
-        raise TypeError("`verbose` must be a boolean.")
-
-    # Convert types
-    if type(step) == int:
-        step = float(step)
-
-    # Select cavities
-    if selection is not None:
-        cavities = _select_cavities(cavities, selection)
-
-    # Get number of cavities
-    ncav = int(cavities.max() - 1)
-
-    # Get cavities shape
-    nx, ny, nz = cavities.shape
-
-    # Find openings
-    nopenings, openings = _openings(
-        nx * ny * nz, cavities, depths, ncav, openings_cutoff, step, nthreads, verbose
-    )
-
-    # Reshape openings
-    openings = openings.reshape(nx, ny, nz)
-
-    # Calculate openings areas
-    if verbose:
-        print("> Estimating openings area")
-    aopenings = _area(openings, step, nopenings, nthreads)
-
-    # Find which openings belongs to each cavity
-    opening2cavity = _openings2cavities(nopenings, cavities, openings, nthreads)
-
-    # Process openings
-    aopenings = _process_openings(aopenings, opening2cavity)
-
-    return nopenings, openings, aopenings
          
-
-
-
          [docs]def export(
-    fn: Union[str, pathlib.Path],
-    cavities: Optional[numpy.ndarray],
-    surface: Optional[numpy.ndarray],
-    vertices: Union[numpy.ndarray, List[List[float]]],
-    step: Union[float, int] = 0.6,
-    B: Optional[numpy.ndarray] = None,
-    output_hydropathy: Union[str, pathlib.Path] = "hydropathy.pdb",
-    scales: Optional[numpy.ndarray] = None,
-    selection: Optional[Union[List[int], List[str]]] = None,
-    nthreads: Optional[int] = None,
-    append: bool = False,
-    model: int = 0,
-) -> None:
-    """Export cavitiy (H) and surface (HA) points to PDB-formatted file with
-    a variable (B; optional) in B-factor column, and hydropathy to
-    PDB-formatted file in B-factor column at surface points (HA).
-
-    Parameters
-    ----------
-    fn : Union[str, pathlib.Path]
-        A path to PDB file for writing cavities.
-    cavities : numpy.ndarray, optional
-        Cavity points in the 3D grid (cavities[nx][ny][nz]).
-        Cavities array has integer labels in each position, that are:
-
-            * -1: bulk points;
-
-            * 0: biomolecule points;
-
-            * 1: empty space points;
-
-            * >=2: cavity points.
-
-        The empty space points are regions that do not meet the chosen
-        volume cutoff to be considered a cavity.
-    surface : numpy.ndarray, optional
-        Surface points in the 3D grid (surface[nx][ny][nz]). If None, surface
-        is a numpy.zeros array with same shape of cavities.
-        Surface array has integer labels in each position, that are:
-
-            * -1: bulk points;
-
-            * 0: biomolecule or empty space points;
-
-            * >=2: surface points.
-
-        The empty space points are regions that do not meet the chosen
-        volume cutoff to be considered a cavity.
-    vertices : Union[numpy.ndarray, List[List[float]]]
-        A numpy.ndarray or a list with xyz vertices coordinates (origin,
-        X-axis, Y-axis, Z-axis).
-    step : Union[float, int], optional
-        Grid spacing (A), by default 0.6.
-    B : numpy.ndarray, optional
-        A numpy.ndarray with values to be mapped on B-factor column in cavity
-        points (B[nx][ny][nz]), by default None.
-    output_hydropathy : Union[str, pathlib.Path], optional
-        A path to hydropathy PDB file (surface points mapped with a
-        hydrophobicity scale), by default `hydropathy.pdb`.
-    scales : numpy.ndarray, optional
-        A numpy.ndarray with hydrophobicity scale values to be mapped on
-        B-factor column in surface points (scales[nx][ny][nz]), by default
-        None.
-    selection : Union[List[int], List[str]], optional
-        A list of integer labels or a list of cavity names to be selected, by default None.
-    nthreads : int, optional
-        Number of threads, by default None. If None, the number of threads is
-        `os.cpu_count() - 1`.
-    append : bool, optional
-        Whether to append cavities to the PDB file, by default False.
-    model : int, optional
-        Model number, by default 0.
-
-    Raises
-    ------
-    TypeError
-        `fn` must be a string or pathlib.Path.
-    TypeError
-        `cavities` must be a numpy.ndarray.
-    ValueError
-        `cavities` has the incorrect shape. It must be (nx, ny, nz).
-    TypeError
-        `surface` must be a numpy.ndarray.
-    ValueError
-        `surface` has the incorrect shape. It must be (nx, ny, nz).
-    TypeError
-        `vertices` must be a list or a numpy.ndarray.
-    ValueError
-        `vertices` has incorrect shape. It must be (4, 3).
-    TypeError
-        `step` must be a positive real number.
-    ValueError
-        `step` must be a positive real number.
-    TypeError
-        `B` must be a numpy.ndarray.
-    ValueError
-        `B` has the incorrect shape. It must be (nx, ny, nz).
-    TypeError
-        `output_hydropathy` must be a string.
-    TypeError
-        `scales` must be a numpy.ndarray.
-    ValueError
-        `scales` has the incorrect shape. It must be (nx, ny, nz).
-    TypeError
-        `selection` must be a list of strings (cavity names) or integers (cavity labels).
-    ValueError
-        Invalid `selection`: {selection}.
-    TypeError
-        `nthreads` must be a positive integer.
-    ValueError
-        `nthreads` must be a positive integer.
-    TypeError
-        `append` must be a boolean.
-    TypeError
-        `model` must be a integer.
-    RuntimeError
-        User must define `surface` when not defining `cavities`.
-
-    Note
-    ----
-    The cavity nomenclature is based on the integer label. The cavity marked
-    with 2, the first integer corresponding to a cavity, is KAA, the cavity
-    marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
-    
-    See Also
-    --------
-    detect
-    spatial
-    depth
-    hydropathy
-    write_results
-
-    Example
-    -------
-    With the cavity and surface points identified and depth and hydrophobicity scale mapped in the 3D grid, we can:
-
-    * Export cavity points
-
-    >>> from pyKVFinder import export
-    >>> export('cavity_wo_surface.pdb', cavities, None, vertices)
-
-    * Export cavity and surface points
-
-    >>> export('cavities.pdb', cavities, surface, vertices)
-
-    * Export cavity and surface points with depth mapped on them
-
-    >>> export('cavities_with_depth.pdb', cavities, surface, vertices, B=depths)
-
-    * Export surface points with hydrophobicity_scale mapped on them
-
-    >>> export(None, None, surface, vertices, output_hydropathy='hydropathy.pdb', scales=scales)
-
-    * Export all
-
-    >>> export('cavities.pdb', cavities, surface, vertices, B=depths, output_hydropathy='hydropathy.pdb', scales=scales)
-
-    """
-    from _pyKVFinder import _export, _export_b
-
-    # Check arguments
-    if fn is not None:
-        if type(fn) not in [str, pathlib.Path]:
-            raise TypeError("`fn` must be a string or a pathlib.Path.")
-        os.makedirs(os.path.abspath(os.path.dirname(fn)), exist_ok=True)
-    if cavities is not None:
-        if type(cavities) not in [numpy.ndarray]:
-            raise TypeError("`cavities` must be a numpy.ndarray.")
-        elif len(cavities.shape) != 3:
-            raise ValueError(
-                "`cavities` has the incorrect shape. It must be (nx, ny, nz)."
-            )
-    if surface is not None:
-        if type(surface) not in [numpy.ndarray]:
-            raise TypeError("`surface` must be a numpy.ndarray.")
-        elif len(surface.shape) != 3:
-            raise ValueError(
-                "`surface` has the incorrect shape. It must be (nx, ny, nz)."
-            )
-    if type(vertices) not in [numpy.ndarray, list]:
-        raise TypeError("`vertices` must be a list or a numpy.ndarray.")
-    elif numpy.asarray(vertices).shape != (4, 3):
-        raise ValueError("`vertices` has incorrect shape. It must be (4, 3).")
-    if type(step) not in [float, int]:
-        raise TypeError("`step` must be a positive real number.")
-    elif step <= 0.0:
-        raise ValueError("`step` must be a positive real number.")
-    if B is not None:
-        if type(B) not in [numpy.ndarray]:
-            raise TypeError("`B` must be a numpy.ndarray.")
-        elif len(B.shape) != 3:
-            raise ValueError("`B` has the incorrect shape. It must be (nx, ny, nz).")
-    if output_hydropathy is not None:
-        if type(output_hydropathy) not in [str, pathlib.Path]:
-            raise TypeError("`output_hydropathy` must be a string or a pathlib.Path.")
-        os.makedirs(os.path.abspath(os.path.dirname(output_hydropathy)), exist_ok=True)
-    if scales is not None:
-        if type(scales) not in [numpy.ndarray]:
-            raise TypeError("`scales` must be a numpy.ndarray.")
-        elif len(scales.shape) != 3:
-            raise ValueError(
-                "`scales` has the incorrect shape. It must be (nx, ny, nz)."
-            )
-    if selection is not None:
-        # Check selection types
-        if all(isinstance(x, int) for x in selection):
-            pass
-        elif all(isinstance(x, str) for x in selection):
-            selection = [_get_cavity_label(sele) for sele in selection]
-        else:
-            raise TypeError(
-                "`selection` must be a list of strings (cavity names) or integers (cavity labels)."
-            )
-        # Check if selection includes valid cavity labels
-        if any(x < 2 for x in selection):
-            raise ValueError(f"Invalid `selection`: {selection}.")
-    if nthreads is None:
-        nthreads = os.cpu_count() - 1
-    else:
-        if type(nthreads) not in [int]:
-            raise TypeError("`nthreads` must be a positive integer.")
-        elif nthreads <= 0:
-            raise ValueError("`nthreads` must be a positive integer.")
-    if type(append) not in [bool]:
-        raise TypeError("`append` must be a boolean.")
-    if type(model) not in [int]:
-        raise TypeError("`model` must be a integer.")
-
-    # Convert types
-    if type(vertices) == list:
-        vertices = numpy.asarray(vertices)
-    if type(step) == int:
-        step = float(step)
-
-    # Convert numpy.ndarray data types
-    vertices = vertices.astype("float64") if vertices.dtype != "float64" else vertices
-    if B is not None:
-        B = B.astype("float64") if B.dtype != "float64" else B
-    if scales is not None:
-        scales = scales.astype("float64") if scales.dtype != "float64" else scales
-
-    # Get sincos: sine and cossine of the grid rotation angles (sina, cosa, sinb, cosb)
-    sincos = _get_sincos(vertices)
-
-    # Unpack vertices
-    P1, P2, P3, P4 = vertices
-
-    # If surface is None, create an empty grid
-    if cavities is not None:
-        if surface is None:
-            surface = numpy.zeros(cavities.shape, dtype="int32")
-        else:
-            surface = surface.astype("int32") if surface.dtype != "int32" else surface
-
-    # Select cavities
-    if selection is not None:
-        surface = _select_cavities(surface, selection)
-        if cavities is not None:
-            cavities = _select_cavities(cavities, selection)
-
-    if cavities is None:
-
-        if surface is None:
-            raise RuntimeError(f"User must define `surface` when not defining `cavities`.")
-        else:
-            # Get number of cavities
-            ncav = int(surface.max() - 1)
-
-            # Export hydropathy
-            _export_b(
-                output_hydropathy,
-                surface,
-                surface,
-                scales,
-                P1,
-                sincos,
-                step,
-                ncav,
-                nthreads,
-                append,
-                model,
-            )
-    else:
-        # Check and convert cavities dtype
-        cavities = cavities.astype("int32") if cavities.dtype != "int32" else cavities
-
-        # Get number of cavities
-        ncav = int(cavities.max() - 1)
-
-        # Export cavities
-        if B is None:
-            _export(
-                fn, cavities, surface, P1, sincos, step, ncav, nthreads, append, model
-            )
-        else:
-            _export_b(
-                fn,
-                cavities,
-                surface,
-                B,
-                P1,
-                sincos,
-                step,
-                ncav,
-                nthreads,
-                append,
-                model,
-            )
-
-        # Export hydropathy surface points
-        if scales is None:
-            pass
-        else:
-            _export_b(
-                output_hydropathy,
-                surface,
-                surface,
-                scales,
-                P1,
-                sincos,
-                step,
-                ncav,
-                nthreads,
-                append,
-                model,
-            )
          
-
-
-
          [docs]def export_openings(
-    fn: Union[str, pathlib.Path],
-    openings: numpy.ndarray,
-    vertices: Union[numpy.ndarray, List[List[float]]],
-    step: Union[float, int] = 0.6,
-    selection: Optional[Union[List[int], List[str]]] = None,
-    nthreads: Optional[int] = None,
-    append: bool = False,
-    model: int = 0,
-) -> None:
-    """Export opening points (H) to a PDB-formatted file.
-
-    Parameters
-    ----------
-    fn : Union[str, pathlib.Path]
-        A path to PDB file for writing openings.
-    openings : numpy.ndarray
-        Openings points in the 3D grid (openings[nx][ny][nz]).
-        Openings array has integer labels in each position, that are:
-
-            * -1: bulk points;
-
-            * 0: cavity or biomolecule points;
-
-            * 1: empty space points;
-
-            * >=2: Opening points.
-
-        The empty space points are regions that do not meet the chosen
-        openings cutoff to be considered an opening.
-    vertices : Union[numpy.ndarray, List[List[float]]]
-        A numpy.ndarray or a list with xyz vertices coordinates (origin,
-        X-axis, Y-axis, Z-axis).
-    step : Union[float, int], optional
-        Grid spacing (A), by default 0.6.
-    selection : Union[List[int], List[str]], optional
-        A list of integer labels or a list of opening names to be selected, by default None.
-    nthreads : int, optional
-        Number of threads, by default None. If None, the number of threads is
-        `os.cpu_count() - 1`.
-    append : bool, optional
-        Whether to append openings to the PDB file, by default False.
-    model : int, optional
-        Model number, by default 0.
-
-    Raises
-    ------
-    TypeError
-        `openings` must be a numpy.ndarray.
-    ValueError
-        `openings` has the incorrect shape. It must be (nx, ny, nz).
-    TypeError
-        `vertices` must be a list or a numpy.ndarray.
-    ValueError
-        `vertices` has incorrect shape. It must be (4, 3).
-    TypeError
-        `step` must be a positive real number.
-    ValueError
-        `step` must be a positive real number.
-    TypeError
-        `selection` must be a list of strings (opening names) or integers (opening labels).
-    ValueError
-        Invalid `selection`: {selection}.
-    TypeError
-        `nthreads` must be a positive integer.
-    ValueError
-        `nthreads` must be a positive integer.
-    TypeError
-        `append` must be a boolean.
-    TypeError
-        `model` must be a integer.
-    TypeError
-        `fn` must be a string or pathlib.Path.
-
-    Note
-    ----
-    The opening nomenclature is based on the integer label. The opening marked
-    with 2, the first integer corresponding to a opening, is OAA, the opening
-    marked with 3 is OAB, the opening marked with 4 is OAC and so on.
-
-    See Also
-    --------
-    export
-    detect
-    depths
-    openings
-
-    Example
-    -------
-    With the opening points identified with ``openings``, we can export them to a PDB-formatted file:
-
-    >>> from pyKVFinder import export_openings
-    >>> export_openings('openings.pdb', openings, vertices)
-    """
-    from _pyKVFinder import _export_openings
-
-    # Check arguments
-    if type(openings) not in [numpy.ndarray]:
-        raise TypeError("`openings` must be a numpy.ndarray.")
-    elif len(openings.shape) != 3:
-        raise ValueError("`openings` has the incorrect shape. It must be (nx, ny, nz).")
-    if type(vertices) not in [numpy.ndarray, list]:
-        raise TypeError("`vertices` must be a list or a numpy.ndarray.")
-    elif numpy.asarray(vertices).shape != (4, 3):
-        raise ValueError("`vertices` has incorrect shape. It must be (4, 3).")
-    if type(step) not in [float, int]:
-        raise TypeError("`step` must be a positive real number.")
-    elif step <= 0.0:
-        raise ValueError("`step` must be a positive real number.")
-    if selection is not None:
-        # Check selection types
-        if all(isinstance(x, int) for x in selection):
-            pass
-        elif all(isinstance(x, str) for x in selection):
-            selection = [_get_opening_label(sele) for sele in selection]
-        else:
-            raise TypeError(
-                "`selection` must be a list of strings (cavity names) or integers (cavity labels)."
-            )
-        # Check if selection includes valid cavity labels
-        if any(x < 2 for x in selection):
-            raise ValueError(f"Invalid `selection`: {selection}.")
-    if nthreads is None:
-        nthreads = os.cpu_count() - 1
-    else:
-        if type(nthreads) not in [int]:
-            raise TypeError("`nthreads` must be a positive integer.")
-        elif nthreads <= 0:
-            raise ValueError("`nthreads` must be a positive integer.")
-    if type(append) not in [bool]:
-        raise TypeError("`append` must be a boolean.")
-    if type(model) not in [int]:
-        raise TypeError("`model` must be a integer.")
-
-    # Convert types
-    if type(vertices) == list:
-        vertices = numpy.asarray(vertices)
-    if type(step) == int:
-        step = float(step)
-
-    # Convert numpy.ndarray data types
-    vertices = vertices.astype("float64") if vertices.dtype != "float64" else vertices
-
-    # Get sincos: sine and cossine of the grid rotation angles (sina, cosa, sinb, cosb)
-    sincos = _get_sincos(vertices)
-
-    # Create base directories of results
-    if fn is not None:
-        if type(fn) not in [str, pathlib.Path]:
-            raise TypeError("`fn` must be a string or a pathlib.Path.")
-        os.makedirs(os.path.abspath(os.path.dirname(fn)), exist_ok=True)
-
-    # Unpack vertices
-    P1, _, _, _ = vertices
-
-    # Select cavities
-    if selection is not None:
-        openings = _select_cavities(openings, selection)
-
-    # Get number of openings
-    nopenings = int(openings.max() - 1)
-
-    # Export openings
-    _export_openings(fn, openings, P1, sincos, step, nopenings, nthreads, append, model)
          
-
          
-
-           
          
-          
          
-          
-        
          
-      
          
-    
          
-  
          
-   
-
-
-
\ No newline at end of file
diff --git a/docs/source/_build/html/_modules/pyKVFinder/main.html b/docs/source/_build/html/_modules/pyKVFinder/main.html
deleted file mode 100644
index 019c0edf..00000000
--- a/docs/source/_build/html/_modules/pyKVFinder/main.html
+++ /dev/null
@@ -1,1967 +0,0 @@
-
-
-
-  
-  
-  pyKVFinder.main — pyKVFinder 0.5.0 documentation
-      
-      
-    
-  
-  
-        
-        
-        
-        
-        
-    
-    
-     
-
-
- 
-  
          
-    
-
-    
          
-
-      
          
-        
          
-          
          
-  
-  
          
-
          
-          
          
-           
          
-             
-  
          Source code for pyKVFinder.main
          -import logging
-import os
-import pathlib
-import time
-from datetime import datetime
-from typing import Any, Dict, List, Tuple, Optional, Union
-
-import numpy
-
-from .argparser import argparser
-from .grid import (
-    _get_dimensions,
-    _get_sincos,
-    constitutional,
-    depth,
-    detect,
-    export,
-    get_vertices,
-    get_vertices_from_file,
-    hydropathy,
-    spatial,
-)
-from .utils import (
-    _write_parameters,
-    calculate_frequencies,
-    plot_frequencies,
-    read_pdb,
-    read_vdw,
-    read_xyz,
-    write_results,
-)
-
-__all__ = ["run_workflow", "pyKVFinderResults", "Molecule"]
-
-VDW = os.path.join(os.path.abspath(os.path.dirname(__file__)), "data/vdw.dat")
-
-
-def cli() -> None:
-    """pyKVFinder Command Line Interface (CLI).
-
-    Parameters
-    ----------
-    None
-
-    Returns
-    -------
-    None
-
-    Example
-    -------
-    Usage: pyKVFinder [-h] [-v] [--version] [-b <str>] [-O <str>]
-                      [--nthreads <int>] [-d <str>] [-s <float>] [-i <float>]
-                      [-o <float>] [-V <float>] [-R <float>] [-S <str>]
-                      [--ignore_backbone] [-D] [--plot_frequencies]
-                      [-B <.toml>] [-L (<.pdb> | <.xyz>)] [--ligand_cutoff <float>]
-                      (<.pdb> | <.xyz>)
-    """
-    # Start time
-    start_time = time.time()
-
-    # Load pyKVFinder argument parser
-    parser = argparser()
-
-    # Parse command-line arguments
-    args = parser.parse_args()
-
-    # Get base name from input file if not defined by user
-    if args.base_name is None:
-        args.base_name = os.path.basename(
-            args.input.replace(".pdb", "").replace(".xyz", "")
-        )
-
-    # Create output directory
-    os.makedirs(args.output_directory, exist_ok=True)
-
-    # Print message to stdout
-    print(f"[PID {os.getpid()}] Running pyKVFinder for: {args.input}")
-
-    # Start logging
-    logging.basicConfig(
-        filename=f"{os.path.join(args.output_directory, 'KVFinder.log')}",
-        level=logging.INFO,
-        format="%(message)s",
-    )
-    logging.info("=" * 80)
-    logging.info(
-        f"Date: {datetime.now().strftime('%a %d %B, %Y')}\nTime: {datetime.now().strftime('%H:%M:%S')}\n"
-    )
-    logging.info(f"[ Running pyKVFinder for: {args.input} ]")
-    logging.info(f"> vdW radii file: {args.dictionary}")
-
-    if args.verbose:
-        print("> Loading atomic dictionary file")
-    vdw = read_vdw(args.dictionary)
-
-    if args.verbose:
-        print("> Reading PDB coordinates")
-    if args.input.endswith(".pdb"):
-        atomic = read_pdb(args.input, vdw, args.model)
-    elif args.input.endswith(".xyz"):
-        atomic = read_xyz(args.input, vdw)
-
-    if args.ligand:
-        if args.verbose:
-            print("> Reading ligand coordinates")
-        if args.ligand.endswith(".pdb"):
-            latomic = read_pdb(args.ligand, vdw)
-        elif args.ligand.endswith(".xyz"):
-            latomic = read_xyz(args.ligand, vdw)
-    else:
-        latomic = None
-
-    if args.verbose:
-        print("> Calculating 3D grid dimensions")
-    if args.box:
-        # Get vertices from file
-        args.vertices, atomic = get_vertices_from_file(
-            args.box,
-            atomic,
-            args.step,
-            args.probe_in,
-            args.probe_out,
-            args.nthreads,
-        )
-
-        # Set flag to boolean
-        args.box = True
-    else:
-        # Get vertices from input
-        args.vertices = get_vertices(atomic, args.probe_out, args.step)
-
-        # Set flag to boolean
-        args.box = False
-
-    # Calculate distance between points
-    nx, ny, nz = _get_dimensions(args.vertices, args.step)
-
-    # Calculate sin and cos of angles a and b
-    args.sincos = _get_sincos(args.vertices)
-
-    if args.verbose:
-        print(f"p1: {args.vertices[0]}")
-        print(f"p2: {args.vertices[1]}")
-        print(f"p3: {args.vertices[2]}")
-        print(f"p4: {args.vertices[3]}")
-        print(f"Dimensions: (nx:{nx}, ny:{ny}, nz:{nz})")
-        print(f"sina: {args.sincos[0]:.2f}\tsinb: {args.sincos[2]:.2f}")
-        print(f"cosa: {args.sincos[1]:.2f}\tcosb: {args.sincos[3]:.2f}")
-
-    # Logging parameters
-    logging.info(f"> Step: {args.step} \u00c5")
-    logging.info(f"> Probe In: {args.probe_in} \u00c5")
-    logging.info(f"> Probe Out: {args.probe_out} \u00c5")
-    logging.info(f"> Voxel volume: {args.step * args.step * args.step} \u00c5\u00b3")
-    logging.info(f"> p1: {args.vertices[0]}")
-    logging.info(f"> p2: {args.vertices[1]}")
-    logging.info(f"> p3: {args.vertices[2]}")
-    logging.info(f"> p4: {args.vertices[3]}")
-    logging.info(f"> Dimensions: (nx:{nx}, ny:{ny}, nz:{nz})")
-    logging.info(f"> sina: {args.sincos[0]:.2f}\tcosa: {args.sincos[1]:.2f}")
-    logging.info(f"> sinb: {args.sincos[2]:.2f}\tcosb: {args.sincos[3]:.2f}")
-
-    # Cavity detection
-    ncav, cavities = detect(
-        atomic,
-        args.vertices,
-        args.step,
-        args.probe_in,
-        args.probe_out,
-        args.removal_distance,
-        args.volume_cutoff,
-        latomic,
-        args.ligand_cutoff,
-        args.box,
-        args.surface,
-        args.nthreads,
-        args.verbose,
-    )
-
-    # Cavities were found
-    if ncav > 0:
-        # Spatial characterization
-        surface, volume, area = spatial(
-            cavities, args.step, None, args.nthreads, args.verbose
-        )
-
-        # Constitutional characterization
-        residues = constitutional(
-            cavities,
-            atomic,
-            args.vertices,
-            args.step,
-            args.probe_in,
-            args.ignore_backbone,
-            None,
-            args.nthreads,
-            args.verbose,
-        )
-        frequencies = calculate_frequencies(residues)
-
-        # Depth characterization
-        if args.depth:
-            depths, max_depth, avg_depth = depth(
-                cavities, args.step, None, args.nthreads, args.verbose
-            )
-        else:
-            depths, max_depth, avg_depth = None, None, None
-
-        # Plot bar charts of frequencies
-        if args.plot_frequencies:
-            output_plot = os.path.join(
-                args.output_directory, f"{args.base_name}.barplot.pdf"
-            )
-            plot_frequencies(frequencies, output_plot)
-
-        # Hydropathy characterization
-        if args.hydropathy:
-            # Map hydrophobicity scales
-            scales, avg_hydropathy = hydropathy(
-                surface,
-                atomic,
-                args.vertices,
-                args.step,
-                args.probe_in,
-                args.hydropathy,
-                args.ignore_backbone,
-                None,
-                args.nthreads,
-                args.verbose,
-            )
-            output_hydropathy = os.path.join(
-                args.output_directory,
-                f"{args.base_name}.{list(avg_hydropathy.keys())[-1]}.pdb",
-            )
-        else:
-            scales, avg_hydropathy, output_hydropathy = None, None, None
-
-        # Export cavities
-        output_cavity = os.path.join(
-            args.output_directory, f"{args.base_name}.KVFinder.output.pdb"
-        )
-        export(
-            output_cavity,
-            cavities,
-            surface,
-            args.vertices,
-            args.step,
-            depths,
-            output_hydropathy,
-            scales,
-            None,
-            args.nthreads,
-        )
-
-        # Write results
-        output_results = os.path.join(
-            args.output_directory, f"{args.base_name}.KVFinder.results.toml"
-        )
-        write_results(
-            output_results,
-            args.input,
-            args.ligand,
-            output_cavity,
-            output_hydropathy,
-            volume,
-            area,
-            max_depth,
-            avg_depth,
-            avg_hydropathy,
-            residues,
-            frequencies,
-            args.step,
-        )
-
-        # Write parameters
-        _write_parameters(args)
-    else:
-        print("> No cavities detected!")
-
-    # Elapsed time
-    elapsed_time = time.time() - start_time
-    print(f"[ \033[1mElapsed time:\033[0m {elapsed_time:.4f}s ]")
-    logging.info(f"[ Elapsed time (s): {elapsed_time:.4f}s ]\n")
-
-    return 0
-
-
-
          [docs]class pyKVFinderResults(object):
-    """A class containing pyKVFinder detection and characterization results.
-
-    Parameters
-    ----------
-    cavities : numpy.ndarray
-        Cavity points in the 3D grid (cavities[nx][ny][nz]).
-        Cavities array has integer labels in each position, that are:
-
-            * -1: bulk points;
-
-            * 0: biomolecule points;
-
-            * 1: empty space points;
-
-            * >=2: cavity points.
-
-        The empty space points are regions that do not meet the chosen
-        volume cutoff to be considered a cavity.
-    surface : numpy.ndarray
-        Surface points in the 3D grid (surface[nx][ny][nz]).
-        Surface array has integer labels in each position, that are:
-
-            * -1: bulk points;
-
-            * 0: biomolecule or empty space points;
-
-            * >=2: surface points.
-
-        The empty space points are regions that do not meet the chosen
-        volume cutoff to be considered a cavity.
-    depths : numpy.ndarray, optional
-        A numpy.ndarray with depth of cavity points (depth[nx][ny][nz]).
-    scales : numpy.ndarray, optional
-        A numpy.ndarray with hydrophobicity scale value mapped at surface
-        points (scales[nx][ny][nz]).
-    volume : Dict[str, float]
-        A dictionary with volume of each detected cavity.
-    area : Dict[str, float]
-        A dictionary with area of each detected cavity.
-    max_depth : Dict[str, float], optional
-        A dictionary with maximum depth of each detected cavity.
-    avg_depth : Dict[str, float], optional
-        A dictionary with average depth of each detected cavity.
-    avg_hydropathy : Dict[str, float], optional
-        A dictionary with average hydropathy for each detected cavity and
-        the range of the hydrophobicity scale (min, max).
-    residues: Dict[str, List[List[str]]]
-        A dictionary with a list of interface residues for each detected
-        cavity.
-    frequencies : Dict[str, Dict[str, Dict[str, int]]], optional
-        A dictionary with frequencies of residues and class for
-        residues of each detected cavity.
-    _vertices : numpy.ndarray
-        A numpy.ndarray or a list with xyz vertices coordinates (origin,
-        X-axis, Y-axis, Z-axis).
-    _step : float
-        Grid spacing (A).
-    _input : Union[str, pathlib.Path], optional
-        A path to input PDB or XYZ file, by default None.
-    _ligand : Union[str, pathlib.Path], optional
-        A path to ligand PDB or XYZ file, by default None.
-
-    Attributes
-    ----------
-    cavities : numpy.ndarray
-        Cavity points in the 3D grid (cavities[nx][ny][nz]).
-        Cavities array has integer labels in each position, that are:
-
-            * -1: bulk points;
-
-            * 0: biomolecule points;
-
-            * 1: empty space points;
-
-            * >=2: cavity points.
-
-        The empty space points are regions that do not meet the chosen
-        volume cutoff to be considered a cavity.
-    surface : numpy.ndarray
-        Surface points in the 3D grid (surface[nx][ny][nz]).
-        Surface array has integer labels in each position, that are:
-
-            * -1: bulk points;
-
-            * 0: biomolecule or empty space points;
-
-            * >=2: surface points.
-
-        The empty space points are regions that do not meet the chosen
-        volume cutoff to be considered a cavity.
-    depths : numpy.ndarray, optional
-        A numpy.ndarray with depth of cavity points (depth[nx][ny][nz]).
-    scales : numpy.ndarray, optional
-        A numpy.ndarray with hydrophobicity scale value mapped at surface
-        points (scales[nx][ny][nz]).
-    ncav : int
-        Number of cavities.
-    volume : Dict[str, float]
-        A dictionary with volume of each detected cavity.
-    area : Dict[str, float]
-        A dictionary with area of each detected cavity.
-    max_depth : Dict[str, float], optional
-        A dictionary with maximum depth of each detected cavity.
-    avg_depth : Dict[str, float], optional
-        A dictionary with average depth of each detected cavity.
-    avg_hydropathy : Dict[str, float], optional
-        A dictionary with average hydropathy for each detected cavity and
-        the range of the hydrophobicity scale (min, max).
-    residues: Dict[str, List[List[str]]]
-        A dictionary with a list of interface residues for each detected
-        cavity.
-    frequencies : Dict[str, Dict[str, Dict[str, int]]], optional
-        A dictionary with frequencies of residues and class for
-        residues of each detected cavity.
-    _vertices : numpy.ndarray
-        A numpy.ndarray or a list with xyz vertices coordinates (origin,
-        X-axis, Y-axis, Z-axis).
-    _step : float
-        Grid spacing (A).
-    _input : Union[str, pathlib.Path], optional
-        A path to input PDB or XYZ file, by default None.
-    _ligand : Union[str, pathlib.Path], optional
-        A path to ligand PDB or XYZ file, by default None.
-    """
-
-    def __init__(
-        self,
-        cavities: numpy.ndarray,
-        surface: numpy.ndarray,
-        depths: Optional[numpy.ndarray],
-        scales: Optional[numpy.ndarray],
-        volume: Dict[str, float],
-        area: Dict[str, float],
-        max_depth: Optional[Dict[str, float]],
-        avg_depth: Optional[Dict[str, float]],
-        avg_hydropathy: Optional[Dict[str, float]],
-        residues: Dict[str, List[List[str]]],
-        frequencies: Optional[Dict[str, Dict[str, Dict[str, int]]]],
-        _vertices: numpy.ndarray,
-        _step: Union[float, int],
-        _input: Optional[Union[str, pathlib.Path]] = None,
-        _ligand: Optional[Union[str, pathlib.Path]] = None,
-    ):
-        self.cavities = cavities
-        self.surface = surface
-        self.depths = depths
-        self.scales = scales
-        self.volume = volume
-        self.ncav = cavities.max() - 1
-        self.area = area
-        self.max_depth = max_depth
-        self.avg_depth = avg_depth
-        self.avg_hydropathy = avg_hydropathy
-        self.residues = residues
-        self.frequencies = frequencies
-        self._vertices = _vertices
-        self._step = _step
-        self._input = os.path.abspath(_input)
-        self._ligand = os.path.abspath(_ligand) if _ligand else None
-
-    def __repr__(self):
-        return "<pyKVFinderResults object>"
-
-
          [docs]    def export(
-        self,
-        output: Union[str, pathlib.Path] = "cavity.pdb",
-        output_hydropathy: Union[str, pathlib.Path] = "hydropathy.pdb",
-        nthreads: Optional[int] = None,
-    ) -> None:
-        """Exports cavitiy (H) and surface (HA) points to PDB-formatted file
-        with a variable (B; optional) in B-factor column, and hydropathy to
-        PDB-formatted file in B-factor column at surface points (HA).
-
-        Parameters
-        ----------
-        output : Union[str, pathlib.Path]), optional
-            A path to PDB file for writing cavities, by default `cavity.pdb`.
-        output_hydropathy : Union[str, pathlib.Path], optional
-            A path to PDB file for writing hydropathy at surface points, by
-            default `hydropathy.pdb`.
-        nthreads : int, optional
-            Number of threads, by default None. If None, the number of threads is
-            `os.cpu_count() - 1`.
-
-        Note
-        ----
-        The cavity nomenclature is based on the integer label. The cavity
-        marked with 2, the first integer corresponding to a cavity, is KAA,
-        the cavity marked with 3 is KAB, the cavity marked with 4 is KAC
-        and so on.
-
-        Example
-        -------
-        >>> from pyKVFinder import pyKVFinder
-        >>> import os
-        >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
-        >>> results = pyKVFinder(pdb)
-        >>> results.export()
-        """
-        export(
-            output,
-            self.cavities,
-            self.surface,
-            self._vertices,
-            self._step,
-            self.depths,
-            output_hydropathy,
-            self.scales,
-            None,
-            nthreads,
-        )
          
-
-
          [docs]    def write(
-        self,
-        fn: Union[str, pathlib.Path] = "results.toml",
-        output: Optional[Union[str, pathlib.Path]] = None,
-        output_hydropathy: Optional[Union[str, pathlib.Path]] = None,
-    ) -> None:
-        """
-        Writes file paths and cavity characterization to TOML-formatted file
-
-        Parameters
-        ----------
-        fn : Union[str, pathlib.Path], optional
-            A path to TOML-formatted file for writing file paths and cavity
-            characterization (volume, area, depth and interface residues)
-            per cavity detected, by default `results.toml`.
-        output : Union[str, pathlib.Path], optional
-            A path to a cavity PDB file, by default None.
-        output_hydropathy : Union[str, pathlib.Path], optional
-            A path to PDB file for writing hydropathy at surface points, by
-            default None.
-
-        Note
-        ----
-        The cavity nomenclature is based on the integer label. The cavity
-        marked with 2, the first integer corresponding to a cavity, is KAA,
-        the cavity marked with 3 is KAB, the cavity marked with 4 is KAC
-        and so on.
-
-        Example
-        -------
-        >>> from pyKVFinder import pyKVFinder
-        >>> import os
-        >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
-        >>> results = pyKVFinder(pdb)
-        >>> results.write()
-        """
-        write_results(
-            fn,
-            self._input,
-            self._ligand,
-            output,
-            output_hydropathy,
-            self.volume,
-            self.area,
-            self.max_depth,
-            self.avg_depth,
-            self.avg_hydropathy,
-            self.residues,
-            self.frequencies,
-            self._step,
-        )
          
-
-
          [docs]    def plot_frequencies(self, pdf: Union[str, pathlib.Path] = "barplots.pdf"):
-        """Plot bar charts of frequencies (residues and classes of residues) in
-        a PDF file.
-
-        Parameters
-        ----------
-        pdf : Union[str, pathlib.Path], optional
-            A path to a PDF file, by default `barplots.pdf`.
-
-        Note
-        ----
-        The cavity nomenclature is based on the integer label. The cavity
-        marked with 2, the first integer corresponding to a cavity, is KAA,
-        the cavity marked with 3 is KAB, the cavity marked with 4 is KAC
-        and so on.
-
-        Note
-        ----
-        The classes of residues are:
-
-        * Aliphatic apolar (R1): Alanine, Glycine, Isoleucine, Leucine, Methionine, Valine.
-
-        * Aromatic (R2): Phenylalanine, Tryptophan, Tyrosine.
-
-        * Polar Uncharged (R3): Asparagine, Cysteine, Glutamine, Proline, Serine, Threonine.
-
-        * Negatively charged (R4): Aspartate, Glutamate.
-
-        * Positively charged (R5): Arginine, Histidine, Lysine.
-
-        * Non-standard (RX): Non-standard residues
-
-        Example
-        -------
-        >>> from pyKVFinder import pyKVFinder
-        >>> import os
-        >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
-        >>> results = pyKVFinder(pdb)
-        >>> results.plot_frequencies()
-        """
-        plot_frequencies(self.frequencies, pdf)
          
-
-
          [docs]    def export_all(
-        self,
-        fn: Union[str, pathlib.Path] = "results.toml",
-        output: Union[str, pathlib.Path] = "cavity.pdb",
-        output_hydropathy: Union[str, pathlib.Path] = "hydropathy.pdb",
-        include_frequencies_pdf: bool = False,
-        pdf: Union[str, pathlib.Path] = "barplots.pdf",
-        nthreads: Optional[int] = None,
-    ) -> None:
-        """Exports cavities and characterization to PDB-formatted files,
-        writes file paths and characterization to a TOML-formatted file, and
-        optionally plot bar charts of frequencies (residues and classes of
-        residues) in a PDF file.
-
-        Parameters
-        ----------
-        fn : Union[str, pathlib.Path], optional
-            A path to TOML-formatted file for writing file paths and
-            cavity characterization (volume, area and interface residues)
-            per cavity detected, by default `results.toml`.
-        output : Union[str, pathlib.Path], optional
-            A path to PDB file for writing cavities, by default `cavity.pdb`.
-        output_hydropathy : Union[str, pathlib.Path], optional
-            A path to PDB file for writing hydropathy at surface points,
-            by default `hydropathy.pdb`.
-        include_frequencies_pdf : bool, optional
-            Whether to plot frequencies (residues and classes of residues)
-            to PDF file, by default False.
-        pdf : Union[str, pathlib.Path], optional
-            A path to a PDF file, by default `barplots.pdf`.
-        nthreads : int, optional
-            Number of threads, by default None. If None, the number of threads is
-            `os.cpu_count() - 1`.
-
-        Note
-        ----
-        The cavity nomenclature is based on the integer label. The cavity
-        marked with 2, the first integer corresponding to a cavity, is KAA,
-        the cavity marked with 3 is KAB, the cavity marked with 4 is KAC
-        and so on.
-
-        Note
-        ----
-        The classes of residues are:
-
-        * Aliphatic apolar (R1): Alanine, Glycine, Isoleucine, Leucine, Methionine, Valine.
-
-        * Aromatic (R2): Phenylalanine, Tryptophan, Tyrosine.
-
-        * Polar Uncharged (R3): Asparagine, Cysteine, Glutamine, Proline, Serine, Threonine.
-
-        * Negatively charged (R4): Aspartate, Glutamate.
-
-        * Positively charged (R5): Arginine, Histidine, Lysine.
-
-        * Non-standard (RX): Non-standard residues.
-
-        Example
-        -------
-        >>> from pyKVFinder import pyKVFinder
-        >>> import os
-        >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
-        >>> results = pyKVFinder(pdb)
-        >>> results.export_all()
-
-        Yet, we can set a ``include_frequencies_pdf`` flag to True to plot the bar charts of the frequencies in a PDF file.
-
-        >>> results.export_all(include_frequencies_pdf=True)
-        """
-        # Export cavity PDB file
-        self.export(output, output_hydropathy, nthreads)
-        # Write KVFinder results TOML
-        self.write(fn, output, output_hydropathy)
-        # Plot bar charts of frequencies
-        if include_frequencies_pdf:
-            self.plot_frequencies(pdf)
          
-
-
-
          [docs]def run_workflow(
-    input: Union[str, pathlib.Path],
-    ligand: Optional[Union[str, pathlib.Path]] = None,
-    vdw: Optional[Union[str, pathlib.Path]] = None,
-    box: Optional[Union[str, pathlib.Path]] = None,
-    step: Union[float, int] = 0.6,
-    probe_in: Union[float, int] = 1.4,
-    probe_out: Union[float, int] = 4.0,
-    removal_distance: Union[float, int] = 2.4,
-    volume_cutoff: Union[float, int] = 5.0,
-    ligand_cutoff: Union[float, int] = 5.0,
-    include_depth: bool = False,
-    include_hydropathy: bool = False,
-    hydrophobicity_scale: Union[str, pathlib.Path] = "EisenbergWeiss",
-    surface: str = "SES",
-    ignore_backbone: bool = False,
-    model: Optional[int] = None,
-    nthreads: Optional[int] = None,
-    verbose: bool = False,
-) -> pyKVFinderResults:
-    """Detects and characterizes cavities (volume, area, depth [optional],
-    hydropathy [optional] and interface residues).
-
-    Parameters
-    ----------
-    input : Union[str, pathlib.Path]
-        A path to a target structure file, in PDB or XYZ format, to detect and characterize cavities.
-    ligand : Union[str, pathlib.Path], optional
-        A path to ligand file, in PDB or XYZ format, by default None.
-    vdw : Union[str, pathlib.Path], optional
-        A path to a van der Waals radii file, by default None. If None, apply the built-in van der
-        Waals radii file: `vdw.dat`.
-    box : Union[str, pathlib.Path], optional
-        A path to box configuration file (TOML-formatted), by default None.
-    step : Union[float, int], optional
-        Grid spacing (A), by default 0.6.
-    probe_in : Union[float, int], optional
-        Probe In size (A), by default 1.4.
-    probe_out : Union[float, int], optional
-        Probe Out size (A), by default 4.0.
-    removal_distance : Union[float, int], optional
-        Length to be removed from the cavity-bulk frontier (A), by default 2.4.
-    volume_cutoff : Union[float, int], optional
-        Cavities volume filter (A3), by default 5.0.
-    ligand_cutoff : Union[float, int], optional
-        Radius value to limit a space around a ligand (A), by default 5.0.
-    include_depth : bool, optional
-        Whether to characterize the depth of the detected cavities, by
-        default False.
-    include_hydropathy : bool, optional
-        Whether to characterize the hydropathy of the detected cavities, by
-        default False.
-    hydrophobicity_scale : Union[str, pathlib.Path], optional
-        Name of a built-in hydrophobicity scale (EisenbergWeiss, HessaHeijne,
-        KyteDoolitte, MoonFleming, WimleyWhite, ZhaoLondon) or a path to a
-        TOML-formatted file with a custom hydrophobicity scale, by default
-        `EisenbergWeiss`.
-    surface : str, optional
-        Keywords options are SES (Solvent Excluded Surface) or SAS (Solvent
-        Accessible Surface), by default SES.
-    ignore_backbone : bool, optional
-        Whether to ignore backbone atoms (C, CA, N, O) when defining interface
-        residues, by default False.
-    model : int, optional
-        Model number, by default None. If None, keep atoms from all models.
-    nthreads : int, optional
-        Number of threads, by default None. If None, the number of threads is
-        `os.cpu_count() - 1`.
-    verbose : bool, optional
-        Print extra information to standard output, by default False.
-
-    Returns
-    -------
-    results : pyKVFinderResults
-        A class with the following attributes defined:
-
-            * cavities : numpy.ndarray
-
-                Cavity points in the 3D grid (cavities[nx][ny][nz]).
-                Cavities array has integer labels in each position, that are:
-
-                * -1: bulk points;
-                * 0: biomolecule points;
-                * 1: empty space points;
-                * >=2: cavity points.
-
-                The empty space points are regions that do not meet the chosen
-                volume cutoff to be considered a cavity.
-
-            * surface : numpy.ndarray
-
-                Surface points in the 3D grid (surface[nx][ny][nz]).
-                Surface array has integer labels in each position, that are:
-
-                * -1: bulk points;
-                * 0: biomolecule or empty space points;
-                * >=2: surface points.
-
-                The empty space points are regions that do not meet the chosen
-                volume cutoff to be considered a cavity.
-
-            * depths : numpy.ndarray, optional
-
-                A numpy.ndarray with depth of cavity points (depth[nx][ny][nz]).
-
-            * scales : numpy.ndarray, optional
-
-                A numpy.ndarray with hydrophobicity scale value mapped at surface
-                points (scales[nx][ny][nz]).
-
-            * ncav : int
-
-                Number of cavities.
-
-            * volume : Dict[str, float]
-
-                A dictionary with volume of each detected cavity.
-
-            * area : Dict[str, float]
-
-                A dictionary with area of each detected cavity.
-
-            * max_depth : Dict[str, float], optional
-
-                A dictionary with maximum depth of each detected cavity.
-
-            * avg_depth : Dict[str, float], optional
-
-                A dictionary with average depth of each detected cavity.
-
-            * avg_hydropathy : Dict[str, float], optional
-
-                A dictionary with average hydropathy for each detected cavity and
-                the range of the hydrophobicity scale (min, max).
-
-            * residues: Dict[str, List[List[str]]]
-
-                A dictionary with a list of interface residues for each detected
-                cavity.
-
-            * frequencies : Dict[str, Dict[str, Dict[str, int]]], optional
-
-                A dictionary with frequencies of residues and class for
-                residues of each detected cavity.
-
-            * _vertices : numpy.ndarray
-
-                A numpy.ndarray or a list with xyz vertices coordinates (origin,
-                X-axis, Y-axis, Z-axis).
-
-            * _step : float
-
-                Grid spacing (A).
-
-            * _input : Union[str, pathlib.Path], optional
-
-                A path to input PDB or XYZ file.
-
-            * _ligand : Union[str, pathlib.Path], optional
-
-                A path to ligand PDB or XYZ file.
-
-    Raises
-    ------
-    TypeError
-        `input` must have .pdb or .xyz extension.
-    TypeError
-        `ligand` must have .pdb or .xyz extension.
-
-    Note
-    ----
-    The cavity nomenclature is based on the integer label. The cavity marked
-    with 2, the first integer corresponding to a cavity, is KAA, the cavity
-    marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
-
-    Note
-    ----
-    The classes of residues are:
-
-    * Aliphatic apolar (R1): Alanine, Glycine, Isoleucine, Leucine, Methionine, Valine.
-
-    * Aromatic (R2): Phenylalanine, Tryptophan, Tyrosine.
-
-    * Polar Uncharged (R3): Asparagine, Cysteine, Glutamine, Proline, Serine, Threonine.
-
-    * Negatively charged (R4): Aspartate, Glutamate.
-
-    * Positively charged (R5): Arginine, Histidine, Lysine.
-
-    * Non-standard (RX): Non-standard residues.
-
-    See Also
-    --------
-    pyKVFinderResults
-
-    Example
-    -------
-    The **standard workflow** for cavity detection with spatial (surface points, volume, area) and constitutional (interface residues and their frequencies) characterization  can be run at once with one command:
-
-    >>> import os
-    >>> import pyKVFinder
-    >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
-    >>> results = pyKVFinder.run_workflow(pdb)
-    >>> results
-    <pyKVFinderResults object>
-    >>> results.cavities
-    array([[[-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            ...,
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1]],
-           ...,
-           [[-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            ...,
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
-    >>> results.surface
-    array([[[-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            ...,
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1]],
-           ...,
-           [[-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            ...,
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
-    >>> results.ncav
-    >>> 18
-    >>> results.volume
-    {'KAA': 137.16, 'KAB': 47.52, 'KAC': 66.96, 'KAD': 8.21, 'KAE': 43.63, 'KAF': 12.53, 'KAG': 6.26, 'KAH': 520.13, 'KAI': 12.31, 'KAJ': 26.57, 'KAK': 12.31, 'KAL': 33.91, 'KAM': 23.11, 'KAN': 102.82, 'KAO': 6.05, 'KAP': 15.55, 'KAQ': 7.99, 'KAR': 7.78}
-    >>> results.area
-    {'KAA': 126.41, 'KAB': 62.37, 'KAC': 74.57, 'KAD': 19.06, 'KAE': 57.08, 'KAF': 22.77, 'KAG': 15.38, 'KAH': 496.97, 'KAI': 30.58, 'KAJ': 45.64, 'KAK': 30.58, 'KAL': 45.58, 'KAM': 45.25, 'KAN': 129.77, 'KAO': 12.28, 'KAP': 25.04, 'KAQ': 13.46, 'KAR': 16.6}
-    >>> results.residues
-    {'KAA': [['14', 'E', 'SER'], ['15', 'E', 'VAL'], ['18', 'E', 'PHE'], ['19', 'E', 'LEU'], ['100', 'E', 'PHE'], ['152', 'E', 'LEU'], ['155', 'E', 'GLU'], ['156', 'E', 'TYR'], ['292', 'E', 'LYS'], ['302', 'E', 'TRP'], ['303', 'E', 'ILE'], ['306', 'E', 'TYR']], 'KAB': [['18', 'E', 'PHE'], ['22', 'E', 'ALA'], ['25', 'E', 'ASP'], ['26', 'E', 'PHE'], ['29', 'E', 'LYS'], ['97', 'E', 'ALA'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['156', 'E', 'TYR']], 'KAC': [['141', 'E', 'PRO'], ['142', 'E', 'HIS'], ['144', 'E', 'ARG'], ['145', 'E', 'PHE'], ['148', 'E', 'ALA'], ['299', 'E', 'THR'], ['300', 'E', 'THR'], ['305', 'E', 'ILE'], ['310', 'E', 'VAL'], ['311', 'E', 'GLU'], ['313', 'E', 'PRO']], 'KAD': [['122', 'E', 'TYR'], ['124', 'E', 'ALA'], ['176', 'E', 'GLN'], ['318', 'E', 'PHE'], ['320', 'E', 'GLY'], ['321', 'E', 'PRO'], ['322', 'E', 'GLY'], ['323', 'E', 'ASP']], 'KAE': [['95', 'E', 'LEU'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['100', 'E', 'PHE'], ['103', 'E', 'LEU'], ['104', 'E', 'VAL'], ['105', 'E', 'LYS'], ['106', 'E', 'LEU']], 'KAF': [['123', 'E', 'VAL'], ['124', 'E', 'ALA'], ['175', 'E', 'ASP'], ['176', 'E', 'GLN'], ['181', 'E', 'GLN']], 'KAG': [['34', 'E', 'SER'], ['37', 'E', 'THR'], ['96', 'E', 'GLN'], ['106', 'E', 'LEU'], ['107', 'E', 'GLU'], ['108', 'E', 'PHE'], ['109', 'E', 'SER']], 'KAH': [['49', 'E', 'LEU'], ['50', 'E', 'GLY'], ['51', 'E', 'THR'], ['52', 'E', 'GLY'], ['53', 'E', 'SER'], ['54', 'E', 'PHE'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['72', 'E', 'LYS'], ['74', 'E', 'LEU'], ['84', 'E', 'GLN'], ['87', 'E', 'HIS'], ['88', 'E', 'THR'], ['91', 'E', 'GLU'], ['104', 'E', 'VAL'], ['120', 'E', 'MET'], ['121', 'E', 'GLU'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['166', 'E', 'ASP'], ['168', 'E', 'LYS'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['184', 'E', 'ASP'], ['186', 'E', 'GLY'], ['187', 'E', 'PHE'], ['201', 'E', 'THR'], ['327', 'E', 'PHE']], 'KAI': [['131', 'E', 'HIS'], ['138', 'E', 'PHE'], ['142', 'E', 'HIS'], ['146', 'E', 'TYR'], ['174', 'E', 'ILE'], ['314', 'E', 'PHE']], 'KAJ': [['33', 'E', 'PRO'], ['89', 'E', 'LEU'], ['92', 'E', 'LYS'], ['93', 'E', 'ARG'], ['96', 'E', 'GLN'], ['349', 'E', 'GLU'], ['350', 'E', 'PHE']], 'KAK': [['157', 'E', 'LEU'], ['162', 'E', 'LEU'], ['163', 'E', 'ILE'], ['164', 'E', 'TYR'], ['185', 'E', 'PHE'], ['188', 'E', 'ALA']], 'KAL': [['49', 'E', 'LEU'], ['127', 'E', 'GLU'], ['129', 'E', 'PHE'], ['130', 'E', 'SER'], ['326', 'E', 'ASN'], ['327', 'E', 'PHE'], ['328', 'E', 'ASP'], ['330', 'E', 'TYR']], 'KAM': [['51', 'E', 'THR'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['73', 'E', 'ILE'], ['74', 'E', 'LEU'], ['75', 'E', 'ASP'], ['115', 'E', 'ASN'], ['335', 'E', 'ILE'], ['336', 'E', 'ARG']], 'KAN': [['165', 'E', 'ARG'], ['166', 'E', 'ASP'], ['167', 'E', 'LEU'], ['199', 'E', 'CYS'], ['200', 'E', 'GLY'], ['201', 'E', 'THR'], ['204', 'E', 'TYR'], ['205', 'E', 'LEU'], ['206', 'E', 'ALA'], ['209', 'E', 'ILE'], ['219', 'E', 'VAL'], ['220', 'E', 'ASP'], ['223', 'E', 'ALA']], 'KAO': [['48', 'E', 'THR'], ['51', 'E', 'THR'], ['56', 'E', 'ARG'], ['330', 'E', 'TYR'], ['331', 'E', 'GLU']], 'KAP': [['222', 'E', 'TRP'], ['238', 'E', 'PHE'], ['253', 'E', 'GLY'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['273', 'E', 'LEU']], 'KAQ': [['207', 'E', 'PRO'], ['208', 'E', 'GLU'], ['211', 'E', 'LEU'], ['213', 'E', 'LYS'], ['275', 'E', 'VAL'], ['277', 'E', 'LEU']], 'KAR': [['237', 'E', 'PRO'], ['238', 'E', 'PHE'], ['249', 'E', 'LYS'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['256', 'E', 'ARG']]}
-    >>> results.frequencies
-    {'KAA': {'RESIDUES': {'GLU': 1, 'ILE': 1, 'LEU': 2, 'LYS': 1, 'PHE': 2, 'SER': 1, 'TRP': 1, 'TYR': 2, 'VAL': 1}, 'CLASS': {'R1': 4, 'R2': 5, 'R3': 1, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAB': {'RESIDUES': {'ALA': 2, 'ASN': 1, 'ASP': 1, 'LYS': 1, 'PHE': 2, 'TYR': 1, 'VAL': 1}, 'CLASS': {'R1': 3, 'R2': 3, 'R3': 1, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAC': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'GLU': 1, 'HIS': 1, 'ILE': 1, 'PHE': 1, 'PRO': 2, 'THR': 2, 'VAL': 1}, 'CLASS': {'R1': 5, 'R2': 1, 'R3': 2, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAD': {'RESIDUES': {'ALA': 1, 'ASP': 1, 'GLN': 1, 'GLY': 2, 'PHE': 1, 'PRO': 1, 'TYR': 1}, 'CLASS': {'R1': 4, 'R2': 2, 'R3': 1, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAE': {'RESIDUES': {'ASN': 1, 'LEU': 3, 'LYS': 1, 'PHE': 1, 'VAL': 2}, 'CLASS': {'R1': 5, 'R2': 1, 'R3': 1, 'R4': 0, 'R5': 1, 'RX': 0}}, 'KAF': {'RESIDUES': {'ALA': 1, 'ASP': 1, 'GLN': 2, 'VAL': 1}, 'CLASS': {'R1': 2, 'R2': 0, 'R3': 2, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAG': {'RESIDUES': {'GLN': 1, 'GLU': 1, 'LEU': 1, 'PHE': 1, 'SER': 2, 'THR': 1}, 'CLASS': {'R1': 1, 'R2': 1, 'R3': 4, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAH': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'ASN': 1, 'ASP': 2, 'GLN': 1, 'GLU': 4, 'GLY': 4, 'HIS': 1, 'LEU': 3, 'LYS': 2, 'MET': 1, 'PHE': 3, 'SER': 1, 'THR': 4, 'TYR': 1, 'VAL': 3}, 'CLASS': {'R1': 11, 'R2': 4, 'R3': 8, 'R4': 6, 'R5': 4, 'RX': 0}}, 'KAI': {'RESIDUES': {'HIS': 2, 'ILE': 1, 'PHE': 2, 'TYR': 1}, 'CLASS': {'R1': 1, 'R2': 3, 'R3': 0, 'R4': 0, 'R5': 2, 'RX': 0}}, 'KAJ': {'RESIDUES': {'ARG': 1, 'GLN': 1, 'GLU': 1, 'LEU': 1, 'LYS': 1, 'PHE': 1, 'PRO': 1}, 'CLASS': {'R1': 2, 'R2': 1, 'R3': 1, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAK': {'RESIDUES': {'ALA': 1, 'ILE': 1, 'LEU': 2, 'PHE': 1, 'TYR': 1}, 'CLASS': {'R1': 4, 'R2': 2, 'R3': 0, 'R4': 0, 'R5': 0, 'RX': 0}}, 'KAL': {'RESIDUES': {'ASN': 1, 'ASP': 1, 'GLU': 1, 'LEU': 1, 'PHE': 2, 'SER': 1, 'TYR': 1}, 'CLASS': {'R1': 1, 'R2': 3, 'R3': 2, 'R4': 2, 'R5': 0, 'RX': 0}}, 'KAM': {'RESIDUES': {'ARG': 2, 'ASN': 1, 'ASP': 1, 'GLY': 1, 'ILE': 2, 'LEU': 1, 'THR': 1}, 'CLASS': {'R1': 4, 'R2': 0, 'R3': 2, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAN': {'RESIDUES': {'ALA': 2, 'ARG': 1, 'ASP': 2, 'CYS': 1, 'GLY': 1, 'ILE': 1, 'LEU': 2, 'THR': 1, 'TYR': 1, 'VAL': 1}, 'CLASS': {'R1': 7, 'R2': 1, 'R3': 2, 'R4': 2, 'R5': 1, 'RX': 0}}, 'KAO': {'RESIDUES': {'ARG': 1, 'GLU': 1, 'THR': 2, 'TYR': 1}, 'CLASS': {'R1': 0, 'R2': 1, 'R3': 2, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAP': {'RESIDUES': {'GLY': 1, 'LEU': 1, 'LYS': 1, 'PHE': 1, 'TRP': 1, 'VAL': 1}, 'CLASS': {'R1': 3, 'R2': 2, 'R3': 0, 'R4': 0, 'R5': 1, 'RX': 0}}, 'KAQ': {'RESIDUES': {'GLU': 1, 'LEU': 2, 'LYS': 1, 'PRO': 1, 'VAL': 1}, 'CLASS': {'R1': 4, 'R2': 0, 'R3': 0, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAR': {'RESIDUES': {'ARG': 1, 'LYS': 2, 'PHE': 1, 'PRO': 1, 'VAL': 1}, 'CLASS': {'R1': 2, 'R2': 1, 'R3': 0, 'R4': 0, 'R5': 3, 'RX': 0}}}
-
-    However, users may opt to perform cavity detection in a segmented space through ligand adjustment and/or box adjustment modes.
-
-    The cavity detection can be limited around the target ligand(s), which will be passed to pyKVFinder through a *.pdb* or a *.xyz* files. Thus, the detected cavities are limited within a radius (``ligand_cutoff``) of the target ligand(s).
-
-    >>> ligand = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'ADN.pdb')
-    >>> results = pyKVFinder.run_workflow(pdb, ligand)
-    >>> results
-    <pyKVFinderResults object>
-    >>> results.cavities
-    array([[[-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            ...,
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1]],
-           ...,
-           [[-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            ...,
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
-    >>> results.surface
-    array([[[-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            ...,
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1]],
-           ...,
-           [[-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            ...,
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
-    >>> results.ncav
-    >>> 18
-    >>> results.volume
-    {'KAA': 365.04, 'KAB': 16.85}
-    >>> results.area
-    {'KAA': 328.79, 'KAB': 23.15}
-    >>> results.residues
-    {'KAA': [['49', 'E', 'LEU'], ['50', 'E', 'GLY'], ['51', 'E', 'THR'], ['52', 'E', 'GLY'], ['53', 'E', 'SER'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['72', 'E', 'LYS'], ['104', 'E', 'VAL'], ['120', 'E', 'MET'], ['121', 'E', 'GLU'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['166', 'E', 'ASP'], ['168', 'E', 'LYS'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['184', 'E', 'ASP'], ['327', 'E', 'PHE']], 'KAB': [['49', 'E', 'LEU'], ['127', 'E', 'GLU'], ['130', 'E', 'SER'], ['326', 'E', 'ASN'], ['327', 'E', 'PHE'], ['328', 'E', 'ASP'], ['330', 'E', 'TYR']]}
-    >>> results.frequencies
-    {'KAA': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'ASN': 1, 'ASP': 2, 'GLU': 3, 'GLY': 3, 'LEU': 2, 'LYS': 2, 'MET': 1, 'PHE': 1, 'SER': 1, 'THR': 2, 'TYR': 1, 'VAL': 3}, 'CLASS': {'R1': 9, 'R2': 2, 'R3': 5, 'R4': 5, 'R5': 3, 'RX': 0}}, 'KAB': {'RESIDUES': {'ASN': 1, 'ASP': 1, 'GLU': 1, 'LEU': 1, 'PHE': 1, 'SER': 1, 'TYR': 1}, 'CLASS': {'R1': 1, 'R2': 2, 'R3': 2, 'R4': 2, 'R5': 0, 'RX': 0}}}
-
-    Further, we can also perform cavity detection on a custom 3D grid, where we can explore closed regions with a custom box, which can be defined by a *.toml* file (see `Box configuration file template`).
-
-    >>> fn = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'custom-box.toml')
-    >>> with open(fn, 'r') as f:
-    ...     print(f.read())
-    [box]
-    p1 = [3.11, 7.34, 1.59]
-    p2 = [11.51, 7.34, 1.59]
-    p3 = [3.11, 10.74, 1.59]
-    p4 = [3.11, 7.34, 6.19]
-    >>> results = pyKVFinder.run_workflow(pdb, box=fn)
-    >>> results
-    <pyKVFinderResults object>
-    >>> results.cavities
-    array([[[-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            ...,
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1]],
-           ...,
-           [[-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            ...,
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
-    >>> results.surface
-    array([[[-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            ...,
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1]],
-           ...,
-           [[-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            ...,
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1],
-            [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
-    >>> results.ncav
-    >>> 1
-    >>> results.volume
-    {'KAA': 115.78}
-    >>> results.area
-    {'KAA': 33.91}
-    >>> results.residues
-    {'KAA': [['49', 'E', 'LEU'], ['50', 'E', 'GLY'], ['51', 'E', 'THR'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['104', 'E', 'VAL'], ['121', 'E', 'GLU'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['327', 'E', 'PHE']]}
-    >>> results.frequencies
-    {'KAA': {'RESIDUES': {'ALA': 1, 'ASN': 1, 'GLU': 3, 'GLY': 1, 'LEU': 2, 'PHE': 1, 'THR': 2, 'TYR': 1, 'VAL': 3}, 'CLASS': {'R1': 7, 'R2': 2, 'R3': 3, 'R4': 3, 'R5': 0, 'RX': 0}}}
-
-    However, users may opt to perform the **full workflow** for cavity detection with spatial (surface points, volume and area), constitutional (interface residues and their frequencies), hydropathy and depth characterization. This full workflow can be run with one command by setting some parameters of ``run_workflow`` function:
-
-    >>> results = pyKVFinder.run_workflow(pdb, include_depth=True, include_hydropathy=True, hydrophobicity_scale='EisenbergWeiss')
-    >>> results.depths
-    array([[[0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            ...,
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.]],
-           ...,
-           [[0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            ...,
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.]]])
-    >>> results.scales
-    array([[[0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            ...,
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.]],
-           ...,
-           [[0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            ...,
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.],
-            [0., 0., 0., ..., 0., 0., 0.]]])
-    >>> results.avg_depth
-    {'KAA': 1.35, 'KAB': 0.91, 'KAC': 0.68, 'KAD': 0.32, 'KAE': 0.99, 'KAF': 0.24, 'KAG': 0.1, 'KAH': 3.91, 'KAI': 0.0, 'KAJ': 0.96, 'KAK': 0.0, 'KAL': 1.07, 'KAM': 0.24, 'KAN': 0.0, 'KAO': 0.29, 'KAP': 0.7, 'KAQ': 0.22, 'KAR': 0.12}
-    >>> results.max_depth
-    {'KAA': 3.79, 'KAB': 2.68, 'KAC': 2.62, 'KAD': 0.85, 'KAE': 3.0, 'KAF': 0.85, 'KAG': 0.6, 'KAH': 10.73, 'KAI': 0.0, 'KAJ': 2.24, 'KAK': 0.0, 'KAL': 3.0, 'KAM': 1.2, 'KAN': 0.0, 'KAO': 1.04, 'KAP': 2.08, 'KAQ': 0.85, 'KAR': 0.6}
-    >>> results.avg_hydropathy
-    {'KAA': -0.73, 'KAB': -0.05, 'KAC': -0.07, 'KAD': -0.62, 'KAE': -0.81, 'KAF': -0.14, 'KAG': -0.33, 'KAH': -0.17, 'KAI': -0.4, 'KAJ': 0.62, 'KAK': -0.99, 'KAL': 0.36, 'KAM': -0.33, 'KAN': 0.18, 'KAO': 0.88, 'KAP': -0.96, 'KAQ': 0.48, 'KAR': 0.24, 'EisenbergWeiss': [-1.42, 2.6]}
-    """
-    if verbose:
-        print("> Loading atomic dictionary file")
-    if vdw is not None:
-        vdw = read_vdw(vdw)
-    else:
-        vdw = read_vdw(VDW)
-
-    if verbose:
-        print("> Reading PDB coordinates")
-    if input.endswith(".pdb"):
-        atomic = read_pdb(input, vdw, model)
-    elif input.endswith(".xyz"):
-        atomic = read_xyz(input, vdw)
-    else:
-        raise TypeError("`target` must have .pdb or .xyz extension.")
-
-    if ligand:
-        if verbose:
-            print("> Reading ligand coordinates")
-        if ligand.endswith(".pdb"):
-            latomic = read_pdb(ligand, vdw)
-        elif ligand.endswith(".xyz"):
-            latomic = read_xyz(ligand, vdw)
-        else:
-            raise TypeError("`ligand` must have .pdb or .xyz extension.")
-    else:
-        latomic = None
-
-    if verbose:
-        print("> Calculating 3D grid dimensions")
-    if box:
-        # Get vertices from file
-        vertices, atomic = get_vertices_from_file(
-            box, atomic, step, probe_in, probe_out, nthreads
-        )
-
-        # Set flag to boolean
-        box = True
-    else:
-        # Get vertices from input
-        vertices = get_vertices(atomic, probe_out, step)
-
-        # Set flag to boolean
-        box = False
-
-    # Calculate distance between points
-    nx, ny, nz = _get_dimensions(vertices, step)
-    if verbose:
-        print(f"Dimensions: (nx:{nx}, ny:{ny}, nz:{nz})")
-
-    # Calculate sin and cos of angles a and b
-    sincos = _get_sincos(vertices)
-    if verbose:
-        print(f"sina: {sincos[0]:.2f}\tsinb: {sincos[2]:.2f}")
-        print(f"cosa: {sincos[1]:.2f}\tcosb: {sincos[3]:.2f}")
-
-    # Cavity detection
-    ncav, cavities = detect(
-        atomic,
-        vertices,
-        step,
-        probe_in,
-        probe_out,
-        removal_distance,
-        volume_cutoff,
-        latomic,
-        ligand_cutoff,
-        box,
-        surface,
-        nthreads,
-        verbose,
-    )
-
-    if ncav > 0:
-        # Spatial characterization
-        surface, volume, area = spatial(cavities, step, None, nthreads, verbose)
-
-        # Constitutional characterization
-        residues = constitutional(
-            cavities,
-            atomic,
-            vertices,
-            step,
-            probe_in,
-            ignore_backbone,
-            None,
-            nthreads,
-            verbose,
-        )
-        frequencies = calculate_frequencies(residues)
-
-        # Depth characterization
-        if include_depth:
-            depths, max_depth, avg_depth = depth(
-                cavities, step, None, nthreads, verbose
-            )
-        else:
-            depths, max_depth, avg_depth = None, None, None
-
-        # Hydropathy hydrophobicity scales
-        if include_hydropathy:
-            scales, avg_hydropathy = hydropathy(
-                surface,
-                atomic,
-                vertices,
-                step,
-                probe_in,
-                hydrophobicity_scale,
-                ignore_backbone,
-                None,
-                nthreads,
-                verbose,
-            )
-        else:
-            scales, avg_hydropathy = None, None
-    else:
-        print("Warning: No cavities detected, returning None!")
-        return None
-
-    # Return dict
-    results = pyKVFinderResults(
-        cavities,
-        surface,
-        depths,
-        scales,
-        volume,
-        area,
-        max_depth,
-        avg_depth,
-        avg_hydropathy,
-        residues,
-        frequencies,
-        vertices,
-        step,
-        input,
-        ligand,
-    )
-
-    return results
          
-
-
-
          [docs]class Molecule(object):
-    """A class for representing molecular structures.
-
-    Parameters
-    ----------
-    molecule : Union[str, pathlib.Path]
-        A file path to the molecule in either PDB or XYZ format
-    radii : Union[str, pathlib.Path, Dict[str, Any]], optional
-        A file path to a van der Waals radii file or a dictionary of VDW radii, by default None. If None, apply the built-in van der Waals radii file: `vdw.dat`.
-    model : int, optional
-        The model number of a multi-model PDB file, by default None. If None, keep atoms from all models.
-    nthreads : int, optional
-        Number of threads, by default None. If None, the number of threads is `os.cpu_count() - 1`.
-    verbose : bool, optional
-        Print extra information to standard output, by default False.
-
-    Attributes
-    ----------
-    _atomic : numpy.ndarray
-        A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates and radius) for each atom.
-    _dim : tuple
-        Grid dimensions.
-    _grid : numpy.ndarray
-        Molecule points in the 3D grid (grid[nx][ny][nz]).
-        Grid array has integer labels in each position, that are:
-
-            * 0: molecule points;
-
-            * 1: solvent points.
-    _molecule : Union[str, pathlib.Path]
-        A file path to the molecule in either PDB or XYZ format.
-    _padding : float
-        The length to add to each direction of the 3D grid.
-    _probe : float
-        Spherical probe size to define the molecular surface based on a molecular representation.
-    _radii : Dict[str, Any]
-        A dictionary containing radii values, by default None.
-    _representation : str, optional
-        Molecular surface representation. Keywords options are vdW (van der Waals surface), SES (Solvent Excluded Surface) or SAS (Solvent Accessible Surface), by default SES.
-    _rotation : numpy.ndarray
-        A numpy.ndarray with sine and cossine of the grid rotation angles (sina, cosa, sinb, cosb).
-    _step : float
-        Grid spacing (A).
-    _vertices : numpy.ndarray
-        A numpy.ndarray or a list with xyz vertices coordinates (origin, X-axis, Y-axis, Z-axis).
-    nthreads : int
-        Number of threads for parallel processing.
-    verbose : bool
-        Whether to print extra information to standard output.
-
-    Note
-    ----
-    The van der Waals radii file defines the radius values for each atom by residue and when not defined, it uses a generic value based on the atom type. The function by default loads the built-in van der Waals radii file: ``vdw.dat``.
-
-    See Also
-    --------
-    read_vdw
-
-    Example
-    -------
-    The ``Molecule`` class loads the target molecular structure (ClO4) into pyKVFinder. class.
-
-    >>> import os
-    >>> from pyKVFinder import Molecule
-    >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'ClO4.pdb')
-    >>> molecule = Molecule(pdb)
-    >>> molecule
-    >>> <pyKVFinder.main.Molecule object at 0x7f5ddacf2230>
-
-    The van der Waals radii can be define by:
-
-        * creating a Python dictionary:
-
-        >>> # PyMOL (v2.5.0) vdW radii values
-        >>> vdw = {'GEN': {'CL': 1.75, 'O': 1.52}}
-        >>> molecule = Molecule(pdb, radii=vdw)
-        >>> molecule.radii
-        {'GEN': {'CL': 1.75, 'O': 1.52}}
-
-        * specifying a *.dat* file following template of `van der Waals radii file`.
-
-        >>> from pyKVFinder import read_vdw
-        >>> # ChimeraX vdW radii values
-        >>> with open('vdw.dat', 'w') as f:
-        ...     f.write('>GEN\\nCL\\t\\t1.98\\nO\\t\\t1.46\\n')
-        >>> vdw = read_vdw('vdw.dat')
-        >>> molecule = Molecule(pdb, radii=vdw)
-        >>> molecule.radii
-        {'GEN': {'CL': 1.98, 'O': 1.46}}
-    """
-
-    def __init__(
-        self,
-        molecule: Union[str, pathlib.Path],
-        radii: Union[str, pathlib.Path, Dict[str, Any]] = None,
-        model: Optional[int] = None,
-        nthreads: Optional[int] = None,
-        verbose: bool = False,
-    ):
-        """Initialize the Molecule object with molecule, radii, model, nthreads and verbose.
-
-        Parameters
-        ----------
-        molecule : Union[str, pathlib.Path]
-            A file path to the molecule in either PDB or XYZ format.
-        radii : Union[str, pathlib.Path, Dict[str, Any]], optional
-            A file path to a van der Waals radii file or a dictionary of VDW radii, by default None. If None, apply the built-in van der Waals radii file: `vdw.dat`.
-        model : int, optional
-            The model number of a multi-model PDB file, by default None. If None, keep atoms from all models.
-        nthreads : int, optional
-            Number of threads, by default None. If None, the number of threads is `os.cpu_count() - 1`.
-        verbose : bool, optional
-            Print extra information to standard output, by default False.
-
-        Raises
-        ------
-        TypeError
-            `molecule` must be a string or a pathlib.Path.
-        TypeError
-            `molecule` must have .pdb or .xyz extension.
-        TypeError
-            `nthreads` must be a positive integer.
-        ValueError
-            `nthreads` must be a positive integer.
-        """
-
-        # Attributes
-        self._grid = None
-        self._step = None
-        self._padding = None
-        self._probe = None
-        self._representation = None
-        self._vertices = None
-        self._dim = None
-        self._rotation = None
-        self.verbose = verbose
-
-        # Molecule
-        if type(molecule) not in [str, pathlib.Path]:
-            raise TypeError("`molecule` must be a string or a pathlib.Path.")
-        self._molecule = os.path.realpath(molecule)
-
-        # van der Waals radii
-        if self.verbose:
-            print("> Loading van der Waals radii")
-        if radii is None:
-            # default
-            self._radii = read_vdw(VDW)
-        elif type(radii) in [str, pathlib.Path]:
-            # vdw file
-            self._radii = read_vdw(radii)
-        elif type(radii) in [dict]:
-            # Processed dictionary
-            self._radii = radii
-
-        # Atomic information
-        if self.verbose:
-            print("> Reading molecule coordinates")
-        if molecule.endswith(".pdb"):
-            self._atomic = read_pdb(molecule, self.radii, model)
-        elif molecule.endswith(".xyz"):
-            self._atomic = read_xyz(molecule, self.radii)
-        else:
-            raise TypeError("`molecule` must have .pdb or .xyz extension.")
-
-        # Number of threads
-        if nthreads is not None:
-            if type(nthreads) not in [int]:
-                raise TypeError("`nthreads` must be a positive integer.")
-            elif nthreads <= 0:
-                raise ValueError("`nthreads` must be a positive integer.")
-            else:
-                self.nthreads = nthreads
-        else:
-            self.nthreads = os.cpu_count() - 1
-
-    @property
-    def atomic(self) -> numpy.ndarray:
-        """Get _atomic attribute."""
-        return self._atomic
-
-    @property
-    def dim(self) -> Tuple[int, int, int]:
-        """Get _dim attribute"""
-        return self._dim
-
-    @property
-    def grid(self) -> numpy.ndarray:
-        """Get _grid attribute."""
-        return self._grid
-
-    @property
-    def molecule(self) -> Union[str, pathlib.Path]:
-        """Get _molecule attribute."""
-        return self._molecule
-
-    @property
-    def nx(self) -> int:
-        """Get grid units in X-axis."""
-        if self._dim is not None:
-            return self._dim[0]
-
-    @property
-    def ny(self) -> int:
-        """Get grid units in Y-axis."""
-        if self._dim is not None:
-            return self._dim[1]
-
-    @property
-    def nz(self) -> int:
-        """Get grid units in Z-axis."""
-        if self._dim is not None:
-            return self._dim[2]
-
-    @property
-    def p1(self) -> numpy.ndarray:
-        """Get origin of the 3D grid."""
-        if self._vertices is not None:
-            return self._vertices[0]
-
-    @property
-    def p2(self) -> numpy.ndarray:
-        """Get X-axis max of the 3D grid."""
-        if self._vertices is not None:
-            return self._vertices[1]
-
-    @property
-    def p3(self) -> numpy.ndarray:
-        """Get Y-axis max of the 3D grid."""
-        if self._vertices is not None:
-            return self._vertices[2]
-
-    @property
-    def p4(self) -> numpy.ndarray:
-        """Get Z-axis max of the 3D grid."""
-        if self._vertices is not None:
-            return self._vertices[3]
-
-    @property
-    def padding(self) -> float:
-        """Get _padding attribute."""
-        return self._padding
-
-    @property
-    def probe(self) -> float:
-        """Get _probe attribute."""
-        return self._probe
-
-    @property
-    def radii(self) -> Dict[str, Any]:
-        """Get _radii attribute."""
-        return self._radii
-
-    @property
-    def representation(self) -> str:
-        """Get _representation attribute."""
-        return self._representation
-
-    @property
-    def rotation(self) -> numpy.ndarray:
-        """Get _rotation attribute."""
-        return self._rotation
-
-    @property
-    def step(self) -> float:
-        """Get _step attribute."""
-        if self._step is not None:
-            return self._step
-
-    @property
-    def vertices(self) -> numpy.ndarray:
-        """Get _vertices attribute."""
-        return self._vertices
-
-    @property
-    def xyzr(self) -> numpy.ndarray:
-        """Get xyz coordinates and radius of molecule atoms."""
-        return self._atomic[:, 4:].astype(numpy.float64)
-
-    def _set_grid(self, padding: Optional[float] = None) -> None:
-        """Define the 3D grid for the target molecule.
-
-        Parameters
-        ----------
-        padding : float, optional
-            The length to add to each direction of the 3D grid, by default None. If None, automatically define the length based on molecule coordinates, probe size, grid spacing and atom radii.
-
-        Raises
-        ------
-        TypeError
-            `padding` must be a non-negative real number.
-        ValueError
-            `padding` must be a non-negative real number.
-        """
-        # Padding
-        if padding is not None:
-            if type(padding) not in [int, float]:
-                raise TypeError("`padding` must be a non-negative real number.")
-            elif padding < 0.0:
-                raise ValueError("`padding` must be a non-negative real number.")
-            else:
-                self._padding = padding
-        else:
-            self._padding = self._get_padding()
-
-        # 3D grid
-        if self.verbose:
-            print("> Calculating 3D grid")
-        self._vertices = get_vertices(self.atomic, self.padding, self.step)
-        self._dim = _get_dimensions(self.vertices, self.step)
-        self._rotation = _get_sincos(self.vertices)
-        if self.verbose:
-            print(f"p1: {self.vertices[0]}")
-            print(f"p2: {self.vertices[1]}")
-            print(f"p3: {self.vertices[2]}")
-            print(f"p4: {self.vertices[3]}")
-            print("nx: {}, ny: {}, nz: {}".format(*self.dim))
-            print("sina: {}, sinb: {}, cosa: {}, cosb: {}".format(*self.rotation))
-
-    def _get_padding(self) -> float:
-        """Automatically define the padding based on molecule coordinates, probe size, grid spacing and atom radii.
-
-        Returns
-        -------
-        padding : float
-            The length to add to each direction of the 3D grid.
-        """
-        padding = 1.1 * self.xyzr[:, 3].max()
-        if self.representation in ["SES", "SAS"]:
-            padding += self._probe
-        return float(padding.round(decimals=1))
-
-
          [docs]    def vdw(self, step: float = 0.6, padding: Optional[float] = None) -> None:
-        """Fill the 3D grid with the molecule as the van der Waals surface representation.
-
-        Parameters
-        ----------
-        step : float, optional
-            Grid spacing (A), by default 0.6.
-        padding : float, optional
-            The length to add to each direction of the 3D grid, by default None. If None, automatically define the length based on molecule coordinates, probe size, grid spacing and atom radii.
-
-        Raises
-        ------
-        TypeError
-            `step` must be a positive real number.
-        ValueError
-            `step` must be a positive real number.
-
-        Example
-        -------
-        The ``Molecule.vdw()`` method takes a grid spacing and returns a NumPy array with the molecule points representing the vdW surface in the 3D grid.
-
-        >>> # Grid Spacing (step): 0.1
-        >>> step = 0.1
-        >>> molecule.vdw(step=step)
-        >>> molecule.grid
-        array([[[1, 1, 1, ..., 1, 1, 1],
-                [1, 1, 1, ..., 1, 1, 1],
-                [1, 1, 1, ..., 1, 1, 1],
-                ...,
-                [1, 1, 1, ..., 1, 1, 1],
-                [1, 1, 1, ..., 1, 1, 1],
-                [1, 1, 1, ..., 1, 1, 1]],
-               ...,
-               [[1, 1, 1, ..., 1, 1, 1],
-                [1, 1, 1, ..., 1, 1, 1],
-                [1, 1, 1, ..., 1, 1, 1],
-                ...,
-                [1, 1, 1, ..., 1, 1, 1],
-                [1, 1, 1, ..., 1, 1, 1],
-                [1, 1, 1, ..., 1, 1, 1]]], dtype=int32)
-        """
-        from _pyKVFinder import _fill_receptor
-
-        # Check arguments
-        if type(step) not in [int, float]:
-            raise TypeError("`step` must be a postive real number.")
-        elif step <= 0.0:
-            raise ValueError("`step` must be a positive real number.")
-        else:
-            self._step = step
-
-        # Attributes
-        self._representation = "vdW"
-        self._probe = None
-
-        # Define 3D grid
-        self._set_grid(padding)
-
-        # van der Waals atoms (hard sphere model) to grid
-        if self.verbose:
-            print("> Inserting atoms with van der Waals radii into 3D grid")
-        self._grid = _fill_receptor(
-            self.nx * self.ny * self.nz,
-            self.nx,
-            self.ny,
-            self.nz,
-            self.xyzr,
-            self.p1,
-            self.rotation,
-            self.step,
-            0.0,
-            False,
-            self.nthreads,
-            self.verbose,
-        ).reshape(self.nx, self.ny, self.nz)
          
-
-
          [docs]    def surface(
-        self,
-        step: float = 0.6,
-        probe: float = 1.4,
-        surface: str = "SES",
-        padding: Optional[float] = None,
-    ) -> None:
-        """Fill the 3D grid with the molecule as the van der Waals surface representation.
-
-        Parameters
-        ----------
-        step : float, optional
-            Grid spacing (A), by default 0.6.
-        probe : float, optional
-            Spherical probe size to define the molecular surface based on a molecular representation, by default 1.4.
-        surface : str, optional
-            Molecular surface representation. Keywords options are vdW (van der Waals surface), SES (Solvent Excluded Surface) or SAS (Solvent Accessible Surface), by default "SES".
-        padding : float, optional
-            The length to add to each direction of the 3D grid, by default None. If None, automatically define the length based on molecule coordinates, probe size, grid spacing and atom radii.
-
-        Raises
-        ------
-        TypeError
-            `step` must be a positive real number.
-        ValueError
-            `step` must be a positive real number.
-        TypeError
-            `probe_out` must be a positive real number.
-        ValueError
-            `probe_out` must be a positive real number.
-
-        Example
-        -------
-        The ``Molecule.surface()`` method takes the grid spacing, the spherical probe size to model the surface, the surface representation and returns a NumPy array with the molecule points representing the SES in the 3D grid.
-
-        The molecular surface can be modelled as:
-
-            * Solvent Excluded Surface (SES):
-
-            >>> # Surface Representation: SES
-            >>> surface = 'SES'
-            >>> # Grid Spacing (step): 0.1
-            >>> step = 0.1
-            >>> # Spherical Probe (probe): 1.4
-            >>> probe = 1.4
-            >>> molecule.surface(step=step, probe=probe, surface=surface)
-            >>> molecule.grid
-            array([[[1, 1, 1, ..., 1, 1, 1],
-                    [1, 1, 1, ..., 1, 1, 1],
-                    [1, 1, 1, ..., 1, 1, 1],
-                    ...,
-                    [1, 1, 1, ..., 1, 1, 1],
-                    [1, 1, 1, ..., 1, 1, 1],
-                    [1, 1, 1, ..., 1, 1, 1]],
-                   ...,
-                   [[1, 1, 1, ..., 1, 1, 1],
-                    [1, 1, 1, ..., 1, 1, 1],
-                    [1, 1, 1, ..., 1, 1, 1],
-                    ...,
-                    [1, 1, 1, ..., 1, 1, 1],
-                    [1, 1, 1, ..., 1, 1, 1],
-                    [1, 1, 1, ..., 1, 1, 1]]], dtype=int32)
-
-        The molecular surface can be modelled as:
-
-            * Solvent Accessible Surface (SAS):
-
-            >>> # Surface Representation: SAS
-            >>> surface = 'SAS'
-            >>> # Grid Spacing (step): 0.1
-            >>> step = 0.1
-            >>> # Spherical Probe (probe): 1.4
-            >>> probe = 1.4
-            >>> molecule.surface(step=step, probe=probe, surface=surface)
-            >>> molecule.grid
-            array([[[1, 1, 1, ..., 1, 1, 1],
-                    [1, 1, 1, ..., 1, 1, 1],
-                    [1, 1, 1, ..., 1, 1, 1],
-                    ...,
-                    [1, 1, 1, ..., 1, 1, 1],
-                    [1, 1, 1, ..., 1, 1, 1],
-                    [1, 1, 1, ..., 1, 1, 1]],
-                   ...,
-                   [[1, 1, 1, ..., 1, 1, 1],
-                    [1, 1, 1, ..., 1, 1, 1],
-                    [1, 1, 1, ..., 1, 1, 1],
-                    ...,
-                    [1, 1, 1, ..., 1, 1, 1],
-                    [1, 1, 1, ..., 1, 1, 1],
-                    [1, 1, 1, ..., 1, 1, 1]]], dtype=int32)
-        """
-        from _pyKVFinder import _fill_receptor
-
-        # Check arguments
-        if type(step) not in [int, float]:
-            raise TypeError("`step` must be a postive real number.")
-        elif step <= 0.0:
-            raise ValueError("`step` must be a positive real number.")
-        else:
-            self._step = step
-
-        # Probe
-        if type(probe) not in [int, float, numpy.float64]:
-            raise TypeError("`probe_out` must be a non-negative real number.")
-        elif probe <= 0.0:
-            raise ValueError("`probe_out` must be a non-negative real number.")
-        self._probe = probe
-
-        # Surface
-        if surface == "SES":
-            if self.verbose:
-                print("> Surface representation: Solvent Excluded Surface (SES).")
-            self._representation = surface
-            surface = True
-        elif surface == "SAS":
-            if self.verbose:
-                print("> Surface representation: Solvent Accessible Surface (SAS).")
-            self._representation = surface
-            surface = False
-        else:
-            raise ValueError(f"`surface` must be SAS or SES, not {surface}.")
-
-        # Define 3D grid
-        self._set_grid(padding)
-
-        # Molecular surface (SES or SAS) to grid
-        self._grid = _fill_receptor(
-            self.nx * self.ny * self.nz,
-            self.nx,
-            self.ny,
-            self.nz,
-            self.xyzr,
-            self.p1,
-            self.rotation,
-            self.step,
-            self.probe,
-            surface,
-            self.nthreads,
-            self.verbose,
-        ).reshape(self.nx, self.ny, self.nz)
          
-
-
          [docs]    def volume(self) -> float:
-        """Estimate the volume of the molecule based on the molecular surface representation, ie, vdW, SES or SAS representations.
-
-        Returns
-        -------
-        volume : float
-            Molecular volume (A³).
-
-        Example
-        -------
-        With the molecular surface modelled by ``Molecule.vdw()`` or ``Molecule.surface()``, the volume can be estimated by running:
-
-        >>> molecule.volume()
-        90.8
-        """
-        from _pyKVFinder import _volume
-
-        if self.grid is not None:
-            volume = _volume(
-                (self.grid == 0).astype(numpy.int32) * 2, self.step, 1, self.nthreads
-            )
-            return float(volume.round(decimals=2))
          
-
-
          [docs]    def preview(self, **kwargs) -> None:
-        """Preview the molecular surface in the 3D grid.
-
-        Example
-        -------
-        With the molecular surface modelled by ``Molecule.vdw()`` or ``Molecule.surface()``, the modelled molecule in the 3D grid can be previewed by running:
-
-        >>> molecule.preview()
-        """
-        if self.grid is not None:
-            from plotly.express import scatter_3d
-
-            x, y, z = numpy.nonzero(self.grid == 0)
-            fig = scatter_3d(x=x, y=y, z=z, **kwargs)
-            fig.update_layout(
-                scene_xaxis_showticklabels=False,
-                scene_yaxis_showticklabels=False,
-                scene_zaxis_showticklabels=False,
-            )
-            fig.show()
          
-
-
          [docs]    def export(
-        self,
-        fn: Union[str, pathlib.Path] = "molecule.pdb",
-    ) -> None:
-        """Export molecule points (H) to a PDB-formatted file.
-
-        Parameters
-        ----------
-        fn : Union[str, pathlib.Path], optional
-            A file path to the molecular volume in the grid-based rerpesentation in PDB format, by default "molecule.pdb".
-
-        Raises
-        ------
-        TypeError
-            `fn` must be a string or a pathlib.Path.
-
-        Example
-        -------
-        With the molecular surface modelled by ``Molecule.vdw()`` or ``Molecule.surface()``, the modelled molecule in the 3D grid can be exported to a PDB-formatted file by running:
-        
-        >>> molecule.export('model.pdb')
-        """
-        # Filename (fn)
-        if type(fn) not in [str, pathlib.Path]:
-            raise TypeError("`fn` must be a string or a pathlib.Path.")
-        os.makedirs(os.path.abspath(os.path.dirname(fn)), exist_ok=True)
-
-        # Save grid to PDB file
-        export(
-            fn, (self.grid == 0).astype(numpy.int32) * 2, None, self.vertices, self.step
-        )
          
-
          
-
-           
          
-          
          
-          
-        
          
-      
          
-    
          
-  
          
-   
-
-
-
\ No newline at end of file
diff --git a/docs/source/_build/html/_modules/pyKVFinder/utils.html b/docs/source/_build/html/_modules/pyKVFinder/utils.html
deleted file mode 100644
index 7e51c6d7..00000000
--- a/docs/source/_build/html/_modules/pyKVFinder/utils.html
+++ /dev/null
@@ -1,1477 +0,0 @@
-
-
-
-  
-  
-  pyKVFinder.utils — pyKVFinder 0.5.0 documentation
-      
-      
-    
-  
-  
-        
-        
-        
-        
-        
-    
-    
-     
-
-
- 
-  
          
-    
-
-    
          
-
-      
          
-        
          
-          
          
-  
-  
          
-
          
-          
          
-           
          
-             
-  
          Source code for pyKVFinder.utils
          -import argparse
-import logging
-import os
-import pathlib
-from typing import Dict, List, Optional, Union
-
-import numpy
-
-__all__ = [
-    "read_vdw",
-    "read_pdb",
-    "read_xyz",
-    "read_cavity",
-    "calculate_frequencies",
-    "plot_frequencies",
-    "write_results",
-]
-
-VDW = os.path.join(os.path.abspath(os.path.dirname(__file__)), "data/vdw.dat")
-
-
-
          [docs]def read_vdw(
-    fn: Optional[Union[str, pathlib.Path]] = None
-) -> Dict[str, Dict[str, float]]:
-    """Reads van der Waals radii from .dat file.
-
-    Parameters
-    ----------
-    fn : Optional[Union[str, pathlib.Path]], optional
-        A path to a van der Waals radii file, by default None. If None, apply the built-in van der
-        Waals radii file: `vdw.dat`.
-
-    Returns
-    -------
-    vdw : Dict[str, Dict[str, float]]
-        A dictionary containing radii values.
-
-    Raises
-    ------
-    TypeError
-        `fn` must be a string or a pathlib.Path.
-    ValueError
-        A line in `vdw` has incorrect format. The values must be double
-        tab-separated.
-    ValueError
-        A line in `vdw` has an incorrect radius type for an atom.
-
-    Note
-    ----
-    The van der Waals radii file defines the radius values for each
-    atom by residue and when not defined, it uses a generic value
-    based on the atom type (see ``van der Waals file template``).
-    The package contains a built-in van der Waals radii file: ``vdw.dat``.
-
-    See Also
-    --------
-    read_pdb
-    read_xyz
-    Molecule
-
-    Example
-    -------
-    The ``read_vdw`` function takes the `built-in dictionary <https://github.com/LBC-LNBio/pyKVFinder/blob/master/pyKVFinder/data/vdw.dat>`_ when a *.dat* file is not specified.
-
-    >>> from pyKVFinder import read_vdw
-    >>> vdw = read_vdw()
-    >>> vdw
-    {'ALA': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB1': 1.487, '1HB': 1.487, 'HB2': 1.487, '2HB': 1.487, 'HB3': 1.487, '3HB': 1.487, 'C': 1.908, 'O': 1.6612}, 'ARG': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG2': 1.487, '2HG': 1.487, 'HG3': 1.487, 'HG1': 1.487, '1HG': 1.487, 'CD': 1.908, 'HD2': 1.387, '1HD': 1.387, '2HD': 1.387, 'HD3': 1.387, 'HD1': 1.387, 'NE': 1.75, 'HE': 0.6, 'CZ': 1.908, 'NH1': 1.75, 'HH11': 0.6, '1HH1': 0.6, 'HH12': 0.6, '2HH1': 0.6, 'NH2': 1.75, 'HH21': 0.6, '2HH2': 0.6, 'HH22': 0.6, '1HH2': 0.6, 'C': 1.908, 'O': 1.6612}, 'ASH': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.908, 'OD1': 1.6612, 'OD2': 1.721, 'HD2': 0.0001, 'C': 1.908, 'O': 1.6612}, 'ASN': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'OD1': 1.6612, 'ND2': 1.824, 'HD21': 0.6, '1HD2': 0.6, 'HD22': 0.6, '2HD2': 0.6, 'C': 1.908, 'O': 1.6612}, 'ASP': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'OD1': 1.6612, 'OD2': 1.6612, 'C': 1.908, 'O': 1.6612}, 'CYM': {'N': 1.824, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB3': 1.387, 'HB2': 1.387, 'SG': 2.0, 'C': 1.908, 'O': 1.6612}, 'CYS': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.387, '2HB': 1.387, '1HB': 1.387, 'HB3': 1.387, 'HB1': 1.387, 'SG': 2.0, 'HG': 0.6, 'C': 1.908, 'O': 1.6612}, 'CYX': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.387, 'HB3': 1.387, 'SG': 2.0, 'C': 1.908, 'O': 1.6612}, 'GLH': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.908, 'HG2': 1.487, 'HG3': 1.487, 'CD': 1.908, 'OE1': 1.6612, 'OE2': 1.721, 'HE2': 0.0001, 'C': 1.908, 'O': 1.6612}, 'GLN': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG2': 1.487, '2HG': 1.487, 'HG3': 1.487, 'HG1': 1.487, '1HG': 1.487, 'CD': 1.908, 'OE1': 1.6612, 'NE2': 1.824, 'HE21': 0.6, '1HE2': 0.6, 'HE22': 0.6, '2HE2': 0.6, 'C': 1.908, 'O': 1.6612}, 'GLU': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG2': 1.487, '2HG': 1.487, 'HG3': 1.487, 'HG1': 1.487, '1HG': 1.487, 'CD': 1.908, 'OE1': 1.6612, 'OE2': 1.6612, 'C': 1.908, 'O': 1.6612}, 'GLY': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA2': 1.387, 'HA1': 1.387, '1HA': 1.387, '2HA': 1.387, 'HA3': 1.387, 'C': 1.908, 'O': 1.6612}, 'HID': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.85, 'ND1': 1.75, 'HD1': 0.6, 'CE1': 1.85, 'HE1': 1.359, 'NE2': 1.75, 'CD2': 2.0, 'HD2': 1.409, 'C': 1.908, 'O': 1.6612}, 'HIE': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.85, 'ND1': 1.75, 'CE1': 1.85, 'HE1': 1.359, 'NE2': 1.75, 'HE2': 0.6, 'CD2': 2.0, 'HD2': 1.409, 'C': 1.908, 'O': 1.6612}, 'HIP': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.85, 'ND1': 1.75, 'HD1': 0.6, 'CE1': 1.85, 'HE1': 1.359, 'NE2': 1.75, 'HE2': 0.6, 'CD2': 2.0, 'HD2': 1.409, 'C': 1.908, 'O': 1.6612}, 'ILE': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB': 1.487, 'CG2': 1.908, 'HG21': 1.487, '1HG2': 1.487, 'HG22': 1.487, '2HG2': 1.487, 'HG23': 1.487, '3HG2': 1.487, 'CG1': 1.908, 'HG12': 1.487, '2HG1': 1.487, 'HG13': 1.487, 'HG11': 1.487, '1HG1': 1.487, 'CD1': 1.908, 'HD11': 1.487, '1HD1': 1.487, 'HD12': 1.487, '2HD1': 1.487, 'HD13': 1.487, '3HD1': 1.487, 'C': 1.908, 'O': 1.6612}, 'LEU': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG': 1.487, 'CD1': 1.908, 'HD11': 1.487, '1HD1': 1.487, 'HD12': 1.487, '2HD1': 1.487, 'HD13': 1.487, '3HD1': 1.487, 'CD2': 1.908, 'HD21': 1.487, '1HD2': 1.487, 'HD22': 1.487, '2HD2': 1.487, 'HD23': 1.487, '3HD2': 1.487, 'C': 1.908, 'O': 1.6612}, 'LYN': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.908, 'HG2': 1.487, 'HG3': 1.487, 'CD': 1.908, 'HD2': 1.487, 'HD3': 1.487, 'CE': 1.908, 'HE2': 1.1, 'HE3': 1.1, 'NZ': 1.824, 'HZ2': 0.6, 'HZ3': 0.6, 'C': 1.908, 'O': 1.6612}, 'LYS': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG2': 1.487, '2HG': 1.487, 'HG3': 1.487, 'HG1': 1.487, '1HG': 1.487, 'CD': 1.908, 'HD2': 1.487, '1HD': 1.487, '2HD': 1.487, 'HD3': 1.487, 'HD1': 1.487, 'CE': 1.908, 'HE2': 1.1, '2HE': 1.1, 'HE3': 1.1, '1HE': 1.1, 'HE1': 1.1, 'NZ': 1.824, 'HZ1': 0.6, '1HZ': 0.6, 'HZ2': 0.6, '2HZ': 0.6, 'HZ3': 0.6, '3HZ': 0.6, 'C': 1.908, 'O': 1.6612}, 'MET': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG2': 1.387, '2HG': 1.387, 'HG3': 1.387, 'HG1': 1.387, '1HG': 1.387, 'SD': 2.0, 'CE': 1.908, 'HE1': 1.387, '1HE': 1.387, 'HE2': 1.387, '2HE': 1.387, 'HE3': 1.387, '3HE': 1.387, 'C': 1.908, 'O': 1.6612}, 'PHE': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'CD1': 1.908, 'HD1': 1.459, 'CE1': 1.908, 'HE1': 1.459, 'CZ': 1.908, 'HZ': 1.459, 'CE2': 1.908, 'HE2': 1.459, 'CD2': 1.908, 'HD2': 1.459, 'C': 1.908, 'O': 1.6612}, 'PRO': {'N': 1.824, 'CD': 1.908, 'HD2': 1.387, '1HD': 1.387, '2HD': 1.387, 'HD3': 1.387, 'HD1': 1.387, 'CG': 1.908, 'HG2': 1.487, '2HG': 1.487, 'HG3': 1.487, 'HG1': 1.487, '1HG': 1.487, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CA': 1.908, 'HA': 1.387, 'C': 1.908, 'O': 1.6612}, 'SER': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.387, '2HB': 1.387, '1HB': 1.387, 'HB3': 1.387, 'HB1': 1.387, 'OG': 1.721, 'HG': 0.0001, 'C': 1.908, 'O': 1.6612}, 'THR': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB': 1.387, 'CG2': 1.908, 'HG21': 1.487, '1HG2': 1.487, 'HG22': 1.487, '2HG2': 1.487, 'HG23': 1.487, '3HG2': 1.487, 'OG1': 1.721, 'HG1': 0.0001, 'C': 1.908, 'O': 1.6612}, 'TRP': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.85, 'CD1': 2.0, 'HD1': 1.409, 'NE1': 1.75, 'HE1': 0.6, 'CE2': 1.85, 'CZ2': 1.908, 'HZ2': 1.459, 'CH2': 1.908, 'HH2': 1.459, 'CZ3': 1.908, 'HZ3': 1.459, 'CE3': 1.908, 'HE3': 1.459, 'CD2': 1.85, 'C': 1.908, 'O': 1.6612}, 'TYR': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'CD1': 1.908, 'HD1': 1.459, 'CE1': 1.908, 'HE1': 1.459, 'CZ': 1.908, 'OH': 1.721, 'HH': 0.0001, 'CE2': 1.908, 'HE2': 1.459, 'CD2': 1.908, 'HD2': 1.459, 'C': 1.908, 'O': 1.6612}, 'VAL': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB': 1.487, 'CG1': 1.908, 'CG2': 1.908, 'HG11': 1.487, '1HG2': 1.487, '1HG1': 1.487, 'HG21': 1.487, 'HG12': 1.487, '2HG1': 1.487, 'HG22': 1.487, '2HG2': 1.487, 'HG13': 1.487, '3HG2': 1.487, '3HG1': 1.487, 'HG23': 1.487, 'C': 1.908, 'O': 1.6612}, 'HIS': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.85, 'ND1': 1.75, 'HD1': 0.6, 'CE1': 1.85, 'HE1': 1.359, 'NE2': 1.75, 'CD2': 2.0, 'HD2': 1.409, 'C': 1.908, 'O': 1.6612}, 'PTR': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.908, 'CD1': 1.908, 'HD1': 1.459, 'CE1': 1.908, 'HE1': 1.459, 'CZ': 1.908, 'CE2': 1.908, 'HE2': 1.459, 'CD2': 1.908, 'HD2': 1.459, 'OH': 1.6837, 'P': 2.1, 'O1P': 1.85, 'O2P': 1.85, 'O3P': 1.85, 'C': 1.908, 'O': 1.6612}, 'SEP': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.387, 'HB3': 1.387, '1HB': 1.387, '2HB': 1.387, 'OG': 1.6837, 'P': 2.1, 'O1P': 1.85, 'O2P': 1.85, 'O3P': 1.85, 'C': 1.908, 'O': 1.6612}, 'TPO': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB': 1.387, 'CG2': 1.908, 'HG21': 1.487, 'HG22': 1.487, 'HG23': 1.487, '1HG2': 1.487, '2HG2': 1.487, '3HG2': 1.487, 'OG1': 1.6837, 'P': 2.1, 'O1P': 1.85, 'O2P': 1.85, 'O3P': 1.85, 'C': 1.908, 'O': 1.6612}, 'H2D': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.85, 'ND1': 1.75, 'CE1': 1.85, 'HE1': 1.359, 'NE2': 1.75, 'HE2': 0.6, 'CD2': 2.0, 'HD2': 1.409, 'P': 2.1, 'O1P': 1.85, 'O2P': 1.85, 'O3P': 1.85, 'C': 1.908, 'O': 1.6612}, 'Y1P': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.908, 'CD1': 1.908, 'HD1': 1.459, 'CE1': 1.908, 'HE1': 1.459, 'CZ': 1.908, 'CE2': 1.908, 'HE2': 1.459, 'CD2': 1.908, 'HD2': 1.459, 'OG': 1.6837, 'P': 2.1, 'O1P': 1.721, 'O2P': 1.6612, 'O3P': 1.6612, 'H1P': 0.0001, 'C': 1.908, 'O': 1.6612}, 'T1P': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB': 1.387, 'CG2': 1.908, 'HG21': 1.487, 'HG22': 1.487, 'HG23': 1.487, 'OG': 1.6837, 'P': 2.1, 'O1P': 1.721, 'O2P': 1.6612, 'O3P': 1.6612, 'H1P': 0.0001, 'C': 1.908, 'O': 1.6612}, 'S1P': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.387, 'HB3': 1.387, 'OG': 1.6837, 'P': 2.1, 'O1P': 1.721, 'O2P': 1.6612, 'O3P': 1.6612, 'H1P': 0.0001, 'C': 1.908, 'O': 1.6612}, 'GEN': {'AC': 2.0, 'AG': 1.72, 'AL': 2.0, 'AM': 2.0, 'AR': 1.88, 'AS': 1.85, 'AT': 2.0, 'AU': 1.66, 'B': 2.0, 'BA': 2.0, 'BE': 2.0, 'BH': 2.0, 'BI': 2.0, 'BK': 2.0, 'BR': 1.85, 'C': 1.66, 'CA': 2.0, 'CD': 1.58, 'CE': 2.0, 'CF': 2.0, 'CL': 1.75, 'CM': 2.0, 'CO': 2.0, 'CR': 2.0, 'CS': 2.0, 'CU': 1.4, 'DB': 2.0, 'DS': 2.0, 'DY': 2.0, 'ER': 2.0, 'ES': 2.0, 'EU': 2.0, 'F': 1.47, 'FE': 2.0, 'FM': 2.0, 'FR': 2.0, 'GA': 1.87, 'GD': 2.0, 'GE': 2.0, 'H': 0.91, 'HE': 1.4, 'HF': 2.0, 'HG': 1.55, 'HO': 2.0, 'HS': 2.0, 'I': 1.98, 'IN': 1.93, 'IR': 2.0, 'K': 2.75, 'KR': 2.02, 'LA': 2.0, 'LI': 1.82, 'LR': 2.0, 'LU': 2.0, 'MD': 2.0, 'MG': 1.73, 'MN': 2.0, 'MO': 2.0, 'MT': 2.0, 'N': 1.97, 'NA': 2.27, 'NB': 2.0, 'ND': 2.0, 'NE': 1.54, 'NI': 1.63, 'NO': 2.0, 'NP': 2.0, 'O': 1.69, 'OS': 2.0, 'P': 2.1, 'PA': 2.0, 'PB': 2.02, 'PD': 1.63, 'PM': 2.0, 'PO': 2.0, 'PR': 2.0, 'PT': 1.72, 'PU': 2.0, 'RA': 2.0, 'RB': 2.0, 'RE': 2.0, 'RF': 2.0, 'RH': 2.0, 'RN': 2.0, 'RU': 2.0, 'S': 2.09, 'SB': 2.0, 'SC': 2.0, 'SE': 1.9, 'SG': 2.0, 'SI': 2.1, 'SM': 2.0, 'SN': 2.17, 'SR': 2.0, 'TA': 2.0, 'TB': 2.0, 'TC': 2.0, 'TE': 2.06, 'TH': 2.0, 'TI': 2.0, 'TL': 1.96, 'TM': 2.0, 'U': 1.86, 'V': 2.0, 'W': 2.0, 'XE': 2.16, 'Y': 2.0, 'YB': 2.0, 'ZN': 1.39, 'ZR': 2.0}}
-
-    The van der Waals radii can be define by:
-
-        * creating a Python dictionary:
-
-        >>> vdw = {'GEN': {'C': 1.66, 'CA': 2.0, 'N': 1.97, 'O': 1.69, 'H': 0.91}}
-
-        * specifying a *.dat* file following template of `van der Waals radii file`.
-
-        >>> with open('vdw.dat', 'w') as f:
-        ...     f.write('>GEN\\nC\\t\\t1.66\\nCA\\t\\t2.00\\nN\\t\\t1.97\\nO\\t\\t1.69\\nH\\t\\t0.91\\n')
-        >>> vdw = read_vdw('vdw.dat')
-        >>> vdw
-        {'GEN': {'C': 1.66, 'CA': 2.0, 'N': 1.97, 'O': 1.69, 'H': 0.91}}
-    """
-    # Check argument
-    if fn is not None:
-        if type(fn) not in [str, pathlib.Path]:
-            raise TypeError("`fn` must be a string or a pathlib.Path.")
-    else:
-        # Define default vdw file
-        fn = VDW
-
-    # Create vdw dictionary
-    vdw = {}
-
-    # Open fn
-    with open(fn, "r") as f:
-        # Read line with data only (ignore empty lines)
-        lines = [
-            line.replace(" ", "")
-            for line in f.read().splitlines()
-            if line.replace("\t\t", "")
-        ]
-        for line in lines:
-            if not line.startswith("#"):
-                if line.startswith(">"):
-                    res = line.replace(">", "").replace("\t\t", "").replace(" ", "")
-                    vdw[res] = {}
-                else:
-                    try:
-                        atom, radius = line.split("\t\t")
-                    except ValueError:
-                        if len(line.split("\t\t")) != 2:
-                            raise ValueError(
-                                "A line in `vdw` has incorrect format. \
-The values must be double tab-separated."
-                            )
-                    try:
-                        vdw[res][atom] = float(radius)
-                    except ValueError:
-                        raise ValueError(
-                            "A line in `vdw` has an incorrect radius type for \
-an atom."
-                        )
-
-    return vdw
          
-
-
-def _process_pdb_line(
-    line: str, vdw: Dict[str, Dict[str, float]]
-) -> List[Union[str, float, int]]:
-    """Extracts ATOM and HETATM information of PDB line.
-
-    Parameters
-    ----------
-    line : str
-        A line of a valid PDB file
-    vdw : Dict[str, Dict[str, Dict[str, float]]]
-        A dictionary containing radii values.
-
-    Returns
-    -------
-    atomic : List[Union[str, float, int]]
-        A list with resnum, chain, resname, atom name, xyz coordinates and radius.
-    """
-    # Get PDB infomation
-    atom = line[12:16].strip()
-    resname = line[17:20].strip()
-    resnum = int(line[22:26])
-    chain = line[21]
-    x = float(line[30:38])
-    y = float(line[38:46])
-    z = float(line[46:54])
-    atom_symbol = line[76:78].strip().upper()
-
-    # Get atom and radius from vdw
-    if resname in vdw.keys() and atom in vdw[resname].keys():
-        radius = vdw[resname][atom]
-    else:
-        radius = vdw["GEN"][atom_symbol]
-        logging.info(
-            f"Warning: Atom {atom} of residue {resname} \
-not found in dictionary."
-        )
-        logging.info(
-            f"Warning: Using generic atom {atom_symbol} \
-radius: {radius} \u00c5."
-        )
-
-    # Prepare output
-    atomic = [resnum, chain, resname, atom, x, y, z, radius]
-
-    return atomic
-
-
-
          [docs]def read_pdb(
-    fn: Union[str, pathlib.Path],
-    vdw: Optional[Dict[str, Dict[str, float]]] = None,
-    model: Optional[int] = None,
-) -> numpy.ndarray:
-    """Reads PDB file into numpy.ndarrays.
-
-    Parameters
-    ----------
-    fn : Union[str, pathlib.Path]
-        A path to PDB file.
-    vdw : Dict[str, Dict[str, float]], optional
-        A dictionary containing radii values, by default None. If None, use output of ``read_vdw()``.
-    model : int, optional
-        The model number of a multi-model PDB file, by default None. If None, keep atoms from all models.
-
-    Returns
-    -------
-    atomic : numpy.ndarray
-        A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
-        and radius) for each atom.
-
-    Raises
-    ------
-    TypeError
-        `fn` must be a string or a pathlib.Path.
-
-    Note
-    ----
-    The van der Waals radii file defines the radius values for each atom by residue and when not defined, it uses a generic value based on the atom type. The function by default loads the built-in van der Waals radii file: `vdw.dat`.
-
-    See Also
-    --------
-    read_vdw
-    read_xyz
-    get_vertices
-    get_vertices_from_file
-    detect
-    constitutional
-    hydropathy
-
-    Example
-    -------
-    With the vdW radii dictionary loaded with ``read_vdw``, we can read a target PDB file into Numpy array (atomic data):
-
-    >>> import os
-    >>> import pyKVFinder
-    >>> from pyKVFinder import read_pdb
-    >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
-    >>> atomic = read_pdb(pdb)
-    >>> atomic
-    array([['13', 'E', 'GLU', ..., '-15.642', '-14.858', '1.824'],
-       ['13', 'E', 'GLU', ..., '-14.62', '-15.897', '1.908'],
-       ['13', 'E', 'GLU', ..., '-13.357', '-15.508', '1.908'],
-       ...,
-       ['350', 'E', 'PHE', ..., '18.878', '-9.885', '1.908'],
-       ['350', 'E', 'PHE', ..., '17.624', '-9.558', '1.908'],
-       ['350', 'E', 'PHE', ..., '19.234', '-13.442', '1.69']],
-      dtype='<U32')
-
-    .. warning::
-        The function takes the `built-in dictionary <https://github.com/LBC-LNBio/pyKVFinder/blob/master/pyKVFinder/data/vdw.dat>`_ when the ``vdw`` argument is not specified. If you wish to use a custom van der Waals radii file, you must read it with ``read_vdw`` as shown earlier and pass it as ``read_pdb(pdb, vdw=vdw)``.
-    """
-    # Check arguments
-    if type(fn) not in [str, pathlib.Path]:
-        raise TypeError("`fn` must be a string or a pathlib.Path.")
-    if model is not None:
-        if type(model) not in [int]:
-            raise TypeError("`model` must be an integer.")
-
-    # Define default vdw file
-    if vdw is None:
-        vdw = read_vdw(VDW)
-
-    # Create lists
-    atomic = []
-
-    # Keep all models
-    keep = True if model is None else False
-
-    # Read file and process atoms
-    with open(fn, "r") as f:
-        for line in f.readlines():
-            if model is not None:
-                if line[:5] == "MODEL":
-                    nmodel = int(line[5:].replace(" ", "").rstrip("\n"))
-                    keep = True if model == nmodel else False
-            if keep:
-                if line[:4] == "ATOM" or line[:6] == "HETATM":
-                    atomic.append(_process_pdb_line(line, vdw))
-
-    return numpy.asarray(atomic)
          
-
-
-
          [docs]def read_xyz(
-    fn: Union[str, pathlib.Path], vdw: Optional[Dict[str, Dict[str, float]]] = None
-) -> numpy.ndarray:
-    """Reads XYZ file into numpy.ndarrays.
-
-    Parameters
-    ----------
-    fn : Union[str, pathlib.Path]
-        A path to XYZ file.
-    vdw : Dict[str, Dict[str, float]], optional
-        A dictionary containing radii values, by default None. If None, use output of ``read_vdw()``.
-
-    Returns
-    -------
-    atomic : numpy.ndarray
-        A numpy array with atomic data (residue number, chain, residue name, atom name, xyz coordinates
-        and radius) for each atom.
-
-    Raises
-    ------
-    TypeError
-        `fn` must be a string or a pathlib.Path.
-
-    Note
-    ----
-    The van der Waals radii file defines the radius values for each atom
-    by residue and when not defined, it uses a generic value based on the
-    atom type. The function by default loads the built-in van der Waals radii
-    file: `vdw.dat`.
-
-    See Also
-    --------
-    read_vdw
-    read_pdb
-    get_vertices
-    get_vertices_from_file
-    detect
-    constitutional
-    hydropathy
-
-    Example
-    -------
-    With the vdW radii dictionary loaded with ``pyKVFinder.read_vdw``, we can read a target XYZ file into Numpy arrays (atomic information and atomic coordinates):
-
-    >>> import os
-    >>> import pyKVFinder
-    >>> from pyKVFinder import read_xyz
-    >>> xyz = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.xyz')
-    >>> atomic = read_xyz(xyz)
-    >>> atominfo
-    array([['1', 'A', 'UNK', ..., '-15.642', '-14.858', '1.97'],
-       ['2', 'A', 'UNK', ..., '-14.62', '-15.897', '1.66'],
-       ['3', 'A', 'UNK', ..., '-13.357', '-15.508', '1.66'],
-       ...,
-       ['2790', 'A', 'UNK', ..., '18.878', '-9.885', '1.66'],
-       ['2791', 'A', 'UNK', ..., '17.624001', '-9.558', '1.66'],
-       ['2792', 'A', 'UNK', ..., '19.233999', '-13.442', '1.69']],
-      dtype='<U32')
-
-    .. warning::
-        The function takes the `built-in dictionary <https://github.com/LBC-LNBio/pyKVFinder/blob/master/pyKVFinder/data/vdw.dat>`_ when the ``vdw`` argument is not specified. If you wish to use a custom van der Waals radii file, you must read it with ``read_vdw`` as shown earlier and pass it as ``read_xyz(xyz, vdw=vdw)``.
-
-    """
-    # Check arguments
-    if type(fn) not in [str, pathlib.Path]:
-        raise TypeError("`fn` must be a string or a pathlib.Path.")
-
-    # Define default vdw file
-    if vdw is None:
-        vdw = read_vdw(VDW)
-
-    # Create lists
-    atomic = []
-
-    # Start resnum
-    resnum = 0
-
-    # Read XYZ file
-    with open(fn, "r") as f:
-        for line in f.readlines():
-            line = line.split()
-            if len(line) == 4:
-                # Get PDB information
-                atom_symbol = line[0]
-                x = float(line[1])
-                y = float(line[2])
-                z = float(line[3])
-
-                # Get radius (generic value)
-                radius = vdw["GEN"][atom_symbol]
-
-                # Get resnum
-                resnum += 1
-
-                # Append data
-                atomic.append([resnum, "A", "UNK", atom_symbol, x, y, z, radius])
-
-    return numpy.asarray(atomic)
          
-
-
-def _read_cavity(cavity: Union[str, pathlib.Path]) -> numpy.ndarray:
-    """Reads xyz coordinates and labels of a cavities file into numpy.ndarray.
-
-    Parameters
-    ----------
-    cavity : Union[str, pathlib.Path]
-        A path to a PDB-formatted file of cavities.
-
-    Returns
-    -------
-    xyzl : numpy.ndarray
-        A numpy.ndarray with xyz coordinates and cavity label for each cavity point.
-    """
-    from .grid import _get_cavity_label
-
-    # Create xyzl (xyz coordinates and cavity label)
-    xyzl = []
-
-    # Read cavity file into list
-    with open(cavity, "r") as f:
-        for line in f.readlines():
-            if line[:4] == "ATOM" or line[:6] == "HETATM":
-                x = float(line[30:38])
-                y = float(line[38:46])
-                z = float(line[46:54])
-                label = _get_cavity_label(line[17:20].strip())
-                xyzl.append([x, y, z, label])
-
-    return numpy.asarray(xyzl)
-
-
-
          [docs]def read_cavity(
-    cavity: Union[str, pathlib.Path],
-    receptor: Union[str, pathlib.Path],
-    step: Union[float, int] = 0.6,
-    probe_in: Union[float, int] = 1.4,
-    probe_out: Union[float, int] = 4.0,
-    surface: str = "SES",
-    vdw: Optional[Dict[str, Dict[str, float]]] = None,
-    nthreads: Optional[int] = None,
-    verbose: bool = False,
-) -> numpy.ndarray:
-    """Read cavities and receptor inside a 3D grid.
-
-    Parameters
-    ----------
-    cavity : Union[str, pathlib.Path]
-        A path to a PDB file of cavities.
-    receptor : Union[str, pathlib.Path]
-        A path to a PDB or XYZ file of the receptor.
-    step : Union[float, int], optional
-        Grid spacing (A), by default 0.6.
-    probe_in : Union[float, int], optional
-        Probe In size (A), by default 1.4.
-    probe_out : Union[float, int], optional
-        Probe Out size (A), by default 4.0.
-    surface : str, optional
-        Surface representation. Keywords options are SES (Solvent Excluded Surface) or SAS (Solvent
-        Accessible Surface), by default "SES".
-    vdw : Dict[str, Dict[str, float]], optional
-        A dictionary containing radii values, by default None. If None, use output of ``read_vdw()``.
-    nthreads : Optional[int], optional
-        Number of threads, by default None. If None, the number of threads is
-        `os.cpu_count() - 1`.
-    verbose : bool, optional
-        Print extra information to standard output, by default False.
-
-    Returns
-    -------
-    grid : numpy.ndarray
-        Cavity and receptor points in the 3D grid (grid[nx][ny][nz]).
-        Grid array has integer labels in each position, that are:
-
-            * -1: bulk points or empty space points;
-
-            * 0: biomolecule points;
-
-            * >=2: cavity points.
-
-    Raises
-    ------
-    TypeError
-        `cavity` must be a string or a pathlib.Path.
-    TypeError
-        `receptor` must be a string or a pathlib.Path.
-    TypeError
-        `target` must have .pdb or .xyz extension.
-    TypeError
-        `step` must be a positive real number.
-    ValueError
-        `step` must be a positive real number.
-    TypeError
-        `probe_in` must be a non-negative real number.
-    ValueError
-        `probe_in` must be a non-negative real number.
-    TypeError
-        `probe_out` must be a non-negative real number.
-    ValueError
-        `probe_out` must be a non-negative real number.
-    ValueError
-        `probe_out` must be greater than `probe_in`.
-    TypeError
-        `surface` must be a str.
-    TypeError
-        `nthreads` must be a positive integer.
-    ValueError
-        `nthreads` must be a positive integer.
-    TypeError
-        `verbose` must be a boolean.
-    ValueError
-        `surface` must be SAS or SES, not {surface}.
-
-    Note
-    ----
-    The function takes the `built-in dictionary <https://github.com/LBC-LNBio/pyKVFinder/blob/master/pyKVFinder/data/vdw.dat>`_ when the ``vdw`` argument is not specified. If you wish to use a custom van der Waals radii file, you must read it with ``read_vdw`` as shown earlier and pass it as ``read_cavity(cavity, receptor, vdw=vdw)``.
-
-    See Also
-    --------
-    read_pdb
-    read_xyz
-    get_vertices
-    get_vertices_from_file
-    spatial
-    depth
-    constitutional
-    hydropathy
-    export
-
-    Example
-    -------
-    With a previously calculated cavity, that can be manually curated in a molecular visualization software, such as PyMOL, we can read it with its respective receptor back to pyKVFinder:
-
-    >>> import os
-    >>> import pyKVFinder
-    >>> from pyKVFinder import read_cavity
-    >>> cavity = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.KVFinder.output.pdb')
-    >>> receptor = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
-    >>> grid = read_cavity(cavity, receptor)
-    >>> grid
-    array([[[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]],
-       ...,
-       [[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
-    """
-    from _pyKVFinder import _fill_cavity, _fill_receptor
-
-    from .grid import _get_dimensions, _get_sincos, get_vertices
-
-    # Check arguments
-    if type(cavity) not in [str, pathlib.Path]:
-        raise TypeError("`cavity` must be a string or a pathlib.Path.")
-    if type(receptor) not in [str, pathlib.Path]:
-        raise TypeError("`receptor` must be a string or a pathlib.Path.")
-    elif not receptor.endswith(".pdb") and not receptor.endswith(".xyz"):
-        raise TypeError("`receptor` must have .pdb or .xyz extension.")
-    if type(step) not in [float, int]:
-        raise TypeError("`step` must be a positive real number.")
-    elif step <= 0.0:
-        raise ValueError("`step` must be a positive real number.")
-    if type(probe_in) not in [float, int]:
-        raise TypeError("`probe_in` must be a non-negative real number.")
-    elif probe_in < 0.0:
-        raise ValueError("`probe_in` must be a non-negative real number.")
-    if type(probe_out) not in [float, int]:
-        raise TypeError("`probe_out` must be a non-negative real number.")
-    elif probe_out < 0.0:
-        raise ValueError("`probe_out` must be a non-negative real number.")
-    elif probe_out < probe_in:
-        raise ValueError("`probe_out` must be greater than `probe_in`.")
-    if type(surface) not in [str]:
-        raise TypeError("`surface` must be a str.")
-    if nthreads is None:
-        nthreads = os.cpu_count() - 1
-    else:
-        if type(nthreads) not in [int]:
-            raise TypeError("`nthreads` must be a positive integer.")
-        elif nthreads <= 0:
-            raise ValueError("`nthreads` must be a positive integer.")
-    if type(verbose) not in [bool]:
-        raise TypeError("`verbose` must be a boolean.")
-
-    # Convert types
-    if type(step) == int:
-        step = float(step)
-    if type(probe_in) == int:
-        probe_in = float(probe_in)
-    if type(probe_out) == int:
-        probe_out = float(probe_out)
-
-    # Insert receptor inside 3D grid
-    if verbose:
-        print(f"> Inserting {receptor} into 3D grid")
-
-    # Define default vdw file
-    if vdw is None:
-        vdw = read_vdw(VDW)
-
-    # Load receptor coordinates and radii
-    if receptor.endswith(".pdb"):
-        atomic = read_pdb(receptor, vdw)
-    elif receptor.endswith(".xyz"):
-        atomic = read_xyz(receptor, vdw)
-
-    # Extract xyzr from atomic
-    xyzr = atomic[:, 4:].astype(numpy.float64)
-
-    # Get vertices
-    vertices = get_vertices(atomic, probe_out, step)
-
-    # Get sincos
-    sincos = _get_sincos(vertices)
-
-    # Get dimensions
-    nx, ny, nz = _get_dimensions(vertices, step)
-
-    # Unpack vertices
-    P1, P2, P3, P4 = vertices
-
-    # Calculate number of voxels
-    nvoxels = nx * ny * nz
-
-    if surface == "SES":
-        if verbose:
-            print("> Surface representation: Solvent Excluded Surface (SES)")
-        surface = True
-    elif surface == "SAS":
-        if verbose:
-            print("> Surface representation: Solvent Accessible Surface (SAS)")
-        surface = False
-    else:
-        raise ValueError(f"`surface` must be SAS or SES, not {surface}.")
-
-    # Fill grid with receptor
-    grid = _fill_receptor(
-        nvoxels,
-        nx,
-        ny,
-        nz,
-        xyzr,
-        P1,
-        sincos,
-        step,
-        probe_in,
-        surface,
-        nthreads,
-        verbose,
-    ).reshape(nx, ny, nz)
-
-    # Insert cavities inside 3D grid
-    if verbose:
-        print(f"> Inserting {cavity} into 3D grid")
-
-    # Load cavities coordinates and labels
-    xyzl = _read_cavity(cavity)
-
-    # Fill grid with cavities
-    _fill_cavity(grid, xyzl, P1, sincos, step, nthreads)
-
-    return grid
          
-
-
-def _process_box(args: argparse.Namespace) -> Dict[str, List[float]]:
-    """Gets xyz coordinates of 3D grid vertices.
-
-    Parameters
-    ----------
-    args (argparse.Namespace)
-        Arguments passes by argparser CLI.
-
-    Returns
-    -------
-    box : Dict[str, List[float]]
-        A dictionary with a xyz coordinates (p1: origin,
-        p2: X-axis, p3: Y-axis, p4: Z-axis) for each point.
-    """
-    # Create box parameter
-    box = {
-        "p1": args.vertices[0],
-        "p2": args.vertices[1],
-        "p3": args.vertices[2],
-        "p4": args.vertices[3],
-    }
-
-    # Adjust if box adjustment mode
-    if args.box:
-        # Get probe out additions
-        # p1 = (x1, y1, z1)
-        x1 = (
-            -(args.probe_out * args.sincos[3])
-            - (args.probe_out * args.sincos[0] * args.sincos[2])
-            + (args.probe_out * args.sincos[1] * args.sincos[2])
-        )
-        y1 = -(args.probe_out * args.sincos[1]) - (args.probe_out * args.sincos[0])
-        z1 = (
-            -(args.probe_out * args.sincos[2])
-            + (args.probe_out * args.sincos[0] * args.sincos[3])
-            - (args.probe_out * args.sincos[1] * args.sincos[3])
-        )
-        # p2 = (x2, y2, z2)
-        x2 = (
-            (args.probe_out * args.sincos[3])
-            - (args.probe_out * args.sincos[0] * args.sincos[2])
-            + (args.probe_out * args.sincos[1] * args.sincos[2])
-        )
-        y2 = -(args.probe_out * args.sincos[1]) - (args.probe_out * args.sincos[0])
-        z2 = (
-            (args.probe_out * args.sincos[2])
-            + (args.probe_out * args.sincos[0] * args.sincos[3])
-            - (args.probe_out * args.sincos[1] * args.sincos[3])
-        )
-        # p3 = (x3, y3, z3)
-        x3 = (
-            -(args.probe_out * args.sincos[3])
-            + (args.probe_out * args.sincos[0] * args.sincos[2])
-            + (args.probe_out * args.sincos[1] * args.sincos[2])
-        )
-        y3 = (args.probe_out * args.sincos[1]) - (args.probe_out * args.sincos[0])
-        z3 = (
-            -(args.probe_out * args.sincos[2])
-            - (args.probe_out * args.sincos[0] * args.sincos[3])
-            - (args.probe_out * args.sincos[1] * args.sincos[3])
-        )
-        # p4 = (x4, y4, z4)
-        x4 = (
-            -(args.probe_out * args.sincos[3])
-            - (args.probe_out * args.sincos[0] * args.sincos[2])
-            - (args.probe_out * args.sincos[1] * args.sincos[2])
-        )
-        y4 = -(args.probe_out * args.sincos[1]) + (args.probe_out * args.sincos[0])
-        z4 = (
-            -(args.probe_out * args.sincos[2])
-            + (args.probe_out * args.sincos[0] * args.sincos[3])
-            + (args.probe_out * args.sincos[1] * args.sincos[3])
-        )
-
-        # Remove probe out addition
-        box["p1"] -= numpy.array([x1, y1, z1])
-        box["p2"] -= numpy.array([x2, y2, z2])
-        box["p3"] -= numpy.array([x3, y3, z3])
-        box["p4"] -= numpy.array([x4, y4, z4])
-
-    # Prepare to dict to toml module
-    box["p1"] = numpy.around(box["p1"], 2).tolist()
-    box["p2"] = numpy.around(box["p2"], 2).tolist()
-    box["p3"] = numpy.around(box["p3"], 2).tolist()
-    box["p4"] = numpy.around(box["p4"], 2).tolist()
-
-    return box
-
-
-def _write_parameters(args: argparse.Namespace) -> None:
-    """Writes parameters used in cavity detection and characterization of
-    pyKVFinder to TOML-formatted file.
-
-    Parameters
-    ----------
-    args : argparse.Namespace
-        Arguments passes by argparser CLI.
-    """
-    import toml
-
-    # Parameters filename
-    fn = os.path.join(args.output_directory, f"{args.base_name}.parameters.toml")
-
-    # Parameters dict
-    parameters = {
-        "FILES": {
-            "INPUT": args.input,
-            "LIGAND": args.ligand,
-            "BASE_NAME": args.base_name,
-            "OUTPUT_DIRECTORY": args.output_directory,
-            "DICTIONARY": args.dictionary,
-        },
-        "SETTINGS": {
-            "MODES": {
-                "BOX_ADJUSTMENT": args.box,
-                "LIGAND_ADJUSTMENT": True if args.ligand else False,
-                "DEPTH": args.depth,
-                "SURFACE": args.surface,
-                "IGNORE_BACKBONE": args.ignore_backbone,
-            },
-            "STEP": args.step,
-            "PROBES": {
-                "PROBE_IN": args.probe_in,
-                "PROBE_OUT": args.probe_out,
-            },
-            "CUTOFFS": {
-                "VOLUME_CUTOFF": args.volume_cutoff,
-                "LIGAND_CUTOFF": args.ligand_cutoff,
-                "REMOVAL_DISTANCE": args.removal_distance,
-            },
-            "BOX": _process_box(args),
-        },
-    }
-
-    # Write to TOML file
-    with open(fn, "w") as param:
-        toml.dump(parameters, param)
-
-
-
          [docs]def calculate_frequencies(
-    residues: Dict[str, List[List[str]]]
-) -> Dict[str, Dict[str, Dict[str, int]]]:
-    """Calculate frequencies of residues and class of residues
-    (R1, R2, R3, R4 and R5) for detected cavities.
-
-    Parameters
-    ----------
-    residues : Dict[str, List[List[str]]]
-        A dictionary with a list of interface residues for each detected
-        cavity.
-
-    Returns
-    -------
-    frequencies : Dict[str, Dict[str, Dict[str, int]]]
-        A dictionary with frequencies of residues and class for
-        residues of each detected cavity.
-
-    Note
-    ----
-    The cavity nomenclature is based on the integer label. The cavity
-    marked with 2, the first integer corresponding to a cavity, is KAA, the
-    cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
-
-    Note
-    ----
-    The classes of residues are:
-
-    * Aliphatic apolar (R1): Alanine, Glycine, Isoleucine, Leucine, Methionine, Valine.
-
-    * Aromatic (R2): Phenylalanine, Tryptophan, Tyrosine.
-
-    * Polar Uncharged (R3): Asparagine, Cysteine, Glutamine, Proline, Serine, Threonine.
-
-    * Negatively charged (R4): Aspartate, Glutamate.
-
-    * Positively charged (R5): Arginine, Histidine, Lysine.
-
-    * Non-standard (RX): Non-standard residues.
-
-    See Also
-    --------
-    constitutional
-    plot_frequencies
-    write_results
-
-    Example
-    -------
-    With the interface residues identified with ``constitutional``, we can calculate residues and classes of residues frequencies:
-
-    >>> from pyKVFinder import calculate_frequencies
-    >>> residues
-    {'KAA': [['49', 'E', 'LEU'], ['50', 'E', 'GLY'], ['51', 'E', 'THR'], ['52', 'E', 'GLY'], ['53', 'E', 'SER'], ['54', 'E', 'PHE'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['72', 'E', 'LYS'], ['74', 'E', 'LEU'], ['84', 'E', 'GLN'], ['87', 'E', 'HIS'], ['88', 'E', 'THR'], ['91', 'E', 'GLU'], ['104', 'E', 'VAL'], ['120', 'E', 'MET'], ['121', 'E', 'GLU'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['166', 'E', 'ASP'], ['168', 'E', 'LYS'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['184', 'E', 'ASP'], ['186', 'E', 'GLY'], ['187', 'E', 'PHE'], ['201', 'E', 'THR'], ['327', 'E', 'PHE']]}
-    >>> frequencies = calculate_frequencies(residues)
-    >>> frequencies
-    {'KAA': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'ASN': 1, 'ASP': 2, 'GLN': 1, 'GLU': 4, 'GLY': 4, 'HIS': 1, 'LEU': 3, 'LYS': 2, 'MET': 1, 'PHE': 3, 'SER': 1, 'THR': 4, 'TYR': 1, 'VAL': 3}, 'CLASS': {'R1': 11, 'R2': 4, 'R3': 8, 'R4': 6, 'R5': 4, 'RX': 0}}}
-    """
-    # Create a dict for frequencies
-    frequencies = {}
-
-    # Get cavity name and residues list for each detected cavity
-    for name, reslist in residues.items():
-        # Create a dict for cavity name
-        frequencies[name] = {
-            "RESIDUES": {},
-            "CLASS": {},
-        }
-        # Get unique residues names
-        residues = [res[2] for res in reslist]
-        reslist = sorted(list(set(residues)))
-
-        # Get residues frequencies
-        for res in reslist:
-            frequencies[name]["RESIDUES"][res] = residues.count(res)
-
-        # Get class frequencies
-        frequencies[name]["CLASS"]["R1"] = (
-            frequencies[name]["RESIDUES"].get("ALA", 0)
-            + frequencies[name]["RESIDUES"].get("GLY", 0)
-            + frequencies[name]["RESIDUES"].get("ILE", 0)
-            + frequencies[name]["RESIDUES"].get("LEU", 0)
-            + frequencies[name]["RESIDUES"].get("PRO", 0)
-            + frequencies[name]["RESIDUES"].get("VAL", 0)
-        )
-        frequencies[name]["CLASS"]["R2"] = (
-            frequencies[name]["RESIDUES"].get("PHE", 0)
-            + frequencies[name]["RESIDUES"].get("TRP", 0)
-            + frequencies[name]["RESIDUES"].get("TYR", 0)
-        )
-        frequencies[name]["CLASS"]["R3"] = (
-            frequencies[name]["RESIDUES"].get("ASN", 0)
-            + frequencies[name]["RESIDUES"].get("CYS", 0)
-            + frequencies[name]["RESIDUES"].get("GLN", 0)
-            + frequencies[name]["RESIDUES"].get("MET", 0)
-            + frequencies[name]["RESIDUES"].get("SER", 0)
-            + frequencies[name]["RESIDUES"].get("THR", 0)
-        )
-        frequencies[name]["CLASS"]["R4"] = frequencies[name]["RESIDUES"].get(
-            "ASP", 0
-        ) + frequencies[name]["RESIDUES"].get("GLU", 0)
-        frequencies[name]["CLASS"]["R5"] = (
-            frequencies[name]["RESIDUES"].get("ARG", 0)
-            + frequencies[name]["RESIDUES"].get("HIS", 0)
-            + frequencies[name]["RESIDUES"].get("LYS", 0)
-        )
-        frequencies[name]["CLASS"]["RX"] = len(residues) - sum(
-            frequencies[name]["CLASS"].values()
-        )
-
-    return frequencies
          
-
-
-
          [docs]def plot_frequencies(
-    frequencies: Dict[str, Dict[str, Dict[str, int]]],
-    fn: Union[str, pathlib.Path] = "barplots.pdf",
-) -> None:
-    """Plot bar charts of calculated frequencies (residues and classes of
-    residues) for each detected cavity in a target PDF file.
-
-    Parameters
-    ----------
-    frequencies : Dict[str, Dict[str, Dict[str, int]]]
-        A dictionary with frequencies of residues and class for
-        residues of each detected cavity.
-    fn : Union[str, pathlib.Path], optional
-        A path to PDF file for plotting bar charts of frequencies, by
-        default `barplots.pdf`.
-
-    Raises
-    ------
-    TypeError
-        `fn` must be a string or a pathlib.Path.
-
-    Note
-    ----
-    The cavity nomenclature is based on the integer label. The cavity
-    marked with 2, the first integer corresponding to a cavity, is KAA, the
-    cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
-
-    Note
-    ----
-    The classes of residues are:
-
-    * Aliphatic apolar (R1): Alanine, Glycine, Isoleucine, Leucine, Methionine, Valine.
-
-    * Aromatic (R2): Phenylalanine, Tryptophan, Tyrosine.
-
-    * Polar Uncharged (R3): Asparagine, Cysteine, Glutamine, Proline, Serine, Threonine.
-
-    * Negatively charged (R4): Aspartate, Glutamate.
-
-    * Positively charged (R5): Arginine, Histidine, Lysine.
-
-    * Non-standard (RX): Non-standard residues.
-
-    See Also
-    --------
-    calculate_frequencies
-
-    Example
-    -------
-    With the residues and classes of residues frequencies calculated with ``calculate_frequencies``, we can plot the bar charts of these frequencies in a PDF file.
-
-    >>> from pyKVFinder import plot_frequencies
-    >>> frequencies
-    {'KAA': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'ASN': 1, 'ASP': 2, 'GLN': 1, 'GLU': 4, 'GLY': 4, 'HIS': 1, 'LEU': 3, 'LYS': 2, 'MET': 1, 'PHE': 3, 'SER': 1, 'THR': 4, 'TYR': 1, 'VAL': 3}, 'CLASS': {'R1': 11, 'R2': 4, 'R3': 8, 'R4': 6, 'R5': 4, 'RX': 0}}}
-    >>> plot_frequencies(frequencies, fn='barplots.pdf')
-
-    .. image:: ../_images/barplots.png
-        :width: 600
-        :align: center
-    """
-    import matplotlib.pyplot as plt
-    from matplotlib.backends.backend_pdf import PdfPages
-
-    # Check arguments
-    if type(fn) not in [str, pathlib.Path]:
-        raise TypeError("`fn` must be a string or a pathlib.Path.")
-
-    # Create base directories of output PDF file
-    os.makedirs(os.path.abspath(os.path.dirname(fn)), exist_ok=True)
-
-    # Create a dictionary for standard amino acids
-    tmp = {
-        "ALA": 0,
-        "ARG": 0,
-        "ASN": 0,
-        "ASP": 0,
-        "CYS": 0,
-        "GLN": 0,
-        "GLU": 0,
-        "GLY": 0,
-        "HIS": 0,
-        "ILE": 0,
-        "LEU": 0,
-        "LYS": 0,
-        "MET": 0,
-        "PHE": 0,
-        "PRO": 0,
-        "SER": 0,
-        "THR": 0,
-        "TRP": 0,
-        "TYR": 0,
-        "VAL": 0,
-    }
-
-    with PdfPages(fn) as pdf:
-        # Standardize data
-        ymax = 0
-        for cavity_tag in frequencies.keys():
-            # Include missing residues
-            frequencies[cavity_tag]["RESIDUES"] = {
-                **tmp,
-                **frequencies[cavity_tag]["RESIDUES"],
-            }
-            # Get y maximum
-            if ymax < max(frequencies[cavity_tag]["CLASS"].values()):
-                ymax = max(frequencies[cavity_tag]["CLASS"].values())
-        ymax += 1
-
-        # Pdf plots
-        for cavity_tag in frequencies.keys():
-            # Create page
-            fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(16, 9), dpi=300)
-            fig.suptitle(r"Cavity " + f"{cavity_tag}", fontsize=30)
-
-            # Frequency residues
-            x = list(frequencies[cavity_tag]["RESIDUES"].keys())
-            y = frequencies[cavity_tag]["RESIDUES"].values()
-            colors = [
-                "tab:cyan",
-                "tab:purple",
-                "tab:green",
-                "tab:red",
-                "tab:green",
-                "tab:green",
-                "tab:red",
-                "tab:cyan",
-                "tab:purple",
-                "tab:cyan",
-                "tab:cyan",
-                "tab:purple",
-                "tab:green",
-                "tab:orange",
-                "tab:cyan",
-                "tab:green",
-                "tab:green",
-                "tab:orange",
-                "tab:orange",
-                "tab:cyan",
-            ]
-            for _ in range(len(x) - len(colors)):
-                colors.append("tab:gray")
-
-            ax1.bar(x, y, align="center", edgecolor="black", color=colors)
-            ax1.set_xlabel(None)
-            ax1.set_xlim(-1, len(x))
-            ax1.tick_params(axis="x", labelsize=15, rotation=45)
-            ax1.tick_params(axis="y", labelsize=20)
-            ax1.set_ylabel(r"Frequency", fontsize=20)
-            ax1.set_ylim(0, ymax)
-            ax1.grid(which="major", axis="y", linestyle="--")
-
-            # Frequency classes
-            x = list(frequencies[cavity_tag]["CLASS"].keys())
-            y = frequencies[cavity_tag]["CLASS"].values()
-            colors = [
-                "tab:cyan",
-                "tab:orange",
-                "tab:green",
-                "tab:red",
-                "tab:purple",
-                "tab:gray",
-            ]
-
-            ax2.bar(x=x, height=y, align="center", edgecolor="black", color=colors)
-            ax2.set_xlabel(None)
-            ax2.set_xlim(-1, len(x))
-            ax2.tick_params(axis="x", labelsize=20)
-            ax2.tick_params(axis="y", labelsize=20)
-            ax2.set_ylabel(None)
-            ax2.set_ylim(0, ymax)
-            ax2.grid(which="major", axis="y", linestyle="--")
-
-            # Legend
-            labels = [
-                r"Aliphatic apolar",
-                r"Aromatic",
-                r"Polar uncharged",
-                r"Negatively charged",
-                r"Positively charged",
-                r"Non-standard",
-            ]
-            handles = [
-                plt.Rectangle((0, 0), 1, 1, facecolor=colors[label], edgecolor="black")
-                for label in range(len(labels))
-            ]
-            fig.legend(
-                handles,
-                labels,
-                fontsize=15,
-                fancybox=True,
-                shadow=True,
-                loc="lower center",
-                ncol=6,
-            )
-
-            # Adjust plots
-            fig.tight_layout()
-            fig.subplots_adjust(bottom=0.12)
-
-            # Save page
-            pdf.savefig()
-            plt.close()
          
-
-
-
          [docs]def write_results(
-    fn: Union[str, pathlib.Path],
-    input: Optional[Union[str, pathlib.Path]],
-    ligand: Optional[Union[str, pathlib.Path]],
-    output: Optional[Union[str, pathlib.Path]],
-    output_hydropathy: Optional[Union[str, pathlib.Path]] = None,
-    volume: Optional[Dict[str, float]] = None,
-    area: Optional[Dict[str, float]] = None,
-    max_depth: Optional[Dict[str, float]] = None,
-    avg_depth: Optional[Dict[str, float]] = None,
-    avg_hydropathy: Optional[Dict[str, float]] = None,
-    residues: Optional[Dict[str, List[List[str]]]] = None,
-    frequencies: Optional[Dict[str, Dict[str, Dict[str, int]]]] = None,
-    step: Union[float, int] = 0.6,
-) -> None:
-    """Writes file paths and cavity characterization to TOML-formatted file.
-
-    Parameters
-    ----------
-    fn : Union[str, pathlib.Path]
-        A path to TOML-formatted file for writing file paths and
-        cavity characterization (volume, area, depth [optional] and interface
-        residues) per cavity detected.
-    input : Union[str, pathlib.Path], optional
-        A path to input PDB or XYZ file.
-    ligand : Union[str, pathlib.Path], optional
-        A path to ligand PDB or XYZ file.
-    output : Union[str, pathlib.Path], optional
-        A path to cavity PDB file.
-    output_hydropathy : Union[str, pathlib.Path], optional
-        A path to hydropathy PDB file (surface points mapped with a
-        hydrophobicity scale), by default None.
-    volume : Dict[str, float], optional
-        A dictionary with volume of each detected cavity, by default None.
-    area : Dict[str, float], optional
-        A dictionary with area of each detected cavity, by default None.
-    max_depth : Dict[str, float], optional
-        A dictionary with maximum depth of each detected cavity, by default
-        None.
-    avg_depth : Dict[str, float], optional
-        A dictionary with average depth of each detected cavity, by default
-        None.
-    avg_hydropapthy : Dict[str, float], optional
-        A dictionary with average hydropathy of each detected cavity and range
-        of the hydrophobicity scale mapped, by default None.
-    residues : Dict[str, List[List[str]]], optional
-        A dictionary with interface residues of each detected cavity, by
-        default None.
-    frequencies : Dict[str, Dict[str, Dict[str, int]]], optional
-        A dictionary with frequencies of interface residues and classes of
-        residues of each detected cavity, by default None.
-    step : Union[float, int], optional
-        Grid spacing (A), by default 0.6.
-
-    Raises
-    ------
-    TypeError
-        `fn` must be a string or a pathlib.Path.
-    TypeError
-        `input` must be a string or a pathlib.Path.
-    TypeError
-        `ligand` must be a string or a pathlib.Path.
-    TypeError
-        `output` must be a string or a pathlib.Path.
-    TypeError
-        `output_hydropathy` must be a string or a pathlib.Path.
-    TypeError
-        `volume` must be a dictionary.
-    TypeError
-        `area` must be a dictionary.
-    TypeError
-        `max_depth` must be a dictionary.
-    TypeError
-        `avg_depth` must be a dictionary.
-    TypeError
-        `avg_hydropathy` must be a dictionary.
-    TypeError
-        `residues` must be a dictionary.
-    TypeError
-        `frequencies` must be a dictionary.
-    TypeError
-        `step` must be a positive real number.
-    ValueError
-        `step` must be a positive real number.
-
-    Note
-    ----
-    The cavity nomenclature is based on the integer label. The cavity
-    marked with 2, the first integer corresponding to a cavity, is KAA, the
-    cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
-
-    See Also
-    --------
-    detect
-    spatial
-    depth
-    constitutional
-    hydropathy
-    export
-
-    Example
-    -------
-    With the cavity and surface points identified and depth and hydrophobicity scale mapped in the 3D grid, we can:
-
-    * Write cavity detection:
-
-    >>> from pyKVFinder import write_results
-    >>> import os
-    >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
-    >>> write_results('results.toml', input=pdb, ligand=None, output='cavities.pdb')
-
-    * Write spatial characterization
-
-    >>> volume
-    {'KAA': 137.16, 'KAB': 47.52, 'KAC': 66.96, 'KAD': 8.21, 'KAE': 43.63, 'KAF': 12.53, 'KAG': 6.26, 'KAH': 520.13, 'KAI': 12.31, 'KAJ': 26.57, 'KAK': 12.31, 'KAL': 33.91, 'KAM': 23.11, 'KAN': 102.82, 'KAO': 6.05, 'KAP': 15.55, 'KAQ': 7.99, 'KAR': 7.78}
-    >>> area
-    {'KAA': 120.52, 'KAB': 58.76, 'KAC': 72.06, 'KAD': 17.62, 'KAE': 56.44, 'KAF': 22.53, 'KAG': 15.38, 'KAH': 489.25, 'KAI': 29.87, 'KAJ': 44.85, 'KAK': 30.58, 'KAL': 43.59, 'KAM': 45.25, 'KAN': 129.77, 'KAO': 11.57, 'KAP': 24.8, 'KAQ': 12.59, 'KAR': 15.97}
-    >>> write_results('results.toml', input=pdb, ligand=None, output=None, volume=volume, area=area)
-
-    * Write constitutional characterization
-
-    >>> residues
-    {'KAA': [['14', 'E', 'SER'], ['15', 'E', 'VAL'], ['18', 'E', 'PHE'], ['19', 'E', 'LEU'], ['100', 'E', 'PHE'], ['152', 'E', 'LEU'], ['155', 'E', 'GLU'], ['156', 'E', 'TYR'], ['292', 'E', 'LYS'], ['302', 'E', 'TRP'], ['303', 'E', 'ILE'], ['306', 'E', 'TYR']], 'KAB': [['18', 'E', 'PHE'], ['22', 'E', 'ALA'], ['25', 'E', 'ASP'], ['26', 'E', 'PHE'], ['29', 'E', 'LYS'], ['97', 'E', 'ALA'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['156', 'E', 'TYR']], 'KAC': [['141', 'E', 'PRO'], ['142', 'E', 'HIS'], ['144', 'E', 'ARG'], ['145', 'E', 'PHE'], ['148', 'E', 'ALA'], ['299', 'E', 'THR'], ['300', 'E', 'THR'], ['305', 'E', 'ILE'], ['310', 'E', 'VAL'], ['311', 'E', 'GLU'], ['313', 'E', 'PRO']], 'KAD': [['122', 'E', 'TYR'], ['124', 'E', 'ALA'], ['176', 'E', 'GLN'], ['318', 'E', 'PHE'], ['320', 'E', 'GLY'], ['321', 'E', 'PRO'], ['322', 'E', 'GLY'], ['323', 'E', 'ASP']], 'KAE': [['95', 'E', 'LEU'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['100', 'E', 'PHE'], ['103', 'E', 'LEU'], ['104', 'E', 'VAL'], ['105', 'E', 'LYS'], ['106', 'E', 'LEU']], 'KAF': [['123', 'E', 'VAL'], ['124', 'E', 'ALA'], ['175', 'E', 'ASP'], ['176', 'E', 'GLN'], ['181', 'E', 'GLN']], 'KAG': [['34', 'E', 'SER'], ['37', 'E', 'THR'], ['96', 'E', 'GLN'], ['106', 'E', 'LEU'], ['107', 'E', 'GLU'], ['108', 'E', 'PHE'], ['109', 'E', 'SER']], 'KAH': [['49', 'E', 'LEU'], ['50', 'E', 'GLY'], ['51', 'E', 'THR'], ['52', 'E', 'GLY'], ['53', 'E', 'SER'], ['54', 'E', 'PHE'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['72', 'E', 'LYS'], ['74', 'E', 'LEU'], ['84', 'E', 'GLN'], ['87', 'E', 'HIS'], ['88', 'E', 'THR'], ['91', 'E', 'GLU'], ['104', 'E', 'VAL'], ['120', 'E', 'MET'], ['121', 'E', 'GLU'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['166', 'E', 'ASP'], ['168', 'E', 'LYS'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['184', 'E', 'ASP'], ['186', 'E', 'GLY'], ['187', 'E', 'PHE'], ['201', 'E', 'THR'], ['327', 'E', 'PHE']], 'KAI': [['131', 'E', 'HIS'], ['138', 'E', 'PHE'], ['142', 'E', 'HIS'], ['146', 'E', 'TYR'], ['174', 'E', 'ILE'], ['314', 'E', 'PHE']], 'KAJ': [['33', 'E', 'PRO'], ['89', 'E', 'LEU'], ['92', 'E', 'LYS'], ['93', 'E', 'ARG'], ['96', 'E', 'GLN'], ['349', 'E', 'GLU'], ['350', 'E', 'PHE']], 'KAK': [['157', 'E', 'LEU'], ['162', 'E', 'LEU'], ['163', 'E', 'ILE'], ['164', 'E', 'TYR'], ['185', 'E', 'PHE'], ['188', 'E', 'ALA']], 'KAL': [['49', 'E', 'LEU'], ['127', 'E', 'GLU'], ['129', 'E', 'PHE'], ['130', 'E', 'SER'], ['326', 'E', 'ASN'], ['327', 'E', 'PHE'], ['328', 'E', 'ASP'], ['330', 'E', 'TYR']], 'KAM': [['51', 'E', 'THR'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['73', 'E', 'ILE'], ['74', 'E', 'LEU'], ['75', 'E', 'ASP'], ['115', 'E', 'ASN'], ['335', 'E', 'ILE'], ['336', 'E', 'ARG']], 'KAN': [['165', 'E', 'ARG'], ['166', 'E', 'ASP'], ['167', 'E', 'LEU'], ['199', 'E', 'CYS'], ['200', 'E', 'GLY'], ['201', 'E', 'THR'], ['204', 'E', 'TYR'], ['205', 'E', 'LEU'], ['206', 'E', 'ALA'], ['209', 'E', 'ILE'], ['219', 'E', 'VAL'], ['220', 'E', 'ASP'], ['223', 'E', 'ALA']], 'KAO': [['48', 'E', 'THR'], ['51', 'E', 'THR'], ['56', 'E', 'ARG'], ['330', 'E', 'TYR'], ['331', 'E', 'GLU']], 'KAP': [['222', 'E', 'TRP'], ['238', 'E', 'PHE'], ['253', 'E', 'GLY'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['273', 'E', 'LEU']], 'KAQ': [['207', 'E', 'PRO'], ['208', 'E', 'GLU'], ['211', 'E', 'LEU'], ['213', 'E', 'LYS'], ['275', 'E', 'VAL'], ['277', 'E', 'LEU']], 'KAR': [['237', 'E', 'PRO'], ['238', 'E', 'PHE'], ['249', 'E', 'LYS'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['256', 'E', 'ARG']]}
-    >>> frequencies
-    {'KAA': {'RESIDUES': {'GLU': 1, 'ILE': 1, 'LEU': 2, 'LYS': 1, 'PHE': 2, 'SER': 1, 'TRP': 1, 'TYR': 2, 'VAL': 1}, 'CLASS': {'R1': 4, 'R2': 5, 'R3': 1, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAB': {'RESIDUES': {'ALA': 2, 'ASN': 1, 'ASP': 1, 'LYS': 1, 'PHE': 2, 'TYR': 1, 'VAL': 1}, 'CLASS': {'R1': 3, 'R2': 3, 'R3': 1, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAC': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'GLU': 1, 'HIS': 1, 'ILE': 1, 'PHE': 1, 'PRO': 2, 'THR': 2, 'VAL': 1}, 'CLASS': {'R1': 5, 'R2': 1, 'R3': 2, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAD': {'RESIDUES': {'ALA': 1, 'ASP': 1, 'GLN': 1, 'GLY': 2, 'PHE': 1, 'PRO': 1, 'TYR': 1}, 'CLASS': {'R1': 4, 'R2': 2, 'R3': 1, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAE': {'RESIDUES': {'ASN': 1, 'LEU': 3, 'LYS': 1, 'PHE': 1, 'VAL': 2}, 'CLASS': {'R1': 5, 'R2': 1, 'R3': 1, 'R4': 0, 'R5': 1, 'RX': 0}}, 'KAF': {'RESIDUES': {'ALA': 1, 'ASP': 1, 'GLN': 2, 'VAL': 1}, 'CLASS': {'R1': 2, 'R2': 0, 'R3': 2, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAG': {'RESIDUES': {'GLN': 1, 'GLU': 1, 'LEU': 1, 'PHE': 1, 'SER': 2, 'THR': 1}, 'CLASS': {'R1': 1, 'R2': 1, 'R3': 4, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAH': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'ASN': 1, 'ASP': 2, 'GLN': 1, 'GLU': 4, 'GLY': 4, 'HIS': 1, 'LEU': 3, 'LYS': 2, 'MET': 1, 'PHE': 3, 'SER': 1, 'THR': 4, 'TYR': 1, 'VAL': 3}, 'CLASS': {'R1': 11, 'R2': 4, 'R3': 8, 'R4': 6, 'R5': 4, 'RX': 0}}, 'KAI': {'RESIDUES': {'HIS': 2, 'ILE': 1, 'PHE': 2, 'TYR': 1}, 'CLASS': {'R1': 1, 'R2': 3, 'R3': 0, 'R4': 0, 'R5': 2, 'RX': 0}}, 'KAJ': {'RESIDUES': {'ARG': 1, 'GLN': 1, 'GLU': 1, 'LEU': 1, 'LYS': 1, 'PHE': 1, 'PRO': 1}, 'CLASS': {'R1': 2, 'R2': 1, 'R3': 1, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAK': {'RESIDUES': {'ALA': 1, 'ILE': 1, 'LEU': 2, 'PHE': 1, 'TYR': 1}, 'CLASS': {'R1': 4, 'R2': 2, 'R3': 0, 'R4': 0, 'R5': 0, 'RX': 0}}, 'KAL': {'RESIDUES': {'ASN': 1, 'ASP': 1, 'GLU': 1, 'LEU': 1, 'PHE': 2, 'SER': 1, 'TYR': 1}, 'CLASS': {'R1': 1, 'R2': 3, 'R3': 2, 'R4': 2, 'R5': 0, 'RX': 0}}, 'KAM': {'RESIDUES': {'ARG': 2, 'ASN': 1, 'ASP': 1, 'GLY': 1, 'ILE': 2, 'LEU': 1, 'THR': 1}, 'CLASS': {'R1': 4, 'R2': 0, 'R3': 2, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAN': {'RESIDUES': {'ALA': 2, 'ARG': 1, 'ASP': 2, 'CYS': 1, 'GLY': 1, 'ILE': 1, 'LEU': 2, 'THR': 1, 'TYR': 1, 'VAL': 1}, 'CLASS': {'R1': 7, 'R2': 1, 'R3': 2, 'R4': 2, 'R5': 1, 'RX': 0}}, 'KAO': {'RESIDUES': {'ARG': 1, 'GLU': 1, 'THR': 2, 'TYR': 1}, 'CLASS': {'R1': 0, 'R2': 1, 'R3': 2, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAP': {'RESIDUES': {'GLY': 1, 'LEU': 1, 'LYS': 1, 'PHE': 1, 'TRP': 1, 'VAL': 1}, 'CLASS': {'R1': 3, 'R2': 2, 'R3': 0, 'R4': 0, 'R5': 1, 'RX': 0}}, 'KAQ': {'RESIDUES': {'GLU': 1, 'LEU': 2, 'LYS': 1, 'PRO': 1, 'VAL': 1}, 'CLASS': {'R1': 4, 'R2': 0, 'R3': 0, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAR': {'RESIDUES': {'ARG': 1, 'LYS': 2, 'PHE': 1, 'PRO': 1, 'VAL': 1}, 'CLASS': {'R1': 2, 'R2': 1, 'R3': 0, 'R4': 0, 'R5': 3, 'RX': 0}}}
-    >>> write_results('results.toml', input=pdb, ligand=None, output=output_cavity, volume=volume, area=area, residues=residues, frequencies=frequencies)
-
-    * Write depth characterization
-
-    >>> max_depth
-    {'KAA': 3.79, 'KAB': 2.68, 'KAC': 2.62, 'KAD': 0.85, 'KAE': 3.0, 'KAF': 0.85, 'KAG': 0.6, 'KAH': 10.73, 'KAI': 2.55, 'KAJ': 2.24, 'KAK': 0.0, 'KAL': 3.0, 'KAM': 1.2, 'KAN': 0.0, 'KAO': 1.04, 'KAP': 2.08, 'KAQ': 0.85, 'KAR': 0.6}
-    >>> avg_depth
-    {'KAA': 1.28, 'KAB': 0.86, 'KAC': 0.67, 'KAD': 0.29, 'KAE': 0.98, 'KAF': 0.24, 'KAG': 0.1, 'KAH': 3.75, 'KAI': 1.5, 'KAJ': 0.96, 'KAK': 0.0, 'KAL': 1.0, 'KAM': 0.24, 'KAN': 0.0, 'KAO': 0.29, 'KAP': 0.7, 'KAQ': 0.22, 'KAR': 0.12}
-    >>> write_results('results.toml', input=pdb, ligand=None, output=None, max_depth=max_depth, avg_depth=avg_depth)
-
-    * Write hydropathy characterization
-
-    >>> avg_hydropathy
-    {'KAA': -0.73, 'KAB': -0.06, 'KAC': -0.07, 'KAD': -0.62, 'KAE': -0.81, 'KAF': -0.14, 'KAG': -0.33, 'KAH': -0.16, 'KAI': -0.4, 'KAJ': 0.62, 'KAK': -0.99, 'KAL': 0.35, 'KAM': -0.33, 'KAN': 0.18, 'KAO': 0.88, 'KAP': -0.96, 'KAQ': 0.48, 'KAR': 0.24, 'EisenbergWeiss': [-1.42, 2.6]}
-    >>> write_results('results.toml', input=pdb, ligand=None, output=None, output_hydropathy='hydropathy.pdb', avg_hydropathy=avg_hydropathy)
-
-    * Write all
-
-    >>> write_results('results.toml', input=pdb, ligand=None, output='cavities.pdb', output_hydropathy='hydropathy.pdb', volume=volume, area=area, max_depth=max_depth, avg_depth=avg_depth, avg_hydropathy=avg_hydropathy, residues=residues, frequencies=frequencies)
-
-    """
-    import toml
-
-    # Check arguments
-    if type(fn) not in [str, pathlib.Path]:
-        raise TypeError("`fn` must be a string or a pathlib.Path.")
-    if input is not None:
-        if type(input) not in [str, pathlib.Path]:
-            raise TypeError("`input` must be a string or a pathlib.Path.")
-    if ligand is not None:
-        if type(ligand) not in [str, pathlib.Path]:
-            raise TypeError("`ligand` must be a string or a pathlib.Path.")
-    if output is not None:
-        if type(output) not in [str, pathlib.Path]:
-            raise TypeError("`output` must be a string or a pathlib.Path.")
-    if output_hydropathy is not None:
-        if type(output_hydropathy) not in [str, pathlib.Path]:
-            raise TypeError("`output_hydropathy` must be a string or a pathlib.Path.")
-    if volume is not None:
-        if type(volume) not in [dict]:
-            raise TypeError("`volume` must be a dictionary.")
-    if area is not None:
-        if type(area) not in [dict]:
-            raise TypeError("`area` must be a dictionary.")
-    if max_depth is not None:
-        if type(max_depth) not in [dict]:
-            raise TypeError("`max_depth` must be a dictionary.")
-    if avg_depth is not None:
-        if type(avg_depth) not in [dict]:
-            raise TypeError("`avg_depth` must be a dictionary.")
-    if avg_hydropathy is not None:
-        if type(avg_hydropathy) not in [dict]:
-            raise TypeError("`avg_hydropathy` must be a dictionary.")
-    if residues is not None:
-        if type(residues) not in [dict]:
-            raise TypeError("`residues` must be a dictionary.")
-    if frequencies is not None:
-        if type(frequencies) not in [dict]:
-            raise TypeError("`frequencies` must be a dictionary.")
-    if type(step) not in [float, int]:
-        raise TypeError("`step` must be a positive real number.")
-    elif step <= 0.0:
-        raise ValueError("`step` must be a positive real number.")
-
-    # Convert types
-    if type(step) == int:
-        step = float(step)
-
-    # Create base directories of results
-    os.makedirs(os.path.abspath(os.path.dirname(fn)), exist_ok=True)
-
-    # Prepare paths
-    input = os.path.abspath(input)
-    if ligand:
-        ligand = os.path.abspath(ligand)
-    if output:
-        output = os.path.abspath(output)
-    if output_hydropathy:
-        output_hydropathy = os.path.abspath(output_hydropathy)
-
-    # Create output dictionary for results file
-    files = {
-        "INPUT": input,
-        "LIGAND": ligand,
-        "OUTPUT": output,
-        "HYDROPATHY": output_hydropathy,
-    }
-    parameters = {
-        "STEP": step,
-    }
-    results = (
-        {
-            "VOLUME": volume,
-            "AREA": area,
-            "MAX_DEPTH": max_depth,
-            "AVG_DEPTH": avg_depth,
-            "AVG_HYDROPATHY": avg_hydropathy,
-            "RESIDUES": residues,
-            "FREQUENCY": frequencies,
-        }
-        if (volume is not None)
-        or (area is not None)
-        or (max_depth is not None)
-        or (avg_depth is not None)
-        or (avg_hydropathy is not None)
-        or (residues is not None)
-        or (frequencies is not None)
-        else None
-    )
-
-    # Create base directories of results TOML file
-    os.makedirs(os.path.abspath(os.path.dirname(fn)), exist_ok=True)
-
-    # Write results to TOML file
-    with open(fn, "w") as f:
-        f.write("# pyKVFinder results\n\n")
-        toml.dump(
-            {
-                "FILES": files,
-                "PARAMETERS": parameters,
-                "RESULTS": results,
-            },
-            f,
-        )
          
-
          
-
-           
          
-          
          
-          
-        
          
-      
          
-    
          
-  
          
-   
-
-
-
\ No newline at end of file
diff --git a/docs/source/_build/html/_sources/_about/index.rst.txt b/docs/source/_build/html/_sources/_about/index.rst.txt
deleted file mode 100644
index 36d5e702..00000000
--- a/docs/source/_build/html/_sources/_about/index.rst.txt
+++ /dev/null
@@ -1,50 +0,0 @@
-.. raw:: html
-
-    
          About
          
-
-Issues
-======
-
-pyKVFinder package uses GitHub for project management. Please help us by reporting any problems or requests.
-
-On `Issues `_ page, you can file a:
-
-.. toctree::
-    
-    Bug Report 
-    Request for a new feature 
-
-Only make sure the bug or request has not already been reported. Click on “Search” and enter some keywords to search.
-
-Thank you for helping us improve pyKVFinder!
-
-Scientific team
-===============
-
-pyKVFinder was developed by:
-
-- João Victor da Silva Guerra
-- Helder Veras Ribeiro Filho
-- Gabriel Ernesto Jara
-- Leandro Oliveira Bortot
-- José Geraldo de Carvalho Pereira
-- Paulo Sergio Lopes de Oliveira
-
-Computational Biology Laboratory (`LBC `_), Brazilian Biosciences National Laboratory (`LNBio `_), Brazilian Center for Research in Energy and Materials (`CNPEM `_)
-
-If you have any further questions, inquires or if you wish to contribute to KVFinder project, please contact us at joao.guerra@lnbio.cnpem.br or paulo.oliveira@lnbio.cnpem.br.
-
-Citing pyKVFinder
-=================
-
-Guerra, J.V.d., Ribeiro-Filho, H.V., Jara, G.E. et al. pyKVFinder: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science. BMC Bioinformatics 22, 607 (2021). `https://doi.org/10.1186/s12859-021-04519-4 `_.
-
-Funding
-=======
-
-This work was supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) [Grant Number 2018/00629-0], Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) [Grant Number 350244/2020-0], and Brazilian Center for Research in Energy and Materials (CNPEM).
-
-License
-=======
-
-The software is licensed under the terms of the GNU General Public License version 3 (GPL3) and is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
diff --git a/docs/source/_build/html/_sources/_api_reference/Molecule.rst.txt b/docs/source/_build/html/_sources/_api_reference/Molecule.rst.txt
deleted file mode 100644
index 1a94fcd7..00000000
--- a/docs/source/_build/html/_sources/_api_reference/Molecule.rst.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-pyKVFinder.Molecule
-===================
-
-.. autoclass:: pyKVFinder.Molecule
-    :members:
diff --git a/docs/source/_build/html/_sources/_api_reference/calculate_frequencies.rst.txt b/docs/source/_build/html/_sources/_api_reference/calculate_frequencies.rst.txt
deleted file mode 100644
index c0cf1da6..00000000
--- a/docs/source/_build/html/_sources/_api_reference/calculate_frequencies.rst.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-pyKVFinder.calculate_frequencies
-================================
-
-.. autofunction:: pyKVFinder.calculate_frequencies
diff --git a/docs/source/_build/html/_sources/_api_reference/constitutional.rst.txt b/docs/source/_build/html/_sources/_api_reference/constitutional.rst.txt
deleted file mode 100644
index 435ec154..00000000
--- a/docs/source/_build/html/_sources/_api_reference/constitutional.rst.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-pyKVFinder.constitutional
-=========================
-
-.. autofunction:: pyKVFinder.constitutional
diff --git a/docs/source/_build/html/_sources/_api_reference/depth.rst.txt b/docs/source/_build/html/_sources/_api_reference/depth.rst.txt
deleted file mode 100644
index 6a539ff1..00000000
--- a/docs/source/_build/html/_sources/_api_reference/depth.rst.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-pyKVFinder.depth
-================
-
-.. autofunction:: pyKVFinder.depth
diff --git a/docs/source/_build/html/_sources/_api_reference/detect.rst.txt b/docs/source/_build/html/_sources/_api_reference/detect.rst.txt
deleted file mode 100644
index 6b7d5c16..00000000
--- a/docs/source/_build/html/_sources/_api_reference/detect.rst.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-pyKVFinder.detect
-=================
-
-.. autofunction:: pyKVFinder.detect
diff --git a/docs/source/_build/html/_sources/_api_reference/export.rst.txt b/docs/source/_build/html/_sources/_api_reference/export.rst.txt
deleted file mode 100644
index 75cf0f41..00000000
--- a/docs/source/_build/html/_sources/_api_reference/export.rst.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-pyKVFinder.export
-=================
-
-.. autofunction:: pyKVFinder.export
diff --git a/docs/source/_build/html/_sources/_api_reference/export_openings.rst.txt b/docs/source/_build/html/_sources/_api_reference/export_openings.rst.txt
deleted file mode 100644
index 1c7c3d33..00000000
--- a/docs/source/_build/html/_sources/_api_reference/export_openings.rst.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-pyKVFinder.export_openings
-==========================
-
-.. autofunction:: pyKVFinder.export_openings
diff --git a/docs/source/_build/html/_sources/_api_reference/get_vertices.rst.txt b/docs/source/_build/html/_sources/_api_reference/get_vertices.rst.txt
deleted file mode 100644
index 14bca8fa..00000000
--- a/docs/source/_build/html/_sources/_api_reference/get_vertices.rst.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-pyKVFinder.get_vertices
-=======================
-
-.. autofunction:: pyKVFinder.get_vertices
diff --git a/docs/source/_build/html/_sources/_api_reference/get_vertices_from_file.rst.txt b/docs/source/_build/html/_sources/_api_reference/get_vertices_from_file.rst.txt
deleted file mode 100644
index 217efee7..00000000
--- a/docs/source/_build/html/_sources/_api_reference/get_vertices_from_file.rst.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-pyKVFinder.get_vertices_from_file
-=================================
-
-.. autofunction:: pyKVFinder.get_vertices_from_file
diff --git a/docs/source/_build/html/_sources/_api_reference/hydropathy.rst.txt b/docs/source/_build/html/_sources/_api_reference/hydropathy.rst.txt
deleted file mode 100644
index f4318500..00000000
--- a/docs/source/_build/html/_sources/_api_reference/hydropathy.rst.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-pyKVFinder.hydropathy
-=====================
-
-.. autofunction:: pyKVFinder.hydropathy
diff --git a/docs/source/_build/html/_sources/_api_reference/openings.rst.txt b/docs/source/_build/html/_sources/_api_reference/openings.rst.txt
deleted file mode 100644
index 9c0ea59d..00000000
--- a/docs/source/_build/html/_sources/_api_reference/openings.rst.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-pyKVFinder.openings
-===================
-
-.. autofunction:: pyKVFinder.openings
diff --git a/docs/source/_build/html/_sources/_api_reference/plot_frequencies.rst.txt b/docs/source/_build/html/_sources/_api_reference/plot_frequencies.rst.txt
deleted file mode 100644
index 73232df4..00000000
--- a/docs/source/_build/html/_sources/_api_reference/plot_frequencies.rst.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-pyKVFinder.plot_frequencies
-===========================
-
-.. autofunction:: pyKVFinder.plot_frequencies
diff --git a/docs/source/_build/html/_sources/_api_reference/pyKVFinderResults.rst.txt b/docs/source/_build/html/_sources/_api_reference/pyKVFinderResults.rst.txt
deleted file mode 100644
index 67d17f1d..00000000
--- a/docs/source/_build/html/_sources/_api_reference/pyKVFinderResults.rst.txt
+++ /dev/null
@@ -1,5 +0,0 @@
-pyKVFinder.pyKVFinderResults
-============================
-
-.. autoclass:: pyKVFinder.pyKVFinderResults
-    :members:
diff --git a/docs/source/_build/html/_sources/_api_reference/read_cavity.rst.txt b/docs/source/_build/html/_sources/_api_reference/read_cavity.rst.txt
deleted file mode 100644
index e65ab82b..00000000
--- a/docs/source/_build/html/_sources/_api_reference/read_cavity.rst.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-pyKVFinder.read_cavity
-======================
-
-.. autofunction:: pyKVFinder.read_cavity
diff --git a/docs/source/_build/html/_sources/_api_reference/read_pdb.rst.txt b/docs/source/_build/html/_sources/_api_reference/read_pdb.rst.txt
deleted file mode 100644
index 55e3c150..00000000
--- a/docs/source/_build/html/_sources/_api_reference/read_pdb.rst.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-pyKVFinder.read_pdb
-===================
-
-.. autofunction:: pyKVFinder.read_pdb
diff --git a/docs/source/_build/html/_sources/_api_reference/read_vdw.rst.txt b/docs/source/_build/html/_sources/_api_reference/read_vdw.rst.txt
deleted file mode 100644
index 354f7244..00000000
--- a/docs/source/_build/html/_sources/_api_reference/read_vdw.rst.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-pyKVFinder.read_vdw
--------------------
-
-.. autofunction:: pyKVFinder.read_vdw
diff --git a/docs/source/_build/html/_sources/_api_reference/read_xyz.rst.txt b/docs/source/_build/html/_sources/_api_reference/read_xyz.rst.txt
deleted file mode 100644
index 95fa58ef..00000000
--- a/docs/source/_build/html/_sources/_api_reference/read_xyz.rst.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-pyKVFinder.read_xyz
-===================
-
-.. autofunction:: pyKVFinder.read_xyz
diff --git a/docs/source/_build/html/_sources/_api_reference/run_workflow.rst.txt b/docs/source/_build/html/_sources/_api_reference/run_workflow.rst.txt
deleted file mode 100644
index 4c429035..00000000
--- a/docs/source/_build/html/_sources/_api_reference/run_workflow.rst.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-pyKVFinder.run_workflow
-=======================
-
-.. autofunction:: pyKVFinder.run_workflow(input: Union[str, pathlib.Path], ligand: Optional[Union[str, pathlib.Path]] = None, vdw: Optional[Union[str, pathlib.Path]] = None, box: Optional[Union[str, pathlib.Path]] = None, step: Union[float, int] = 0.6, probe_in: Union[float, int] = 1.4, probe_out: Union[float, int] = 4.0, removal_distance: Union[float, int] = 2.4, volume_cutoff: Union[float, int] = 5.0, ligand_cutoff: Union[float, int] = 5.0, include_depth: bool = False, include_hydropathy: bool = False, hydrophobicity_scale: Union[str, pathlib.Path] = 'EisenbergWeiss', surface: str = 'SES', ignore_backbone: bool = False, model: Optional[int] = None, nthreads: Optional[int] = None, verbose: bool = False) -> pyKVFinder.pyKVFinderResults
diff --git a/docs/source/_build/html/_sources/_api_reference/spatial.rst.txt b/docs/source/_build/html/_sources/_api_reference/spatial.rst.txt
deleted file mode 100644
index 87f5bcb5..00000000
--- a/docs/source/_build/html/_sources/_api_reference/spatial.rst.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-pyKVFinder.spatial
-==================
-
-.. autofunction:: pyKVFinder.spatial
diff --git a/docs/source/_build/html/_sources/_api_reference/write_results.rst.txt b/docs/source/_build/html/_sources/_api_reference/write_results.rst.txt
deleted file mode 100644
index 8124d11a..00000000
--- a/docs/source/_build/html/_sources/_api_reference/write_results.rst.txt
+++ /dev/null
@@ -1,4 +0,0 @@
-pyKVFinder.write_results
-========================
-
-.. autofunction:: pyKVFinder.write_results
diff --git a/docs/source/_build/html/_sources/_cfg_files/box_file_template.rst.txt b/docs/source/_build/html/_sources/_cfg_files/box_file_template.rst.txt
deleted file mode 100644
index c0d5d330..00000000
--- a/docs/source/_build/html/_sources/_cfg_files/box_file_template.rst.txt
+++ /dev/null
@@ -1,51 +0,0 @@
-Box configuration file template
-###############################
-
-There are three methods for defining a custom 3D grid in pyKVFinder.
-
-The first directly defines four vertices of the 3D grid (origin, X-axis, Y-axis and Z-axis), an example is shown below:
-
-.. code-block:: TOML
-
-  [box]
-  # px = [x, y, z]
-  p1 = [0.0, 0.0, 0.0]
-  p2 = [1.0, 0.0, 0.0]
-  p3 = [0.0, 1.0, 0.0]
-  p4 = [0.0, 0.0, 1.0]
-
-Example: `custom-box.toml `_.
-
-The second defines a list of residues and a padding, the template is shown below:
-
-.. code-block:: TOML
-
-  [box]
-  residues = [ ["resnum", "chain", "resname",], ["resnum", "chain", "resname",], ]
-  padding =  3.5
-
-Example: `residues-box.toml `_.
-
-The third uses `parKVFinder `_'s TOML-formatted parameters file created by its PyMOL plugin.
-
-.. code-block:: python
-
-	[SETTINGS.visiblebox.p1]
-	x = 0.0
-	y = 0.0
-	z = 0.0
-
-	[SETTINGS.visiblebox.p2]
-	x = 1.0
-	y = 0.0
-	z = 0.0
-
-	[SETTINGS.visiblebox.p3]
-	x = 0.0
-	y = 1.0
-	z = 0.0
-
-	[SETTINGS.visiblebox.p4]
-	x = 0.0
-	y = 0.0
-	z = 1.0
diff --git a/docs/source/_build/html/_sources/_cfg_files/hydrophobicity_scale_file_template.rst.txt b/docs/source/_build/html/_sources/_cfg_files/hydrophobicity_scale_file_template.rst.txt
deleted file mode 100644
index 3c7ae099..00000000
--- a/docs/source/_build/html/_sources/_cfg_files/hydrophobicity_scale_file_template.rst.txt
+++ /dev/null
@@ -1,44 +0,0 @@
-Hydrophobicity scale file template
-##################################
-
-The hydrophobicity scale file defines the name of the scale and the hydrophobicity value for each residue and when not defined, it assigns zero to the missing residues. The package contains six built-in hydrophobicity scales: `Eisenberg & Weiss `_ [1], `Hessa & Heijne `_ [2], `Kyte & Doolittle `_ [3], `Moon & Fleming `_ [4], `Wimley & White `_ [5] and `Zhao & London `_ [6]. However, the user can define its own file with a mandatory format and pass it to pyKVFinder. The format is shown below:
-
-.. code-block:: TOML
-
-    [EisenbergWeiss]
-    ALA = -0.64
-    ARG = 2.6
-    ASN = 0.8
-    ASP = 0.92
-    CYS = -0.3
-    GLN = 0.87
-    GLU = 0.76
-    GLY = -0.49
-    HIS = 0.41
-    ILE = -1.42
-    LEU = -1.09
-    LYS = 1.54
-    MET = -0.66
-    PHE = -1.22
-    PRO = -0.12
-    SER = 0.18
-    THR = 0.05
-    TRP = -0.83
-    TYR = -0.27
-    VAL = -1.11
-
-.. raw:: html
-
-    
          References
          
-
-1. Eisenberg D, Weiss RM, Terwilliger TC. The hydrophobic moment detects periodicity in protein hydrophobicity. Proceedings of the National Academy of Sciences. 1984;81. 
-
-2. Hessa T, Kim H, Bihlmaier K, Lundin C, Boekel J, Andersson H, et al. Recognition of transmembrane helices by the endoplasmic reticulum translocon. Nature. 2005;433. 
-
-3. Kyte J, Doolittle RF. A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology. 1982;157. 
-
-4. Moon CP, Fleming KG. Side-chain hydrophobicity scale derived from transmembrane protein folding into lipid bilayers. Proceedings of the National Academy of Sciences. 2011;108. 
-
-5. Wimley WC, White SH. Experimentally determined hydrophobicity scale for proteins at membrane interfaces. Nature Structural & Molecular Biology. 1996;3. 
-
-6. Zhao G, London E. An amino acid “transmembrane tendency” scale that approaches the theoretical limit to accuracy for prediction of transmembrane helices: Relationship to biological hydrophobicity. Protein Science. 2006;15. 
diff --git a/docs/source/_build/html/_sources/_cli/index.rst.txt b/docs/source/_build/html/_sources/_cli/index.rst.txt
deleted file mode 100644
index fb3b771c..00000000
--- a/docs/source/_build/html/_sources/_cli/index.rst.txt
+++ /dev/null
@@ -1,240 +0,0 @@
-.. raw:: html
-
-    
          Command-line interface
          
-
-In addition to pyKVFinder package, a command-line interface (CLI) is available to ease cavity detection and characterization with the full set of customizable parameters.
-
-.. code-block:: bash
-
-  $ pyKVFinder
-  Usage: pyKVFinder [-h] [-v] [--version] [-b ] [-O ]
-                    [--nthreads ] [-d ] [-s ] [-i ]
-                    [-o ] [-V ] [-R ] [-S ]
-                    [--ignore_backbone] [-D] [--plot_frequencies]
-                    [--hydropathy [{EisenbergWeiss, HessaHeijne, KyteDoolittle, 
-                    MoonFleming, WimleyWhite, ZhaoLondon, <.toml>}]]
-                    [-B <.toml>] [-L (<.pdb> | <.xyz>)] [--ligand_cutoff ]
-                    (<.pdb> | <.xyz>)
-
-Positional arguments
---------------------
-
-The positional arguments are:
-
-* ``(<.pdb> | <.xyz>)``: A path to a target PDB or XYZ file.
-  
-  .. code-block:: bash
-    
-    $ pyKVFinder <.pdb>
-
-Optional arguments
-------------------
-
-The optional arguments are:
-
-* ``-h`` or ``--help``: Show help message.
-  
-  .. code-block:: bash
-    
-    $ pyKVFinder -h
-    $ pyKVFinder --help
-
-* ``--version``: Display pyKVFinder version.
-  
-  .. code-block:: bash
-
-    $ pyKVFinder --version
-
-* ``-v`` or ``--verbose``: Print extra information to standard output.
-
-  .. code-block:: bash
-
-    $ pyKVFinder <.pdb> --verbose
-
-  :Default: ``False``
-
-* ``-b `` or ``--base_name ``: A prefix for output files.
-
-  .. code-block:: bash
-
-    $ pyKVFinder <.pdb> -b 
-    $ pyKVFinder <.pdb> --base_name 
-
-  :Default: Prefix of target PDB file (<.pdb>)
-
-* ``-O `` or ``--output_directory ``: A path to a directory for output files.
-
-  .. code-block:: bash
-
-    $ pyKVFinder <.pdb> -O 
-    $ pyKVFinder <.pdb> --output_directory 
-
-  :Default: Current working directory
-
-* ``--nthreads ``: Number of threads to apply in parallel routines.
-
-  .. code-block:: bash
-
-    $ pyKVFinder <.pdb> --nthreads 
-
-  :Default: ``os.cpu_count() - 1``
-
-Detection and characterization
-******************************
-
-The arguments for adjusting biomolecular detection are:
-
-* ``-d `` or ``--dictionary ``: A path to a van der Waals radii file (see template).
-
-  .. code-block:: bash
-
-    $ pyKVFinder <.pdb> -d 
-    $ pyKVFinder <.pdb> --dictionary 
-
-  :Default: ``vdw.dat``
-
-* ``-s `` or ``--step ``: Grid spacing (A).
-
-  .. code-block:: bash
-
-    $ pyKVFinder <.pdb> -s 
-    $ pyKVFinder <.pdb> --step 
-
-  :Default: ``0.6``
-
-* ``-i `` or ``--probe_in ``: Probe In size (A).
-
-  .. code-block:: bash
-
-    $ pyKVFinder <.pdb> -i 
-    $ pyKVFinder <.pdb> --probe_in 
-
-  :Default: ``1.4``
-
-* ``-o `` or ``--probe_out ``: Probe Out size (A).
-
-  .. code-block:: bash
-
-    $ pyKVFinder <.pdb> -o 
-    $ pyKVFinder <.pdb> --probe_out 
-
-  :Default: ``4.0``
-
-* ``-V `` or ``--volume_cutoff ``: Cavities volume filter (A3).
-
-  .. code-block:: bash
-
-    $ pyKVFinder <.pdb> -V 
-    $ pyKVFinder <.pdb> --volume_cutoff 
-
-  :Default: ``5.0``
-
-* ``-R `` or ``--removal_distance ``: Length to be removed from the cavity-bulk frontier (A).
-
-  .. code-block:: bash
-
-    $ pyKVFinder <.pdb> -R 
-    $ pyKVFinder <.pdb> --removal_distance 
-
-  :Default: ``2.4``
-
-* ``-S `` or ``--surface ``: A surface representation. Options are: ``SES`` and ``SAS``. SES specifies solvent excluded surface and SAS specifies solvent accessible surface.
-
-  .. code-block:: bash
-
-    $ pyKVFinder <.pdb> -S 
-    $ pyKVFinder <.pdb> --surface 
-
-  :Default: ``SES``
-
-* ``--ignore_backbone``: Ignore backbone contacts to cavity when defining interface residues.
-
-  .. code-block:: bash
-
-    $ pyKVFinder <.pdb> --ignore_backbone
-
-  :Default: ``None``
-
-Extra characterization
-**********************
-
-The parameters for additional characterization are:
-
-* ``--D or --depth``: Characterize the depth of the detected cavities. This mode includes depth of each cavity point as the B-factor in the cavity PDB file and maximum and average depth of the detected cavities in the results file.
-
-  .. code-block:: bash
-
-    $ pyKVFinder <.pdb> -D
-    $ pyKVFinder <.pdb> --depth
-
-  :Default: ``None``
-
-* ``--plot_frequencies``: Plot bar charts of calculated frequencies (residues and classes of residues) of the detected cavities in a PDF file. The classes of residues are aliphatic apolar (R1), aromatic (R2), polar uncharged (R3), negatively charged (R4), positively charged (R5) and non-standard (RX) residues.
-
-  .. code-block:: bash
-
-    $ pyKVFinder <.pdb> --plot_frequencies
-
-  :Default: ``None``
-
-* ``--hydropathy [{EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, WimleyWhite, ZhaoLondon, <.toml>}]``: Characterize the hydropathy of the detected cavities. This mode maps a target hydrophobicity scale as B-factor at surface points of the detected cavities. Also, it calculates the average hydropathy of each detected cavity. The constant hydrophobicity scale is EisenbergWeiss.
-
-  .. code-block:: bash
-
-    $ pyKVFinder <.pdb> --hydropathy
-
-  In addition, the user can define one of the built-in hydrophobicity scale. The built-in hydrophobicity scales are: EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, WimleyWhite and ZhaoLondon.
-
-  .. code-block:: bash
-
-    $ pyKVFinder <.pdb> --hydropathy EisenbergWeiss
-    $ pyKVFinder <.pdb> --hydropathy HessaHeijne
-    $ pyKVFinder <.pdb> --hydropathy KyteDoolittle
-    $ pyKVFinder <.pdb> --hydropathy MoonFleming
-    $ pyKVFinder <.pdb> --hydropathy WimleyWhite
-    $ pyKVFinder <.pdb> --hydropathy ZhaoLondon
-
-  Further, the user can also define a custom hydrophobicity scale file via a TOML-formatted file (see template).
-
-  .. code-block:: bash
-
-    $ pyKVFinder <.pdb> --hydropathy <.toml>
-
-  :Default: ``None``
-  :Constant: ``EisenbergWeiss``
-
-Box adjusment
-*************
-
-The box adjustment argument is:
-
-* ``-B <.toml>`` or ``--box <.toml>``: A path to TOML-formatted file with box parameters (see template). Adjust the 3D grid based on a list of residues (["resnum", "chain"]) and a padding or a set of four vertices (p1: origin, p2: X-axis max, p3: Y-axis max, p4: Z-axis max) with xyz coordinates ([x, y, z]).
-
-  .. code-block:: bash
-
-    $ pyKVFinder <.pdb> -B <.toml>
-    $ pyKVFinder <.pdb> --box <.toml>
-
-  :Default: ``None``
-
-Ligand adjustment
-*****************
-
-The ligand adjustment arguments are:
-
-* ``-L (<.pdb> | <.xyz>)`` or ``--ligand (<.pdb> | <.xyz>)``: A path to a ligand PDB or XYZ file to limit the cavities within a radius (ligand_cutoff) around it.
-
-  .. code-block:: bash
-
-    $ pyKVFinder <.pdb> -L <.pdb>
-    $ pyKVFinder <.pdb> --ligand <.pdb>
-
-  :Default: ``None``
-
-* ``--ligand_cutoff ``: A radius value to limit a space around the defined ligand.
-
-  .. code-block:: bash
-
-    $ pyKVFinder <.pdb> -L <.pdb> --ligand_cutoff 
-
-  :Default: ``5.0``
diff --git a/docs/source/_build/html/_sources/_installation/index.rst.txt b/docs/source/_build/html/_sources/_installation/index.rst.txt
deleted file mode 100644
index d4e7388d..00000000
--- a/docs/source/_build/html/_sources/_installation/index.rst.txt
+++ /dev/null
@@ -1,57 +0,0 @@
-Requirements
-============
-
-If you don’t have Python v3 and/or SWIG yet, the installation procedure differs depending on the operating system.
-
-Python and SWIG can be installed with conda, or with a package manager on Linux and macOS.
-
-Package managers
-----------------
-
-On Linux:
-
-.. code-block:: bash
-    
-  sudo apt install python3 swig
-
-On macOS:
-
-.. code-block:: bash
-    
-  brew install python3 swig
-
-.. note:: 
-
-  Users can use their preferred package manager to install SWIG and Python v3.
-
-Conda
------
-
-If you use conda, you can install Python v3 and SWIG from the defaults channel:
-
-.. code-block:: bash
-    
-  # Use an environment rather than install in base environement (recommended)
-  conda create -n myenv python=3
-  conda activate myenv
-  # The SWIG install command
-  conda install swig
-
-Installation
-============
-
-The prerequisites for installing pyKVFinder is Python v3 and SWIG. If you don’t have Python and/or SWIG yet, please refer to this `section `_.
-
-To install the latest release on `PyPI `_, 
-run:
-
-.. code-block:: bash
-
-  pip install pyKVFinder
-
-Or to install the latest developmental version, run:
-
-.. code-block:: bash
-
-  git clone https://github.com/LBC-LNBio/pyKVFinder.git
-  pip install pyKVFinder
diff --git a/docs/source/_build/html/_sources/_tutorial/index.rst.txt b/docs/source/_build/html/_sources/_tutorial/index.rst.txt
deleted file mode 100644
index 154aebcf..00000000
--- a/docs/source/_build/html/_sources/_tutorial/index.rst.txt
+++ /dev/null
@@ -1,1125 +0,0 @@
-.. raw:: html
-
-    
          Tutorial
          
-
-This section is an introductory overview of pyKVFinder features. For detailed reference documentation of the functions and classes contained in the package, see the `API reference <../_api_reference/index.html>`_.
-
-Before reading this section, you should know a bit of Python. If you would like to refresh your memory, refer to this `Python tutorial `_.
-
-First of all, import pyKVFinder package on Python:
-
-.. code-block:: python
-
-  >>> import pyKVFinder
-
-Cavity detection and characterization
-#####################################
-
-All files used on this tutorial can be found in our package and in our `GitHub repository `_:
-
-* `1FMO.pdb `_
-* `ADN.pdb `_
-
-In this tutorial, we will use pyKVFinder on a catalytic subunit of a cAMP-dependent protein kinase (cADK) to identify and characterize its cavities.
-
-pyKVFinder can be imported as a Python package in Python environment and users can decide to run the full pyKVFinder `workflow `_ through the single pyKVFinder function or run pyKVFinder functions in a `stepwise `_ fashion.
-
-Standard workflow
-*****************
-
-The **standard workflow** for cavity detection with spatial and constitutional characterization (volume, area and interface residues) can be run at once with one command:
-
-.. code-block:: python
-
-  >>> import os
-  >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
-  >>> results = pyKVFinder.run_workflow(pdb)
-  >>> results
-  
-
-Inside the *pyKVFinderResults object*, cavity and surface points, number of cavities, volume, area, and interface residues and their frequencies are stored as attributes. Below, we show how to access them:
-
-.. code-block:: python
-  
-  >>> results.cavities
-  array([[[-1, -1, -1, ..., -1, -1, -1],
-          [-1, -1, -1, ..., -1, -1, -1],
-          [-1, -1, -1, ..., -1, -1, -1],
-          ...,
-          [-1, -1, -1, ..., -1, -1, -1],
-          [-1, -1, -1, ..., -1, -1, -1],
-          [-1, -1, -1, ..., -1, -1, -1]],
-
-        ...,
-
-        [[-1, -1, -1, ..., -1, -1, -1],
-          [-1, -1, -1, ..., -1, -1, -1],
-          [-1, -1, -1, ..., -1, -1, -1],
-          ...,
-          [-1, -1, -1, ..., -1, -1, -1],
-          [-1, -1, -1, ..., -1, -1, -1],
-          [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
-  >>> results.surface
-  array([[[-1, -1, -1, ..., -1, -1, -1],
-          [-1, -1, -1, ..., -1, -1, -1],
-          [-1, -1, -1, ..., -1, -1, -1],
-          ...,
-          [-1, -1, -1, ..., -1, -1, -1],
-          [-1, -1, -1, ..., -1, -1, -1],
-          [-1, -1, -1, ..., -1, -1, -1]],
-
-        ...,
-
-        [[-1, -1, -1, ..., -1, -1, -1],
-          [-1, -1, -1, ..., -1, -1, -1],
-          [-1, -1, -1, ..., -1, -1, -1],
-          ...,
-          [-1, -1, -1, ..., -1, -1, -1],
-          [-1, -1, -1, ..., -1, -1, -1],
-          [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
-  >>> results.ncav
-  >>> 18
-  >>> results.volume
-  {'KAA': 137.16, 'KAB': 47.52, 'KAC': 66.96, 'KAD': 8.21, 'KAE': 43.63, 'KAF': 12.53, 'KAG': 6.26, 'KAH': 520.13, 'KAI': 12.31, 'KAJ': 26.57, 'KAK': 12.31, 'KAL': 33.91, 'KAM': 23.11, 'KAN': 102.82, 'KAO': 6.05, 'KAP': 15.55, 'KAQ': 7.99, 'KAR': 7.78}
-  >>> results.area
-  {'KAA': 126.41, 'KAB': 62.37, 'KAC': 74.57, 'KAD': 19.06, 'KAE': 57.08, 'KAF': 22.77, 'KAG': 15.38, 'KAH': 496.97, 'KAI': 30.58, 'KAJ': 45.64, 'KAK': 30.58, 'KAL': 45.58, 'KAM': 45.25, 'KAN': 129.77, 'KAO': 12.28, 'KAP': 25.04, 'KAQ': 13.46, 'KAR': 16.6}
-  >>> results.residues
-  {'KAA': [['14', 'E', 'SER'], ['15', 'E', 'VAL'], ['18', 'E', 'PHE'], ['19', 'E', 'LEU'], ['100', 'E', 'PHE'], ['152', 'E', 'LEU'], ['155', 'E', 'GLU'], ['156', 'E', 'TYR'], ['292', 'E', 'LYS'], ['302', 'E', 'TRP'], ['303', 'E', 'ILE'], ['306', 'E', 'TYR']], 'KAB': [['18', 'E', 'PHE'], ['22', 'E', 'ALA'], ['25', 'E', 'ASP'], ['26', 'E', 'PHE'], ['29', 'E', 'LYS'], ['97', 'E', 'ALA'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['156', 'E', 'TYR']], 'KAC': [['141', 'E', 'PRO'], ['142', 'E', 'HIS'], ['144', 'E', 'ARG'], ['145', 'E', 'PHE'], ['148', 'E', 'ALA'], ['299', 'E', 'THR'], ['300', 'E', 'THR'], ['305', 'E', 'ILE'], ['310', 'E', 'VAL'], ['311', 'E', 'GLU'], ['313', 'E', 'PRO']], 'KAD': [['122', 'E', 'TYR'], ['124', 'E', 'ALA'], ['176', 'E', 'GLN'], ['318', 'E', 'PHE'], ['320', 'E', 'GLY'], ['321', 'E', 'PRO'], ['322', 'E', 'GLY'], ['323', 'E', 'ASP']], 'KAE': [['95', 'E', 'LEU'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['100', 'E', 'PHE'], ['103', 'E', 'LEU'], ['104', 'E', 'VAL'], ['105', 'E', 'LYS'], ['106', 'E', 'LEU']], 'KAF': [['123', 'E', 'VAL'], ['124', 'E', 'ALA'], ['175', 'E', 'ASP'], ['176', 'E', 'GLN'], ['181', 'E', 'GLN']], 'KAG': [['34', 'E', 'SER'], ['37', 'E', 'THR'], ['96', 'E', 'GLN'], ['106', 'E', 'LEU'], ['107', 'E', 'GLU'], ['108', 'E', 'PHE'], ['109', 'E', 'SER']], 'KAH': [['49', 'E', 'LEU'], ['50', 'E', 'GLY'], ['51', 'E', 'THR'], ['52', 'E', 'GLY'], ['53', 'E', 'SER'], ['54', 'E', 'PHE'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['72', 'E', 'LYS'], ['74', 'E', 'LEU'], ['84', 'E', 'GLN'], ['87', 'E', 'HIS'], ['88', 'E', 'THR'], ['91', 'E', 'GLU'], ['104', 'E', 'VAL'], ['120', 'E', 'MET'], ['121', 'E', 'GLU'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['166', 'E', 'ASP'], ['168', 'E', 'LYS'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['184', 'E', 'ASP'], ['186', 'E', 'GLY'], ['187', 'E', 'PHE'], ['201', 'E', 'THR'], ['327', 'E', 'PHE']], 'KAI': [['131', 'E', 'HIS'], ['138', 'E', 'PHE'], ['142', 'E', 'HIS'], ['146', 'E', 'TYR'], ['174', 'E', 'ILE'], ['314', 'E', 'PHE']], 'KAJ': [['33', 'E', 'PRO'], ['89', 'E', 'LEU'], ['92', 'E', 'LYS'], ['93', 'E', 'ARG'], ['96', 'E', 'GLN'], ['349', 'E', 'GLU'], ['350', 'E', 'PHE']], 'KAK': [['157', 'E', 'LEU'], ['162', 'E', 'LEU'], ['163', 'E', 'ILE'], ['164', 'E', 'TYR'], ['185', 'E', 'PHE'], ['188', 'E', 'ALA']], 'KAL': [['49', 'E', 'LEU'], ['127', 'E', 'GLU'], ['129', 'E', 'PHE'], ['130', 'E', 'SER'], ['326', 'E', 'ASN'], ['327', 'E', 'PHE'], ['328', 'E', 'ASP'], ['330', 'E', 'TYR']], 'KAM': [['51', 'E', 'THR'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['73', 'E', 'ILE'], ['74', 'E', 'LEU'], ['75', 'E', 'ASP'], ['115', 'E', 'ASN'], ['335', 'E', 'ILE'], ['336', 'E', 'ARG']], 'KAN': [['165', 'E', 'ARG'], ['166', 'E', 'ASP'], ['167', 'E', 'LEU'], ['199', 'E', 'CYS'], ['200', 'E', 'GLY'], ['201', 'E', 'THR'], ['204', 'E', 'TYR'], ['205', 'E', 'LEU'], ['206', 'E', 'ALA'], ['209', 'E', 'ILE'], ['219', 'E', 'VAL'], ['220', 'E', 'ASP'], ['223', 'E', 'ALA']], 'KAO': [['48', 'E', 'THR'], ['51', 'E', 'THR'], ['56', 'E', 'ARG'], ['330', 'E', 'TYR'], ['331', 'E', 'GLU']], 'KAP': [['222', 'E', 'TRP'], ['238', 'E', 'PHE'], ['253', 'E', 'GLY'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['273', 'E', 'LEU']], 'KAQ': [['207', 'E', 'PRO'], ['208', 'E', 'GLU'], ['211', 'E', 'LEU'], ['213', 'E', 'LYS'], ['275', 'E', 'VAL'], ['277', 'E', 'LEU']], 'KAR': [['237', 'E', 'PRO'], ['238', 'E', 'PHE'], ['249', 'E', 'LYS'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['256', 'E', 'ARG']]}
-  >>> results.frequencies
-  {'KAA': {'RESIDUES': {'GLU': 1, 'ILE': 1, 'LEU': 2, 'LYS': 1, 'PHE': 2, 'SER': 1, 'TRP': 1, 'TYR': 2, 'VAL': 1}, 'CLASS': {'R1': 4, 'R2': 5, 'R3': 1, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAB': {'RESIDUES': {'ALA': 2, 'ASN': 1, 'ASP': 1, 'LYS': 1, 'PHE': 2, 'TYR': 1, 'VAL': 1}, 'CLASS': {'R1': 3, 'R2': 3, 'R3': 1, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAC': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'GLU': 1, 'HIS': 1, 'ILE': 1, 'PHE': 1, 'PRO': 2, 'THR': 2, 'VAL': 1}, 'CLASS': {'R1': 5, 'R2': 1, 'R3': 2, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAD': {'RESIDUES': {'ALA': 1, 'ASP': 1, 'GLN': 1, 'GLY': 2, 'PHE': 1, 'PRO': 1, 'TYR': 1}, 'CLASS': {'R1': 4, 'R2': 2, 'R3': 1, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAE': {'RESIDUES': {'ASN': 1, 'LEU': 3, 'LYS': 1, 'PHE': 1, 'VAL': 2}, 'CLASS': {'R1': 5, 'R2': 1, 'R3': 1, 'R4': 0, 'R5': 1, 'RX': 0}}, 'KAF': {'RESIDUES': {'ALA': 1, 'ASP': 1, 'GLN': 2, 'VAL': 1}, 'CLASS': {'R1': 2, 'R2': 0, 'R3': 2, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAG': {'RESIDUES': {'GLN': 1, 'GLU': 1, 'LEU': 1, 'PHE': 1, 'SER': 2, 'THR': 1}, 'CLASS': {'R1': 1, 'R2': 1, 'R3': 4, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAH': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'ASN': 1, 'ASP': 2, 'GLN': 1, 'GLU': 4, 'GLY': 4, 'HIS': 1, 'LEU': 3, 'LYS': 2, 'MET': 1, 'PHE': 3, 'SER': 1, 'THR': 4, 'TYR': 1, 'VAL': 3}, 'CLASS': {'R1': 11, 'R2': 4, 'R3': 8, 'R4': 6, 'R5': 4, 'RX': 0}}, 'KAI': {'RESIDUES': {'HIS': 2, 'ILE': 1, 'PHE': 2, 'TYR': 1}, 'CLASS': {'R1': 1, 'R2': 3, 'R3': 0, 'R4': 0, 'R5': 2, 'RX': 0}}, 'KAJ': {'RESIDUES': {'ARG': 1, 'GLN': 1, 'GLU': 1, 'LEU': 1, 'LYS': 1, 'PHE': 1, 'PRO': 1}, 'CLASS': {'R1': 2, 'R2': 1, 'R3': 1, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAK': {'RESIDUES': {'ALA': 1, 'ILE': 1, 'LEU': 2, 'PHE': 1, 'TYR': 1}, 'CLASS': {'R1': 4, 'R2': 2, 'R3': 0, 'R4': 0, 'R5': 0, 'RX': 0}}, 'KAL': {'RESIDUES': {'ASN': 1, 'ASP': 1, 'GLU': 1, 'LEU': 1, 'PHE': 2, 'SER': 1, 'TYR': 1}, 'CLASS': {'R1': 1, 'R2': 3, 'R3': 2, 'R4': 2, 'R5': 0, 'RX': 0}}, 'KAM': {'RESIDUES': {'ARG': 2, 'ASN': 1, 'ASP': 1, 'GLY': 1, 'ILE': 2, 'LEU': 1, 'THR': 1}, 'CLASS': {'R1': 4, 'R2': 0, 'R3': 2, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAN': {'RESIDUES': {'ALA': 2, 'ARG': 1, 'ASP': 2, 'CYS': 1, 'GLY': 1, 'ILE': 1, 'LEU': 2, 'THR': 1, 'TYR': 1, 'VAL': 1}, 'CLASS': {'R1': 7, 'R2': 1, 'R3': 2, 'R4': 2, 'R5': 1, 'RX': 0}}, 'KAO': {'RESIDUES': {'ARG': 1, 'GLU': 1, 'THR': 2, 'TYR': 1}, 'CLASS': {'R1': 0, 'R2': 1, 'R3': 2, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAP': {'RESIDUES': {'GLY': 1, 'LEU': 1, 'LYS': 1, 'PHE': 1, 'TRP': 1, 'VAL': 1}, 'CLASS': {'R1': 3, 'R2': 2, 'R3': 0, 'R4': 0, 'R5': 1, 'RX': 0}}, 'KAQ': {'RESIDUES': {'GLU': 1, 'LEU': 2, 'LYS': 1, 'PRO': 1, 'VAL': 1}, 'CLASS': {'R1': 4, 'R2': 0, 'R3': 0, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAR': {'RESIDUES': {'ARG': 1, 'LYS': 2, 'PHE': 1, 'PRO': 1, 'VAL': 1}, 'CLASS': {'R1': 2, 'R2': 1, 'R3': 0, 'R4': 0, 'R5': 3, 'RX': 0}}}
-
-.. note::
-  
-  The cavity nomenclature is based on the integer label. The cavity marked with 2, the first integer corresponding to a cavity, is KAA, the cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
-
-.. note::
-
-  The cavity points belonging to the same cavity receive the same integer label in the grid. The code numbering is the following:
-    
-    * -1: bulk points.
-    * 0: biomolecule points.
-    * 1: empty space points.
-    * >=2: cavity points.
-
-.. note::
-
-  The surface points belonging to the same cavity receive the same integer label in the grid. The code numbering is the following:
-    
-    * -1: bulk points.
-    * 0: biomolecule or empty space points.
-    * >=2: cavity points.
-
-.. note::
-
-  The ``pyKVFinder.run_workflow`` function uses default parameter specifications and therefore parameters can be adjusted to users’ needs.
-
-.. seealso::
-
-  * `pyKVFinder.run_workflow <../_api_reference/run_workflow>`_
-
-With these attributes, we can write the detected cavities and the characterization to files. Further, we can set a flag to plot the bar charts of the frequencies in a PDF file. Below, we illustrate the usage:
-
-.. code-block:: python
-
-  >>> results.export_all(fn='results.toml', output='cavity.pdb', include_frequencies_pdf=True, pdf='barplots.pdf')
-
-.. note::
-
-  The ``pyKVFinder.pyKVFinderResults.export_all`` methods uses default parameter specifications, except for ``include_frequencies_pdf`` parameter, and therefore parameters can be adjusted to users’ needs.
-
-.. seealso::
-
-  * `pyKVFinder.pyKVFinderResults <../_api_reference/pyKVFinderResults.html>`_
-
-Full workflow
-*************
-
-However, users may opt to perform the **full workflow** for cavity detection with spatial (volume and area), constitutional (interface residues), hydropathy and depth characterization. This full workflow can be run with one command by setting some parameters of ``pyKVFinder.run_workflow`` function:
-
-.. code-block:: python
-
-  >>> results = pyKVFinder.run_workflow(pdb, include_depth=True, include_hydropathy=True, hydrophobicity_scale='EisenbergWeiss')
-
-Inside the *pyKVFinderResults object*, in addition to cavity and surface points, volume, area, and interface residues and their frequencies showed above, depth and hydropathy points, average depth, maximum depth and average hydropathy are also stored as attributes. Below, we show how to access them:
-
-.. code-block:: python
-
-  >>> results.depths
-  array([[[0., 0., 0., ..., 0., 0., 0.],
-          [0., 0., 0., ..., 0., 0., 0.],
-          [0., 0., 0., ..., 0., 0., 0.],
-          ...,
-          [0., 0., 0., ..., 0., 0., 0.],
-          [0., 0., 0., ..., 0., 0., 0.],
-          [0., 0., 0., ..., 0., 0., 0.]],
-
-        ...,
-
-        [[0., 0., 0., ..., 0., 0., 0.],
-          [0., 0., 0., ..., 0., 0., 0.],
-          [0., 0., 0., ..., 0., 0., 0.],
-          ...,
-          [0., 0., 0., ..., 0., 0., 0.],
-          [0., 0., 0., ..., 0., 0., 0.],
-          [0., 0., 0., ..., 0., 0., 0.]]])
-  >>> results.scales
-  array([[[0., 0., 0., ..., 0., 0., 0.],
-          [0., 0., 0., ..., 0., 0., 0.],
-          [0., 0., 0., ..., 0., 0., 0.],
-          ...,
-          [0., 0., 0., ..., 0., 0., 0.],
-          [0., 0., 0., ..., 0., 0., 0.],
-          [0., 0., 0., ..., 0., 0., 0.]],
-
-        ...,
-
-        [[0., 0., 0., ..., 0., 0., 0.],
-          [0., 0., 0., ..., 0., 0., 0.],
-          [0., 0., 0., ..., 0., 0., 0.],
-          ...,
-          [0., 0., 0., ..., 0., 0., 0.],
-          [0., 0., 0., ..., 0., 0., 0.],
-          [0., 0., 0., ..., 0., 0., 0.]]])
-  >>> results.avg_depth
-  {'KAA': 1.35, 'KAB': 0.91, 'KAC': 0.68, 'KAD': 0.32, 'KAE': 0.99, 'KAF': 0.24, 'KAG': 0.1, 'KAH': 3.91, 'KAI': 0.0, 'KAJ': 0.96, 'KAK': 0.0, 'KAL': 1.07, 'KAM': 0.24, 'KAN': 0.0, 'KAO': 0.29, 'KAP': 0.7, 'KAQ': 0.22, 'KAR': 0.12}
-  >>> results.max_depth
-  {'KAA': 3.79, 'KAB': 2.68, 'KAC': 2.62, 'KAD': 0.85, 'KAE': 3.0, 'KAF': 0.85, 'KAG': 0.6, 'KAH': 10.73, 'KAI': 0.0, 'KAJ': 2.24, 'KAK': 0.0, 'KAL': 3.0, 'KAM': 1.2, 'KAN': 0.0, 'KAO': 1.04, 'KAP': 2.08, 'KAQ': 0.85, 'KAR': 0.6}
-  >>> results.avg_hydropathy
-  {'KAA': -0.73, 'KAB': -0.05, 'KAC': -0.07, 'KAD': -0.62, 'KAE': -0.81, 'KAF': -0.14, 'KAG': -0.33, 'KAH': -0.17, 'KAI': -0.4, 'KAJ': 0.62, 'KAK': -0.99, 'KAL': 0.36, 'KAM': -0.33, 'KAN': 0.18, 'KAO': 0.88, 'KAP': -0.96, 'KAQ': 0.48, 'KAR': 0.24, 'EisenbergWeiss': [-1.42, 2.6]}
-
-.. note::
-  
-  The cavity nomenclature is based on the integer label. The cavity marked with 2, the first integer corresponding to a cavity, is KAA, the cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
-
-.. note::
-
-  The ``pyKVFinder.run_workflow`` function uses default parameter specifications, except for ``include_depth`` and ``include_hydropathy`` parameters, and therefore parameters can be adjusted to users’ needs.
-
-.. seealso::
-
-  * `pyKVFinder.run_workflow <../_api_reference/run_workflow>`_
-
-With these attributes, we can write the detected cavities with depth annotated on B-factor column, the surface cavity points with hydrophobicity scale annotated on B-factor column, and the characterization to files. Below, we illustrate the usage:
-
-.. code-block:: python
-
-  >>> results.export_all(fn='results.toml', output='cavity.pdb', output_hydropathy='hydropathy.pdb', include_frequencies_pdf=False)
-
-.. note::
-
-  The ``pyKVFinder.pyKVFinderResults.export_all`` methods uses default parameter specifications, and therefore parameters can be adjusted to users’ needs.
-
-.. seealso::
-
-  * `pyKVFinder.pyKVFinderResults <../_api_reference/pyKVFinderResults.html>`_
-
-Separated steps
-***************
-
-If users prefer, instead of running ``pyKVFinder.run_workflow`` function, you can apply the cavity detection and characterization in a step-by-step fashion. Below we describe each step in detail.
-
-1. Loading van der Waals radii dictionary
-=========================================
-
-The `van der Waals radii file <../_cfg_files/vdw_file_template.html>`_ define the radius values for each residue and when not defined, it uses a generic value based on the atom type. ``pyKVFinder.read_vdw`` takes a vdW radii file (*.dat*) and returns a dictionary contaning radii values for each atom of each residue.
-
-.. code-block:: python
-
-  >>> vdw = pyKVFinder.read_vdw()
-  >>> vdw
-  {'ALA': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB1': 1.487, '1HB': 1.487, 'HB2': 1.487, '2HB': 1.487, 'HB3': 1.487, '3HB': 1.487, 'C': 1.908, 'O': 1.6612}, 'ARG': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG2': 1.487, '2HG': 1.487, 'HG3': 1.487, 'HG1': 1.487, '1HG': 1.487, 'CD': 1.908, 'HD2': 1.387, '1HD': 1.387, '2HD': 1.387, 'HD3': 1.387, 'HD1': 1.387, 'NE': 1.75, 'HE': 0.6, 'CZ': 1.908, 'NH1': 1.75, 'HH11': 0.6, '1HH1': 0.6, 'HH12': 0.6, '2HH1': 0.6, 'NH2': 1.75, 'HH21': 0.6, '2HH2': 0.6, 'HH22': 0.6, '1HH2': 0.6, 'C': 1.908, 'O': 1.6612}, 'ASH': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.908, 'OD1': 1.6612, 'OD2': 1.721, 'HD2': 0.0001, 'C': 1.908, 'O': 1.6612}, 'ASN': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'OD1': 1.6612, 'ND2': 1.824, 'HD21': 0.6, '1HD2': 0.6, 'HD22': 0.6, '2HD2': 0.6, 'C': 1.908, 'O': 1.6612}, 'ASP': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'OD1': 1.6612, 'OD2': 1.6612, 'C': 1.908, 'O': 1.6612}, 'CYM': {'N': 1.824, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB3': 1.387, 'HB2': 1.387, 'SG': 2.0, 'C': 1.908, 'O': 1.6612}, 'CYS': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.387, '2HB': 1.387, '1HB': 1.387, 'HB3': 1.387, 'HB1': 1.387, 'SG': 2.0, 'HG': 0.6, 'C': 1.908, 'O': 1.6612}, 'CYX': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.387, 'HB3': 1.387, 'SG': 2.0, 'C': 1.908, 'O': 1.6612}, 'GLH': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.908, 'HG2': 1.487, 'HG3': 1.487, 'CD': 1.908, 'OE1': 1.6612, 'OE2': 1.721, 'HE2': 0.0001, 'C': 1.908, 'O': 1.6612}, 'GLN': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG2': 1.487, '2HG': 1.487, 'HG3': 1.487, 'HG1': 1.487, '1HG': 1.487, 'CD': 1.908, 'OE1': 1.6612, 'NE2': 1.824, 'HE21': 0.6, '1HE2': 0.6, 'HE22': 0.6, '2HE2': 0.6, 'C': 1.908, 'O': 1.6612}, 'GLU': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG2': 1.487, '2HG': 1.487, 'HG3': 1.487, 'HG1': 1.487, '1HG': 1.487, 'CD': 1.908, 'OE1': 1.6612, 'OE2': 1.6612, 'C': 1.908, 'O': 1.6612}, 'GLY': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA2': 1.387, 'HA1': 1.387, '1HA': 1.387, '2HA': 1.387, 'HA3': 1.387, 'C': 1.908, 'O': 1.6612}, 'HID': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.85, 'ND1': 1.75, 'HD1': 0.6, 'CE1': 1.85, 'HE1': 1.359, 'NE2': 1.75, 'CD2': 2.0, 'HD2': 1.409, 'C': 1.908, 'O': 1.6612}, 'HIE': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.85, 'ND1': 1.75, 'CE1': 1.85, 'HE1': 1.359, 'NE2': 1.75, 'HE2': 0.6, 'CD2': 2.0, 'HD2': 1.409, 'C': 1.908, 'O': 1.6612}, 'HIP': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.85, 'ND1': 1.75, 'HD1': 0.6, 'CE1': 1.85, 'HE1': 1.359, 'NE2': 1.75, 'HE2': 0.6, 'CD2': 2.0, 'HD2': 1.409, 'C': 1.908, 'O': 1.6612}, 'ILE': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB': 1.487, 'CG2': 1.908, 'HG21': 1.487, '1HG2': 1.487, 'HG22': 1.487, '2HG2': 1.487, 'HG23': 1.487, '3HG2': 1.487, 'CG1': 1.908, 'HG12': 1.487, '2HG1': 1.487, 'HG13': 1.487, 'HG11': 1.487, '1HG1': 1.487, 'CD1': 1.908, 'HD11': 1.487, '1HD1': 1.487, 'HD12': 1.487, '2HD1': 1.487, 'HD13': 1.487, '3HD1': 1.487, 'C': 1.908, 'O': 1.6612}, 'LEU': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG': 1.487, 'CD1': 1.908, 'HD11': 1.487, '1HD1': 1.487, 'HD12': 1.487, '2HD1': 1.487, 'HD13': 1.487, '3HD1': 1.487, 'CD2': 1.908, 'HD21': 1.487, '1HD2': 1.487, 'HD22': 1.487, '2HD2': 1.487, 'HD23': 1.487, '3HD2': 1.487, 'C': 1.908, 'O': 1.6612}, 'LYN': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.908, 'HG2': 1.487, 'HG3': 1.487, 'CD': 1.908, 'HD2': 1.487, 'HD3': 1.487, 'CE': 1.908, 'HE2': 1.1, 'HE3': 1.1, 'NZ': 1.824, 'HZ2': 0.6, 'HZ3': 0.6, 'C': 1.908, 'O': 1.6612}, 'LYS': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG2': 1.487, '2HG': 1.487, 'HG3': 1.487, 'HG1': 1.487, '1HG': 1.487, 'CD': 1.908, 'HD2': 1.487, '1HD': 1.487, '2HD': 1.487, 'HD3': 1.487, 'HD1': 1.487, 'CE': 1.908, 'HE2': 1.1, '2HE': 1.1, 'HE3': 1.1, '1HE': 1.1, 'HE1': 1.1, 'NZ': 1.824, 'HZ1': 0.6, '1HZ': 0.6, 'HZ2': 0.6, '2HZ': 0.6, 'HZ3': 0.6, '3HZ': 0.6, 'C': 1.908, 'O': 1.6612}, 'MET': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG2': 1.387, '2HG': 1.387, 'HG3': 1.387, 'HG1': 1.387, '1HG': 1.387, 'SD': 2.0, 'CE': 1.908, 'HE1': 1.387, '1HE': 1.387, 'HE2': 1.387, '2HE': 1.387, 'HE3': 1.387, '3HE': 1.387, 'C': 1.908, 'O': 1.6612}, 'PHE': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'CD1': 1.908, 'HD1': 1.459, 'CE1': 1.908, 'HE1': 1.459, 'CZ': 1.908, 'HZ': 1.459, 'CE2': 1.908, 'HE2': 1.459, 'CD2': 1.908, 'HD2': 1.459, 'C': 1.908, 'O': 1.6612}, 'PRO': {'N': 1.824, 'CD': 1.908, 'HD2': 1.387, '1HD': 1.387, '2HD': 1.387, 'HD3': 1.387, 'HD1': 1.387, 'CG': 1.908, 'HG2': 1.487, '2HG': 1.487, 'HG3': 1.487, 'HG1': 1.487, '1HG': 1.487, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CA': 1.908, 'HA': 1.387, 'C': 1.908, 'O': 1.6612}, 'SER': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.387, '2HB': 1.387, '1HB': 1.387, 'HB3': 1.387, 'HB1': 1.387, 'OG': 1.721, 'HG': 0.0001, 'C': 1.908, 'O': 1.6612}, 'THR': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB': 1.387, 'CG2': 1.908, 'HG21': 1.487, '1HG2': 1.487, 'HG22': 1.487, '2HG2': 1.487, 'HG23': 1.487, '3HG2': 1.487, 'OG1': 1.721, 'HG1': 0.0001, 'C': 1.908, 'O': 1.6612}, 'TRP': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.85, 'CD1': 2.0, 'HD1': 1.409, 'NE1': 1.75, 'HE1': 0.6, 'CE2': 1.85, 'CZ2': 1.908, 'HZ2': 1.459, 'CH2': 1.908, 'HH2': 1.459, 'CZ3': 1.908, 'HZ3': 1.459, 'CE3': 1.908, 'HE3': 1.459, 'CD2': 1.85, 'C': 1.908, 'O': 1.6612}, 'TYR': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'CD1': 1.908, 'HD1': 1.459, 'CE1': 1.908, 'HE1': 1.459, 'CZ': 1.908, 'OH': 1.721, 'HH': 0.0001, 'CE2': 1.908, 'HE2': 1.459, 'CD2': 1.908, 'HD2': 1.459, 'C': 1.908, 'O': 1.6612}, 'VAL': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB': 1.487, 'CG1': 1.908, 'CG2': 1.908, 'HG11': 1.487, '1HG2': 1.487, '1HG1': 1.487, 'HG21': 1.487, 'HG12': 1.487, '2HG1': 1.487, 'HG22': 1.487, '2HG2': 1.487, 'HG13': 1.487, '3HG2': 1.487, '3HG1': 1.487, 'HG23': 1.487, 'C': 1.908, 'O': 1.6612}, 'HIS': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.85, 'ND1': 1.75, 'HD1': 0.6, 'CE1': 1.85, 'HE1': 1.359, 'NE2': 1.75, 'CD2': 2.0, 'HD2': 1.409, 'C': 1.908, 'O': 1.6612}, 'PTR': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.908, 'CD1': 1.908, 'HD1': 1.459, 'CE1': 1.908, 'HE1': 1.459, 'CZ': 1.908, 'CE2': 1.908, 'HE2': 1.459, 'CD2': 1.908, 'HD2': 1.459, 'OH': 1.6837, 'P': 2.1, 'O1P': 1.85, 'O2P': 1.85, 'O3P': 1.85, 'C': 1.908, 'O': 1.6612}, 'SEP': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.387, 'HB3': 1.387, '1HB': 1.387, '2HB': 1.387, 'OG': 1.6837, 'P': 2.1, 'O1P': 1.85, 'O2P': 1.85, 'O3P': 1.85, 'C': 1.908, 'O': 1.6612}, 'TPO': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB': 1.387, 'CG2': 1.908, 'HG21': 1.487, 'HG22': 1.487, 'HG23': 1.487, '1HG2': 1.487, '2HG2': 1.487, '3HG2': 1.487, 'OG1': 1.6837, 'P': 2.1, 'O1P': 1.85, 'O2P': 1.85, 'O3P': 1.85, 'C': 1.908, 'O': 1.6612}, 'H2D': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.85, 'ND1': 1.75, 'CE1': 1.85, 'HE1': 1.359, 'NE2': 1.75, 'HE2': 0.6, 'CD2': 2.0, 'HD2': 1.409, 'P': 2.1, 'O1P': 1.85, 'O2P': 1.85, 'O3P': 1.85, 'C': 1.908, 'O': 1.6612}, 'Y1P': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.908, 'CD1': 1.908, 'HD1': 1.459, 'CE1': 1.908, 'HE1': 1.459, 'CZ': 1.908, 'CE2': 1.908, 'HE2': 1.459, 'CD2': 1.908, 'HD2': 1.459, 'OG': 1.6837, 'P': 2.1, 'O1P': 1.721, 'O2P': 1.6612, 'O3P': 1.6612, 'H1P': 0.0001, 'C': 1.908, 'O': 1.6612}, 'T1P': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB': 1.387, 'CG2': 1.908, 'HG21': 1.487, 'HG22': 1.487, 'HG23': 1.487, 'OG': 1.6837, 'P': 2.1, 'O1P': 1.721, 'O2P': 1.6612, 'O3P': 1.6612, 'H1P': 0.0001, 'C': 1.908, 'O': 1.6612}, 'S1P': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.387, 'HB3': 1.387, 'OG': 1.6837, 'P': 2.1, 'O1P': 1.721, 'O2P': 1.6612, 'O3P': 1.6612, 'H1P': 0.0001, 'C': 1.908, 'O': 1.6612}, 'GEN': {'AC': 2.0, 'AG': 1.72, 'AL': 2.0, 'AM': 2.0, 'AR': 1.88, 'AS': 1.85, 'AT': 2.0, 'AU': 1.66, 'B': 2.0, 'BA': 2.0, 'BE': 2.0, 'BH': 2.0, 'BI': 2.0, 'BK': 2.0, 'BR': 1.85, 'C': 1.66, 'CA': 2.0, 'CD': 1.58, 'CE': 2.0, 'CF': 2.0, 'CL': 1.75, 'CM': 2.0, 'CO': 2.0, 'CR': 2.0, 'CS': 2.0, 'CU': 1.4, 'DB': 2.0, 'DS': 2.0, 'DY': 2.0, 'ER': 2.0, 'ES': 2.0, 'EU': 2.0, 'F': 1.47, 'FE': 2.0, 'FM': 2.0, 'FR': 2.0, 'GA': 1.87, 'GD': 2.0, 'GE': 2.0, 'H': 0.91, 'HE': 1.4, 'HF': 2.0, 'HG': 1.55, 'HO': 2.0, 'HS': 2.0, 'I': 1.98, 'IN': 1.93, 'IR': 2.0, 'K': 2.75, 'KR': 2.02, 'LA': 2.0, 'LI': 1.82, 'LR': 2.0, 'LU': 2.0, 'MD': 2.0, 'MG': 1.73, 'MN': 2.0, 'MO': 2.0, 'MT': 2.0, 'N': 1.97, 'NA': 2.27, 'NB': 2.0, 'ND': 2.0, 'NE': 1.54, 'NI': 1.63, 'NO': 2.0, 'NP': 2.0, 'O': 1.69, 'OS': 2.0, 'P': 2.1, 'PA': 2.0, 'PB': 2.02, 'PD': 1.63, 'PM': 2.0, 'PO': 2.0, 'PR': 2.0, 'PT': 1.72, 'PU': 2.0, 'RA': 2.0, 'RB': 2.0, 'RE': 2.0, 'RF': 2.0, 'RH': 2.0, 'RN': 2.0, 'RU': 2.0, 'S': 2.09, 'SB': 2.0, 'SC': 2.0, 'SE': 1.9, 'SG': 2.0, 'SI': 2.1, 'SM': 2.0, 'SN': 2.17, 'SR': 2.0, 'TA': 2.0, 'TB': 2.0, 'TC': 2.0, 'TE': 2.06, 'TH': 2.0, 'TI': 2.0, 'TL': 1.96, 'TM': 2.0, 'U': 1.86, 'V': 2.0, 'W': 2.0, 'XE': 2.16, 'Y': 2.0, 'YB': 2.0, 'ZN': 1.39, 'ZR': 2.0}}
-
-.. note::
-
-  The function takes the `built-in dictionary `_ when a *.dat* file is not specified. Otherwise, user must specify a *.dat* file following template of `van der Waals radii file <../_cfg_files/vdw_file_template.html>`_.
-
-  This step is only necessary if you are reading a custom van der Waals radii file to use in ``pyKVFinder.read_pdb``.
-
-.. seealso::
-
-  * `pyKVFinder.read_vdw <../_api_reference/read_vdw.html>`_
-
-2. Loading data from target structure
-=====================================
-
-``pyKVFinder.read_pdb`` takes a target *.pdb* file and returns a NumPy array (``atomic``) with residue number, chain identifier, residue name, atom name, xyz coordinates and radius, considering a van der Waals radii dictionary, for each atom.
-
-.. code-block:: python
-
-  >>> import os
-  >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
-  >>> atomic = pyKVFinder.read_pdb(pdb)
-  >>> atomic
-  array([['13', 'E', 'GLU', ..., '-15.642', '-14.858', '1.824'],
-       ['13', 'E', 'GLU', ..., '-14.62', '-15.897', '1.908'],
-       ['13', 'E', 'GLU', ..., '-13.357', '-15.508', '1.908'],
-       ...,
-       ['350', 'E', 'PHE', ..., '18.878', '-9.885', '1.908'],
-       ['350', 'E', 'PHE', ..., '17.624', '-9.558', '1.908'],
-       ['350', 'E', 'PHE', ..., '19.234', '-13.442', '1.69']],
-      dtype='`_, when the ``vdw`` argument is not specified. If you wish to use a custom van der Waals radii file, you must read it with ``pyKVFinder.read_vdw`` as shown earlier and pass it as ``pyKVFinder.read_pdb(pdb, vdw=vdw)``.
-
-.. note::
-
-  The structural data can be also read from a *.xyz* file with ``pyKVFinder.read_xyz`` function. However, XYZ format does not provide information about chain identifier and residue name, thus this fields will have `A` and `UNK`, respectively.
-
-.. seealso::
-
-  * `pyKVFinder.read_pdb <../_api_reference/read_pdb.html>`_
-  * `pyKVFinder.read_xyz <../_api_reference/read_xyz.html>`_
-
-3. Dimensioning the 3D grid
-===========================
-
-The pyKVFinder 3D grid must be calculated based on the target *.pdb* or *.xyz* file, the Probe Out diameter and the grid spacing. 
-
-``pyKVFinder.get_vertices`` takes the NumPy array with residue number, chain identifier, residue name, atom name, xyz coordinates and radius for each atom, and the Probe Out (``probe_out``) and grid spacing (``step``) that will be applied in the detection, and returns a NumPy array with vertice coordinates (origin, X-axis, Y-axis, Z-axis) of the 3D grid.
-
-.. code-block:: python
-
-  >>> # Default Probe Out (probe_out): 4.0
-  >>> probe_out = 4.0
-  >>> # Default Grid Spacing (step): 0.6
-  >>> step = 0.6
-  >>> vertices = pyKVFinder.get_vertices(atomic, probe_out=probe_out, step=step)
-  >>> vertices
-  array([[-19.911, -32.125, -30.806],
-       [ 40.188, -32.125, -30.806],
-       [-19.911,  43.446, -30.806],
-       [-19.911, -32.125,  27.352]])
-
-.. note::
-  
-  If the ``probe_out`` and ``step`` values are not defined, the function automatically sets them to the default values. So, you can call the function by ``pyKVFinder.get_vertices(atomic)``.
-
-.. seealso::
-
-  * `pyKVFinder.get_vertices <../_api_reference/get_vertices.html>`_
-
-4. Detecting biomolecular cavities
-==================================
-
-``pyKVFinder.detect`` takes the NumPy array with residue number, chain identifier, residue name, atom name, xyz coordinates and radius for each atom, a NumPy array with vertices and a collection of detection parameters (``step``, ``probe_in``, ``probe_out``, ``removal_distance``, ``volume_cutoff``, ``surface``), and returns a tuple with the number of detected cavities and a NumPy array with the cavity points in the 3D grid.
-
-.. code-block:: python
-  
-  >>> # Default Grid Spacing (step): 0.6
-  >>> step = 0.6  
-  >>> # Default Probe In (probe_in): 1.4
-  >>> probe_in = 1.4
-  >>> # Default Probe Out (probe_out): 4.0
-  >>> probe_out = 4.0
-  >>> # Default Removal Distance (removal_distance): 2.4
-  >>> removal_distance = 2.4
-  >>> # Default Volume Cutoff (volume_cutoff): 5.0
-  >>> volume_cutoff = 5.0
-  >>> # Default Surface Representation (surface): 'SES'
-  >>> surface = 'SES'
-  >>> ncav, cavities = pyKVFinder.detect(atomic, vertices, step=step, probe_in=probe_in, probe_out=probe_out, removal_distance=removal_distance, volume_cutoff=volume_cutoff, surface=surface)
-  >>> ncav
-  18
-  >>> cavities
-  array([[[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]],
-
-       ...,
-
-       [[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
-  
-.. note::
-
-  If any of the detection parameters (``step``, ``probe_in``, ``probe_out``, ``removal_distance``, ``volume_cutoff``, ``surface``) are not defined, the function automatically sets them to the default values. So, you can call the function by ``pyKVFinder.detect(atomic, vertices)``.
-
-.. note::
-
-  The cavity points belonging to the same cavity receive the same integer label in the grid. The code numbering is the following:
-    
-    * -1: bulk points.
-    * 0: biomolecule points.
-    * 1: empty space points.
-    * >=2: cavity points.
-
-.. seealso::
-
-  * `pyKVFinder.detect <../_api_reference/detect.html>`_
-
-4.1 Detecting biomolecular cavities with ligand adjustment
-----------------------------------------------------------
-
-The cavity detection can be limited around the target ligand(s), which will be passed to pyKVFinder through a *.pdb* or *.xyz* file. Thus, the detected cavities are limited within a radius (``ligand_cutoff``) of the target ligand(s).
-
-First, ``pyKVFinder.read_pdb`` takes an `adenosine `_ as the target ligand and returns the NumPy array with residue number, chain identifier, residue name, atom name, xyz coordinates and radius for each atom of the ligand.
-
-.. code-block:: python
-
-  >>> ligand = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'ADN.pdb')
-  >>> latomic = pyKVFinder.read_pdb(ligand)
-  >>> latomic
-  array([['351', 'E', 'ADN', "C5'", '11.087', '9.79', '2.052', '1.66'],
-       ['351', 'E', 'ADN', "O5'", '11.545', '8.52', '1.545', '1.69'],
-       ['351', 'E', 'ADN', "C4'", '10.688', '9.68', '3.523', '1.66'],
-       ['351', 'E', 'ADN', "O4'", '9.714', '10.725', '3.81', '1.69'],
-       ['351', 'E', 'ADN', "C3'", '9.973', '8.374', '3.903', '1.66'],
-       ['351', 'E', 'ADN', "O3'", '10.879', '7.361', '4.304', '1.69'],
-       ['351', 'E', 'ADN', "C2'", '9.115', '8.82', '5.059', '1.66'],
-       ['351', 'E', 'ADN', "O2'", '9.887', '9.034', '6.232', '1.69'],
-       ['351', 'E', 'ADN', "C1'", '8.625', '10.16', '4.5', '1.66'],
-       ['351', 'E', 'ADN', 'N1', '3.499', '10.104', '4.402', '1.97'],
-       ['351', 'E', 'ADN', 'C2', '4.376', '10.259', '5.387', '1.66'],
-       ['351', 'E', 'ADN', 'N3', '5.705', '10.249', '5.351', '1.97'],
-       ['351', 'E', 'ADN', 'C4', '6.136', '10.087', '4.094', '1.66'],
-       ['351', 'E', 'ADN', 'C5', '5.353', '9.952', '2.974', '1.66'],
-       ['351', 'E', 'ADN', 'C6', '3.957', '9.957', '3.146', '1.66'],
-       ['351', 'E', 'ADN', 'N6', '3.083', '9.826', '2.142', '1.97'],
-       ['351', 'E', 'ADN', 'N7', '6.146', '9.791', '1.843', '1.97'],
-       ['351', 'E', 'ADN', 'C8', '7.374', '9.872', '2.291', '1.66'],
-       ['351', 'E', 'ADN', 'N9', '7.444', '10.056', '3.646', '1.97']],
-      dtype='>> # Default Ligand Cutoff (ligand_cutoff): 5.0
-  >>> ligand_cutoff = 5.0
-  >>> ncav_la, cavities_la = pyKVFinder.detect(atomic, vertices, latomic=latomic, ligand_cutoff=ligand_cutoff)
-  >>> ncav_la
-  2
-  >>> cavities_la
-  array([[[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]],
-
-       ...,
-
-       [[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
-
-.. note::
-
-  If the ``ligand_cutoff`` is not defined, the function automatically sets it to the default value. So, you can call the function by ``pyKVFinder.detect(atomic, vertices, latomic=latomic)``.
-
-  The cavity points belonging to the same cavity receive the same integer label in the grid. The code numbering is the following:
-    
-    * -1: bulk points.
-    * 0: biomolecule points.
-    * 1: empty space points.
-    * >=2: cavity points.
-
-.. seealso::
-
-  * `pyKVFinder.read_pdb <../_api_reference/read_pdb.html>`_
-  * `pyKVFinder.read_xyz <../_api_reference/read_xyz.html>`_
-  * `pyKVFinder.detect <../_api_reference/detect.html>`_
-
-5. Performing spatial characterization
-======================================
-
-A spatial characterization, that includes volume, area and defining surface points, is performed on the detected cavities. 
-
-``pyKVFinder.spatial`` takes the detected cavities and the grid spacing (``step``) and and returns a tuple with a NumPy array with the surface points in the 3D grid, a dictionary with the volume of the detected cavities and a dictionary with the area of the detected cavities.
-
-.. code-block:: python
-
-  >>> surface, volume, area = pyKVFinder.spatial(cavities, step=step)
-  >>> surface
-  array([[[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]],
-
-       ...,
-
-       [[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
-  >>> volume
-  {'KAA': 137.16, 'KAB': 47.52, 'KAC': 66.96, 'KAD': 8.21, 'KAE': 43.63, 'KAF': 12.53, 'KAG': 6.26, 'KAH': 520.13, 'KAI': 12.31, 'KAJ': 26.57, 'KAK': 12.31, 'KAL': 33.91, 'KAM': 23.11, 'KAN': 102.82, 'KAO': 6.05, 'KAP': 15.55, 'KAQ': 7.99, 'KAR': 7.78}
-  >>> area
-  {'KAA': 126.41, 'KAB': 62.37, 'KAC': 74.57, 'KAD': 19.06, 'KAE': 57.08, 'KAF': 22.77, 'KAG': 15.38, 'KAH': 496.97, 'KAI': 30.58, 'KAJ': 45.64, 'KAK': 30.58, 'KAL': 45.58, 'KAM': 45.25, 'KAN': 129.77, 'KAO': 12.28, 'KAP': 25.04, 'KAQ': 13.46, 'KAR': 16.6}
-
-.. note::
-
-  The cavity nomenclature is based on the integer label. The cavity marked with 2, the first integer corresponding to a cavity, is KAA, the cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
-
-.. note::
-
-  The surface points belonging to the same cavity receive the same integer label in the grid. The code numbering is the following:
-    
-    * -1: bulk points.
-    * 0: biomolecule or empty space points.
-    * >=2: cavity points.
-
-.. note::
-
-  If the ``step`` is not defined, the function automatically sets it to the default value. So, you can call the function by ``pyKVFinder.spatial(cavities)``.
-
-.. seealso::
-
-  * `pyKVFinder.spatial <../_api_reference/spatial.html>`_  
-
-6. Performing constitutional characterization
-=============================================
-
-A constitutional characterization, that identifies the interface residues, is performed on the detected cavities.
-
-``pyKVFinder.constitutional`` takes the detected cavities, the NumPy array with residue number, chain identifier, residue name, atom name, xyz coordinates and radius for each atom, the NumPy array with vertice coordinates (origin, X-axis, Y-axis, Z-axis) and a collection of detection parameters (``step``, ``probe_in``, ``ignore_backbone``), and returns a dictionary with interface residues of each cavity.
-
-.. code-block:: python
-
-  >>> # Default ignore backbone contacts flag (ignore_backbone): False
-  >>> ignore_backbone = False
-  >>> residues = pyKVFinder.constitutional(cavities, atomic, vertices, step=step, probe_in=probe_in, ignore_backbone=ignore_backbone)
-  >>> residues
-  {'KAA': [['14', 'E', 'SER'], ['15', 'E', 'VAL'], ['18', 'E', 'PHE'], ['19', 'E', 'LEU'], ['100', 'E', 'PHE'], ['152', 'E', 'LEU'], ['155', 'E', 'GLU'], ['156', 'E', 'TYR'], ['292', 'E', 'LYS'], ['302', 'E', 'TRP'], ['303', 'E', 'ILE'], ['306', 'E', 'TYR']], 'KAB': [['18', 'E', 'PHE'], ['22', 'E', 'ALA'], ['25', 'E', 'ASP'], ['26', 'E', 'PHE'], ['29', 'E', 'LYS'], ['97', 'E', 'ALA'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['156', 'E', 'TYR']], 'KAC': [['141', 'E', 'PRO'], ['142', 'E', 'HIS'], ['144', 'E', 'ARG'], ['145', 'E', 'PHE'], ['148', 'E', 'ALA'], ['299', 'E', 'THR'], ['300', 'E', 'THR'], ['305', 'E', 'ILE'], ['310', 'E', 'VAL'], ['311', 'E', 'GLU'], ['313', 'E', 'PRO']], 'KAD': [['122', 'E', 'TYR'], ['124', 'E', 'ALA'], ['176', 'E', 'GLN'], ['318', 'E', 'PHE'], ['320', 'E', 'GLY'], ['321', 'E', 'PRO'], ['322', 'E', 'GLY'], ['323', 'E', 'ASP']], 'KAE': [['95', 'E', 'LEU'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['100', 'E', 'PHE'], ['103', 'E', 'LEU'], ['104', 'E', 'VAL'], ['105', 'E', 'LYS'], ['106', 'E', 'LEU']], 'KAF': [['123', 'E', 'VAL'], ['124', 'E', 'ALA'], ['175', 'E', 'ASP'], ['176', 'E', 'GLN'], ['181', 'E', 'GLN']], 'KAG': [['34', 'E', 'SER'], ['37', 'E', 'THR'], ['96', 'E', 'GLN'], ['106', 'E', 'LEU'], ['107', 'E', 'GLU'], ['108', 'E', 'PHE'], ['109', 'E', 'SER']], 'KAH': [['49', 'E', 'LEU'], ['50', 'E', 'GLY'], ['51', 'E', 'THR'], ['52', 'E', 'GLY'], ['53', 'E', 'SER'], ['54', 'E', 'PHE'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['72', 'E', 'LYS'], ['74', 'E', 'LEU'], ['84', 'E', 'GLN'], ['87', 'E', 'HIS'], ['88', 'E', 'THR'], ['91', 'E', 'GLU'], ['104', 'E', 'VAL'], ['120', 'E', 'MET'], ['121', 'E', 'GLU'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['166', 'E', 'ASP'], ['168', 'E', 'LYS'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['184', 'E', 'ASP'], ['186', 'E', 'GLY'], ['187', 'E', 'PHE'], ['201', 'E', 'THR'], ['327', 'E', 'PHE']], 'KAI': [['131', 'E', 'HIS'], ['138', 'E', 'PHE'], ['142', 'E', 'HIS'], ['146', 'E', 'TYR'], ['174', 'E', 'ILE'], ['314', 'E', 'PHE']], 'KAJ': [['33', 'E', 'PRO'], ['89', 'E', 'LEU'], ['92', 'E', 'LYS'], ['93', 'E', 'ARG'], ['96', 'E', 'GLN'], ['349', 'E', 'GLU'], ['350', 'E', 'PHE']], 'KAK': [['157', 'E', 'LEU'], ['162', 'E', 'LEU'], ['163', 'E', 'ILE'], ['164', 'E', 'TYR'], ['185', 'E', 'PHE'], ['188', 'E', 'ALA']], 'KAL': [['49', 'E', 'LEU'], ['127', 'E', 'GLU'], ['129', 'E', 'PHE'], ['130', 'E', 'SER'], ['326', 'E', 'ASN'], ['327', 'E', 'PHE'], ['328', 'E', 'ASP'], ['330', 'E', 'TYR']], 'KAM': [['51', 'E', 'THR'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['73', 'E', 'ILE'], ['74', 'E', 'LEU'], ['75', 'E', 'ASP'], ['115', 'E', 'ASN'], ['335', 'E', 'ILE'], ['336', 'E', 'ARG']], 'KAN': [['165', 'E', 'ARG'], ['166', 'E', 'ASP'], ['167', 'E', 'LEU'], ['199', 'E', 'CYS'], ['200', 'E', 'GLY'], ['201', 'E', 'THR'], ['204', 'E', 'TYR'], ['205', 'E', 'LEU'], ['206', 'E', 'ALA'], ['209', 'E', 'ILE'], ['219', 'E', 'VAL'], ['220', 'E', 'ASP'], ['223', 'E', 'ALA']], 'KAO': [['48', 'E', 'THR'], ['51', 'E', 'THR'], ['56', 'E', 'ARG'], ['330', 'E', 'TYR'], ['331', 'E', 'GLU']], 'KAP': [['222', 'E', 'TRP'], ['238', 'E', 'PHE'], ['253', 'E', 'GLY'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['273', 'E', 'LEU']], 'KAQ': [['207', 'E', 'PRO'], ['208', 'E', 'GLU'], ['211', 'E', 'LEU'], ['213', 'E', 'LYS'], ['275', 'E', 'VAL'], ['277', 'E', 'LEU']], 'KAR': [['237', 'E', 'PRO'], ['238', 'E', 'PHE'], ['249', 'E', 'LYS'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['256', 'E', 'ARG']]}
-
-If you wish to ignore backbones contacts (C, CA, N, O) with the cavity when defining interface residues, you must set ``ignore_backbone`` flag to ``True``.
-
-.. code-block:: python
-
-  >>> residues_ib = pyKVFinder.constitutional(cavities, atomic, vertices, step=step, probe_in=probe_in, ignore_backbone=True)
-  >>> residues_ib
-  {'KAA': [['15', 'E', 'VAL'], ['18', 'E', 'PHE'], ['19', 'E', 'LEU'], ['100', 'E', 'PHE'], ['152', 'E', 'LEU'], ['155', 'E', 'GLU'], ['156', 'E', 'TYR'], ['292', 'E', 'LYS'], ['302', 'E', 'TRP'], ['303', 'E', 'ILE'], ['306', 'E', 'TYR']], 'KAB': [['18', 'E', 'PHE'], ['22', 'E', 'ALA'], ['25', 'E', 'ASP'], ['26', 'E', 'PHE'], ['29', 'E', 'LYS'], ['99', 'E', 'ASN'], ['156', 'E', 'TYR']], 'KAC': [['144', 'E', 'ARG'], ['145', 'E', 'PHE'], ['148', 'E', 'ALA'], ['299', 'E', 'THR'], ['300', 'E', 'THR'], ['305', 'E', 'ILE'], ['310', 'E', 'VAL'], ['311', 'E', 'GLU'], ['313', 'E', 'PRO']], 'KAD': [['122', 'E', 'TYR'], ['124', 'E', 'ALA'], ['176', 'E', 'GLN'], ['318', 'E', 'PHE']], 'KAE': [['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['103', 'E', 'LEU'], ['105', 'E', 'LYS'], ['106', 'E', 'LEU']], 'KAF': [['123', 'E', 'VAL'], ['175', 'E', 'ASP'], ['181', 'E', 'GLN']], 'KAG': [['34', 'E', 'SER'], ['37', 'E', 'THR'], ['96', 'E', 'GLN'], ['106', 'E', 'LEU'], ['109', 'E', 'SER']], 'KAH': [['49', 'E', 'LEU'], ['53', 'E', 'SER'], ['54', 'E', 'PHE'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['72', 'E', 'LYS'], ['74', 'E', 'LEU'], ['84', 'E', 'GLN'], ['87', 'E', 'HIS'], ['88', 'E', 'THR'], ['91', 'E', 'GLU'], ['104', 'E', 'VAL'], ['120', 'E', 'MET'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['166', 'E', 'ASP'], ['168', 'E', 'LYS'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['184', 'E', 'ASP'], ['187', 'E', 'PHE'], ['201', 'E', 'THR'], ['327', 'E', 'PHE']], 'KAI': [['131', 'E', 'HIS'], ['138', 'E', 'PHE'], ['142', 'E', 'HIS'], ['146', 'E', 'TYR'], ['174', 'E', 'ILE'], ['314', 'E', 'PHE']], 'KAJ': [['33', 'E', 'PRO'], ['89', 'E', 'LEU'], ['92', 'E', 'LYS'], ['93', 'E', 'ARG'], ['96', 'E', 'GLN'], ['349', 'E', 'GLU'], ['350', 'E', 'PHE']], 'KAK': [['157', 'E', 'LEU'], ['162', 'E', 'LEU'], ['164', 'E', 'TYR'], ['185', 'E', 'PHE'], ['188', 'E', 'ALA']], 'KAL': [['127', 'E', 'GLU'], ['129', 'E', 'PHE'], ['130', 'E', 'SER'], ['327', 'E', 'PHE'], ['328', 'E', 'ASP'], ['330', 'E', 'TYR']], 'KAM': [['51', 'E', 'THR'], ['56', 'E', 'ARG'], ['73', 'E', 'ILE'], ['115', 'E', 'ASN'], ['335', 'E', 'ILE']], 'KAN': [['165', 'E', 'ARG'], ['166', 'E', 'ASP'], ['167', 'E', 'LEU'], ['201', 'E', 'THR'], ['204', 'E', 'TYR'], ['205', 'E', 'LEU'], ['206', 'E', 'ALA'], ['209', 'E', 'ILE'], ['219', 'E', 'VAL'], ['220', 'E', 'ASP'], ['223', 'E', 'ALA']], 'KAO': [['48', 'E', 'THR'], ['51', 'E', 'THR'], ['56', 'E', 'ARG'], ['330', 'E', 'TYR']], 'KAP': [['222', 'E', 'TRP'], ['238', 'E', 'PHE'], ['255', 'E', 'VAL'], ['273', 'E', 'LEU']], 'KAQ': [['207', 'E', 'PRO'], ['208', 'E', 'GLU'], ['211', 'E', 'LEU'], ['213', 'E', 'LYS'], ['277', 'E', 'LEU']], 'KAR': [['238', 'E', 'PHE'], ['249', 'E', 'LYS'], ['255', 'E', 'VAL'], ['256', 'E', 'ARG']]}
-
-.. note::
-
-  The cavity nomenclature is based on the integer label. The cavity marked with 2, the first integer corresponding to a cavity, is KAA, the cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
-
-.. note::
-
-  If the ``step``, ``probe_in`` and ``ignore_backbone`` are not defined, the function automatically sets them to the default value. So, you can call the function by ``pyKVFinder.constitutional(cavities, atomic, vertices)``.
-
-.. seealso::
-
-  * `pyKVFinder.constitutional <../_api_reference/constitutional.html>`_  
-
-6.1 Calculating and plotting frequencies
-----------------------------------------
-
-With the interface residues defined, you can also calculate the frequencies of residues and classes of residues. The classes of residues are:
-
-:R1: **Alipathic apolar:** Alanine, Glycine, Isoleucine, Leucine, Methionine, Valine
-:R2: **Aromatic:** Phenylalanine, Tryptophan, Tyrosine
-:R3: **Polar uncharged**: Asparagine, Cysteine, Glutamine, Proline, Serine, Threonine
-:R4: **Negatively charged**: Aspartate, Glutamate
-:R5: **Positively charged**: Arginine, Histidine, Lysine
-:RX: **Non-standard**: Non-standard residues
-
-``pyKVFinder.calculate_frequencies`` takes the dictionary of interface residues calculated above and returns a dictionary with the frequencies of residues and classes of residues of each detected cavity.
-
-.. code-block:: python
-
-  >>> frequencies = pyKVFinder.calculate_frequencies(residues)
-  >>> frequencies
-  {'KAA': {'RESIDUES': {'GLU': 1, 'ILE': 1, 'LEU': 2, 'LYS': 1, 'PHE': 2, 'SER': 1, 'TRP': 1, 'TYR': 2, 'VAL': 1}, 'CLASS': {'R1': 4, 'R2': 5, 'R3': 1, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAB': {'RESIDUES': {'ALA': 2, 'ASN': 1, 'ASP': 1, 'LYS': 1, 'PHE': 2, 'TYR': 1, 'VAL': 1}, 'CLASS': {'R1': 3, 'R2': 3, 'R3': 1, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAC': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'GLU': 1, 'HIS': 1, 'ILE': 1, 'PHE': 1, 'PRO': 2, 'THR': 2, 'VAL': 1}, 'CLASS': {'R1': 5, 'R2': 1, 'R3': 2, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAD': {'RESIDUES': {'ALA': 1, 'ASP': 1, 'GLN': 1, 'GLY': 2, 'PHE': 1, 'PRO': 1, 'TYR': 1}, 'CLASS': {'R1': 4, 'R2': 2, 'R3': 1, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAE': {'RESIDUES': {'ASN': 1, 'LEU': 3, 'LYS': 1, 'PHE': 1, 'VAL': 2}, 'CLASS': {'R1': 5, 'R2': 1, 'R3': 1, 'R4': 0, 'R5': 1, 'RX': 0}}, 'KAF': {'RESIDUES': {'ALA': 1, 'ASP': 1, 'GLN': 2, 'VAL': 1}, 'CLASS': {'R1': 2, 'R2': 0, 'R3': 2, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAG': {'RESIDUES': {'GLN': 1, 'GLU': 1, 'LEU': 1, 'PHE': 1, 'SER': 2, 'THR': 1}, 'CLASS': {'R1': 1, 'R2': 1, 'R3': 4, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAH': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'ASN': 1, 'ASP': 2, 'GLN': 1, 'GLU': 4, 'GLY': 4, 'HIS': 1, 'LEU': 3, 'LYS': 2, 'MET': 1, 'PHE': 3, 'SER': 1, 'THR': 4, 'TYR': 1, 'VAL': 3}, 'CLASS': {'R1': 11, 'R2': 4, 'R3': 8, 'R4': 6, 'R5': 4, 'RX': 0}}, 'KAI': {'RESIDUES': {'HIS': 2, 'ILE': 1, 'PHE': 2, 'TYR': 1}, 'CLASS': {'R1': 1, 'R2': 3, 'R3': 0, 'R4': 0, 'R5': 2, 'RX': 0}}, 'KAJ': {'RESIDUES': {'ARG': 1, 'GLN': 1, 'GLU': 1, 'LEU': 1, 'LYS': 1, 'PHE': 1, 'PRO': 1}, 'CLASS': {'R1': 2, 'R2': 1, 'R3': 1, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAK': {'RESIDUES': {'ALA': 1, 'ILE': 1, 'LEU': 2, 'PHE': 1, 'TYR': 1}, 'CLASS': {'R1': 4, 'R2': 2, 'R3': 0, 'R4': 0, 'R5': 0, 'RX': 0}}, 'KAL': {'RESIDUES': {'ASN': 1, 'ASP': 1, 'GLU': 1, 'LEU': 1, 'PHE': 2, 'SER': 1, 'TYR': 1}, 'CLASS': {'R1': 1, 'R2': 3, 'R3': 2, 'R4': 2, 'R5': 0, 'RX': 0}}, 'KAM': {'RESIDUES': {'ARG': 2, 'ASN': 1, 'ASP': 1, 'GLY': 1, 'ILE': 2, 'LEU': 1, 'THR': 1}, 'CLASS': {'R1': 4, 'R2': 0, 'R3': 2, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAN': {'RESIDUES': {'ALA': 2, 'ARG': 1, 'ASP': 2, 'CYS': 1, 'GLY': 1, 'ILE': 1, 'LEU': 2, 'THR': 1, 'TYR': 1, 'VAL': 1}, 'CLASS': {'R1': 7, 'R2': 1, 'R3': 2, 'R4': 2, 'R5': 1, 'RX': 0}}, 'KAO': {'RESIDUES': {'ARG': 1, 'GLU': 1, 'THR': 2, 'TYR': 1}, 'CLASS': {'R1': 0, 'R2': 1, 'R3': 2, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAP': {'RESIDUES': {'GLY': 1, 'LEU': 1, 'LYS': 1, 'PHE': 1, 'TRP': 1, 'VAL': 1}, 'CLASS': {'R1': 3, 'R2': 2, 'R3': 0, 'R4': 0, 'R5': 1, 'RX': 0}}, 'KAQ': {'RESIDUES': {'GLU': 1, 'LEU': 2, 'LYS': 1, 'PRO': 1, 'VAL': 1}, 'CLASS': {'R1': 4, 'R2': 0, 'R3': 0, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAR': {'RESIDUES': {'ARG': 1, 'LYS': 2, 'PHE': 1, 'PRO': 1, 'VAL': 1}, 'CLASS': {'R1': 2, 'R2': 1, 'R3': 0, 'R4': 0, 'R5': 3, 'RX': 0}}}
-
-.. note::
-
-  The cavity nomenclature is based on the integer label. The cavity marked with 2, the first integer corresponding to a cavity, is KAA, the cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
-
-Afterwards, ``pyKVFinder.plot_frequencies`` takes the dictionary with the frequencies of residues and classes of residues of each detected cavity and a path to a PDF file, and plots the bar charts of calculated frequencies for each detected cavity in a PDF file.
-
-.. code-block:: python
-
-  >>> fn = 'barplots.pdf'
-  >>> pyKVFinder.plot_frequencies(frequencies, fn=fn)
-
-.. note::
-
-  If the ``fn`` is not defined, the function automatically sets it to the default value. So, you can call the function by ``pyKVFinder.plot_frequencies(frequencies)``.
-
-.. seealso::
-
-  * `pyKVFinder.calculate_frequencies <../_api_reference/calculate_frequencies.html>`_  
-  * `pyKVFinder.plot_frequencies <../_api_reference/plot_frequencies.html>`_  
-
-A sample barplot of ``pyKVFinder.plot_frequencies`` is shown below.
-
-.. image:: ../_images/plot-frequencies.png
-    :width: 600
-    :align: center
-
-|
-
-7. Performing hydropathy characterization
-=========================================
-
-A hydropathy characterization, that maps a target hydrophobicity scale on surface points and calculate the average hydropathy, is performed on the surface points of the detected cavities.
-
-``pyKVFinder.hydropathy`` takes the surface points of the detected cavities, the NumPy array with residue number, chain identifier, residue name, atom name, xyz coordinates and radius for each atom, the NumPy array with vertice coordinates (origin, X-axis, Y-axis, Z-axis), a collection of detection parameters (``step``, ``probe_in``) and a target hydrophobicity scale to be mapped on the surface points, and returns a tuple with a NumPy array with the hydropobicity scale mapped to the surface points in the 3D grid and a dictionary with the average hydrophobicity scale of the detected cavities and the range of the chosen hydrophobicity scale.
-
-.. code-block:: python
-  
-  >>> # Default Hydrophobicity Scale (hydropathy): 'EisenbergWeiss'
-  >>> hydrophobicity_scale = 'EisenbergWeiss'
-  >>> scales, avg_hydropathy = pyKVFinder.hydropathy(surface, atomic, vertices, step=step, probe_in=probe_in, hydrophobicity_scale=hydrophobicity_scale, ignore_backbone=ignore_backbone)
-  >>> scales
-  array([[[0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        ...,
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.]],
-
-       ...,
-
-       [[0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        ...,
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.]]])
-  >>> avg_hydropathy
-  {'KAA': -0.73, 'KAB': -0.05, 'KAC': -0.07, 'KAD': -0.62, 'KAE': -0.81, 'KAF': -0.14, 'KAG': -0.33, 'KAH': -0.16, 'KAI': -0.4, 'KAJ': 0.62, 'KAK': -0.99, 'KAL': 0.36, 'KAM': -0.33, 'KAN': 0.18, 'KAO': 0.88, 'KAP': -0.96, 'KAQ': 0.48, 'KAR': 0.24, 'EisenbergWeiss': [-1.42, 2.6]}
-
-.. note::
-
-  The cavity nomenclature is based on the integer label. The cavity marked with 2, the first integer corresponding to a cavity, is KAA, the cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
-
-.. note::
-
-  The ``pyKVFinder.hydropathy`` function accepts six built-in hydrophobicity scales:
-
-    * `EisenbergWeiss `_;
-    * `HessaHeijne `_;
-    * `KyteDoolittle `_;
-    * `MoonFleming `_;
-    * `WimleyWhite `_;
-    * `ZhaoLondon `_.
-
-  Otherwise, user must specify a *.toml* file following `Hydrophobicity Scale File Template `_.
-
-.. note::
-
-  If the ``step``, ``probe_in``, ``hydrophobicity_scale`` and ``ignore_backbone`` are not defined, the function automatically sets them to the default values. So, you can call the function by ``pyKVFinder.hydropathy(surface, atomic, vertices)``.
-
-.. seealso::
-
-  * `pyKVFinder.hydropathy <../_api_reference/hydropathy.html>`_    
-
-8. Performing depth characterization
-====================================
-
-A depth characterization identifies the degree of burial of the binding site. First, it identifies the cavity volume boundary. Subsequently, the depth of each cavity point is heuristically estimated by the shortest Euclidean distance between the cavity point and its respective boundary points. With this, the maximum and average depths for the detected cavities are calculated.
-
-``pyKVFinder.depth`` takes the detected cavities and the grid spacing (``step``) and returns a tuple with a NumPy array with the depth of the cavity points in the 3D grid, a dictionary with the maximum depth of the detected cavities and a dictionary with the average depth of the detected cavities.
-
-.. code-block:: python
-
-  >>> depths, max_depth, avg_depth = pyKVFinder.depth(cavities, step=step)
-  >>> depths
-  array([[[0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        ...,
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.]],
-
-       ...,
-
-       [[0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        ...,
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.]]])
-  >>> max_depth
-  {'KAA': 3.79, 'KAB': 2.68, 'KAC': 2.62, 'KAD': 0.85, 'KAE': 3.0, 'KAF': 0.85, 'KAG': 0.6, 'KAH': 10.73, 'KAI': 0.0, 'KAJ': 2.24, 'KAK': 0.0, 'KAL': 3.0, 'KAM': 1.2, 'KAN': 0.0, 'KAO': 1.04, 'KAP': 2.08, 'KAQ': 0.85, 'KAR': 0.6}
-  >>> avg_depth
-  {'KAA': 1.35, 'KAB': 0.91, 'KAC': 0.68, 'KAD': 0.32, 'KAE': 0.99, 'KAF': 0.24, 'KAG': 0.1, 'KAH': 3.91, 'KAI': 0.0, 'KAJ': 0.96, 'KAK': 0.0, 'KAL': 1.07, 'KAM': 0.24, 'KAN': 0.0, 'KAO': 0.29, 'KAP': 0.7, 'KAQ': 0.22, 'KAR': 0.12}
-
-.. note::
-
-  The cavity nomenclature is based on the integer label. The cavity marked with 2, the first integer corresponding to a cavity, is KAA, the cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
-
-.. note::
-
-  If the ``step`` is not defined, the function automatically sets it to the default value. So, you can call the function by ``pyKVFinder.depth(cavities)``.
-
-.. seealso::
-
-  * `pyKVFinder.depth <../_api_reference/depth.html>`_  
-
-9. Exporting cavities
-=====================
-
-There are four different ways to export the detected cavities to PDB-formatted files. 
-
-9.1 Exporting only cavity points
---------------------------------
-
-.. code-block:: python
-
-  >>> output_cavity = 'cavity_wo_surface.pdb'
-  >>> pyKVFinder.export(output_cavity, cavities, None, vertices, step=step)
-
-9.2 Exporting cavity and surface points
----------------------------------------
-
-.. code-block:: python
-
-  >>> output_cavity = 'cavity.pdb'
-  >>> pyKVFinder.export(output_cavity, cavities, surface, vertices, step=step)
-
-9.3 Exporting cavity and surface points with depth mapped on B-factor
----------------------------------------------------------------------
-
-.. code-block:: python
-
-  >>> output_cavity = 'cavity_with_depth.pdb'
-  >>> pyKVFinder.export(output_cavity, cavities, surface, vertices, step=step, B=depths)
-
-9.4 Exporting cavity and surface points with depth mapped on B-factor and surface points with hydrophobicity scale mapped on B-factor
--------------------------------------------------------------------------------------------------------------------------------------
-
-.. code-block:: python
-
-  >>> output_cavity = 'cavity_with_depth.pdb'
-  >>> output_hydropathy = 'hydropathy.pdb'
-  >>> pyKVFinder.export(output_cavity, cavities, surface, vertices, step=step, B=depths, output_hydropathy=output_hydropathy, scales=scales)
-
-.. note::
-
-  The cavity nomenclature is based on the integer label. The cavity marked with 2, the first integer corresponding to a cavity, is KAA, the cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
-
-.. note::
-
-  If the ``step``, ``B``, ``scales`` and ``output_hydropathy`` are not defined, the function automatically sets them to the default values. So, you can call the function by ``pyKVFinder.export(output_cavity, cavities, surface, vertices)``.
-
-.. seealso::
-
-  * `pyKVFinder.export <../_api_reference/export.html>`_  
-
-10.  Writing results
-====================
-
-The function call depends on the characterizations performed on the detected cavities.
-
-10.1 Cavity detection only
---------------------------
-
-.. code-block:: python
-
-  >>> output_results = 'results.toml'
-  >>> pyKVFinder.write_results(output_results, input=pdb, ligand=None, output=output_cavity, step=step)
-
-10.2 Spatial characterization
------------------------------
-
-.. code-block:: python
-
-  >>> output_results = 'results.toml'
-  >>> pyKVFinder.write_results(output_results, input=pdb, ligand=None, output=output_cavity, volume=volume, area=area, step=step)
-
-10.3 Spatial and constitutional characterization
-------------------------------------------------
-
-.. code-block:: python
-
-  >>> output_results = 'results.toml'
-  >>> pyKVFinder.write_results(output_results, input=pdb, ligand=None, output=output_cavity, volume=volume, area=area, residues=residues, frequencies=frequencies, step=step)
-
-10.4 Spatial, constitutional and depth characterization
--------------------------------------------------------
-
-.. code-block:: python
-
-  >>> output_results = 'results.toml'
-  >>> pyKVFinder.write_results(output_results, input=pdb, ligand=None, output=output_cavity, volume=volume, area=area, max_depth=max_depth, avg_depth=avg_depth, residues=residues, frequencies=frequencies, step=step)
-
-10.5 Spatial, constitutional, depth and hydropathy characterization
--------------------------------------------------------------------
-
-.. code-block:: python
-
-  >>> output_results = 'results.toml'
-  >>> pyKVFinder.write_results(output_results, input=pdb, ligand=None, output=output_cavity, output_hydropathy=output_hydropathy, volume=volume, area=area, max_depth=max_depth, avg_depth=avg_depth, avg_hydropathy=avg_hydropathy, residues=residues, frequencies=frequencies, step=step)
-
-.. note::
-
-  The cavity nomenclature is based on the integer label. The cavity marked with 2, the first integer corresponding to a cavity, is KAA, the cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
-
-.. seealso::
-
-  * `pyKVFinder.write_results <../_api_reference/write_results.html>`_ 
-
-Steered detection
-*****************
-
-All these steps showed so far were performed the detection on the whole target biomolecule; however, we can perform them on a custom 3D grid, where we can explore closed regions with a custom box, which can be defined by a *.toml* file.
-
-There are three methods to define a custom 3D grid as shown in `Box configuration file template `_.
-
-First, we will create a box *.toml* file with: 
-
-- Four vertices of the box (origin, X-axis, Y-axis and Z-axis):
-
-.. code-block:: python
-
-  >>> import toml
-  >>> fn = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'custom-box.toml')
-  >>> box = toml.load(fn)
-  >>> box
-  {'box': {'p1': [3.11, 7.34, 1.59], 'p2': [11.51, 7.34, 1.59], 'p3': [3.11, 10.74, 1.59], 'p4': [3.11, 7.34, 6.19]}}
-
-or
-
-- A list of residues and a padding:
-
-.. code-block:: python
-
-  >>> fn = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'residues-box.toml')
-  >>> box = toml.load(fn)
-  >>> box
-  {'box': {'residues': [['49', 'E', 'LEU'], ['50', 'E', 'GLY'], ['51', 'E', 'THR']], 'padding': 3.5}}
-
-A third way is to define a custom 3D grid with `parKVFinder `_'s TOML-formatted parameters file.
-
-.. code-block:: python
-
-  >>> fn = 'box.toml'
-  >>> box = """
-	[SETTINGS.visiblebox.p1]
-	x = 3.11
-	y = 7.34
-	z = 1.59
-
-	[SETTINGS.visiblebox.p2]
-	x = 11.51
-	y = 7.34
-	z = 1.59
-
-	[SETTINGS.visiblebox.p3]
-	x = 3.11
-	y = 10.74
-	z = 1.59
-
-	[SETTINGS.visiblebox.p4]
-	x = 3.11
-	y = 7.34
-	z = 6.19
-  """
-  >>> with open(fn, 'w') as f:
-  ...     toml.dump(toml.loads(box), f)
-
-.. note::
-
-  Users can create this box with parKVFinder PyMOL plugin (PyMOL2 parKVFinder Tools) and save the parameters file from it.
-
-Workflows
-=========
-
-Then, you can explore the box adjustment mode with the standard and full workflows, defining the ``box`` parameter as the filepath of one box configuration file from above (*custom-box.toml*, *residues-box.toml* or *box.toml*).
-
-For instance, with *custom-box.toml*:
-
-.. code-block:: python
-
-  >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
-  >>> # Box configuration filepath
-  >>> fn = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'custom-box.toml')
-  >>> # Standard workflow
-  >>> results = pyKVFinder.run_workflow(pdb, box=fn)
-  >>> # Full workflow
-  >>> results = pyKVFinder.run_workflow(pdb, box=fn, include_depth=True, include_hydropathy=True, hydrophobicity_scale='EisenbergWeiss')
-
-.. seealso::
-
-  * `pyKVFinder.run_workflow <../_api_reference/run_workflow>`_ 
-
-Separated steps
-===============
-
-If you are running pyKVFinder package in a step-by-step fashion (`Separated steps `_), the steps `3 `_ and `4 `_ are different than before.
-
-- Dimensioning the 3D grid: Instead of calling ``pyKVFinder.get_vertices``, you call ``pyKVFinder.get_vertices_from_file``.
-
-``pyKVFinder.get_vertices_from_file`` takes *.toml* file with box configuration or parKVFinder parameters file, the NumPy array with residue number, chain identifier, residue name, atom name, xyz coordinates and radius for each atom, and a collection of detection parameters (``step``, ``probe_in`` and ``probe_out``), and returns a tuple with a NumPy array with vertice coordinates (origin, X-axis, Y-axis, Z-axis) of the 3D grid and the NumPy array with residue number, chain identifier, residue name, atom name, xyz coordinates and radius for each atom inside the custom box.
-
-Users can define the ``box`` parameter as the filepath of one box configuration file from above (*custom-box.toml*, *residues-box.toml* or *box.toml*). For instance, with *custom-box.toml*:
-
-.. code-block:: python
-
-  >>> vertices, atomic = pyKVFinder.get_vertices_from_file(fn, atomic, step=step, probe_in=probe_in, probe_out=probe_out)
-
-.. note::
-
-  If the ``step``, ``probe_in`` and ``probe_out`` are not defined, the function automatically sets them to the default value. So, you can call the function by ``pyKVFinder.get_vertices_from_file('box.toml', atomic)``.
-
-- Detecting biomolecular cavities: Now, you can explore this box adjustment mode, defining the ``box_adjustment`` parameter as ``True``.
-
-.. code-block:: python
-
-  >>> ncav, cavities = pyKVFinder.detect(atomic, vertices, step=step, probe_in=probe_in, probe_out=probe_out, removal_distance=removal_distance, volume_cutoff=volume_cutoff, box_adjustment=True, surface=surface)
-  >>> ncav
-  1
-  >> cavities
-  array([[[-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      ...,
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1]],
-
-      ...,
-
-      [[-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      ...,
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32) 
-
-.. note::
-
-  If any of the detection parameters (``step``, ``probe_in``, ``probe_out``, ``removal_distance``, ``volume_cutoff``, ``surface``) are not defined, the function automatically sets them to the default value. So, you can call the function by ``pyKVFinder.detect(atomic, vertices, box_adjustment=True)``.
-
-.. warning::
-
-  If you are using box adjusment mode, do not forget to set ``box_adjustment`` flag to ``True``.
-
-.. seealso::
-
-  * `pyKVFinder.get_vertices_from_file <../_api_reference/get_vertices_from_file.html>`_
-  * `pyKVFinder.detect <../_api_reference/detect.html>`_ 
-
-Molecular volume
-################
-
-All files used on this tutorial can be found in our package and in our `GitHub repository `_:
-
-* `ClO4.pdb `_
-
-In this tutorial, we will use pyKVFinder on perchlorate (ClO\ :sub:`4` \) to estimate the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES) and solvent accessible surface (SAS) to represent the molecular surface (see Figure below).
-
-+-------------------------------+--------------------------------+--------------------------------+
-| .. image:: ../_images/vdw.png | .. image:: ../_images/ses.png  | .. image:: ../_images/sas.png  |
-|                               |                                |                                |
-| .. centered:: (a) vdW         | .. centered:: (b) SES          | .. centered:: (c) SAS          |
-+-------------------------------+--------------------------------+--------------------------------+
-| .. centered:: **Molecular surface represenation**                                               |
-+-------------------------------------------------------------------------------------------------+
-
-First, we must load the target molecular structure (ClO\ :sub:`4` \)  into ``pyKVFinder.Molecule`` class. 
-
-.. code-block:: python
-
-  >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'ClO4.pdb')
-  >>> molecule pyKVFinder.Molecule(pdb)
-  >>> molecule
-  
-
-With the atomic information and vdW radii dictionary loaded, the molecule is inserted into a regular 3D grid, considering the vdW radii of any of the atoms. Natively, the vdW radii are taken from the `built-in dictionary `_. In the 3D grid, each voxel corresponds to a molecule (0) or solvent (1) points. Here, we can model our molecule using the vdW surface, SES or SAS.
-
-1. vdW volume
-*************
-
-``Molecule.vdw()`` takes a grid spacing and returns a NumPy array with the molecule points representing the vdW surface in the 3D grid. 
-
-.. code-block:: python
-
-  >>> # Grid Spacing (step): 0.1
-  >>> step = 0.1
-  >>> molecule.vdw(step=step)
-  >>> molecule.grid
-  array([[[1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1],
-          ...,
-          [1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1]],
-        
-          ...,
-
-        [[1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1],
-          ...,
-          [1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1]]], dtype=int32)
-
-.. note::
-
-  If ``step`` is not defined, the function automatically sets it to the default value. So, you can call the function by ``molecule.vdw()``.
-
-We can preview our modelled molecule in the 3D grid by running:
-
-.. code-block:: python
-  
-  >>> molecule.export("vdw-model.pdb")
-
-.. image:: ../_images/vdw-grid.png
-  :width: 500
-  :align: center
-
-We can also export our modelled molecule int the 3D grid by running:
-
-.. code-block:: python
-  
-  >>> molecule.preview()
-
-Now, we can estimate the vdW volume by running:
-
-.. code-block:: python
-  
-  >>> molecule.volume()
-  83.64
-
-2. SES volume
-*************
-
-``Molecule.surface()`` takes the grid spacing, the spherical probe size to model the surface, the SES representation and returns a NumPy array with the molecule points representing the SES in the 3D grid. 
-
-.. code-block:: python
-
-  >>> # Grid Spacing (step): 0.1
-  >>> step = 0.1
-  >>> # Spherical Probe (probe): 1.4
-  >>> probe = 1.4
-  >>> # Surface Representation: SES
-  >>> surface = 'SES'
-  >>> molecule.surface(step=step, probe=probe, surface=surface)
-  >>> molecule.grid
-  array([[[1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1],
-          ...,
-          [1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1]],
-        
-          ...,
-
-        [[1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1],
-          ...,
-          [1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1]]], dtype=int32)
-
-.. note::
-
-  If any of the parameters (``step``, ``probe`` or ``surface``) are not defined, the function automatically sets them to the default values. So, you can call the function by ``molecule.surface()``.
-
-We can preview our modelled molecule in the 3D grid by running:
-
-.. code-block:: python
-  
-  >>> molecule.preview()
-
-.. image:: ../_images/ses-grid.png
-  :width: 500
-  :align: center
-
-Now, we can estimate the vdW volume by running:
-
-.. code-block:: python
-  
-  >>> molecule.volume()
-  90.8
-
-3. SAS volume
-*************
-
-``Molecule.surface()`` takes a grid spacing, a spherical probe to model the surface, a SAS representation and returns a NumPy array with the molecule points representing the SES in the 3D grid. 
-
-.. code-block:: python
-
-  >>> # Grid Spacing (step): 0.1
-  >>> step = 0.1
-  >>> # Spherical Probe (probe): 1.4
-  >>> probe = 1.4
-  >>> # Surface Representation: SAS
-  >>> surface = 'SAS'
-  >>> molecule.surface(step=step, probe=probe, surface=surface)
-  >>> molecule.grid
-  array([[[1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1],
-          ...,
-          [1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1]],
-        
-          ...,
-
-        [[1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1],
-          ...,
-          [1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1],
-          [1, 1, 1, ..., 1, 1, 1]]], dtype=int32)
-
-.. note::
-
-  If any of the parameters (``step`` or ``probe``) are not defined, the function automatically sets them to the default values. So, you can call the function by ``molecule.surface(surface='SAS')``.
-
-We can preview our modelled molecule in the 3D grid by running:
-
-.. code-block:: python
-  
-  >>> molecule.preview()
-
-.. image:: ../_images/sas-grid.png
-  :width: 500
-  :align: center
-
-Now, we can estimate the vdW volume by running:
-
-.. code-block:: python
-  
-  >>> molecule.volume()
-  340.28
-
-Examples
-########
-
-Jupyter notebook `examples `_ are available for:
-
-.. toctree::
-  :maxdepth: 0
-
-  Conservation analysis 
-  Data visualization 
-  Molecular dynamics analysis 
diff --git a/docs/source/_build/html/_sources/index.rst.txt b/docs/source/_build/html/_sources/index.rst.txt
deleted file mode 100644
index 0a6c3acf..00000000
--- a/docs/source/_build/html/_sources/index.rst.txt
+++ /dev/null
@@ -1,60 +0,0 @@
-Welcome to pyKVFinder's documentation!
-======================================
-
-Welcome to the **Python-C parallel KVFinder (pyKVFinder)** documentation, this page was built to help you get started with our cavity detection and characterization package.
-
-* `Installation <_installation/index.html>`_
-* `Tutorial <_tutorial/index.html>`_
-* `API reference <_api_reference/index.html>`_
-* `Command-line interface <_cli/index.html>`_
-* `GitHub repository `_
-* `About <_about/index.html>`_
-
-.. toctree::
-   :maxdepth: 1
-   :caption: Installation
-   :hidden:
-
-   _installation/index
- 
-.. toctree::
-   :maxdepth: 1
-   :caption: Tutorial
-   :hidden:
-   
-   _tutorial/index
-   
-.. toctree::
-   :maxdepth: 1
-   :caption: API Reference
-   :hidden:
-
-   _api_reference/index
-
-.. toctree::
-   :maxdepth: 1
-   :caption: Command-line interface
-   :hidden:
-
-   _cli/index
-
-.. toctree::
-    :maxdepth: 1
-    :caption: Configuration files
-    :hidden:
-
-    vdW radii <_cfg_files/vdw_file_template>
-    Custom grid <_cfg_files/box_file_template>
-    Hydrophobicity scale <_cfg_files/hydrophobicity_scale_file_template>
-
-.. toctree::
-   :maxdepth: 1
-   :caption: Citing pyKVFinder
-   :hidden:
-
-.. toctree::
-   :maxdepth: 1
-   :caption: About
-   :hidden:
-
-   _about/index
diff --git a/docs/source/_build/html/_static/_sphinx_javascript_frameworks_compat.js b/docs/source/_build/html/_static/_sphinx_javascript_frameworks_compat.js
deleted file mode 100644
index 8549469d..00000000
--- a/docs/source/_build/html/_static/_sphinx_javascript_frameworks_compat.js
+++ /dev/null
@@ -1,134 +0,0 @@
-/*
- * _sphinx_javascript_frameworks_compat.js
- * ~~~~~~~~~~
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- * Compatability shim for jQuery and underscores.js.
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- * xref RemovedInSphinx60Warning
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- */
-$u = _.noConflict();
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-/**
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-jQuery.urldecode = function(x) {
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-    return decodeURIComponent(x.replace(/\+/g, ' '));
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-/**
- * small helper function to urlencode strings
- */
-jQuery.urlencode = encodeURIComponent;
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-/**
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-jQuery.getQueryParameters = function(s) {
-    if (typeof s === 'undefined')
-        s = document.location.search;
-    var parts = s.substr(s.indexOf('?') + 1).split('&');
-    var result = {};
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-        var value = jQuery.urldecode(tmp[1]);
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-            result[key].push(value);
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-            result[key] = [value];
-    }
-    return result;
-};
-
-/**
- * highlight a given string on a jquery object by wrapping it in
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- */
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-            jQuery.each(node.childNodes, function() {
-                highlight(this, addItems);
-            });
-        }
-    }
-    var addItems = [];
-    var result = this.each(function() {
-        highlight(this, addItems);
-    });
-    for (var i = 0; i < addItems.length; ++i) {
-        jQuery(addItems[i].parent).before(addItems[i].target);
-    }
-    return result;
-};
-
-/*
- * backward compatibility for jQuery.browser
- * This will be supported until firefox bug is fixed.
- */
-if (!jQuery.browser) {
-    jQuery.uaMatch = function(ua) {
-        ua = ua.toLowerCase();
-
-        var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
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-    };
-    jQuery.browser = {};
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diff --git a/docs/source/_build/html/_static/basic.css b/docs/source/_build/html/_static/basic.css
deleted file mode 100644
index 08896771..00000000
--- a/docs/source/_build/html/_static/basic.css
+++ /dev/null
@@ -1,930 +0,0 @@
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-    width: 90%;
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-          "rect"
-        );
-        const bbox = parent.getBBox();
-        rect.x.baseVal.value = bbox.x;
-        rect.y.baseVal.value = bbox.y;
-        rect.width.baseVal.value = bbox.width;
-        rect.height.baseVal.value = bbox.height;
-        rect.setAttribute("class", className);
-        addItems.push({ parent: parent, target: rect });
-      }
-    }
-  } else if (node.matches && !node.matches("button, select, textarea")) {
-    node.childNodes.forEach((el) => _highlight(el, addItems, text, className));
-  }
-};
-const _highlightText = (thisNode, text, className) => {
-  let addItems = [];
-  _highlight(thisNode, addItems, text, className);
-  addItems.forEach((obj) =>
-    obj.parent.insertAdjacentElement("beforebegin", obj.target)
-  );
-};
-
-/**
- * Small JavaScript module for the documentation.
- */
-const Documentation = {
-  init: () => {
-    Documentation.highlightSearchWords();
-    Documentation.initDomainIndexTable();
-    Documentation.initOnKeyListeners();
-  },
-
-  /**
-   * i18n support
-   */
-  TRANSLATIONS: {},
-  PLURAL_EXPR: (n) => (n === 1 ? 0 : 1),
-  LOCALE: "unknown",
-
-  // gettext and ngettext don't access this so that the functions
-  // can safely bound to a different name (_ = Documentation.gettext)
-  gettext: (string) => {
-    const translated = Documentation.TRANSLATIONS[string];
-    switch (typeof translated) {
-      case "undefined":
-        return string; // no translation
-      case "string":
-        return translated; // translation exists
-      default:
-        return translated[0]; // (singular, plural) translation tuple exists
-    }
-  },
-
-  ngettext: (singular, plural, n) => {
-    const translated = Documentation.TRANSLATIONS[singular];
-    if (typeof translated !== "undefined")
-      return translated[Documentation.PLURAL_EXPR(n)];
-    return n === 1 ? singular : plural;
-  },
-
-  addTranslations: (catalog) => {
-    Object.assign(Documentation.TRANSLATIONS, catalog.messages);
-    Documentation.PLURAL_EXPR = new Function(
-      "n",
-      `return (${catalog.plural_expr})`
-    );
-    Documentation.LOCALE = catalog.locale;
-  },
-
-  /**
-   * highlight the search words provided in the url in the text
-   */
-  highlightSearchWords: () => {
-    const highlight =
-      new URLSearchParams(window.location.search).get("highlight") || "";
-    const terms = highlight.toLowerCase().split(/\s+/).filter(x => x);
-    if (terms.length === 0) return; // nothing to do
-
-    // There should never be more than one element matching "div.body"
-    const divBody = document.querySelectorAll("div.body");
-    const body = divBody.length ? divBody[0] : document.querySelector("body");
-    window.setTimeout(() => {
-      terms.forEach((term) => _highlightText(body, term, "highlighted"));
-    }, 10);
-
-    const searchBox = document.getElementById("searchbox");
-    if (searchBox === null) return;
-    searchBox.appendChild(
-      document
-        .createRange()
-        .createContextualFragment(
-          '
          ' +
-            '' +
-            Documentation.gettext("Hide Search Matches") +
-            "
          "
-        )
-    );
-  },
-
-  /**
-   * helper function to hide the search marks again
-   */
-  hideSearchWords: () => {
-    document
-      .querySelectorAll("#searchbox .highlight-link")
-      .forEach((el) => el.remove());
-    document
-      .querySelectorAll("span.highlighted")
-      .forEach((el) => el.classList.remove("highlighted"));
-    const url = new URL(window.location);
-    url.searchParams.delete("highlight");
-    window.history.replaceState({}, "", url);
-  },
-
-  /**
-   * helper function to focus on search bar
-   */
-  focusSearchBar: () => {
-    document.querySelectorAll("input[name=q]")[0]?.focus();
-  },
-
-  /**
-   * Initialise the domain index toggle buttons
-   */
-  initDomainIndexTable: () => {
-    const toggler = (el) => {
-      const idNumber = el.id.substr(7);
-      const toggledRows = document.querySelectorAll(`tr.cg-${idNumber}`);
-      if (el.src.substr(-9) === "minus.png") {
-        el.src = `${el.src.substr(0, el.src.length - 9)}plus.png`;
-        toggledRows.forEach((el) => (el.style.display = "none"));
-      } else {
-        el.src = `${el.src.substr(0, el.src.length - 8)}minus.png`;
-        toggledRows.forEach((el) => (el.style.display = ""));
-      }
-    };
-
-    const togglerElements = document.querySelectorAll("img.toggler");
-    togglerElements.forEach((el) =>
-      el.addEventListener("click", (event) => toggler(event.currentTarget))
-    );
-    togglerElements.forEach((el) => (el.style.display = ""));
-    if (DOCUMENTATION_OPTIONS.COLLAPSE_INDEX) togglerElements.forEach(toggler);
-  },
-
-  initOnKeyListeners: () => {
-    // only install a listener if it is really needed
-    if (
-      !DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS &&
-      !DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS
-    )
-      return;
-
-    const blacklistedElements = new Set([
-      "TEXTAREA",
-      "INPUT",
-      "SELECT",
-      "BUTTON",
-    ]);
-    document.addEventListener("keydown", (event) => {
-      if (blacklistedElements.has(document.activeElement.tagName)) return; // bail for input elements
-      if (event.altKey || event.ctrlKey || event.metaKey) return; // bail with special keys
-
-      if (!event.shiftKey) {
-        switch (event.key) {
-          case "ArrowLeft":
-            if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break;
-
-            const prevLink = document.querySelector('link[rel="prev"]');
-            if (prevLink && prevLink.href) {
-              window.location.href = prevLink.href;
-              event.preventDefault();
-            }
-            break;
-          case "ArrowRight":
-            if (!DOCUMENTATION_OPTIONS.NAVIGATION_WITH_KEYS) break;
-
-            const nextLink = document.querySelector('link[rel="next"]');
-            if (nextLink && nextLink.href) {
-              window.location.href = nextLink.href;
-              event.preventDefault();
-            }
-            break;
-          case "Escape":
-            if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break;
-            Documentation.hideSearchWords();
-            event.preventDefault();
-        }
-      }
-
-      // some keyboard layouts may need Shift to get /
-      switch (event.key) {
-        case "/":
-          if (!DOCUMENTATION_OPTIONS.ENABLE_SEARCH_SHORTCUTS) break;
-          Documentation.focusSearchBar();
-          event.preventDefault();
-      }
-    });
-  },
-};
-
-// quick alias for translations
-const _ = Documentation.gettext;
-
-_ready(Documentation.init);
diff --git a/docs/source/_build/html/_static/documentation_options.js b/docs/source/_build/html/_static/documentation_options.js
deleted file mode 100644
index 0ce3c191..00000000
--- a/docs/source/_build/html/_static/documentation_options.js
+++ /dev/null
@@ -1,14 +0,0 @@
-var DOCUMENTATION_OPTIONS = {
-    URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
-    VERSION: '0.5.0',
-    LANGUAGE: 'en',
-    COLLAPSE_INDEX: false,
-    BUILDER: 'html',
-    FILE_SUFFIX: '.html',
-    LINK_SUFFIX: '.html',
-    HAS_SOURCE: true,
-    SOURCELINK_SUFFIX: '.txt',
-    NAVIGATION_WITH_KEYS: false,
-    SHOW_SEARCH_SUMMARY: true,
-    ENABLE_SEARCH_SHORTCUTS: false,
-};
\ No newline at end of file
diff --git a/docs/source/_build/html/_static/file.png b/docs/source/_build/html/_static/file.png
deleted file mode 100644
index a858a410..00000000
Binary files a/docs/source/_build/html/_static/file.png and /dev/null differ
diff --git a/docs/source/_build/html/_static/icon.ico b/docs/source/_build/html/_static/icon.ico
deleted file mode 100644
index 04f83ac0..00000000
Binary files a/docs/source/_build/html/_static/icon.ico and /dev/null differ
diff --git a/docs/source/_build/html/_static/jquery-3.6.0.js b/docs/source/_build/html/_static/jquery-3.6.0.js
deleted file mode 100644
index fc6c299b..00000000
--- a/docs/source/_build/html/_static/jquery-3.6.0.js
+++ /dev/null
@@ -1,10881 +0,0 @@
-/*!
- * jQuery JavaScript Library v3.6.0
- * https://jquery.com/
- *
- * Includes Sizzle.js
- * https://sizzlejs.com/
- *
- * Copyright OpenJS Foundation and other contributors
- * Released under the MIT license
- * https://jquery.org/license
- *
- * Date: 2021-03-02T17:08Z
- */
-( function( global, factory ) {
-
-	"use strict";
-
-	if ( typeof module === "object" && typeof module.exports === "object" ) {
-
-		// For CommonJS and CommonJS-like environments where a proper `window`
-		// is present, execute the factory and get jQuery.
-		// For environments that do not have a `window` with a `document`
-		// (such as Node.js), expose a factory as module.exports.
-		// This accentuates the need for the creation of a real `window`.
-		// e.g. var jQuery = require("jquery")(window);
-		// See ticket #14549 for more info.
-		module.exports = global.document ?
-			factory( global, true ) :
-			function( w ) {
-				if ( !w.document ) {
-					throw new Error( "jQuery requires a window with a document" );
-				}
-				return factory( w );
-			};
-	} else {
-		factory( global );
-	}
-
-// Pass this if window is not defined yet
-} )( typeof window !== "undefined" ? window : this, function( window, noGlobal ) {
-
-// Edge <= 12 - 13+, Firefox <=18 - 45+, IE 10 - 11, Safari 5.1 - 9+, iOS 6 - 9.1
-// throw exceptions when non-strict code (e.g., ASP.NET 4.5) accesses strict mode
-// arguments.callee.caller (trac-13335). But as of jQuery 3.0 (2016), strict mode should be common
-// enough that all such attempts are guarded in a try block.
-"use strict";
-
-var arr = [];
-
-var getProto = Object.getPrototypeOf;
-
-var slice = arr.slice;
-
-var flat = arr.flat ? function( array ) {
-	return arr.flat.call( array );
-} : function( array ) {
-	return arr.concat.apply( [], array );
-};
-
-
-var push = arr.push;
-
-var indexOf = arr.indexOf;
-
-var class2type = {};
-
-var toString = class2type.toString;
-
-var hasOwn = class2type.hasOwnProperty;
-
-var fnToString = hasOwn.toString;
-
-var ObjectFunctionString = fnToString.call( Object );
-
-var support = {};
-
-var isFunction = function isFunction( obj ) {
-
-		// Support: Chrome <=57, Firefox <=52
-		// In some browsers, typeof returns "function" for HTML  elements
-		// (i.e., `typeof document.createElement( "object" ) === "function"`).
-		// We don't want to classify *any* DOM node as a function.
-		// Support: QtWeb <=3.8.5, WebKit <=534.34, wkhtmltopdf tool <=0.12.5
-		// Plus for old WebKit, typeof returns "function" for HTML collections
-		// (e.g., `typeof document.getElementsByTagName("div") === "function"`). (gh-4756)
-		return typeof obj === "function" && typeof obj.nodeType !== "number" &&
-			typeof obj.item !== "function";
-	};
-
-
-var isWindow = function isWindow( obj ) {
-		return obj != null && obj === obj.window;
-	};
-
-
-var document = window.document;
-
-
-
-	var preservedScriptAttributes = {
-		type: true,
-		src: true,
-		nonce: true,
-		noModule: true
-	};
-
-	function DOMEval( code, node, doc ) {
-		doc = doc || document;
-
-		var i, val,
-			script = doc.createElement( "script" );
-
-		script.text = code;
-		if ( node ) {
-			for ( i in preservedScriptAttributes ) {
-
-				// Support: Firefox 64+, Edge 18+
-				// Some browsers don't support the "nonce" property on scripts.
-				// On the other hand, just using `getAttribute` is not enough as
-				// the `nonce` attribute is reset to an empty string whenever it
-				// becomes browsing-context connected.
-				// See https://github.com/whatwg/html/issues/2369
-				// See https://html.spec.whatwg.org/#nonce-attributes
-				// The `node.getAttribute` check was added for the sake of
-				// `jQuery.globalEval` so that it can fake a nonce-containing node
-				// via an object.
-				val = node[ i ] || node.getAttribute && node.getAttribute( i );
-				if ( val ) {
-					script.setAttribute( i, val );
-				}
-			}
-		}
-		doc.head.appendChild( script ).parentNode.removeChild( script );
-	}
-
-
-function toType( obj ) {
-	if ( obj == null ) {
-		return obj + "";
-	}
-
-	// Support: Android <=2.3 only (functionish RegExp)
-	return typeof obj === "object" || typeof obj === "function" ?
-		class2type[ toString.call( obj ) ] || "object" :
-		typeof obj;
-}
-/* global Symbol */
-// Defining this global in .eslintrc.json would create a danger of using the global
-// unguarded in another place, it seems safer to define global only for this module
-
-
-
-var
-	version = "3.6.0",
-
-	// Define a local copy of jQuery
-	jQuery = function( selector, context ) {
-
-		// The jQuery object is actually just the init constructor 'enhanced'
-		// Need init if jQuery is called (just allow error to be thrown if not included)
-		return new jQuery.fn.init( selector, context );
-	};
-
-jQuery.fn = jQuery.prototype = {
-
-	// The current version of jQuery being used
-	jquery: version,
-
-	constructor: jQuery,
-
-	// The default length of a jQuery object is 0
-	length: 0,
-
-	toArray: function() {
-		return slice.call( this );
-	},
-
-	// Get the Nth element in the matched element set OR
-	// Get the whole matched element set as a clean array
-	get: function( num ) {
-
-		// Return all the elements in a clean array
-		if ( num == null ) {
-			return slice.call( this );
-		}
-
-		// Return just the one element from the set
-		return num < 0 ? this[ num + this.length ] : this[ num ];
-	},
-
-	// Take an array of elements and push it onto the stack
-	// (returning the new matched element set)
-	pushStack: function( elems ) {
-
-		// Build a new jQuery matched element set
-		var ret = jQuery.merge( this.constructor(), elems );
-
-		// Add the old object onto the stack (as a reference)
-		ret.prevObject = this;
-
-		// Return the newly-formed element set
-		return ret;
-	},
-
-	// Execute a callback for every element in the matched set.
-	each: function( callback ) {
-		return jQuery.each( this, callback );
-	},
-
-	map: function( callback ) {
-		return this.pushStack( jQuery.map( this, function( elem, i ) {
-			return callback.call( elem, i, elem );
-		} ) );
-	},
-
-	slice: function() {
-		return this.pushStack( slice.apply( this, arguments ) );
-	},
-
-	first: function() {
-		return this.eq( 0 );
-	},
-
-	last: function() {
-		return this.eq( -1 );
-	},
-
-	even: function() {
-		return this.pushStack( jQuery.grep( this, function( _elem, i ) {
-			return ( i + 1 ) % 2;
-		} ) );
-	},
-
-	odd: function() {
-		return this.pushStack( jQuery.grep( this, function( _elem, i ) {
-			return i % 2;
-		} ) );
-	},
-
-	eq: function( i ) {
-		var len = this.length,
-			j = +i + ( i < 0 ? len : 0 );
-		return this.pushStack( j >= 0 && j < len ? [ this[ j ] ] : [] );
-	},
-
-	end: function() {
-		return this.prevObject || this.constructor();
-	},
-
-	// For internal use only.
-	// Behaves like an Array's method, not like a jQuery method.
-	push: push,
-	sort: arr.sort,
-	splice: arr.splice
-};
-
-jQuery.extend = jQuery.fn.extend = function() {
-	var options, name, src, copy, copyIsArray, clone,
-		target = arguments[ 0 ] || {},
-		i = 1,
-		length = arguments.length,
-		deep = false;
-
-	// Handle a deep copy situation
-	if ( typeof target === "boolean" ) {
-		deep = target;
-
-		// Skip the boolean and the target
-		target = arguments[ i ] || {};
-		i++;
-	}
-
-	// Handle case when target is a string or something (possible in deep copy)
-	if ( typeof target !== "object" && !isFunction( target ) ) {
-		target = {};
-	}
-
-	// Extend jQuery itself if only one argument is passed
-	if ( i === length ) {
-		target = this;
-		i--;
-	}
-
-	for ( ; i < length; i++ ) {
-
-		// Only deal with non-null/undefined values
-		if ( ( options = arguments[ i ] ) != null ) {
-
-			// Extend the base object
-			for ( name in options ) {
-				copy = options[ name ];
-
-				// Prevent Object.prototype pollution
-				// Prevent never-ending loop
-				if ( name === "__proto__" || target === copy ) {
-					continue;
-				}
-
-				// Recurse if we're merging plain objects or arrays
-				if ( deep && copy && ( jQuery.isPlainObject( copy ) ||
-					( copyIsArray = Array.isArray( copy ) ) ) ) {
-					src = target[ name ];
-
-					// Ensure proper type for the source value
-					if ( copyIsArray && !Array.isArray( src ) ) {
-						clone = [];
-					} else if ( !copyIsArray && !jQuery.isPlainObject( src ) ) {
-						clone = {};
-					} else {
-						clone = src;
-					}
-					copyIsArray = false;
-
-					// Never move original objects, clone them
-					target[ name ] = jQuery.extend( deep, clone, copy );
-
-				// Don't bring in undefined values
-				} else if ( copy !== undefined ) {
-					target[ name ] = copy;
-				}
-			}
-		}
-	}
-
-	// Return the modified object
-	return target;
-};
-
-jQuery.extend( {
-
-	// Unique for each copy of jQuery on the page
-	expando: "jQuery" + ( version + Math.random() ).replace( /\D/g, "" ),
-
-	// Assume jQuery is ready without the ready module
-	isReady: true,
-
-	error: function( msg ) {
-		throw new Error( msg );
-	},
-
-	noop: function() {},
-
-	isPlainObject: function( obj ) {
-		var proto, Ctor;
-
-		// Detect obvious negatives
-		// Use toString instead of jQuery.type to catch host objects
-		if ( !obj || toString.call( obj ) !== "[object Object]" ) {
-			return false;
-		}
-
-		proto = getProto( obj );
-
-		// Objects with no prototype (e.g., `Object.create( null )`) are plain
-		if ( !proto ) {
-			return true;
-		}
-
-		// Objects with prototype are plain iff they were constructed by a global Object function
-		Ctor = hasOwn.call( proto, "constructor" ) && proto.constructor;
-		return typeof Ctor === "function" && fnToString.call( Ctor ) === ObjectFunctionString;
-	},
-
-	isEmptyObject: function( obj ) {
-		var name;
-
-		for ( name in obj ) {
-			return false;
-		}
-		return true;
-	},
-
-	// Evaluates a script in a provided context; falls back to the global one
-	// if not specified.
-	globalEval: function( code, options, doc ) {
-		DOMEval( code, { nonce: options && options.nonce }, doc );
-	},
-
-	each: function( obj, callback ) {
-		var length, i = 0;
-
-		if ( isArrayLike( obj ) ) {
-			length = obj.length;
-			for ( ; i < length; i++ ) {
-				if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) {
-					break;
-				}
-			}
-		} else {
-			for ( i in obj ) {
-				if ( callback.call( obj[ i ], i, obj[ i ] ) === false ) {
-					break;
-				}
-			}
-		}
-
-		return obj;
-	},
-
-	// results is for internal usage only
-	makeArray: function( arr, results ) {
-		var ret = results || [];
-
-		if ( arr != null ) {
-			if ( isArrayLike( Object( arr ) ) ) {
-				jQuery.merge( ret,
-					typeof arr === "string" ?
-						[ arr ] : arr
-				);
-			} else {
-				push.call( ret, arr );
-			}
-		}
-
-		return ret;
-	},
-
-	inArray: function( elem, arr, i ) {
-		return arr == null ? -1 : indexOf.call( arr, elem, i );
-	},
-
-	// Support: Android <=4.0 only, PhantomJS 1 only
-	// push.apply(_, arraylike) throws on ancient WebKit
-	merge: function( first, second ) {
-		var len = +second.length,
-			j = 0,
-			i = first.length;
-
-		for ( ; j < len; j++ ) {
-			first[ i++ ] = second[ j ];
-		}
-
-		first.length = i;
-
-		return first;
-	},
-
-	grep: function( elems, callback, invert ) {
-		var callbackInverse,
-			matches = [],
-			i = 0,
-			length = elems.length,
-			callbackExpect = !invert;
-
-		// Go through the array, only saving the items
-		// that pass the validator function
-		for ( ; i < length; i++ ) {
-			callbackInverse = !callback( elems[ i ], i );
-			if ( callbackInverse !== callbackExpect ) {
-				matches.push( elems[ i ] );
-			}
-		}
-
-		return matches;
-	},
-
-	// arg is for internal usage only
-	map: function( elems, callback, arg ) {
-		var length, value,
-			i = 0,
-			ret = [];
-
-		// Go through the array, translating each of the items to their new values
-		if ( isArrayLike( elems ) ) {
-			length = elems.length;
-			for ( ; i < length; i++ ) {
-				value = callback( elems[ i ], i, arg );
-
-				if ( value != null ) {
-					ret.push( value );
-				}
-			}
-
-		// Go through every key on the object,
-		} else {
-			for ( i in elems ) {
-				value = callback( elems[ i ], i, arg );
-
-				if ( value != null ) {
-					ret.push( value );
-				}
-			}
-		}
-
-		// Flatten any nested arrays
-		return flat( ret );
-	},
-
-	// A global GUID counter for objects
-	guid: 1,
-
-	// jQuery.support is not used in Core but other projects attach their
-	// properties to it so it needs to exist.
-	support: support
-} );
-
-if ( typeof Symbol === "function" ) {
-	jQuery.fn[ Symbol.iterator ] = arr[ Symbol.iterator ];
-}
-
-// Populate the class2type map
-jQuery.each( "Boolean Number String Function Array Date RegExp Object Error Symbol".split( " " ),
-	function( _i, name ) {
-		class2type[ "[object " + name + "]" ] = name.toLowerCase();
-	} );
-
-function isArrayLike( obj ) {
-
-	// Support: real iOS 8.2 only (not reproducible in simulator)
-	// `in` check used to prevent JIT error (gh-2145)
-	// hasOwn isn't used here due to false negatives
-	// regarding Nodelist length in IE
-	var length = !!obj && "length" in obj && obj.length,
-		type = toType( obj );
-
-	if ( isFunction( obj ) || isWindow( obj ) ) {
-		return false;
-	}
-
-	return type === "array" || length === 0 ||
-		typeof length === "number" && length > 0 && ( length - 1 ) in obj;
-}
-var Sizzle =
-/*!
- * Sizzle CSS Selector Engine v2.3.6
- * https://sizzlejs.com/
- *
- * Copyright JS Foundation and other contributors
- * Released under the MIT license
- * https://js.foundation/
- *
- * Date: 2021-02-16
- */
-( function( window ) {
-var i,
-	support,
-	Expr,
-	getText,
-	isXML,
-	tokenize,
-	compile,
-	select,
-	outermostContext,
-	sortInput,
-	hasDuplicate,
-
-	// Local document vars
-	setDocument,
-	document,
-	docElem,
-	documentIsHTML,
-	rbuggyQSA,
-	rbuggyMatches,
-	matches,
-	contains,
-
-	// Instance-specific data
-	expando = "sizzle" + 1 * new Date(),
-	preferredDoc = window.document,
-	dirruns = 0,
-	done = 0,
-	classCache = createCache(),
-	tokenCache = createCache(),
-	compilerCache = createCache(),
-	nonnativeSelectorCache = createCache(),
-	sortOrder = function( a, b ) {
-		if ( a === b ) {
-			hasDuplicate = true;
-		}
-		return 0;
-	},
-
-	// Instance methods
-	hasOwn = ( {} ).hasOwnProperty,
-	arr = [],
-	pop = arr.pop,
-	pushNative = arr.push,
-	push = arr.push,
-	slice = arr.slice,
-
-	// Use a stripped-down indexOf as it's faster than native
-	// https://jsperf.com/thor-indexof-vs-for/5
-	indexOf = function( list, elem ) {
-		var i = 0,
-			len = list.length;
-		for ( ; i < len; i++ ) {
-			if ( list[ i ] === elem ) {
-				return i;
-			}
-		}
-		return -1;
-	},
-
-	booleans = "checked|selected|async|autofocus|autoplay|controls|defer|disabled|hidden|" +
-		"ismap|loop|multiple|open|readonly|required|scoped",
-
-	// Regular expressions
-
-	// http://www.w3.org/TR/css3-selectors/#whitespace
-	whitespace = "[\\x20\\t\\r\\n\\f]",
-
-	// https://www.w3.org/TR/css-syntax-3/#ident-token-diagram
-	identifier = "(?:\\\\[\\da-fA-F]{1,6}" + whitespace +
-		"?|\\\\[^\\r\\n\\f]|[\\w-]|[^\0-\\x7f])+",
-
-	// Attribute selectors: http://www.w3.org/TR/selectors/#attribute-selectors
-	attributes = "\\[" + whitespace + "*(" + identifier + ")(?:" + whitespace +
-
-		// Operator (capture 2)
-		"*([*^$|!~]?=)" + whitespace +
-
-		// "Attribute values must be CSS identifiers [capture 5]
-		// or strings [capture 3 or capture 4]"
-		"*(?:'((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\"|(" + identifier + "))|)" +
-		whitespace + "*\\]",
-
-	pseudos = ":(" + identifier + ")(?:\\((" +
-
-		// To reduce the number of selectors needing tokenize in the preFilter, prefer arguments:
-		// 1. quoted (capture 3; capture 4 or capture 5)
-		"('((?:\\\\.|[^\\\\'])*)'|\"((?:\\\\.|[^\\\\\"])*)\")|" +
-
-		// 2. simple (capture 6)
-		"((?:\\\\.|[^\\\\()[\\]]|" + attributes + ")*)|" +
-
-		// 3. anything else (capture 2)
-		".*" +
-		")\\)|)",
-
-	// Leading and non-escaped trailing whitespace, capturing some non-whitespace characters preceding the latter
-	rwhitespace = new RegExp( whitespace + "+", "g" ),
-	rtrim = new RegExp( "^" + whitespace + "+|((?:^|[^\\\\])(?:\\\\.)*)" +
-		whitespace + "+$", "g" ),
-
-	rcomma = new RegExp( "^" + whitespace + "*," + whitespace + "*" ),
-	rcombinators = new RegExp( "^" + whitespace + "*([>+~]|" + whitespace + ")" + whitespace +
-		"*" ),
-	rdescend = new RegExp( whitespace + "|>" ),
-
-	rpseudo = new RegExp( pseudos ),
-	ridentifier = new RegExp( "^" + identifier + "$" ),
-
-	matchExpr = {
-		"ID": new RegExp( "^#(" + identifier + ")" ),
-		"CLASS": new RegExp( "^\\.(" + identifier + ")" ),
-		"TAG": new RegExp( "^(" + identifier + "|[*])" ),
-		"ATTR": new RegExp( "^" + attributes ),
-		"PSEUDO": new RegExp( "^" + pseudos ),
-		"CHILD": new RegExp( "^:(only|first|last|nth|nth-last)-(child|of-type)(?:\\(" +
-			whitespace + "*(even|odd|(([+-]|)(\\d*)n|)" + whitespace + "*(?:([+-]|)" +
-			whitespace + "*(\\d+)|))" + whitespace + "*\\)|)", "i" ),
-		"bool": new RegExp( "^(?:" + booleans + ")$", "i" ),
-
-		// For use in libraries implementing .is()
-		// We use this for POS matching in `select`
-		"needsContext": new RegExp( "^" + whitespace +
-			"*[>+~]|:(even|odd|eq|gt|lt|nth|first|last)(?:\\(" + whitespace +
-			"*((?:-\\d)?\\d*)" + whitespace + "*\\)|)(?=[^-]|$)", "i" )
-	},
-
-	rhtml = /HTML$/i,
-	rinputs = /^(?:input|select|textarea|button)$/i,
-	rheader = /^h\d$/i,
-
-	rnative = /^[^{]+\{\s*\[native \w/,
-
-	// Easily-parseable/retrievable ID or TAG or CLASS selectors
-	rquickExpr = /^(?:#([\w-]+)|(\w+)|\.([\w-]+))$/,
-
-	rsibling = /[+~]/,
-
-	// CSS escapes
-	// http://www.w3.org/TR/CSS21/syndata.html#escaped-characters
-	runescape = new RegExp( "\\\\[\\da-fA-F]{1,6}" + whitespace + "?|\\\\([^\\r\\n\\f])", "g" ),
-	funescape = function( escape, nonHex ) {
-		var high = "0x" + escape.slice( 1 ) - 0x10000;
-
-		return nonHex ?
-
-			// Strip the backslash prefix from a non-hex escape sequence
-			nonHex :
-
-			// Replace a hexadecimal escape sequence with the encoded Unicode code point
-			// Support: IE <=11+
-			// For values outside the Basic Multilingual Plane (BMP), manually construct a
-			// surrogate pair
-			high < 0 ?
-				String.fromCharCode( high + 0x10000 ) :
-				String.fromCharCode( high >> 10 | 0xD800, high & 0x3FF | 0xDC00 );
-	},
-
-	// CSS string/identifier serialization
-	// https://drafts.csswg.org/cssom/#common-serializing-idioms
-	rcssescape = /([\0-\x1f\x7f]|^-?\d)|^-$|[^\0-\x1f\x7f-\uFFFF\w-]/g,
-	fcssescape = function( ch, asCodePoint ) {
-		if ( asCodePoint ) {
-
-			// U+0000 NULL becomes U+FFFD REPLACEMENT CHARACTER
-			if ( ch === "\0" ) {
-				return "\uFFFD";
-			}
-
-			// Control characters and (dependent upon position) numbers get escaped as code points
-			return ch.slice( 0, -1 ) + "\\" +
-				ch.charCodeAt( ch.length - 1 ).toString( 16 ) + " ";
-		}
-
-		// Other potentially-special ASCII characters get backslash-escaped
-		return "\\" + ch;
-	},
-
-	// Used for iframes
-	// See setDocument()
-	// Removing the function wrapper causes a "Permission Denied"
-	// error in IE
-	unloadHandler = function() {
-		setDocument();
-	},
-
-	inDisabledFieldset = addCombinator(
-		function( elem ) {
-			return elem.disabled === true && elem.nodeName.toLowerCase() === "fieldset";
-		},
-		{ dir: "parentNode", next: "legend" }
-	);
-
-// Optimize for push.apply( _, NodeList )
-try {
-	push.apply(
-		( arr = slice.call( preferredDoc.childNodes ) ),
-		preferredDoc.childNodes
-	);
-
-	// Support: Android<4.0
-	// Detect silently failing push.apply
-	// eslint-disable-next-line no-unused-expressions
-	arr[ preferredDoc.childNodes.length ].nodeType;
-} catch ( e ) {
-	push = { apply: arr.length ?
-
-		// Leverage slice if possible
-		function( target, els ) {
-			pushNative.apply( target, slice.call( els ) );
-		} :
-
-		// Support: IE<9
-		// Otherwise append directly
-		function( target, els ) {
-			var j = target.length,
-				i = 0;
-
-			// Can't trust NodeList.length
-			while ( ( target[ j++ ] = els[ i++ ] ) ) {}
-			target.length = j - 1;
-		}
-	};
-}
-
-function Sizzle( selector, context, results, seed ) {
-	var m, i, elem, nid, match, groups, newSelector,
-		newContext = context && context.ownerDocument,
-
-		// nodeType defaults to 9, since context defaults to document
-		nodeType = context ? context.nodeType : 9;
-
-	results = results || [];
-
-	// Return early from calls with invalid selector or context
-	if ( typeof selector !== "string" || !selector ||
-		nodeType !== 1 && nodeType !== 9 && nodeType !== 11 ) {
-
-		return results;
-	}
-
-	// Try to shortcut find operations (as opposed to filters) in HTML documents
-	if ( !seed ) {
-		setDocument( context );
-		context = context || document;
-
-		if ( documentIsHTML ) {
-
-			// If the selector is sufficiently simple, try using a "get*By*" DOM method
-			// (excepting DocumentFragment context, where the methods don't exist)
-			if ( nodeType !== 11 && ( match = rquickExpr.exec( selector ) ) ) {
-
-				// ID selector
-				if ( ( m = match[ 1 ] ) ) {
-
-					// Document context
-					if ( nodeType === 9 ) {
-						if ( ( elem = context.getElementById( m ) ) ) {
-
-							// Support: IE, Opera, Webkit
-							// TODO: identify versions
-							// getElementById can match elements by name instead of ID
-							if ( elem.id === m ) {
-								results.push( elem );
-								return results;
-							}
-						} else {
-							return results;
-						}
-
-					// Element context
-					} else {
-
-						// Support: IE, Opera, Webkit
-						// TODO: identify versions
-						// getElementById can match elements by name instead of ID
-						if ( newContext && ( elem = newContext.getElementById( m ) ) &&
-							contains( context, elem ) &&
-							elem.id === m ) {
-
-							results.push( elem );
-							return results;
-						}
-					}
-
-				// Type selector
-				} else if ( match[ 2 ] ) {
-					push.apply( results, context.getElementsByTagName( selector ) );
-					return results;
-
-				// Class selector
-				} else if ( ( m = match[ 3 ] ) && support.getElementsByClassName &&
-					context.getElementsByClassName ) {
-
-					push.apply( results, context.getElementsByClassName( m ) );
-					return results;
-				}
-			}
-
-			// Take advantage of querySelectorAll
-			if ( support.qsa &&
-				!nonnativeSelectorCache[ selector + " " ] &&
-				( !rbuggyQSA || !rbuggyQSA.test( selector ) ) &&
-
-				// Support: IE 8 only
-				// Exclude object elements
-				( nodeType !== 1 || context.nodeName.toLowerCase() !== "object" ) ) {
-
-				newSelector = selector;
-				newContext = context;
-
-				// qSA considers elements outside a scoping root when evaluating child or
-				// descendant combinators, which is not what we want.
-				// In such cases, we work around the behavior by prefixing every selector in the
-				// list with an ID selector referencing the scope context.
-				// The technique has to be used as well when a leading combinator is used
-				// as such selectors are not recognized by querySelectorAll.
-				// Thanks to Andrew Dupont for this technique.
-				if ( nodeType === 1 &&
-					( rdescend.test( selector ) || rcombinators.test( selector ) ) ) {
-
-					// Expand context for sibling selectors
-					newContext = rsibling.test( selector ) && testContext( context.parentNode ) ||
-						context;
-
-					// We can use :scope instead of the ID hack if the browser
-					// supports it & if we're not changing the context.
-					if ( newContext !== context || !support.scope ) {
-
-						// Capture the context ID, setting it first if necessary
-						if ( ( nid = context.getAttribute( "id" ) ) ) {
-							nid = nid.replace( rcssescape, fcssescape );
-						} else {
-							context.setAttribute( "id", ( nid = expando ) );
-						}
-					}
-
-					// Prefix every selector in the list
-					groups = tokenize( selector );
-					i = groups.length;
-					while ( i-- ) {
-						groups[ i ] = ( nid ? "#" + nid : ":scope" ) + " " +
-							toSelector( groups[ i ] );
-					}
-					newSelector = groups.join( "," );
-				}
-
-				try {
-					push.apply( results,
-						newContext.querySelectorAll( newSelector )
-					);
-					return results;
-				} catch ( qsaError ) {
-					nonnativeSelectorCache( selector, true );
-				} finally {
-					if ( nid === expando ) {
-						context.removeAttribute( "id" );
-					}
-				}
-			}
-		}
-	}
-
-	// All others
-	return select( selector.replace( rtrim, "$1" ), context, results, seed );
-}
-
-/**
- * Create key-value caches of limited size
- * @returns {function(string, object)} Returns the Object data after storing it on itself with
- *	property name the (space-suffixed) string and (if the cache is larger than Expr.cacheLength)
- *	deleting the oldest entry
- */
-function createCache() {
-	var keys = [];
-
-	function cache( key, value ) {
-
-		// Use (key + " ") to avoid collision with native prototype properties (see Issue #157)
-		if ( keys.push( key + " " ) > Expr.cacheLength ) {
-
-			// Only keep the most recent entries
-			delete cache[ keys.shift() ];
-		}
-		return ( cache[ key + " " ] = value );
-	}
-	return cache;
-}
-
-/**
- * Mark a function for special use by Sizzle
- * @param {Function} fn The function to mark
- */
-function markFunction( fn ) {
-	fn[ expando ] = true;
-	return fn;
-}
-
-/**
- * Support testing using an element
- * @param {Function} fn Passed the created element and returns a boolean result
- */
-function assert( fn ) {
-	var el = document.createElement( "fieldset" );
-
-	try {
-		return !!fn( el );
-	} catch ( e ) {
-		return false;
-	} finally {
-
-		// Remove from its parent by default
-		if ( el.parentNode ) {
-			el.parentNode.removeChild( el );
-		}
-
-		// release memory in IE
-		el = null;
-	}
-}
-
-/**
- * Adds the same handler for all of the specified attrs
- * @param {String} attrs Pipe-separated list of attributes
- * @param {Function} handler The method that will be applied
- */
-function addHandle( attrs, handler ) {
-	var arr = attrs.split( "|" ),
-		i = arr.length;
-
-	while ( i-- ) {
-		Expr.attrHandle[ arr[ i ] ] = handler;
-	}
-}
-
-/**
- * Checks document order of two siblings
- * @param {Element} a
- * @param {Element} b
- * @returns {Number} Returns less than 0 if a precedes b, greater than 0 if a follows b
- */
-function siblingCheck( a, b ) {
-	var cur = b && a,
-		diff = cur && a.nodeType === 1 && b.nodeType === 1 &&
-			a.sourceIndex - b.sourceIndex;
-
-	// Use IE sourceIndex if available on both nodes
-	if ( diff ) {
-		return diff;
-	}
-
-	// Check if b follows a
-	if ( cur ) {
-		while ( ( cur = cur.nextSibling ) ) {
-			if ( cur === b ) {
-				return -1;
-			}
-		}
-	}
-
-	return a ? 1 : -1;
-}
-
-/**
- * Returns a function to use in pseudos for input types
- * @param {String} type
- */
-function createInputPseudo( type ) {
-	return function( elem ) {
-		var name = elem.nodeName.toLowerCase();
-		return name === "input" && elem.type === type;
-	};
-}
-
-/**
- * Returns a function to use in pseudos for buttons
- * @param {String} type
- */
-function createButtonPseudo( type ) {
-	return function( elem ) {
-		var name = elem.nodeName.toLowerCase();
-		return ( name === "input" || name === "button" ) && elem.type === type;
-	};
-}
-
-/**
- * Returns a function to use in pseudos for :enabled/:disabled
- * @param {Boolean} disabled true for :disabled; false for :enabled
- */
-function createDisabledPseudo( disabled ) {
-
-	// Known :disabled false positives: fieldset[disabled] > legend:nth-of-type(n+2) :can-disable
-	return function( elem ) {
-
-		// Only certain elements can match :enabled or :disabled
-		// https://html.spec.whatwg.org/multipage/scripting.html#selector-enabled
-		// https://html.spec.whatwg.org/multipage/scripting.html#selector-disabled
-		if ( "form" in elem ) {
-
-			// Check for inherited disabledness on relevant non-disabled elements:
-			// * listed form-associated elements in a disabled fieldset
-			//   https://html.spec.whatwg.org/multipage/forms.html#category-listed
-			//   https://html.spec.whatwg.org/multipage/forms.html#concept-fe-disabled
-			// * option elements in a disabled optgroup
-			//   https://html.spec.whatwg.org/multipage/forms.html#concept-option-disabled
-			// All such elements have a "form" property.
-			if ( elem.parentNode && elem.disabled === false ) {
-
-				// Option elements defer to a parent optgroup if present
-				if ( "label" in elem ) {
-					if ( "label" in elem.parentNode ) {
-						return elem.parentNode.disabled === disabled;
-					} else {
-						return elem.disabled === disabled;
-					}
-				}
-
-				// Support: IE 6 - 11
-				// Use the isDisabled shortcut property to check for disabled fieldset ancestors
-				return elem.isDisabled === disabled ||
-
-					// Where there is no isDisabled, check manually
-					/* jshint -W018 */
-					elem.isDisabled !== !disabled &&
-					inDisabledFieldset( elem ) === disabled;
-			}
-
-			return elem.disabled === disabled;
-
-		// Try to winnow out elements that can't be disabled before trusting the disabled property.
-		// Some victims get caught in our net (label, legend, menu, track), but it shouldn't
-		// even exist on them, let alone have a boolean value.
-		} else if ( "label" in elem ) {
-			return elem.disabled === disabled;
-		}
-
-		// Remaining elements are neither :enabled nor :disabled
-		return false;
-	};
-}
-
-/**
- * Returns a function to use in pseudos for positionals
- * @param {Function} fn
- */
-function createPositionalPseudo( fn ) {
-	return markFunction( function( argument ) {
-		argument = +argument;
-		return markFunction( function( seed, matches ) {
-			var j,
-				matchIndexes = fn( [], seed.length, argument ),
-				i = matchIndexes.length;
-
-			// Match elements found at the specified indexes
-			while ( i-- ) {
-				if ( seed[ ( j = matchIndexes[ i ] ) ] ) {
-					seed[ j ] = !( matches[ j ] = seed[ j ] );
-				}
-			}
-		} );
-	} );
-}
-
-/**
- * Checks a node for validity as a Sizzle context
- * @param {Element|Object=} context
- * @returns {Element|Object|Boolean} The input node if acceptable, otherwise a falsy value
- */
-function testContext( context ) {
-	return context && typeof context.getElementsByTagName !== "undefined" && context;
-}
-
-// Expose support vars for convenience
-support = Sizzle.support = {};
-
-/**
- * Detects XML nodes
- * @param {Element|Object} elem An element or a document
- * @returns {Boolean} True iff elem is a non-HTML XML node
- */
-isXML = Sizzle.isXML = function( elem ) {
-	var namespace = elem && elem.namespaceURI,
-		docElem = elem && ( elem.ownerDocument || elem ).documentElement;
-
-	// Support: IE <=8
-	// Assume HTML when documentElement doesn't yet exist, such as inside loading iframes
-	// https://bugs.jquery.com/ticket/4833
-	return !rhtml.test( namespace || docElem && docElem.nodeName || "HTML" );
-};
-
-/**
- * Sets document-related variables once based on the current document
- * @param {Element|Object} [doc] An element or document object to use to set the document
- * @returns {Object} Returns the current document
- */
-setDocument = Sizzle.setDocument = function( node ) {
-	var hasCompare, subWindow,
-		doc = node ? node.ownerDocument || node : preferredDoc;
-
-	// Return early if doc is invalid or already selected
-	// Support: IE 11+, Edge 17 - 18+
-	// IE/Edge sometimes throw a "Permission denied" error when strict-comparing
-	// two documents; shallow comparisons work.
-	// eslint-disable-next-line eqeqeq
-	if ( doc == document || doc.nodeType !== 9 || !doc.documentElement ) {
-		return document;
-	}
-
-	// Update global variables
-	document = doc;
-	docElem = document.documentElement;
-	documentIsHTML = !isXML( document );
-
-	// Support: IE 9 - 11+, Edge 12 - 18+
-	// Accessing iframe documents after unload throws "permission denied" errors (jQuery #13936)
-	// Support: IE 11+, Edge 17 - 18+
-	// IE/Edge sometimes throw a "Permission denied" error when strict-comparing
-	// two documents; shallow comparisons work.
-	// eslint-disable-next-line eqeqeq
-	if ( preferredDoc != document &&
-		( subWindow = document.defaultView ) && subWindow.top !== subWindow ) {
-
-		// Support: IE 11, Edge
-		if ( subWindow.addEventListener ) {
-			subWindow.addEventListener( "unload", unloadHandler, false );
-
-		// Support: IE 9 - 10 only
-		} else if ( subWindow.attachEvent ) {
-			subWindow.attachEvent( "onunload", unloadHandler );
-		}
-	}
-
-	// Support: IE 8 - 11+, Edge 12 - 18+, Chrome <=16 - 25 only, Firefox <=3.6 - 31 only,
-	// Safari 4 - 5 only, Opera <=11.6 - 12.x only
-	// IE/Edge & older browsers don't support the :scope pseudo-class.
-	// Support: Safari 6.0 only
-	// Safari 6.0 supports :scope but it's an alias of :root there.
-	support.scope = assert( function( el ) {
-		docElem.appendChild( el ).appendChild( document.createElement( "div" ) );
-		return typeof el.querySelectorAll !== "undefined" &&
-			!el.querySelectorAll( ":scope fieldset div" ).length;
-	} );
-
-	/* Attributes
-	---------------------------------------------------------------------- */
-
-	// Support: IE<8
-	// Verify that getAttribute really returns attributes and not properties
-	// (excepting IE8 booleans)
-	support.attributes = assert( function( el ) {
-		el.className = "i";
-		return !el.getAttribute( "className" );
-	} );
-
-	/* getElement(s)By*
-	---------------------------------------------------------------------- */
-
-	// Check if getElementsByTagName("*") returns only elements
-	support.getElementsByTagName = assert( function( el ) {
-		el.appendChild( document.createComment( "" ) );
-		return !el.getElementsByTagName( "*" ).length;
-	} );
-
-	// Support: IE<9
-	support.getElementsByClassName = rnative.test( document.getElementsByClassName );
-
-	// Support: IE<10
-	// Check if getElementById returns elements by name
-	// The broken getElementById methods don't pick up programmatically-set names,
-	// so use a roundabout getElementsByName test
-	support.getById = assert( function( el ) {
-		docElem.appendChild( el ).id = expando;
-		return !document.getElementsByName || !document.getElementsByName( expando ).length;
-	} );
-
-	// ID filter and find
-	if ( support.getById ) {
-		Expr.filter[ "ID" ] = function( id ) {
-			var attrId = id.replace( runescape, funescape );
-			return function( elem ) {
-				return elem.getAttribute( "id" ) === attrId;
-			};
-		};
-		Expr.find[ "ID" ] = function( id, context ) {
-			if ( typeof context.getElementById !== "undefined" && documentIsHTML ) {
-				var elem = context.getElementById( id );
-				return elem ? [ elem ] : [];
-			}
-		};
-	} else {
-		Expr.filter[ "ID" ] =  function( id ) {
-			var attrId = id.replace( runescape, funescape );
-			return function( elem ) {
-				var node = typeof elem.getAttributeNode !== "undefined" &&
-					elem.getAttributeNode( "id" );
-				return node && node.value === attrId;
-			};
-		};
-
-		// Support: IE 6 - 7 only
-		// getElementById is not reliable as a find shortcut
-		Expr.find[ "ID" ] = function( id, context ) {
-			if ( typeof context.getElementById !== "undefined" && documentIsHTML ) {
-				var node, i, elems,
-					elem = context.getElementById( id );
-
-				if ( elem ) {
-
-					// Verify the id attribute
-					node = elem.getAttributeNode( "id" );
-					if ( node && node.value === id ) {
-						return [ elem ];
-					}
-
-					// Fall back on getElementsByName
-					elems = context.getElementsByName( id );
-					i = 0;
-					while ( ( elem = elems[ i++ ] ) ) {
-						node = elem.getAttributeNode( "id" );
-						if ( node && node.value === id ) {
-							return [ elem ];
-						}
-					}
-				}
-
-				return [];
-			}
-		};
-	}
-
-	// Tag
-	Expr.find[ "TAG" ] = support.getElementsByTagName ?
-		function( tag, context ) {
-			if ( typeof context.getElementsByTagName !== "undefined" ) {
-				return context.getElementsByTagName( tag );
-
-			// DocumentFragment nodes don't have gEBTN
-			} else if ( support.qsa ) {
-				return context.querySelectorAll( tag );
-			}
-		} :
-
-		function( tag, context ) {
-			var elem,
-				tmp = [],
-				i = 0,
-
-				// By happy coincidence, a (broken) gEBTN appears on DocumentFragment nodes too
-				results = context.getElementsByTagName( tag );
-
-			// Filter out possible comments
-			if ( tag === "*" ) {
-				while ( ( elem = results[ i++ ] ) ) {
-					if ( elem.nodeType === 1 ) {
-						tmp.push( elem );
-					}
-				}
-
-				return tmp;
-			}
-			return results;
-		};
-
-	// Class
-	Expr.find[ "CLASS" ] = support.getElementsByClassName && function( className, context ) {
-		if ( typeof context.getElementsByClassName !== "undefined" && documentIsHTML ) {
-			return context.getElementsByClassName( className );
-		}
-	};
-
-	/* QSA/matchesSelector
-	---------------------------------------------------------------------- */
-
-	// QSA and matchesSelector support
-
-	// matchesSelector(:active) reports false when true (IE9/Opera 11.5)
-	rbuggyMatches = [];
-
-	// qSa(:focus) reports false when true (Chrome 21)
-	// We allow this because of a bug in IE8/9 that throws an error
-	// whenever `document.activeElement` is accessed on an iframe
-	// So, we allow :focus to pass through QSA all the time to avoid the IE error
-	// See https://bugs.jquery.com/ticket/13378
-	rbuggyQSA = [];
-
-	if ( ( support.qsa = rnative.test( document.querySelectorAll ) ) ) {
-
-		// Build QSA regex
-		// Regex strategy adopted from Diego Perini
-		assert( function( el ) {
-
-			var input;
-
-			// Select is set to empty string on purpose
-			// This is to test IE's treatment of not explicitly
-			// setting a boolean content attribute,
-			// since its presence should be enough
-			// https://bugs.jquery.com/ticket/12359
-			docElem.appendChild( el ).innerHTML = "" +
-				"";
-
-			// Support: IE8, Opera 11-12.16
-			// Nothing should be selected when empty strings follow ^= or $= or *=
-			// The test attribute must be unknown in Opera but "safe" for WinRT
-			// https://msdn.microsoft.com/en-us/library/ie/hh465388.aspx#attribute_section
-			if ( el.querySelectorAll( "[msallowcapture^='']" ).length ) {
-				rbuggyQSA.push( "[*^$]=" + whitespace + "*(?:''|\"\")" );
-			}
-
-			// Support: IE8
-			// Boolean attributes and "value" are not treated correctly
-			if ( !el.querySelectorAll( "[selected]" ).length ) {
-				rbuggyQSA.push( "\\[" + whitespace + "*(?:value|" + booleans + ")" );
-			}
-
-			// Support: Chrome<29, Android<4.4, Safari<7.0+, iOS<7.0+, PhantomJS<1.9.8+
-			if ( !el.querySelectorAll( "[id~=" + expando + "-]" ).length ) {
-				rbuggyQSA.push( "~=" );
-			}
-
-			// Support: IE 11+, Edge 15 - 18+
-			// IE 11/Edge don't find elements on a `[name='']` query in some cases.
-			// Adding a temporary attribute to the document before the selection works
-			// around the issue.
-			// Interestingly, IE 10 & older don't seem to have the issue.
-			input = document.createElement( "input" );
-			input.setAttribute( "name", "" );
-			el.appendChild( input );
-			if ( !el.querySelectorAll( "[name='']" ).length ) {
-				rbuggyQSA.push( "\\[" + whitespace + "*name" + whitespace + "*=" +
-					whitespace + "*(?:''|\"\")" );
-			}
-
-			// Webkit/Opera - :checked should return selected option elements
-			// http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked
-			// IE8 throws error here and will not see later tests
-			if ( !el.querySelectorAll( ":checked" ).length ) {
-				rbuggyQSA.push( ":checked" );
-			}
-
-			// Support: Safari 8+, iOS 8+
-			// https://bugs.webkit.org/show_bug.cgi?id=136851
-			// In-page `selector#id sibling-combinator selector` fails
-			if ( !el.querySelectorAll( "a#" + expando + "+*" ).length ) {
-				rbuggyQSA.push( ".#.+[+~]" );
-			}
-
-			// Support: Firefox <=3.6 - 5 only
-			// Old Firefox doesn't throw on a badly-escaped identifier.
-			el.querySelectorAll( "\\\f" );
-			rbuggyQSA.push( "[\\r\\n\\f]" );
-		} );
-
-		assert( function( el ) {
-			el.innerHTML = "" +
-				"";
-
-			// Support: Windows 8 Native Apps
-			// The type and name attributes are restricted during .innerHTML assignment
-			var input = document.createElement( "input" );
-			input.setAttribute( "type", "hidden" );
-			el.appendChild( input ).setAttribute( "name", "D" );
-
-			// Support: IE8
-			// Enforce case-sensitivity of name attribute
-			if ( el.querySelectorAll( "[name=d]" ).length ) {
-				rbuggyQSA.push( "name" + whitespace + "*[*^$|!~]?=" );
-			}
-
-			// FF 3.5 - :enabled/:disabled and hidden elements (hidden elements are still enabled)
-			// IE8 throws error here and will not see later tests
-			if ( el.querySelectorAll( ":enabled" ).length !== 2 ) {
-				rbuggyQSA.push( ":enabled", ":disabled" );
-			}
-
-			// Support: IE9-11+
-			// IE's :disabled selector does not pick up the children of disabled fieldsets
-			docElem.appendChild( el ).disabled = true;
-			if ( el.querySelectorAll( ":disabled" ).length !== 2 ) {
-				rbuggyQSA.push( ":enabled", ":disabled" );
-			}
-
-			// Support: Opera 10 - 11 only
-			// Opera 10-11 does not throw on post-comma invalid pseudos
-			el.querySelectorAll( "*,:x" );
-			rbuggyQSA.push( ",.*:" );
-		} );
-	}
-
-	if ( ( support.matchesSelector = rnative.test( ( matches = docElem.matches ||
-		docElem.webkitMatchesSelector ||
-		docElem.mozMatchesSelector ||
-		docElem.oMatchesSelector ||
-		docElem.msMatchesSelector ) ) ) ) {
-
-		assert( function( el ) {
-
-			// Check to see if it's possible to do matchesSelector
-			// on a disconnected node (IE 9)
-			support.disconnectedMatch = matches.call( el, "*" );
-
-			// This should fail with an exception
-			// Gecko does not error, returns false instead
-			matches.call( el, "[s!='']:x" );
-			rbuggyMatches.push( "!=", pseudos );
-		} );
-	}
-
-	rbuggyQSA = rbuggyQSA.length && new RegExp( rbuggyQSA.join( "|" ) );
-	rbuggyMatches = rbuggyMatches.length && new RegExp( rbuggyMatches.join( "|" ) );
-
-	/* Contains
-	---------------------------------------------------------------------- */
-	hasCompare = rnative.test( docElem.compareDocumentPosition );
-
-	// Element contains another
-	// Purposefully self-exclusive
-	// As in, an element does not contain itself
-	contains = hasCompare || rnative.test( docElem.contains ) ?
-		function( a, b ) {
-			var adown = a.nodeType === 9 ? a.documentElement : a,
-				bup = b && b.parentNode;
-			return a === bup || !!( bup && bup.nodeType === 1 && (
-				adown.contains ?
-					adown.contains( bup ) :
-					a.compareDocumentPosition && a.compareDocumentPosition( bup ) & 16
-			) );
-		} :
-		function( a, b ) {
-			if ( b ) {
-				while ( ( b = b.parentNode ) ) {
-					if ( b === a ) {
-						return true;
-					}
-				}
-			}
-			return false;
-		};
-
-	/* Sorting
-	---------------------------------------------------------------------- */
-
-	// Document order sorting
-	sortOrder = hasCompare ?
-	function( a, b ) {
-
-		// Flag for duplicate removal
-		if ( a === b ) {
-			hasDuplicate = true;
-			return 0;
-		}
-
-		// Sort on method existence if only one input has compareDocumentPosition
-		var compare = !a.compareDocumentPosition - !b.compareDocumentPosition;
-		if ( compare ) {
-			return compare;
-		}
-
-		// Calculate position if both inputs belong to the same document
-		// Support: IE 11+, Edge 17 - 18+
-		// IE/Edge sometimes throw a "Permission denied" error when strict-comparing
-		// two documents; shallow comparisons work.
-		// eslint-disable-next-line eqeqeq
-		compare = ( a.ownerDocument || a ) == ( b.ownerDocument || b ) ?
-			a.compareDocumentPosition( b ) :
-
-			// Otherwise we know they are disconnected
-			1;
-
-		// Disconnected nodes
-		if ( compare & 1 ||
-			( !support.sortDetached && b.compareDocumentPosition( a ) === compare ) ) {
-
-			// Choose the first element that is related to our preferred document
-			// Support: IE 11+, Edge 17 - 18+
-			// IE/Edge sometimes throw a "Permission denied" error when strict-comparing
-			// two documents; shallow comparisons work.
-			// eslint-disable-next-line eqeqeq
-			if ( a == document || a.ownerDocument == preferredDoc &&
-				contains( preferredDoc, a ) ) {
-				return -1;
-			}
-
-			// Support: IE 11+, Edge 17 - 18+
-			// IE/Edge sometimes throw a "Permission denied" error when strict-comparing
-			// two documents; shallow comparisons work.
-			// eslint-disable-next-line eqeqeq
-			if ( b == document || b.ownerDocument == preferredDoc &&
-				contains( preferredDoc, b ) ) {
-				return 1;
-			}
-
-			// Maintain original order
-			return sortInput ?
-				( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) :
-				0;
-		}
-
-		return compare & 4 ? -1 : 1;
-	} :
-	function( a, b ) {
-
-		// Exit early if the nodes are identical
-		if ( a === b ) {
-			hasDuplicate = true;
-			return 0;
-		}
-
-		var cur,
-			i = 0,
-			aup = a.parentNode,
-			bup = b.parentNode,
-			ap = [ a ],
-			bp = [ b ];
-
-		// Parentless nodes are either documents or disconnected
-		if ( !aup || !bup ) {
-
-			// Support: IE 11+, Edge 17 - 18+
-			// IE/Edge sometimes throw a "Permission denied" error when strict-comparing
-			// two documents; shallow comparisons work.
-			/* eslint-disable eqeqeq */
-			return a == document ? -1 :
-				b == document ? 1 :
-				/* eslint-enable eqeqeq */
-				aup ? -1 :
-				bup ? 1 :
-				sortInput ?
-				( indexOf( sortInput, a ) - indexOf( sortInput, b ) ) :
-				0;
-
-		// If the nodes are siblings, we can do a quick check
-		} else if ( aup === bup ) {
-			return siblingCheck( a, b );
-		}
-
-		// Otherwise we need full lists of their ancestors for comparison
-		cur = a;
-		while ( ( cur = cur.parentNode ) ) {
-			ap.unshift( cur );
-		}
-		cur = b;
-		while ( ( cur = cur.parentNode ) ) {
-			bp.unshift( cur );
-		}
-
-		// Walk down the tree looking for a discrepancy
-		while ( ap[ i ] === bp[ i ] ) {
-			i++;
-		}
-
-		return i ?
-
-			// Do a sibling check if the nodes have a common ancestor
-			siblingCheck( ap[ i ], bp[ i ] ) :
-
-			// Otherwise nodes in our document sort first
-			// Support: IE 11+, Edge 17 - 18+
-			// IE/Edge sometimes throw a "Permission denied" error when strict-comparing
-			// two documents; shallow comparisons work.
-			/* eslint-disable eqeqeq */
-			ap[ i ] == preferredDoc ? -1 :
-			bp[ i ] == preferredDoc ? 1 :
-			/* eslint-enable eqeqeq */
-			0;
-	};
-
-	return document;
-};
-
-Sizzle.matches = function( expr, elements ) {
-	return Sizzle( expr, null, null, elements );
-};
-
-Sizzle.matchesSelector = function( elem, expr ) {
-	setDocument( elem );
-
-	if ( support.matchesSelector && documentIsHTML &&
-		!nonnativeSelectorCache[ expr + " " ] &&
-		( !rbuggyMatches || !rbuggyMatches.test( expr ) ) &&
-		( !rbuggyQSA     || !rbuggyQSA.test( expr ) ) ) {
-
-		try {
-			var ret = matches.call( elem, expr );
-
-			// IE 9's matchesSelector returns false on disconnected nodes
-			if ( ret || support.disconnectedMatch ||
-
-				// As well, disconnected nodes are said to be in a document
-				// fragment in IE 9
-				elem.document && elem.document.nodeType !== 11 ) {
-				return ret;
-			}
-		} catch ( e ) {
-			nonnativeSelectorCache( expr, true );
-		}
-	}
-
-	return Sizzle( expr, document, null, [ elem ] ).length > 0;
-};
-
-Sizzle.contains = function( context, elem ) {
-
-	// Set document vars if needed
-	// Support: IE 11+, Edge 17 - 18+
-	// IE/Edge sometimes throw a "Permission denied" error when strict-comparing
-	// two documents; shallow comparisons work.
-	// eslint-disable-next-line eqeqeq
-	if ( ( context.ownerDocument || context ) != document ) {
-		setDocument( context );
-	}
-	return contains( context, elem );
-};
-
-Sizzle.attr = function( elem, name ) {
-
-	// Set document vars if needed
-	// Support: IE 11+, Edge 17 - 18+
-	// IE/Edge sometimes throw a "Permission denied" error when strict-comparing
-	// two documents; shallow comparisons work.
-	// eslint-disable-next-line eqeqeq
-	if ( ( elem.ownerDocument || elem ) != document ) {
-		setDocument( elem );
-	}
-
-	var fn = Expr.attrHandle[ name.toLowerCase() ],
-
-		// Don't get fooled by Object.prototype properties (jQuery #13807)
-		val = fn && hasOwn.call( Expr.attrHandle, name.toLowerCase() ) ?
-			fn( elem, name, !documentIsHTML ) :
-			undefined;
-
-	return val !== undefined ?
-		val :
-		support.attributes || !documentIsHTML ?
-			elem.getAttribute( name ) :
-			( val = elem.getAttributeNode( name ) ) && val.specified ?
-				val.value :
-				null;
-};
-
-Sizzle.escape = function( sel ) {
-	return ( sel + "" ).replace( rcssescape, fcssescape );
-};
-
-Sizzle.error = function( msg ) {
-	throw new Error( "Syntax error, unrecognized expression: " + msg );
-};
-
-/**
- * Document sorting and removing duplicates
- * @param {ArrayLike} results
- */
-Sizzle.uniqueSort = function( results ) {
-	var elem,
-		duplicates = [],
-		j = 0,
-		i = 0;
-
-	// Unless we *know* we can detect duplicates, assume their presence
-	hasDuplicate = !support.detectDuplicates;
-	sortInput = !support.sortStable && results.slice( 0 );
-	results.sort( sortOrder );
-
-	if ( hasDuplicate ) {
-		while ( ( elem = results[ i++ ] ) ) {
-			if ( elem === results[ i ] ) {
-				j = duplicates.push( i );
-			}
-		}
-		while ( j-- ) {
-			results.splice( duplicates[ j ], 1 );
-		}
-	}
-
-	// Clear input after sorting to release objects
-	// See https://github.com/jquery/sizzle/pull/225
-	sortInput = null;
-
-	return results;
-};
-
-/**
- * Utility function for retrieving the text value of an array of DOM nodes
- * @param {Array|Element} elem
- */
-getText = Sizzle.getText = function( elem ) {
-	var node,
-		ret = "",
-		i = 0,
-		nodeType = elem.nodeType;
-
-	if ( !nodeType ) {
-
-		// If no nodeType, this is expected to be an array
-		while ( ( node = elem[ i++ ] ) ) {
-
-			// Do not traverse comment nodes
-			ret += getText( node );
-		}
-	} else if ( nodeType === 1 || nodeType === 9 || nodeType === 11 ) {
-
-		// Use textContent for elements
-		// innerText usage removed for consistency of new lines (jQuery #11153)
-		if ( typeof elem.textContent === "string" ) {
-			return elem.textContent;
-		} else {
-
-			// Traverse its children
-			for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) {
-				ret += getText( elem );
-			}
-		}
-	} else if ( nodeType === 3 || nodeType === 4 ) {
-		return elem.nodeValue;
-	}
-
-	// Do not include comment or processing instruction nodes
-
-	return ret;
-};
-
-Expr = Sizzle.selectors = {
-
-	// Can be adjusted by the user
-	cacheLength: 50,
-
-	createPseudo: markFunction,
-
-	match: matchExpr,
-
-	attrHandle: {},
-
-	find: {},
-
-	relative: {
-		">": { dir: "parentNode", first: true },
-		" ": { dir: "parentNode" },
-		"+": { dir: "previousSibling", first: true },
-		"~": { dir: "previousSibling" }
-	},
-
-	preFilter: {
-		"ATTR": function( match ) {
-			match[ 1 ] = match[ 1 ].replace( runescape, funescape );
-
-			// Move the given value to match[3] whether quoted or unquoted
-			match[ 3 ] = ( match[ 3 ] || match[ 4 ] ||
-				match[ 5 ] || "" ).replace( runescape, funescape );
-
-			if ( match[ 2 ] === "~=" ) {
-				match[ 3 ] = " " + match[ 3 ] + " ";
-			}
-
-			return match.slice( 0, 4 );
-		},
-
-		"CHILD": function( match ) {
-
-			/* matches from matchExpr["CHILD"]
-				1 type (only|nth|...)
-				2 what (child|of-type)
-				3 argument (even|odd|\d*|\d*n([+-]\d+)?|...)
-				4 xn-component of xn+y argument ([+-]?\d*n|)
-				5 sign of xn-component
-				6 x of xn-component
-				7 sign of y-component
-				8 y of y-component
-			*/
-			match[ 1 ] = match[ 1 ].toLowerCase();
-
-			if ( match[ 1 ].slice( 0, 3 ) === "nth" ) {
-
-				// nth-* requires argument
-				if ( !match[ 3 ] ) {
-					Sizzle.error( match[ 0 ] );
-				}
-
-				// numeric x and y parameters for Expr.filter.CHILD
-				// remember that false/true cast respectively to 0/1
-				match[ 4 ] = +( match[ 4 ] ?
-					match[ 5 ] + ( match[ 6 ] || 1 ) :
-					2 * ( match[ 3 ] === "even" || match[ 3 ] === "odd" ) );
-				match[ 5 ] = +( ( match[ 7 ] + match[ 8 ] ) || match[ 3 ] === "odd" );
-
-				// other types prohibit arguments
-			} else if ( match[ 3 ] ) {
-				Sizzle.error( match[ 0 ] );
-			}
-
-			return match;
-		},
-
-		"PSEUDO": function( match ) {
-			var excess,
-				unquoted = !match[ 6 ] && match[ 2 ];
-
-			if ( matchExpr[ "CHILD" ].test( match[ 0 ] ) ) {
-				return null;
-			}
-
-			// Accept quoted arguments as-is
-			if ( match[ 3 ] ) {
-				match[ 2 ] = match[ 4 ] || match[ 5 ] || "";
-
-			// Strip excess characters from unquoted arguments
-			} else if ( unquoted && rpseudo.test( unquoted ) &&
-
-				// Get excess from tokenize (recursively)
-				( excess = tokenize( unquoted, true ) ) &&
-
-				// advance to the next closing parenthesis
-				( excess = unquoted.indexOf( ")", unquoted.length - excess ) - unquoted.length ) ) {
-
-				// excess is a negative index
-				match[ 0 ] = match[ 0 ].slice( 0, excess );
-				match[ 2 ] = unquoted.slice( 0, excess );
-			}
-
-			// Return only captures needed by the pseudo filter method (type and argument)
-			return match.slice( 0, 3 );
-		}
-	},
-
-	filter: {
-
-		"TAG": function( nodeNameSelector ) {
-			var nodeName = nodeNameSelector.replace( runescape, funescape ).toLowerCase();
-			return nodeNameSelector === "*" ?
-				function() {
-					return true;
-				} :
-				function( elem ) {
-					return elem.nodeName && elem.nodeName.toLowerCase() === nodeName;
-				};
-		},
-
-		"CLASS": function( className ) {
-			var pattern = classCache[ className + " " ];
-
-			return pattern ||
-				( pattern = new RegExp( "(^|" + whitespace +
-					")" + className + "(" + whitespace + "|$)" ) ) && classCache(
-						className, function( elem ) {
-							return pattern.test(
-								typeof elem.className === "string" && elem.className ||
-								typeof elem.getAttribute !== "undefined" &&
-									elem.getAttribute( "class" ) ||
-								""
-							);
-				} );
-		},
-
-		"ATTR": function( name, operator, check ) {
-			return function( elem ) {
-				var result = Sizzle.attr( elem, name );
-
-				if ( result == null ) {
-					return operator === "!=";
-				}
-				if ( !operator ) {
-					return true;
-				}
-
-				result += "";
-
-				/* eslint-disable max-len */
-
-				return operator === "=" ? result === check :
-					operator === "!=" ? result !== check :
-					operator === "^=" ? check && result.indexOf( check ) === 0 :
-					operator === "*=" ? check && result.indexOf( check ) > -1 :
-					operator === "$=" ? check && result.slice( -check.length ) === check :
-					operator === "~=" ? ( " " + result.replace( rwhitespace, " " ) + " " ).indexOf( check ) > -1 :
-					operator === "|=" ? result === check || result.slice( 0, check.length + 1 ) === check + "-" :
-					false;
-				/* eslint-enable max-len */
-
-			};
-		},
-
-		"CHILD": function( type, what, _argument, first, last ) {
-			var simple = type.slice( 0, 3 ) !== "nth",
-				forward = type.slice( -4 ) !== "last",
-				ofType = what === "of-type";
-
-			return first === 1 && last === 0 ?
-
-				// Shortcut for :nth-*(n)
-				function( elem ) {
-					return !!elem.parentNode;
-				} :
-
-				function( elem, _context, xml ) {
-					var cache, uniqueCache, outerCache, node, nodeIndex, start,
-						dir = simple !== forward ? "nextSibling" : "previousSibling",
-						parent = elem.parentNode,
-						name = ofType && elem.nodeName.toLowerCase(),
-						useCache = !xml && !ofType,
-						diff = false;
-
-					if ( parent ) {
-
-						// :(first|last|only)-(child|of-type)
-						if ( simple ) {
-							while ( dir ) {
-								node = elem;
-								while ( ( node = node[ dir ] ) ) {
-									if ( ofType ?
-										node.nodeName.toLowerCase() === name :
-										node.nodeType === 1 ) {
-
-										return false;
-									}
-								}
-
-								// Reverse direction for :only-* (if we haven't yet done so)
-								start = dir = type === "only" && !start && "nextSibling";
-							}
-							return true;
-						}
-
-						start = [ forward ? parent.firstChild : parent.lastChild ];
-
-						// non-xml :nth-child(...) stores cache data on `parent`
-						if ( forward && useCache ) {
-
-							// Seek `elem` from a previously-cached index
-
-							// ...in a gzip-friendly way
-							node = parent;
-							outerCache = node[ expando ] || ( node[ expando ] = {} );
-
-							// Support: IE <9 only
-							// Defend against cloned attroperties (jQuery gh-1709)
-							uniqueCache = outerCache[ node.uniqueID ] ||
-								( outerCache[ node.uniqueID ] = {} );
-
-							cache = uniqueCache[ type ] || [];
-							nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ];
-							diff = nodeIndex && cache[ 2 ];
-							node = nodeIndex && parent.childNodes[ nodeIndex ];
-
-							while ( ( node = ++nodeIndex && node && node[ dir ] ||
-
-								// Fallback to seeking `elem` from the start
-								( diff = nodeIndex = 0 ) || start.pop() ) ) {
-
-								// When found, cache indexes on `parent` and break
-								if ( node.nodeType === 1 && ++diff && node === elem ) {
-									uniqueCache[ type ] = [ dirruns, nodeIndex, diff ];
-									break;
-								}
-							}
-
-						} else {
-
-							// Use previously-cached element index if available
-							if ( useCache ) {
-
-								// ...in a gzip-friendly way
-								node = elem;
-								outerCache = node[ expando ] || ( node[ expando ] = {} );
-
-								// Support: IE <9 only
-								// Defend against cloned attroperties (jQuery gh-1709)
-								uniqueCache = outerCache[ node.uniqueID ] ||
-									( outerCache[ node.uniqueID ] = {} );
-
-								cache = uniqueCache[ type ] || [];
-								nodeIndex = cache[ 0 ] === dirruns && cache[ 1 ];
-								diff = nodeIndex;
-							}
-
-							// xml :nth-child(...)
-							// or :nth-last-child(...) or :nth(-last)?-of-type(...)
-							if ( diff === false ) {
-
-								// Use the same loop as above to seek `elem` from the start
-								while ( ( node = ++nodeIndex && node && node[ dir ] ||
-									( diff = nodeIndex = 0 ) || start.pop() ) ) {
-
-									if ( ( ofType ?
-										node.nodeName.toLowerCase() === name :
-										node.nodeType === 1 ) &&
-										++diff ) {
-
-										// Cache the index of each encountered element
-										if ( useCache ) {
-											outerCache = node[ expando ] ||
-												( node[ expando ] = {} );
-
-											// Support: IE <9 only
-											// Defend against cloned attroperties (jQuery gh-1709)
-											uniqueCache = outerCache[ node.uniqueID ] ||
-												( outerCache[ node.uniqueID ] = {} );
-
-											uniqueCache[ type ] = [ dirruns, diff ];
-										}
-
-										if ( node === elem ) {
-											break;
-										}
-									}
-								}
-							}
-						}
-
-						// Incorporate the offset, then check against cycle size
-						diff -= last;
-						return diff === first || ( diff % first === 0 && diff / first >= 0 );
-					}
-				};
-		},
-
-		"PSEUDO": function( pseudo, argument ) {
-
-			// pseudo-class names are case-insensitive
-			// http://www.w3.org/TR/selectors/#pseudo-classes
-			// Prioritize by case sensitivity in case custom pseudos are added with uppercase letters
-			// Remember that setFilters inherits from pseudos
-			var args,
-				fn = Expr.pseudos[ pseudo ] || Expr.setFilters[ pseudo.toLowerCase() ] ||
-					Sizzle.error( "unsupported pseudo: " + pseudo );
-
-			// The user may use createPseudo to indicate that
-			// arguments are needed to create the filter function
-			// just as Sizzle does
-			if ( fn[ expando ] ) {
-				return fn( argument );
-			}
-
-			// But maintain support for old signatures
-			if ( fn.length > 1 ) {
-				args = [ pseudo, pseudo, "", argument ];
-				return Expr.setFilters.hasOwnProperty( pseudo.toLowerCase() ) ?
-					markFunction( function( seed, matches ) {
-						var idx,
-							matched = fn( seed, argument ),
-							i = matched.length;
-						while ( i-- ) {
-							idx = indexOf( seed, matched[ i ] );
-							seed[ idx ] = !( matches[ idx ] = matched[ i ] );
-						}
-					} ) :
-					function( elem ) {
-						return fn( elem, 0, args );
-					};
-			}
-
-			return fn;
-		}
-	},
-
-	pseudos: {
-
-		// Potentially complex pseudos
-		"not": markFunction( function( selector ) {
-
-			// Trim the selector passed to compile
-			// to avoid treating leading and trailing
-			// spaces as combinators
-			var input = [],
-				results = [],
-				matcher = compile( selector.replace( rtrim, "$1" ) );
-
-			return matcher[ expando ] ?
-				markFunction( function( seed, matches, _context, xml ) {
-					var elem,
-						unmatched = matcher( seed, null, xml, [] ),
-						i = seed.length;
-
-					// Match elements unmatched by `matcher`
-					while ( i-- ) {
-						if ( ( elem = unmatched[ i ] ) ) {
-							seed[ i ] = !( matches[ i ] = elem );
-						}
-					}
-				} ) :
-				function( elem, _context, xml ) {
-					input[ 0 ] = elem;
-					matcher( input, null, xml, results );
-
-					// Don't keep the element (issue #299)
-					input[ 0 ] = null;
-					return !results.pop();
-				};
-		} ),
-
-		"has": markFunction( function( selector ) {
-			return function( elem ) {
-				return Sizzle( selector, elem ).length > 0;
-			};
-		} ),
-
-		"contains": markFunction( function( text ) {
-			text = text.replace( runescape, funescape );
-			return function( elem ) {
-				return ( elem.textContent || getText( elem ) ).indexOf( text ) > -1;
-			};
-		} ),
-
-		// "Whether an element is represented by a :lang() selector
-		// is based solely on the element's language value
-		// being equal to the identifier C,
-		// or beginning with the identifier C immediately followed by "-".
-		// The matching of C against the element's language value is performed case-insensitively.
-		// The identifier C does not have to be a valid language name."
-		// http://www.w3.org/TR/selectors/#lang-pseudo
-		"lang": markFunction( function( lang ) {
-
-			// lang value must be a valid identifier
-			if ( !ridentifier.test( lang || "" ) ) {
-				Sizzle.error( "unsupported lang: " + lang );
-			}
-			lang = lang.replace( runescape, funescape ).toLowerCase();
-			return function( elem ) {
-				var elemLang;
-				do {
-					if ( ( elemLang = documentIsHTML ?
-						elem.lang :
-						elem.getAttribute( "xml:lang" ) || elem.getAttribute( "lang" ) ) ) {
-
-						elemLang = elemLang.toLowerCase();
-						return elemLang === lang || elemLang.indexOf( lang + "-" ) === 0;
-					}
-				} while ( ( elem = elem.parentNode ) && elem.nodeType === 1 );
-				return false;
-			};
-		} ),
-
-		// Miscellaneous
-		"target": function( elem ) {
-			var hash = window.location && window.location.hash;
-			return hash && hash.slice( 1 ) === elem.id;
-		},
-
-		"root": function( elem ) {
-			return elem === docElem;
-		},
-
-		"focus": function( elem ) {
-			return elem === document.activeElement &&
-				( !document.hasFocus || document.hasFocus() ) &&
-				!!( elem.type || elem.href || ~elem.tabIndex );
-		},
-
-		// Boolean properties
-		"enabled": createDisabledPseudo( false ),
-		"disabled": createDisabledPseudo( true ),
-
-		"checked": function( elem ) {
-
-			// In CSS3, :checked should return both checked and selected elements
-			// http://www.w3.org/TR/2011/REC-css3-selectors-20110929/#checked
-			var nodeName = elem.nodeName.toLowerCase();
-			return ( nodeName === "input" && !!elem.checked ) ||
-				( nodeName === "option" && !!elem.selected );
-		},
-
-		"selected": function( elem ) {
-
-			// Accessing this property makes selected-by-default
-			// options in Safari work properly
-			if ( elem.parentNode ) {
-				// eslint-disable-next-line no-unused-expressions
-				elem.parentNode.selectedIndex;
-			}
-
-			return elem.selected === true;
-		},
-
-		// Contents
-		"empty": function( elem ) {
-
-			// http://www.w3.org/TR/selectors/#empty-pseudo
-			// :empty is negated by element (1) or content nodes (text: 3; cdata: 4; entity ref: 5),
-			//   but not by others (comment: 8; processing instruction: 7; etc.)
-			// nodeType < 6 works because attributes (2) do not appear as children
-			for ( elem = elem.firstChild; elem; elem = elem.nextSibling ) {
-				if ( elem.nodeType < 6 ) {
-					return false;
-				}
-			}
-			return true;
-		},
-
-		"parent": function( elem ) {
-			return !Expr.pseudos[ "empty" ]( elem );
-		},
-
-		// Element/input types
-		"header": function( elem ) {
-			return rheader.test( elem.nodeName );
-		},
-
-		"input": function( elem ) {
-			return rinputs.test( elem.nodeName );
-		},
-
-		"button": function( elem ) {
-			var name = elem.nodeName.toLowerCase();
-			return name === "input" && elem.type === "button" || name === "button";
-		},
-
-		"text": function( elem ) {
-			var attr;
-			return elem.nodeName.toLowerCase() === "input" &&
-				elem.type === "text" &&
-
-				// Support: IE<8
-				// New HTML5 attribute values (e.g., "search") appear with elem.type === "text"
-				( ( attr = elem.getAttribute( "type" ) ) == null ||
-					attr.toLowerCase() === "text" );
-		},
-
-		// Position-in-collection
-		"first": createPositionalPseudo( function() {
-			return [ 0 ];
-		} ),
-
-		"last": createPositionalPseudo( function( _matchIndexes, length ) {
-			return [ length - 1 ];
-		} ),
-
-		"eq": createPositionalPseudo( function( _matchIndexes, length, argument ) {
-			return [ argument < 0 ? argument + length : argument ];
-		} ),
-
-		"even": createPositionalPseudo( function( matchIndexes, length ) {
-			var i = 0;
-			for ( ; i < length; i += 2 ) {
-				matchIndexes.push( i );
-			}
-			return matchIndexes;
-		} ),
-
-		"odd": createPositionalPseudo( function( matchIndexes, length ) {
-			var i = 1;
-			for ( ; i < length; i += 2 ) {
-				matchIndexes.push( i );
-			}
-			return matchIndexes;
-		} ),
-
-		"lt": createPositionalPseudo( function( matchIndexes, length, argument ) {
-			var i = argument < 0 ?
-				argument + length :
-				argument > length ?
-					length :
-					argument;
-			for ( ; --i >= 0; ) {
-				matchIndexes.push( i );
-			}
-			return matchIndexes;
-		} ),
-
-		"gt": createPositionalPseudo( function( matchIndexes, length, argument ) {
-			var i = argument < 0 ? argument + length : argument;
-			for ( ; ++i < length; ) {
-				matchIndexes.push( i );
-			}
-			return matchIndexes;
-		} )
-	}
-};
-
-Expr.pseudos[ "nth" ] = Expr.pseudos[ "eq" ];
-
-// Add button/input type pseudos
-for ( i in { radio: true, checkbox: true, file: true, password: true, image: true } ) {
-	Expr.pseudos[ i ] = createInputPseudo( i );
-}
-for ( i in { submit: true, reset: true } ) {
-	Expr.pseudos[ i ] = createButtonPseudo( i );
-}
-
-// Easy API for creating new setFilters
-function setFilters() {}
-setFilters.prototype = Expr.filters = Expr.pseudos;
-Expr.setFilters = new setFilters();
-
-tokenize = Sizzle.tokenize = function( selector, parseOnly ) {
-	var matched, match, tokens, type,
-		soFar, groups, preFilters,
-		cached = tokenCache[ selector + " " ];
-
-	if ( cached ) {
-		return parseOnly ? 0 : cached.slice( 0 );
-	}
-
-	soFar = selector;
-	groups = [];
-	preFilters = Expr.preFilter;
-
-	while ( soFar ) {
-
-		// Comma and first run
-		if ( !matched || ( match = rcomma.exec( soFar ) ) ) {
-			if ( match ) {
-
-				// Don't consume trailing commas as valid
-				soFar = soFar.slice( match[ 0 ].length ) || soFar;
-			}
-			groups.push( ( tokens = [] ) );
-		}
-
-		matched = false;
-
-		// Combinators
-		if ( ( match = rcombinators.exec( soFar ) ) ) {
-			matched = match.shift();
-			tokens.push( {
-				value: matched,
-
-				// Cast descendant combinators to space
-				type: match[ 0 ].replace( rtrim, " " )
-			} );
-			soFar = soFar.slice( matched.length );
-		}
-
-		// Filters
-		for ( type in Expr.filter ) {
-			if ( ( match = matchExpr[ type ].exec( soFar ) ) && ( !preFilters[ type ] ||
-				( match = preFilters[ type ]( match ) ) ) ) {
-				matched = match.shift();
-				tokens.push( {
-					value: matched,
-					type: type,
-					matches: match
-				} );
-				soFar = soFar.slice( matched.length );
-			}
-		}
-
-		if ( !matched ) {
-			break;
-		}
-	}
-
-	// Return the length of the invalid excess
-	// if we're just parsing
-	// Otherwise, throw an error or return tokens
-	return parseOnly ?
-		soFar.length :
-		soFar ?
-			Sizzle.error( selector ) :
-
-			// Cache the tokens
-			tokenCache( selector, groups ).slice( 0 );
-};
-
-function toSelector( tokens ) {
-	var i = 0,
-		len = tokens.length,
-		selector = "";
-	for ( ; i < len; i++ ) {
-		selector += tokens[ i ].value;
-	}
-	return selector;
-}
-
-function addCombinator( matcher, combinator, base ) {
-	var dir = combinator.dir,
-		skip = combinator.next,
-		key = skip || dir,
-		checkNonElements = base && key === "parentNode",
-		doneName = done++;
-
-	return combinator.first ?
-
-		// Check against closest ancestor/preceding element
-		function( elem, context, xml ) {
-			while ( ( elem = elem[ dir ] ) ) {
-				if ( elem.nodeType === 1 || checkNonElements ) {
-					return matcher( elem, context, xml );
-				}
-			}
-			return false;
-		} :
-
-		// Check against all ancestor/preceding elements
-		function( elem, context, xml ) {
-			var oldCache, uniqueCache, outerCache,
-				newCache = [ dirruns, doneName ];
-
-			// We can't set arbitrary data on XML nodes, so they don't benefit from combinator caching
-			if ( xml ) {
-				while ( ( elem = elem[ dir ] ) ) {
-					if ( elem.nodeType === 1 || checkNonElements ) {
-						if ( matcher( elem, context, xml ) ) {
-							return true;
-						}
-					}
-				}
-			} else {
-				while ( ( elem = elem[ dir ] ) ) {
-					if ( elem.nodeType === 1 || checkNonElements ) {
-						outerCache = elem[ expando ] || ( elem[ expando ] = {} );
-
-						// Support: IE <9 only
-						// Defend against cloned attroperties (jQuery gh-1709)
-						uniqueCache = outerCache[ elem.uniqueID ] ||
-							( outerCache[ elem.uniqueID ] = {} );
-
-						if ( skip && skip === elem.nodeName.toLowerCase() ) {
-							elem = elem[ dir ] || elem;
-						} else if ( ( oldCache = uniqueCache[ key ] ) &&
-							oldCache[ 0 ] === dirruns && oldCache[ 1 ] === doneName ) {
-
-							// Assign to newCache so results back-propagate to previous elements
-							return ( newCache[ 2 ] = oldCache[ 2 ] );
-						} else {
-
-							// Reuse newcache so results back-propagate to previous elements
-							uniqueCache[ key ] = newCache;
-
-							// A match means we're done; a fail means we have to keep checking
-							if ( ( newCache[ 2 ] = matcher( elem, context, xml ) ) ) {
-								return true;
-							}
-						}
-					}
-				}
-			}
-			return false;
-		};
-}
-
-function elementMatcher( matchers ) {
-	return matchers.length > 1 ?
-		function( elem, context, xml ) {
-			var i = matchers.length;
-			while ( i-- ) {
-				if ( !matchers[ i ]( elem, context, xml ) ) {
-					return false;
-				}
-			}
-			return true;
-		} :
-		matchers[ 0 ];
-}
-
-function multipleContexts( selector, contexts, results ) {
-	var i = 0,
-		len = contexts.length;
-	for ( ; i < len; i++ ) {
-		Sizzle( selector, contexts[ i ], results );
-	}
-	return results;
-}
-
-function condense( unmatched, map, filter, context, xml ) {
-	var elem,
-		newUnmatched = [],
-		i = 0,
-		len = unmatched.length,
-		mapped = map != null;
-
-	for ( ; i < len; i++ ) {
-		if ( ( elem = unmatched[ i ] ) ) {
-			if ( !filter || filter( elem, context, xml ) ) {
-				newUnmatched.push( elem );
-				if ( mapped ) {
-					map.push( i );
-				}
-			}
-		}
-	}
-
-	return newUnmatched;
-}
-
-function setMatcher( preFilter, selector, matcher, postFilter, postFinder, postSelector ) {
-	if ( postFilter && !postFilter[ expando ] ) {
-		postFilter = setMatcher( postFilter );
-	}
-	if ( postFinder && !postFinder[ expando ] ) {
-		postFinder = setMatcher( postFinder, postSelector );
-	}
-	return markFunction( function( seed, results, context, xml ) {
-		var temp, i, elem,
-			preMap = [],
-			postMap = [],
-			preexisting = results.length,
-
-			// Get initial elements from seed or context
-			elems = seed || multipleContexts(
-				selector || "*",
-				context.nodeType ? [ context ] : context,
-				[]
-			),
-
-			// Prefilter to get matcher input, preserving a map for seed-results synchronization
-			matcherIn = preFilter && ( seed || !selector ) ?
-				condense( elems, preMap, preFilter, context, xml ) :
-				elems,
-
-			matcherOut = matcher ?
-
-				// If we have a postFinder, or filtered seed, or non-seed postFilter or preexisting results,
-				postFinder || ( seed ? preFilter : preexisting || postFilter ) ?
-
-					// ...intermediate processing is necessary
-					[] :
-
-					// ...otherwise use results directly
-					results :
-				matcherIn;
-
-		// Find primary matches
-		if ( matcher ) {
-			matcher( matcherIn, matcherOut, context, xml );
-		}
-
-		// Apply postFilter
-		if ( postFilter ) {
-			temp = condense( matcherOut, postMap );
-			postFilter( temp, [], context, xml );
-
-			// Un-match failing elements by moving them back to matcherIn
-			i = temp.length;
-			while ( i-- ) {
-				if ( ( elem = temp[ i ] ) ) {
-					matcherOut[ postMap[ i ] ] = !( matcherIn[ postMap[ i ] ] = elem );
-				}
-			}
-		}
-
-		if ( seed ) {
-			if ( postFinder || preFilter ) {
-				if ( postFinder ) {
-
-					// Get the final matcherOut by condensing this intermediate into postFinder contexts
-					temp = [];
-					i = matcherOut.length;
-					while ( i-- ) {
-						if ( ( elem = matcherOut[ i ] ) ) {
-
-							// Restore matcherIn since elem is not yet a final match
-							temp.push( ( matcherIn[ i ] = elem ) );
-						}
-					}
-					postFinder( null, ( matcherOut = [] ), temp, xml );
-				}
-
-				// Move matched elements from seed to results to keep them synchronized
-				i = matcherOut.length;
-				while ( i-- ) {
-					if ( ( elem = matcherOut[ i ] ) &&
-						( temp = postFinder ? indexOf( seed, elem ) : preMap[ i ] ) > -1 ) {
-
-						seed[ temp ] = !( results[ temp ] = elem );
-					}
-				}
-			}
-
-		// Add elements to results, through postFinder if defined
-		} else {
-			matcherOut = condense(
-				matcherOut === results ?
-					matcherOut.splice( preexisting, matcherOut.length ) :
-					matcherOut
-			);
-			if ( postFinder ) {
-				postFinder( null, results, matcherOut, xml );
-			} else {
-				push.apply( results, matcherOut );
-			}
-		}
-	} );
-}
-
-function matcherFromTokens( tokens ) {
-	var checkContext, matcher, j,
-		len = tokens.length,
-		leadingRelative = Expr.relative[ tokens[ 0 ].type ],
-		implicitRelative = leadingRelative || Expr.relative[ " " ],
-		i = leadingRelative ? 1 : 0,
-
-		// The foundational matcher ensures that elements are reachable from top-level context(s)
-		matchContext = addCombinator( function( elem ) {
-			return elem === checkContext;
-		}, implicitRelative, true ),
-		matchAnyContext = addCombinator( function( elem ) {
-			return indexOf( checkContext, elem ) > -1;
-		}, implicitRelative, true ),
-		matchers = [ function( elem, context, xml ) {
-			var ret = ( !leadingRelative && ( xml || context !== outermostContext ) ) || (
-				( checkContext = context ).nodeType ?
-					matchContext( elem, context, xml ) :
-					matchAnyContext( elem, context, xml ) );
-
-			// Avoid hanging onto element (issue #299)
-			checkContext = null;
-			return ret;
-		} ];
-
-	for ( ; i < len; i++ ) {
-		if ( ( matcher = Expr.relative[ tokens[ i ].type ] ) ) {
-			matchers = [ addCombinator( elementMatcher( matchers ), matcher ) ];
-		} else {
-			matcher = Expr.filter[ tokens[ i ].type ].apply( null, tokens[ i ].matches );
-
-			// Return special upon seeing a positional matcher
-			if ( matcher[ expando ] ) {
-
-				// Find the next relative operator (if any) for proper handling
-				j = ++i;
-				for ( ; j < len; j++ ) {
-					if ( Expr.relative[ tokens[ j ].type ] ) {
-						break;
-					}
-				}
-				return setMatcher(
-					i > 1 && elementMatcher( matchers ),
-					i > 1 && toSelector(
-
-					// If the preceding token was a descendant combinator, insert an implicit any-element `*`
-					tokens
-						.slice( 0, i - 1 )
-						.concat( { value: tokens[ i - 2 ].type === " " ? "*" : "" } )
-					).replace( rtrim, "$1" ),
-					matcher,
-					i < j && matcherFromTokens( tokens.slice( i, j ) ),
-					j < len && matcherFromTokens( ( tokens = tokens.slice( j ) ) ),
-					j < len && toSelector( tokens )
-				);
-			}
-			matchers.push( matcher );
-		}
-	}
-
-	return elementMatcher( matchers );
-}
-
-function matcherFromGroupMatchers( elementMatchers, setMatchers ) {
-	var bySet = setMatchers.length > 0,
-		byElement = elementMatchers.length > 0,
-		superMatcher = function( seed, context, xml, results, outermost ) {
-			var elem, j, matcher,
-				matchedCount = 0,
-				i = "0",
-				unmatched = seed && [],
-				setMatched = [],
-				contextBackup = outermostContext,
-
-				// We must always have either seed elements or outermost context
-				elems = seed || byElement && Expr.find[ "TAG" ]( "*", outermost ),
-
-				// Use integer dirruns iff this is the outermost matcher
-				dirrunsUnique = ( dirruns += contextBackup == null ? 1 : Math.random() || 0.1 ),
-				len = elems.length;
-
-			if ( outermost ) {
-
-				// Support: IE 11+, Edge 17 - 18+
-				// IE/Edge sometimes throw a "Permission denied" error when strict-comparing
-				// two documents; shallow comparisons work.
-				// eslint-disable-next-line eqeqeq
-				outermostContext = context == document || context || outermost;
-			}
-
-			// Add elements passing elementMatchers directly to results
-			// Support: IE<9, Safari
-			// Tolerate NodeList properties (IE: "length"; Safari: ) matching elements by id
-			for ( ; i !== len && ( elem = elems[ i ] ) != null; i++ ) {
-				if ( byElement && elem ) {
-					j = 0;
-
-					// Support: IE 11+, Edge 17 - 18+
-					// IE/Edge sometimes throw a "Permission denied" error when strict-comparing
-					// two documents; shallow comparisons work.
-					// eslint-disable-next-line eqeqeq
-					if ( !context && elem.ownerDocument != document ) {
-						setDocument( elem );
-						xml = !documentIsHTML;
-					}
-					while ( ( matcher = elementMatchers[ j++ ] ) ) {
-						if ( matcher( elem, context || document, xml ) ) {
-							results.push( elem );
-							break;
-						}
-					}
-					if ( outermost ) {
-						dirruns = dirrunsUnique;
-					}
-				}
-
-				// Track unmatched elements for set filters
-				if ( bySet ) {
-
-					// They will have gone through all possible matchers
-					if ( ( elem = !matcher && elem ) ) {
-						matchedCount--;
-					}
-
-					// Lengthen the array for every element, matched or not
-					if ( seed ) {
-						unmatched.push( elem );
-					}
-				}
-			}
-
-			// `i` is now the count of elements visited above, and adding it to `matchedCount`
-			// makes the latter nonnegative.
-			matchedCount += i;
-
-			// Apply set filters to unmatched elements
-			// NOTE: This can be skipped if there are no unmatched elements (i.e., `matchedCount`
-			// equals `i`), unless we didn't visit _any_ elements in the above loop because we have
-			// no element matchers and no seed.
-			// Incrementing an initially-string "0" `i` allows `i` to remain a string only in that
-			// case, which will result in a "00" `matchedCount` that differs from `i` but is also
-			// numerically zero.
-			if ( bySet && i !== matchedCount ) {
-				j = 0;
-				while ( ( matcher = setMatchers[ j++ ] ) ) {
-					matcher( unmatched, setMatched, context, xml );
-				}
-
-				if ( seed ) {
-
-					// Reintegrate element matches to eliminate the need for sorting
-					if ( matchedCount > 0 ) {
-						while ( i-- ) {
-							if ( !( unmatched[ i ] || setMatched[ i ] ) ) {
-								setMatched[ i ] = pop.call( results );
-							}
-						}
-					}
-
-					// Discard index placeholder values to get only actual matches
-					setMatched = condense( setMatched );
-				}
-
-				// Add matches to results
-				push.apply( results, setMatched );
-
-				// Seedless set matches succeeding multiple successful matchers stipulate sorting
-				if ( outermost && !seed && setMatched.length > 0 &&
-					( matchedCount + setMatchers.length ) > 1 ) {
-
-					Sizzle.uniqueSort( results );
-				}
-			}
-
-			// Override manipulation of globals by nested matchers
-			if ( outermost ) {
-				dirruns = dirrunsUnique;
-				outermostContext = contextBackup;
-			}
-
-			return unmatched;
-		};
-
-	return bySet ?
-		markFunction( superMatcher ) :
-		superMatcher;
-}
-
-compile = Sizzle.compile = function( selector, match /* Internal Use Only */ ) {
-	var i,
-		setMatchers = [],
-		elementMatchers = [],
-		cached = compilerCache[ selector + " " ];
-
-	if ( !cached ) {
-
-		// Generate a function of recursive functions that can be used to check each element
-		if ( !match ) {
-			match = tokenize( selector );
-		}
-		i = match.length;
-		while ( i-- ) {
-			cached = matcherFromTokens( match[ i ] );
-			if ( cached[ expando ] ) {
-				setMatchers.push( cached );
-			} else {
-				elementMatchers.push( cached );
-			}
-		}
-
-		// Cache the compiled function
-		cached = compilerCache(
-			selector,
-			matcherFromGroupMatchers( elementMatchers, setMatchers )
-		);
-
-		// Save selector and tokenization
-		cached.selector = selector;
-	}
-	return cached;
-};
-
-/**
- * A low-level selection function that works with Sizzle's compiled
- *  selector functions
- * @param {String|Function} selector A selector or a pre-compiled
- *  selector function built with Sizzle.compile
- * @param {Element} context
- * @param {Array} [results]
- * @param {Array} [seed] A set of elements to match against
- */
-select = Sizzle.select = function( selector, context, results, seed ) {
-	var i, tokens, token, type, find,
-		compiled = typeof selector === "function" && selector,
-		match = !seed && tokenize( ( selector = compiled.selector || selector ) );
-
-	results = results || [];
-
-	// Try to minimize operations if there is only one selector in the list and no seed
-	// (the latter of which guarantees us context)
-	if ( match.length === 1 ) {
-
-		// Reduce context if the leading compound selector is an ID
-		tokens = match[ 0 ] = match[ 0 ].slice( 0 );
-		if ( tokens.length > 2 && ( token = tokens[ 0 ] ).type === "ID" &&
-			context.nodeType === 9 && documentIsHTML && Expr.relative[ tokens[ 1 ].type ] ) {
-
-			context = ( Expr.find[ "ID" ]( token.matches[ 0 ]
-				.replace( runescape, funescape ), context ) || [] )[ 0 ];
-			if ( !context ) {
-				return results;
-
-			// Precompiled matchers will still verify ancestry, so step up a level
-			} else if ( compiled ) {
-				context = context.parentNode;
-			}
-
-			selector = selector.slice( tokens.shift().value.length );
-		}
-
-		// Fetch a seed set for right-to-left matching
-		i = matchExpr[ "needsContext" ].test( selector ) ? 0 : tokens.length;
-		while ( i-- ) {
-			token = tokens[ i ];
-
-			// Abort if we hit a combinator
-			if ( Expr.relative[ ( type = token.type ) ] ) {
-				break;
-			}
-			if ( ( find = Expr.find[ type ] ) ) {
-
-				// Search, expanding context for leading sibling combinators
-				if ( ( seed = find(
-					token.matches[ 0 ].replace( runescape, funescape ),
-					rsibling.test( tokens[ 0 ].type ) && testContext( context.parentNode ) ||
-						context
-				) ) ) {
-
-					// If seed is empty or no tokens remain, we can return early
-					tokens.splice( i, 1 );
-					selector = seed.length && toSelector( tokens );
-					if ( !selector ) {
-						push.apply( results, seed );
-						return results;
-					}
-
-					break;
-				}
-			}
-		}
-	}
-
-	// Compile and execute a filtering function if one is not provided
-	// Provide `match` to avoid retokenization if we modified the selector above
-	( compiled || compile( selector, match ) )(
-		seed,
-		context,
-		!documentIsHTML,
-		results,
-		!context || rsibling.test( selector ) && testContext( context.parentNode ) || context
-	);
-	return results;
-};
-
-// One-time assignments
-
-// Sort stability
-support.sortStable = expando.split( "" ).sort( sortOrder ).join( "" ) === expando;
-
-// Support: Chrome 14-35+
-// Always assume duplicates if they aren't passed to the comparison function
-support.detectDuplicates = !!hasDuplicate;
-
-// Initialize against the default document
-setDocument();
-
-// Support: Webkit<537.32 - Safari 6.0.3/Chrome 25 (fixed in Chrome 27)
-// Detached nodes confoundingly follow *each other*
-support.sortDetached = assert( function( el ) {
-
-	// Should return 1, but returns 4 (following)
-	return el.compareDocumentPosition( document.createElement( "fieldset" ) ) & 1;
-} );
-
-// Support: IE<8
-// Prevent attribute/property "interpolation"
-// https://msdn.microsoft.com/en-us/library/ms536429%28VS.85%29.aspx
-if ( !assert( function( el ) {
-	el.innerHTML = "";
-	return el.firstChild.getAttribute( "href" ) === "#";
-} ) ) {
-	addHandle( "type|href|height|width", function( elem, name, isXML ) {
-		if ( !isXML ) {
-			return elem.getAttribute( name, name.toLowerCase() === "type" ? 1 : 2 );
-		}
-	} );
-}
-
-// Support: IE<9
-// Use defaultValue in place of getAttribute("value")
-if ( !support.attributes || !assert( function( el ) {
-	el.innerHTML = "";
-	el.firstChild.setAttribute( "value", "" );
-	return el.firstChild.getAttribute( "value" ) === "";
-} ) ) {
-	addHandle( "value", function( elem, _name, isXML ) {
-		if ( !isXML && elem.nodeName.toLowerCase() === "input" ) {
-			return elem.defaultValue;
-		}
-	} );
-}
-
-// Support: IE<9
-// Use getAttributeNode to fetch booleans when getAttribute lies
-if ( !assert( function( el ) {
-	return el.getAttribute( "disabled" ) == null;
-} ) ) {
-	addHandle( booleans, function( elem, name, isXML ) {
-		var val;
-		if ( !isXML ) {
-			return elem[ name ] === true ? name.toLowerCase() :
-				( val = elem.getAttributeNode( name ) ) && val.specified ?
-					val.value :
-					null;
-		}
-	} );
-}
-
-return Sizzle;
-
-} )( window );
-
-
-
-jQuery.find = Sizzle;
-jQuery.expr = Sizzle.selectors;
-
-// Deprecated
-jQuery.expr[ ":" ] = jQuery.expr.pseudos;
-jQuery.uniqueSort = jQuery.unique = Sizzle.uniqueSort;
-jQuery.text = Sizzle.getText;
-jQuery.isXMLDoc = Sizzle.isXML;
-jQuery.contains = Sizzle.contains;
-jQuery.escapeSelector = Sizzle.escape;
-
-
-
-
-var dir = function( elem, dir, until ) {
-	var matched = [],
-		truncate = until !== undefined;
-
-	while ( ( elem = elem[ dir ] ) && elem.nodeType !== 9 ) {
-		if ( elem.nodeType === 1 ) {
-			if ( truncate && jQuery( elem ).is( until ) ) {
-				break;
-			}
-			matched.push( elem );
-		}
-	}
-	return matched;
-};
-
-
-var siblings = function( n, elem ) {
-	var matched = [];
-
-	for ( ; n; n = n.nextSibling ) {
-		if ( n.nodeType === 1 && n !== elem ) {
-			matched.push( n );
-		}
-	}
-
-	return matched;
-};
-
-
-var rneedsContext = jQuery.expr.match.needsContext;
-
-
-
-function nodeName( elem, name ) {
-
-	return elem.nodeName && elem.nodeName.toLowerCase() === name.toLowerCase();
-
-}
-var rsingleTag = ( /^<([a-z][^\/\0>:\x20\t\r\n\f]*)[\x20\t\r\n\f]*\/?>(?:<\/\1>|)$/i );
-
-
-
-// Implement the identical functionality for filter and not
-function winnow( elements, qualifier, not ) {
-	if ( isFunction( qualifier ) ) {
-		return jQuery.grep( elements, function( elem, i ) {
-			return !!qualifier.call( elem, i, elem ) !== not;
-		} );
-	}
-
-	// Single element
-	if ( qualifier.nodeType ) {
-		return jQuery.grep( elements, function( elem ) {
-			return ( elem === qualifier ) !== not;
-		} );
-	}
-
-	// Arraylike of elements (jQuery, arguments, Array)
-	if ( typeof qualifier !== "string" ) {
-		return jQuery.grep( elements, function( elem ) {
-			return ( indexOf.call( qualifier, elem ) > -1 ) !== not;
-		} );
-	}
-
-	// Filtered directly for both simple and complex selectors
-	return jQuery.filter( qualifier, elements, not );
-}
-
-jQuery.filter = function( expr, elems, not ) {
-	var elem = elems[ 0 ];
-
-	if ( not ) {
-		expr = ":not(" + expr + ")";
-	}
-
-	if ( elems.length === 1 && elem.nodeType === 1 ) {
-		return jQuery.find.matchesSelector( elem, expr ) ? [ elem ] : [];
-	}
-
-	return jQuery.find.matches( expr, jQuery.grep( elems, function( elem ) {
-		return elem.nodeType === 1;
-	} ) );
-};
-
-jQuery.fn.extend( {
-	find: function( selector ) {
-		var i, ret,
-			len = this.length,
-			self = this;
-
-		if ( typeof selector !== "string" ) {
-			return this.pushStack( jQuery( selector ).filter( function() {
-				for ( i = 0; i < len; i++ ) {
-					if ( jQuery.contains( self[ i ], this ) ) {
-						return true;
-					}
-				}
-			} ) );
-		}
-
-		ret = this.pushStack( [] );
-
-		for ( i = 0; i < len; i++ ) {
-			jQuery.find( selector, self[ i ], ret );
-		}
-
-		return len > 1 ? jQuery.uniqueSort( ret ) : ret;
-	},
-	filter: function( selector ) {
-		return this.pushStack( winnow( this, selector || [], false ) );
-	},
-	not: function( selector ) {
-		return this.pushStack( winnow( this, selector || [], true ) );
-	},
-	is: function( selector ) {
-		return !!winnow(
-			this,
-
-			// If this is a positional/relative selector, check membership in the returned set
-			// so $("p:first").is("p:last") won't return true for a doc with two "p".
-			typeof selector === "string" && rneedsContext.test( selector ) ?
-				jQuery( selector ) :
-				selector || [],
-			false
-		).length;
-	}
-} );
-
-
-// Initialize a jQuery object
-
-
-// A central reference to the root jQuery(document)
-var rootjQuery,
-
-	// A simple way to check for HTML strings
-	// Prioritize #id over  to avoid XSS via location.hash (#9521)
-	// Strict HTML recognition (#11290: must start with <)
-	// Shortcut simple #id case for speed
-	rquickExpr = /^(?:\s*(<[\w\W]+>)[^>]*|#([\w-]+))$/,
-
-	init = jQuery.fn.init = function( selector, context, root ) {
-		var match, elem;
-
-		// HANDLE: $(""), $(null), $(undefined), $(false)
-		if ( !selector ) {
-			return this;
-		}
-
-		// Method init() accepts an alternate rootjQuery
-		// so migrate can support jQuery.sub (gh-2101)
-		root = root || rootjQuery;
-
-		// Handle HTML strings
-		if ( typeof selector === "string" ) {
-			if ( selector[ 0 ] === "<" &&
-				selector[ selector.length - 1 ] === ">" &&
-				selector.length >= 3 ) {
-
-				// Assume that strings that start and end with <> are HTML and skip the regex check
-				match = [ null, selector, null ];
-
-			} else {
-				match = rquickExpr.exec( selector );
-			}
-
-			// Match html or make sure no context is specified for #id
-			if ( match && ( match[ 1 ] || !context ) ) {
-
-				// HANDLE: $(html) -> $(array)
-				if ( match[ 1 ] ) {
-					context = context instanceof jQuery ? context[ 0 ] : context;
-
-					// Option to run scripts is true for back-compat
-					// Intentionally let the error be thrown if parseHTML is not present
-					jQuery.merge( this, jQuery.parseHTML(
-						match[ 1 ],
-						context && context.nodeType ? context.ownerDocument || context : document,
-						true
-					) );
-
-					// HANDLE: $(html, props)
-					if ( rsingleTag.test( match[ 1 ] ) && jQuery.isPlainObject( context ) ) {
-						for ( match in context ) {
-
-							// Properties of context are called as methods if possible
-							if ( isFunction( this[ match ] ) ) {
-								this[ match ]( context[ match ] );
-
-							// ...and otherwise set as attributes
-							} else {
-								this.attr( match, context[ match ] );
-							}
-						}
-					}
-
-					return this;
-
-				// HANDLE: $(#id)
-				} else {
-					elem = document.getElementById( match[ 2 ] );
-
-					if ( elem ) {
-
-						// Inject the element directly into the jQuery object
-						this[ 0 ] = elem;
-						this.length = 1;
-					}
-					return this;
-				}
-
-			// HANDLE: $(expr, $(...))
-			} else if ( !context || context.jquery ) {
-				return ( context || root ).find( selector );
-
-			// HANDLE: $(expr, context)
-			// (which is just equivalent to: $(context).find(expr)
-			} else {
-				return this.constructor( context ).find( selector );
-			}
-
-		// HANDLE: $(DOMElement)
-		} else if ( selector.nodeType ) {
-			this[ 0 ] = selector;
-			this.length = 1;
-			return this;
-
-		// HANDLE: $(function)
-		// Shortcut for document ready
-		} else if ( isFunction( selector ) ) {
-			return root.ready !== undefined ?
-				root.ready( selector ) :
-
-				// Execute immediately if ready is not present
-				selector( jQuery );
-		}
-
-		return jQuery.makeArray( selector, this );
-	};
-
-// Give the init function the jQuery prototype for later instantiation
-init.prototype = jQuery.fn;
-
-// Initialize central reference
-rootjQuery = jQuery( document );
-
-
-var rparentsprev = /^(?:parents|prev(?:Until|All))/,
-
-	// Methods guaranteed to produce a unique set when starting from a unique set
-	guaranteedUnique = {
-		children: true,
-		contents: true,
-		next: true,
-		prev: true
-	};
-
-jQuery.fn.extend( {
-	has: function( target ) {
-		var targets = jQuery( target, this ),
-			l = targets.length;
-
-		return this.filter( function() {
-			var i = 0;
-			for ( ; i < l; i++ ) {
-				if ( jQuery.contains( this, targets[ i ] ) ) {
-					return true;
-				}
-			}
-		} );
-	},
-
-	closest: function( selectors, context ) {
-		var cur,
-			i = 0,
-			l = this.length,
-			matched = [],
-			targets = typeof selectors !== "string" && jQuery( selectors );
-
-		// Positional selectors never match, since there's no _selection_ context
-		if ( !rneedsContext.test( selectors ) ) {
-			for ( ; i < l; i++ ) {
-				for ( cur = this[ i ]; cur && cur !== context; cur = cur.parentNode ) {
-
-					// Always skip document fragments
-					if ( cur.nodeType < 11 && ( targets ?
-						targets.index( cur ) > -1 :
-
-						// Don't pass non-elements to Sizzle
-						cur.nodeType === 1 &&
-							jQuery.find.matchesSelector( cur, selectors ) ) ) {
-
-						matched.push( cur );
-						break;
-					}
-				}
-			}
-		}
-
-		return this.pushStack( matched.length > 1 ? jQuery.uniqueSort( matched ) : matched );
-	},
-
-	// Determine the position of an element within the set
-	index: function( elem ) {
-
-		// No argument, return index in parent
-		if ( !elem ) {
-			return ( this[ 0 ] && this[ 0 ].parentNode ) ? this.first().prevAll().length : -1;
-		}
-
-		// Index in selector
-		if ( typeof elem === "string" ) {
-			return indexOf.call( jQuery( elem ), this[ 0 ] );
-		}
-
-		// Locate the position of the desired element
-		return indexOf.call( this,
-
-			// If it receives a jQuery object, the first element is used
-			elem.jquery ? elem[ 0 ] : elem
-		);
-	},
-
-	add: function( selector, context ) {
-		return this.pushStack(
-			jQuery.uniqueSort(
-				jQuery.merge( this.get(), jQuery( selector, context ) )
-			)
-		);
-	},
-
-	addBack: function( selector ) {
-		return this.add( selector == null ?
-			this.prevObject : this.prevObject.filter( selector )
-		);
-	}
-} );
-
-function sibling( cur, dir ) {
-	while ( ( cur = cur[ dir ] ) && cur.nodeType !== 1 ) {}
-	return cur;
-}
-
-jQuery.each( {
-	parent: function( elem ) {
-		var parent = elem.parentNode;
-		return parent && parent.nodeType !== 11 ? parent : null;
-	},
-	parents: function( elem ) {
-		return dir( elem, "parentNode" );
-	},
-	parentsUntil: function( elem, _i, until ) {
-		return dir( elem, "parentNode", until );
-	},
-	next: function( elem ) {
-		return sibling( elem, "nextSibling" );
-	},
-	prev: function( elem ) {
-		return sibling( elem, "previousSibling" );
-	},
-	nextAll: function( elem ) {
-		return dir( elem, "nextSibling" );
-	},
-	prevAll: function( elem ) {
-		return dir( elem, "previousSibling" );
-	},
-	nextUntil: function( elem, _i, until ) {
-		return dir( elem, "nextSibling", until );
-	},
-	prevUntil: function( elem, _i, until ) {
-		return dir( elem, "previousSibling", until );
-	},
-	siblings: function( elem ) {
-		return siblings( ( elem.parentNode || {} ).firstChild, elem );
-	},
-	children: function( elem ) {
-		return siblings( elem.firstChild );
-	},
-	contents: function( elem ) {
-		if ( elem.contentDocument != null &&
-
-			// Support: IE 11+
-			//  elements with no `data` attribute has an object
-			// `contentDocument` with a `null` prototype.
-			getProto( elem.contentDocument ) ) {
-
-			return elem.contentDocument;
-		}
-
-		// Support: IE 9 - 11 only, iOS 7 only, Android Browser <=4.3 only
-		// Treat the template element as a regular one in browsers that
-		// don't support it.
-		if ( nodeName( elem, "template" ) ) {
-			elem = elem.content || elem;
-		}
-
-		return jQuery.merge( [], elem.childNodes );
-	}
-}, function( name, fn ) {
-	jQuery.fn[ name ] = function( until, selector ) {
-		var matched = jQuery.map( this, fn, until );
-
-		if ( name.slice( -5 ) !== "Until" ) {
-			selector = until;
-		}
-
-		if ( selector && typeof selector === "string" ) {
-			matched = jQuery.filter( selector, matched );
-		}
-
-		if ( this.length > 1 ) {
-
-			// Remove duplicates
-			if ( !guaranteedUnique[ name ] ) {
-				jQuery.uniqueSort( matched );
-			}
-
-			// Reverse order for parents* and prev-derivatives
-			if ( rparentsprev.test( name ) ) {
-				matched.reverse();
-			}
-		}
-
-		return this.pushStack( matched );
-	};
-} );
-var rnothtmlwhite = ( /[^\x20\t\r\n\f]+/g );
-
-
-
-// Convert String-formatted options into Object-formatted ones
-function createOptions( options ) {
-	var object = {};
-	jQuery.each( options.match( rnothtmlwhite ) || [], function( _, flag ) {
-		object[ flag ] = true;
-	} );
-	return object;
-}
-
-/*
- * Create a callback list using the following parameters:
- *
- *	options: an optional list of space-separated options that will change how
- *			the callback list behaves or a more traditional option object
- *
- * By default a callback list will act like an event callback list and can be
- * "fired" multiple times.
- *
- * Possible options:
- *
- *	once:			will ensure the callback list can only be fired once (like a Deferred)
- *
- *	memory:			will keep track of previous values and will call any callback added
- *					after the list has been fired right away with the latest "memorized"
- *					values (like a Deferred)
- *
- *	unique:			will ensure a callback can only be added once (no duplicate in the list)
- *
- *	stopOnFalse:	interrupt callings when a callback returns false
- *
- */
-jQuery.Callbacks = function( options ) {
-
-	// Convert options from String-formatted to Object-formatted if needed
-	// (we check in cache first)
-	options = typeof options === "string" ?
-		createOptions( options ) :
-		jQuery.extend( {}, options );
-
-	var // Flag to know if list is currently firing
-		firing,
-
-		// Last fire value for non-forgettable lists
-		memory,
-
-		// Flag to know if list was already fired
-		fired,
-
-		// Flag to prevent firing
-		locked,
-
-		// Actual callback list
-		list = [],
-
-		// Queue of execution data for repeatable lists
-		queue = [],
-
-		// Index of currently firing callback (modified by add/remove as needed)
-		firingIndex = -1,
-
-		// Fire callbacks
-		fire = function() {
-
-			// Enforce single-firing
-			locked = locked || options.once;
-
-			// Execute callbacks for all pending executions,
-			// respecting firingIndex overrides and runtime changes
-			fired = firing = true;
-			for ( ; queue.length; firingIndex = -1 ) {
-				memory = queue.shift();
-				while ( ++firingIndex < list.length ) {
-
-					// Run callback and check for early termination
-					if ( list[ firingIndex ].apply( memory[ 0 ], memory[ 1 ] ) === false &&
-						options.stopOnFalse ) {
-
-						// Jump to end and forget the data so .add doesn't re-fire
-						firingIndex = list.length;
-						memory = false;
-					}
-				}
-			}
-
-			// Forget the data if we're done with it
-			if ( !options.memory ) {
-				memory = false;
-			}
-
-			firing = false;
-
-			// Clean up if we're done firing for good
-			if ( locked ) {
-
-				// Keep an empty list if we have data for future add calls
-				if ( memory ) {
-					list = [];
-
-				// Otherwise, this object is spent
-				} else {
-					list = "";
-				}
-			}
-		},
-
-		// Actual Callbacks object
-		self = {
-
-			// Add a callback or a collection of callbacks to the list
-			add: function() {
-				if ( list ) {
-
-					// If we have memory from a past run, we should fire after adding
-					if ( memory && !firing ) {
-						firingIndex = list.length - 1;
-						queue.push( memory );
-					}
-
-					( function add( args ) {
-						jQuery.each( args, function( _, arg ) {
-							if ( isFunction( arg ) ) {
-								if ( !options.unique || !self.has( arg ) ) {
-									list.push( arg );
-								}
-							} else if ( arg && arg.length && toType( arg ) !== "string" ) {
-
-								// Inspect recursively
-								add( arg );
-							}
-						} );
-					} )( arguments );
-
-					if ( memory && !firing ) {
-						fire();
-					}
-				}
-				return this;
-			},
-
-			// Remove a callback from the list
-			remove: function() {
-				jQuery.each( arguments, function( _, arg ) {
-					var index;
-					while ( ( index = jQuery.inArray( arg, list, index ) ) > -1 ) {
-						list.splice( index, 1 );
-
-						// Handle firing indexes
-						if ( index <= firingIndex ) {
-							firingIndex--;
-						}
-					}
-				} );
-				return this;
-			},
-
-			// Check if a given callback is in the list.
-			// If no argument is given, return whether or not list has callbacks attached.
-			has: function( fn ) {
-				return fn ?
-					jQuery.inArray( fn, list ) > -1 :
-					list.length > 0;
-			},
-
-			// Remove all callbacks from the list
-			empty: function() {
-				if ( list ) {
-					list = [];
-				}
-				return this;
-			},
-
-			// Disable .fire and .add
-			// Abort any current/pending executions
-			// Clear all callbacks and values
-			disable: function() {
-				locked = queue = [];
-				list = memory = "";
-				return this;
-			},
-			disabled: function() {
-				return !list;
-			},
-
-			// Disable .fire
-			// Also disable .add unless we have memory (since it would have no effect)
-			// Abort any pending executions
-			lock: function() {
-				locked = queue = [];
-				if ( !memory && !firing ) {
-					list = memory = "";
-				}
-				return this;
-			},
-			locked: function() {
-				return !!locked;
-			},
-
-			// Call all callbacks with the given context and arguments
-			fireWith: function( context, args ) {
-				if ( !locked ) {
-					args = args || [];
-					args = [ context, args.slice ? args.slice() : args ];
-					queue.push( args );
-					if ( !firing ) {
-						fire();
-					}
-				}
-				return this;
-			},
-
-			// Call all the callbacks with the given arguments
-			fire: function() {
-				self.fireWith( this, arguments );
-				return this;
-			},
-
-			// To know if the callbacks have already been called at least once
-			fired: function() {
-				return !!fired;
-			}
-		};
-
-	return self;
-};
-
-
-function Identity( v ) {
-	return v;
-}
-function Thrower( ex ) {
-	throw ex;
-}
-
-function adoptValue( value, resolve, reject, noValue ) {
-	var method;
-
-	try {
-
-		// Check for promise aspect first to privilege synchronous behavior
-		if ( value && isFunction( ( method = value.promise ) ) ) {
-			method.call( value ).done( resolve ).fail( reject );
-
-		// Other thenables
-		} else if ( value && isFunction( ( method = value.then ) ) ) {
-			method.call( value, resolve, reject );
-
-		// Other non-thenables
-		} else {
-
-			// Control `resolve` arguments by letting Array#slice cast boolean `noValue` to integer:
-			// * false: [ value ].slice( 0 ) => resolve( value )
-			// * true: [ value ].slice( 1 ) => resolve()
-			resolve.apply( undefined, [ value ].slice( noValue ) );
-		}
-
-	// For Promises/A+, convert exceptions into rejections
-	// Since jQuery.when doesn't unwrap thenables, we can skip the extra checks appearing in
-	// Deferred#then to conditionally suppress rejection.
-	} catch ( value ) {
-
-		// Support: Android 4.0 only
-		// Strict mode functions invoked without .call/.apply get global-object context
-		reject.apply( undefined, [ value ] );
-	}
-}
-
-jQuery.extend( {
-
-	Deferred: function( func ) {
-		var tuples = [
-
-				// action, add listener, callbacks,
-				// ... .then handlers, argument index, [final state]
-				[ "notify", "progress", jQuery.Callbacks( "memory" ),
-					jQuery.Callbacks( "memory" ), 2 ],
-				[ "resolve", "done", jQuery.Callbacks( "once memory" ),
-					jQuery.Callbacks( "once memory" ), 0, "resolved" ],
-				[ "reject", "fail", jQuery.Callbacks( "once memory" ),
-					jQuery.Callbacks( "once memory" ), 1, "rejected" ]
-			],
-			state = "pending",
-			promise = {
-				state: function() {
-					return state;
-				},
-				always: function() {
-					deferred.done( arguments ).fail( arguments );
-					return this;
-				},
-				"catch": function( fn ) {
-					return promise.then( null, fn );
-				},
-
-				// Keep pipe for back-compat
-				pipe: function( /* fnDone, fnFail, fnProgress */ ) {
-					var fns = arguments;
-
-					return jQuery.Deferred( function( newDefer ) {
-						jQuery.each( tuples, function( _i, tuple ) {
-
-							// Map tuples (progress, done, fail) to arguments (done, fail, progress)
-							var fn = isFunction( fns[ tuple[ 4 ] ] ) && fns[ tuple[ 4 ] ];
-
-							// deferred.progress(function() { bind to newDefer or newDefer.notify })
-							// deferred.done(function() { bind to newDefer or newDefer.resolve })
-							// deferred.fail(function() { bind to newDefer or newDefer.reject })
-							deferred[ tuple[ 1 ] ]( function() {
-								var returned = fn && fn.apply( this, arguments );
-								if ( returned && isFunction( returned.promise ) ) {
-									returned.promise()
-										.progress( newDefer.notify )
-										.done( newDefer.resolve )
-										.fail( newDefer.reject );
-								} else {
-									newDefer[ tuple[ 0 ] + "With" ](
-										this,
-										fn ? [ returned ] : arguments
-									);
-								}
-							} );
-						} );
-						fns = null;
-					} ).promise();
-				},
-				then: function( onFulfilled, onRejected, onProgress ) {
-					var maxDepth = 0;
-					function resolve( depth, deferred, handler, special ) {
-						return function() {
-							var that = this,
-								args = arguments,
-								mightThrow = function() {
-									var returned, then;
-
-									// Support: Promises/A+ section 2.3.3.3.3
-									// https://promisesaplus.com/#point-59
-									// Ignore double-resolution attempts
-									if ( depth < maxDepth ) {
-										return;
-									}
-
-									returned = handler.apply( that, args );
-
-									// Support: Promises/A+ section 2.3.1
-									// https://promisesaplus.com/#point-48
-									if ( returned === deferred.promise() ) {
-										throw new TypeError( "Thenable self-resolution" );
-									}
-
-									// Support: Promises/A+ sections 2.3.3.1, 3.5
-									// https://promisesaplus.com/#point-54
-									// https://promisesaplus.com/#point-75
-									// Retrieve `then` only once
-									then = returned &&
-
-										// Support: Promises/A+ section 2.3.4
-										// https://promisesaplus.com/#point-64
-										// Only check objects and functions for thenability
-										( typeof returned === "object" ||
-											typeof returned === "function" ) &&
-										returned.then;
-
-									// Handle a returned thenable
-									if ( isFunction( then ) ) {
-
-										// Special processors (notify) just wait for resolution
-										if ( special ) {
-											then.call(
-												returned,
-												resolve( maxDepth, deferred, Identity, special ),
-												resolve( maxDepth, deferred, Thrower, special )
-											);
-
-										// Normal processors (resolve) also hook into progress
-										} else {
-
-											// ...and disregard older resolution values
-											maxDepth++;
-
-											then.call(
-												returned,
-												resolve( maxDepth, deferred, Identity, special ),
-												resolve( maxDepth, deferred, Thrower, special ),
-												resolve( maxDepth, deferred, Identity,
-													deferred.notifyWith )
-											);
-										}
-
-									// Handle all other returned values
-									} else {
-
-										// Only substitute handlers pass on context
-										// and multiple values (non-spec behavior)
-										if ( handler !== Identity ) {
-											that = undefined;
-											args = [ returned ];
-										}
-
-										// Process the value(s)
-										// Default process is resolve
-										( special || deferred.resolveWith )( that, args );
-									}
-								},
-
-								// Only normal processors (resolve) catch and reject exceptions
-								process = special ?
-									mightThrow :
-									function() {
-										try {
-											mightThrow();
-										} catch ( e ) {
-
-											if ( jQuery.Deferred.exceptionHook ) {
-												jQuery.Deferred.exceptionHook( e,
-													process.stackTrace );
-											}
-
-											// Support: Promises/A+ section 2.3.3.3.4.1
-											// https://promisesaplus.com/#point-61
-											// Ignore post-resolution exceptions
-											if ( depth + 1 >= maxDepth ) {
-
-												// Only substitute handlers pass on context
-												// and multiple values (non-spec behavior)
-												if ( handler !== Thrower ) {
-													that = undefined;
-													args = [ e ];
-												}
-
-												deferred.rejectWith( that, args );
-											}
-										}
-									};
-
-							// Support: Promises/A+ section 2.3.3.3.1
-							// https://promisesaplus.com/#point-57
-							// Re-resolve promises immediately to dodge false rejection from
-							// subsequent errors
-							if ( depth ) {
-								process();
-							} else {
-
-								// Call an optional hook to record the stack, in case of exception
-								// since it's otherwise lost when execution goes async
-								if ( jQuery.Deferred.getStackHook ) {
-									process.stackTrace = jQuery.Deferred.getStackHook();
-								}
-								window.setTimeout( process );
-							}
-						};
-					}
-
-					return jQuery.Deferred( function( newDefer ) {
-
-						// progress_handlers.add( ... )
-						tuples[ 0 ][ 3 ].add(
-							resolve(
-								0,
-								newDefer,
-								isFunction( onProgress ) ?
-									onProgress :
-									Identity,
-								newDefer.notifyWith
-							)
-						);
-
-						// fulfilled_handlers.add( ... )
-						tuples[ 1 ][ 3 ].add(
-							resolve(
-								0,
-								newDefer,
-								isFunction( onFulfilled ) ?
-									onFulfilled :
-									Identity
-							)
-						);
-
-						// rejected_handlers.add( ... )
-						tuples[ 2 ][ 3 ].add(
-							resolve(
-								0,
-								newDefer,
-								isFunction( onRejected ) ?
-									onRejected :
-									Thrower
-							)
-						);
-					} ).promise();
-				},
-
-				// Get a promise for this deferred
-				// If obj is provided, the promise aspect is added to the object
-				promise: function( obj ) {
-					return obj != null ? jQuery.extend( obj, promise ) : promise;
-				}
-			},
-			deferred = {};
-
-		// Add list-specific methods
-		jQuery.each( tuples, function( i, tuple ) {
-			var list = tuple[ 2 ],
-				stateString = tuple[ 5 ];
-
-			// promise.progress = list.add
-			// promise.done = list.add
-			// promise.fail = list.add
-			promise[ tuple[ 1 ] ] = list.add;
-
-			// Handle state
-			if ( stateString ) {
-				list.add(
-					function() {
-
-						// state = "resolved" (i.e., fulfilled)
-						// state = "rejected"
-						state = stateString;
-					},
-
-					// rejected_callbacks.disable
-					// fulfilled_callbacks.disable
-					tuples[ 3 - i ][ 2 ].disable,
-
-					// rejected_handlers.disable
-					// fulfilled_handlers.disable
-					tuples[ 3 - i ][ 3 ].disable,
-
-					// progress_callbacks.lock
-					tuples[ 0 ][ 2 ].lock,
-
-					// progress_handlers.lock
-					tuples[ 0 ][ 3 ].lock
-				);
-			}
-
-			// progress_handlers.fire
-			// fulfilled_handlers.fire
-			// rejected_handlers.fire
-			list.add( tuple[ 3 ].fire );
-
-			// deferred.notify = function() { deferred.notifyWith(...) }
-			// deferred.resolve = function() { deferred.resolveWith(...) }
-			// deferred.reject = function() { deferred.rejectWith(...) }
-			deferred[ tuple[ 0 ] ] = function() {
-				deferred[ tuple[ 0 ] + "With" ]( this === deferred ? undefined : this, arguments );
-				return this;
-			};
-
-			// deferred.notifyWith = list.fireWith
-			// deferred.resolveWith = list.fireWith
-			// deferred.rejectWith = list.fireWith
-			deferred[ tuple[ 0 ] + "With" ] = list.fireWith;
-		} );
-
-		// Make the deferred a promise
-		promise.promise( deferred );
-
-		// Call given func if any
-		if ( func ) {
-			func.call( deferred, deferred );
-		}
-
-		// All done!
-		return deferred;
-	},
-
-	// Deferred helper
-	when: function( singleValue ) {
-		var
-
-			// count of uncompleted subordinates
-			remaining = arguments.length,
-
-			// count of unprocessed arguments
-			i = remaining,
-
-			// subordinate fulfillment data
-			resolveContexts = Array( i ),
-			resolveValues = slice.call( arguments ),
-
-			// the primary Deferred
-			primary = jQuery.Deferred(),
-
-			// subordinate callback factory
-			updateFunc = function( i ) {
-				return function( value ) {
-					resolveContexts[ i ] = this;
-					resolveValues[ i ] = arguments.length > 1 ? slice.call( arguments ) : value;
-					if ( !( --remaining ) ) {
-						primary.resolveWith( resolveContexts, resolveValues );
-					}
-				};
-			};
-
-		// Single- and empty arguments are adopted like Promise.resolve
-		if ( remaining <= 1 ) {
-			adoptValue( singleValue, primary.done( updateFunc( i ) ).resolve, primary.reject,
-				!remaining );
-
-			// Use .then() to unwrap secondary thenables (cf. gh-3000)
-			if ( primary.state() === "pending" ||
-				isFunction( resolveValues[ i ] && resolveValues[ i ].then ) ) {
-
-				return primary.then();
-			}
-		}
-
-		// Multiple arguments are aggregated like Promise.all array elements
-		while ( i-- ) {
-			adoptValue( resolveValues[ i ], updateFunc( i ), primary.reject );
-		}
-
-		return primary.promise();
-	}
-} );
-
-
-// These usually indicate a programmer mistake during development,
-// warn about them ASAP rather than swallowing them by default.
-var rerrorNames = /^(Eval|Internal|Range|Reference|Syntax|Type|URI)Error$/;
-
-jQuery.Deferred.exceptionHook = function( error, stack ) {
-
-	// Support: IE 8 - 9 only
-	// Console exists when dev tools are open, which can happen at any time
-	if ( window.console && window.console.warn && error && rerrorNames.test( error.name ) ) {
-		window.console.warn( "jQuery.Deferred exception: " + error.message, error.stack, stack );
-	}
-};
-
-
-
-
-jQuery.readyException = function( error ) {
-	window.setTimeout( function() {
-		throw error;
-	} );
-};
-
-
-
-
-// The deferred used on DOM ready
-var readyList = jQuery.Deferred();
-
-jQuery.fn.ready = function( fn ) {
-
-	readyList
-		.then( fn )
-
-		// Wrap jQuery.readyException in a function so that the lookup
-		// happens at the time of error handling instead of callback
-		// registration.
-		.catch( function( error ) {
-			jQuery.readyException( error );
-		} );
-
-	return this;
-};
-
-jQuery.extend( {
-
-	// Is the DOM ready to be used? Set to true once it occurs.
-	isReady: false,
-
-	// A counter to track how many items to wait for before
-	// the ready event fires. See #6781
-	readyWait: 1,
-
-	// Handle when the DOM is ready
-	ready: function( wait ) {
-
-		// Abort if there are pending holds or we're already ready
-		if ( wait === true ? --jQuery.readyWait : jQuery.isReady ) {
-			return;
-		}
-
-		// Remember that the DOM is ready
-		jQuery.isReady = true;
-
-		// If a normal DOM Ready event fired, decrement, and wait if need be
-		if ( wait !== true && --jQuery.readyWait > 0 ) {
-			return;
-		}
-
-		// If there are functions bound, to execute
-		readyList.resolveWith( document, [ jQuery ] );
-	}
-} );
-
-jQuery.ready.then = readyList.then;
-
-// The ready event handler and self cleanup method
-function completed() {
-	document.removeEventListener( "DOMContentLoaded", completed );
-	window.removeEventListener( "load", completed );
-	jQuery.ready();
-}
-
-// Catch cases where $(document).ready() is called
-// after the browser event has already occurred.
-// Support: IE <=9 - 10 only
-// Older IE sometimes signals "interactive" too soon
-if ( document.readyState === "complete" ||
-	( document.readyState !== "loading" && !document.documentElement.doScroll ) ) {
-
-	// Handle it asynchronously to allow scripts the opportunity to delay ready
-	window.setTimeout( jQuery.ready );
-
-} else {
-
-	// Use the handy event callback
-	document.addEventListener( "DOMContentLoaded", completed );
-
-	// A fallback to window.onload, that will always work
-	window.addEventListener( "load", completed );
-}
-
-
-
-
-// Multifunctional method to get and set values of a collection
-// The value/s can optionally be executed if it's a function
-var access = function( elems, fn, key, value, chainable, emptyGet, raw ) {
-	var i = 0,
-		len = elems.length,
-		bulk = key == null;
-
-	// Sets many values
-	if ( toType( key ) === "object" ) {
-		chainable = true;
-		for ( i in key ) {
-			access( elems, fn, i, key[ i ], true, emptyGet, raw );
-		}
-
-	// Sets one value
-	} else if ( value !== undefined ) {
-		chainable = true;
-
-		if ( !isFunction( value ) ) {
-			raw = true;
-		}
-
-		if ( bulk ) {
-
-			// Bulk operations run against the entire set
-			if ( raw ) {
-				fn.call( elems, value );
-				fn = null;
-
-			// ...except when executing function values
-			} else {
-				bulk = fn;
-				fn = function( elem, _key, value ) {
-					return bulk.call( jQuery( elem ), value );
-				};
-			}
-		}
-
-		if ( fn ) {
-			for ( ; i < len; i++ ) {
-				fn(
-					elems[ i ], key, raw ?
-						value :
-						value.call( elems[ i ], i, fn( elems[ i ], key ) )
-				);
-			}
-		}
-	}
-
-	if ( chainable ) {
-		return elems;
-	}
-
-	// Gets
-	if ( bulk ) {
-		return fn.call( elems );
-	}
-
-	return len ? fn( elems[ 0 ], key ) : emptyGet;
-};
-
-
-// Matches dashed string for camelizing
-var rmsPrefix = /^-ms-/,
-	rdashAlpha = /-([a-z])/g;
-
-// Used by camelCase as callback to replace()
-function fcamelCase( _all, letter ) {
-	return letter.toUpperCase();
-}
-
-// Convert dashed to camelCase; used by the css and data modules
-// Support: IE <=9 - 11, Edge 12 - 15
-// Microsoft forgot to hump their vendor prefix (#9572)
-function camelCase( string ) {
-	return string.replace( rmsPrefix, "ms-" ).replace( rdashAlpha, fcamelCase );
-}
-var acceptData = function( owner ) {
-
-	// Accepts only:
-	//  - Node
-	//    - Node.ELEMENT_NODE
-	//    - Node.DOCUMENT_NODE
-	//  - Object
-	//    - Any
-	return owner.nodeType === 1 || owner.nodeType === 9 || !( +owner.nodeType );
-};
-
-
-
-
-function Data() {
-	this.expando = jQuery.expando + Data.uid++;
-}
-
-Data.uid = 1;
-
-Data.prototype = {
-
-	cache: function( owner ) {
-
-		// Check if the owner object already has a cache
-		var value = owner[ this.expando ];
-
-		// If not, create one
-		if ( !value ) {
-			value = {};
-
-			// We can accept data for non-element nodes in modern browsers,
-			// but we should not, see #8335.
-			// Always return an empty object.
-			if ( acceptData( owner ) ) {
-
-				// If it is a node unlikely to be stringify-ed or looped over
-				// use plain assignment
-				if ( owner.nodeType ) {
-					owner[ this.expando ] = value;
-
-				// Otherwise secure it in a non-enumerable property
-				// configurable must be true to allow the property to be
-				// deleted when data is removed
-				} else {
-					Object.defineProperty( owner, this.expando, {
-						value: value,
-						configurable: true
-					} );
-				}
-			}
-		}
-
-		return value;
-	},
-	set: function( owner, data, value ) {
-		var prop,
-			cache = this.cache( owner );
-
-		// Handle: [ owner, key, value ] args
-		// Always use camelCase key (gh-2257)
-		if ( typeof data === "string" ) {
-			cache[ camelCase( data ) ] = value;
-
-		// Handle: [ owner, { properties } ] args
-		} else {
-
-			// Copy the properties one-by-one to the cache object
-			for ( prop in data ) {
-				cache[ camelCase( prop ) ] = data[ prop ];
-			}
-		}
-		return cache;
-	},
-	get: function( owner, key ) {
-		return key === undefined ?
-			this.cache( owner ) :
-
-			// Always use camelCase key (gh-2257)
-			owner[ this.expando ] && owner[ this.expando ][ camelCase( key ) ];
-	},
-	access: function( owner, key, value ) {
-
-		// In cases where either:
-		//
-		//   1. No key was specified
-		//   2. A string key was specified, but no value provided
-		//
-		// Take the "read" path and allow the get method to determine
-		// which value to return, respectively either:
-		//
-		//   1. The entire cache object
-		//   2. The data stored at the key
-		//
-		if ( key === undefined ||
-				( ( key && typeof key === "string" ) && value === undefined ) ) {
-
-			return this.get( owner, key );
-		}
-
-		// When the key is not a string, or both a key and value
-		// are specified, set or extend (existing objects) with either:
-		//
-		//   1. An object of properties
-		//   2. A key and value
-		//
-		this.set( owner, key, value );
-
-		// Since the "set" path can have two possible entry points
-		// return the expected data based on which path was taken[*]
-		return value !== undefined ? value : key;
-	},
-	remove: function( owner, key ) {
-		var i,
-			cache = owner[ this.expando ];
-
-		if ( cache === undefined ) {
-			return;
-		}
-
-		if ( key !== undefined ) {
-
-			// Support array or space separated string of keys
-			if ( Array.isArray( key ) ) {
-
-				// If key is an array of keys...
-				// We always set camelCase keys, so remove that.
-				key = key.map( camelCase );
-			} else {
-				key = camelCase( key );
-
-				// If a key with the spaces exists, use it.
-				// Otherwise, create an array by matching non-whitespace
-				key = key in cache ?
-					[ key ] :
-					( key.match( rnothtmlwhite ) || [] );
-			}
-
-			i = key.length;
-
-			while ( i-- ) {
-				delete cache[ key[ i ] ];
-			}
-		}
-
-		// Remove the expando if there's no more data
-		if ( key === undefined || jQuery.isEmptyObject( cache ) ) {
-
-			// Support: Chrome <=35 - 45
-			// Webkit & Blink performance suffers when deleting properties
-			// from DOM nodes, so set to undefined instead
-			// https://bugs.chromium.org/p/chromium/issues/detail?id=378607 (bug restricted)
-			if ( owner.nodeType ) {
-				owner[ this.expando ] = undefined;
-			} else {
-				delete owner[ this.expando ];
-			}
-		}
-	},
-	hasData: function( owner ) {
-		var cache = owner[ this.expando ];
-		return cache !== undefined && !jQuery.isEmptyObject( cache );
-	}
-};
-var dataPriv = new Data();
-
-var dataUser = new Data();
-
-
-
-//	Implementation Summary
-//
-//	1. Enforce API surface and semantic compatibility with 1.9.x branch
-//	2. Improve the module's maintainability by reducing the storage
-//		paths to a single mechanism.
-//	3. Use the same single mechanism to support "private" and "user" data.
-//	4. _Never_ expose "private" data to user code (TODO: Drop _data, _removeData)
-//	5. Avoid exposing implementation details on user objects (eg. expando properties)
-//	6. Provide a clear path for implementation upgrade to WeakMap in 2014
-
-var rbrace = /^(?:\{[\w\W]*\}|\[[\w\W]*\])$/,
-	rmultiDash = /[A-Z]/g;
-
-function getData( data ) {
-	if ( data === "true" ) {
-		return true;
-	}
-
-	if ( data === "false" ) {
-		return false;
-	}
-
-	if ( data === "null" ) {
-		return null;
-	}
-
-	// Only convert to a number if it doesn't change the string
-	if ( data === +data + "" ) {
-		return +data;
-	}
-
-	if ( rbrace.test( data ) ) {
-		return JSON.parse( data );
-	}
-
-	return data;
-}
-
-function dataAttr( elem, key, data ) {
-	var name;
-
-	// If nothing was found internally, try to fetch any
-	// data from the HTML5 data-* attribute
-	if ( data === undefined && elem.nodeType === 1 ) {
-		name = "data-" + key.replace( rmultiDash, "-$&" ).toLowerCase();
-		data = elem.getAttribute( name );
-
-		if ( typeof data === "string" ) {
-			try {
-				data = getData( data );
-			} catch ( e ) {}
-
-			// Make sure we set the data so it isn't changed later
-			dataUser.set( elem, key, data );
-		} else {
-			data = undefined;
-		}
-	}
-	return data;
-}
-
-jQuery.extend( {
-	hasData: function( elem ) {
-		return dataUser.hasData( elem ) || dataPriv.hasData( elem );
-	},
-
-	data: function( elem, name, data ) {
-		return dataUser.access( elem, name, data );
-	},
-
-	removeData: function( elem, name ) {
-		dataUser.remove( elem, name );
-	},
-
-	// TODO: Now that all calls to _data and _removeData have been replaced
-	// with direct calls to dataPriv methods, these can be deprecated.
-	_data: function( elem, name, data ) {
-		return dataPriv.access( elem, name, data );
-	},
-
-	_removeData: function( elem, name ) {
-		dataPriv.remove( elem, name );
-	}
-} );
-
-jQuery.fn.extend( {
-	data: function( key, value ) {
-		var i, name, data,
-			elem = this[ 0 ],
-			attrs = elem && elem.attributes;
-
-		// Gets all values
-		if ( key === undefined ) {
-			if ( this.length ) {
-				data = dataUser.get( elem );
-
-				if ( elem.nodeType === 1 && !dataPriv.get( elem, "hasDataAttrs" ) ) {
-					i = attrs.length;
-					while ( i-- ) {
-
-						// Support: IE 11 only
-						// The attrs elements can be null (#14894)
-						if ( attrs[ i ] ) {
-							name = attrs[ i ].name;
-							if ( name.indexOf( "data-" ) === 0 ) {
-								name = camelCase( name.slice( 5 ) );
-								dataAttr( elem, name, data[ name ] );
-							}
-						}
-					}
-					dataPriv.set( elem, "hasDataAttrs", true );
-				}
-			}
-
-			return data;
-		}
-
-		// Sets multiple values
-		if ( typeof key === "object" ) {
-			return this.each( function() {
-				dataUser.set( this, key );
-			} );
-		}
-
-		return access( this, function( value ) {
-			var data;
-
-			// The calling jQuery object (element matches) is not empty
-			// (and therefore has an element appears at this[ 0 ]) and the
-			// `value` parameter was not undefined. An empty jQuery object
-			// will result in `undefined` for elem = this[ 0 ] which will
-			// throw an exception if an attempt to read a data cache is made.
-			if ( elem && value === undefined ) {
-
-				// Attempt to get data from the cache
-				// The key will always be camelCased in Data
-				data = dataUser.get( elem, key );
-				if ( data !== undefined ) {
-					return data;
-				}
-
-				// Attempt to "discover" the data in
-				// HTML5 custom data-* attrs
-				data = dataAttr( elem, key );
-				if ( data !== undefined ) {
-					return data;
-				}
-
-				// We tried really hard, but the data doesn't exist.
-				return;
-			}
-
-			// Set the data...
-			this.each( function() {
-
-				// We always store the camelCased key
-				dataUser.set( this, key, value );
-			} );
-		}, null, value, arguments.length > 1, null, true );
-	},
-
-	removeData: function( key ) {
-		return this.each( function() {
-			dataUser.remove( this, key );
-		} );
-	}
-} );
-
-
-jQuery.extend( {
-	queue: function( elem, type, data ) {
-		var queue;
-
-		if ( elem ) {
-			type = ( type || "fx" ) + "queue";
-			queue = dataPriv.get( elem, type );
-
-			// Speed up dequeue by getting out quickly if this is just a lookup
-			if ( data ) {
-				if ( !queue || Array.isArray( data ) ) {
-					queue = dataPriv.access( elem, type, jQuery.makeArray( data ) );
-				} else {
-					queue.push( data );
-				}
-			}
-			return queue || [];
-		}
-	},
-
-	dequeue: function( elem, type ) {
-		type = type || "fx";
-
-		var queue = jQuery.queue( elem, type ),
-			startLength = queue.length,
-			fn = queue.shift(),
-			hooks = jQuery._queueHooks( elem, type ),
-			next = function() {
-				jQuery.dequeue( elem, type );
-			};
-
-		// If the fx queue is dequeued, always remove the progress sentinel
-		if ( fn === "inprogress" ) {
-			fn = queue.shift();
-			startLength--;
-		}
-
-		if ( fn ) {
-
-			// Add a progress sentinel to prevent the fx queue from being
-			// automatically dequeued
-			if ( type === "fx" ) {
-				queue.unshift( "inprogress" );
-			}
-
-			// Clear up the last queue stop function
-			delete hooks.stop;
-			fn.call( elem, next, hooks );
-		}
-
-		if ( !startLength && hooks ) {
-			hooks.empty.fire();
-		}
-	},
-
-	// Not public - generate a queueHooks object, or return the current one
-	_queueHooks: function( elem, type ) {
-		var key = type + "queueHooks";
-		return dataPriv.get( elem, key ) || dataPriv.access( elem, key, {
-			empty: jQuery.Callbacks( "once memory" ).add( function() {
-				dataPriv.remove( elem, [ type + "queue", key ] );
-			} )
-		} );
-	}
-} );
-
-jQuery.fn.extend( {
-	queue: function( type, data ) {
-		var setter = 2;
-
-		if ( typeof type !== "string" ) {
-			data = type;
-			type = "fx";
-			setter--;
-		}
-
-		if ( arguments.length < setter ) {
-			return jQuery.queue( this[ 0 ], type );
-		}
-
-		return data === undefined ?
-			this :
-			this.each( function() {
-				var queue = jQuery.queue( this, type, data );
-
-				// Ensure a hooks for this queue
-				jQuery._queueHooks( this, type );
-
-				if ( type === "fx" && queue[ 0 ] !== "inprogress" ) {
-					jQuery.dequeue( this, type );
-				}
-			} );
-	},
-	dequeue: function( type ) {
-		return this.each( function() {
-			jQuery.dequeue( this, type );
-		} );
-	},
-	clearQueue: function( type ) {
-		return this.queue( type || "fx", [] );
-	},
-
-	// Get a promise resolved when queues of a certain type
-	// are emptied (fx is the type by default)
-	promise: function( type, obj ) {
-		var tmp,
-			count = 1,
-			defer = jQuery.Deferred(),
-			elements = this,
-			i = this.length,
-			resolve = function() {
-				if ( !( --count ) ) {
-					defer.resolveWith( elements, [ elements ] );
-				}
-			};
-
-		if ( typeof type !== "string" ) {
-			obj = type;
-			type = undefined;
-		}
-		type = type || "fx";
-
-		while ( i-- ) {
-			tmp = dataPriv.get( elements[ i ], type + "queueHooks" );
-			if ( tmp && tmp.empty ) {
-				count++;
-				tmp.empty.add( resolve );
-			}
-		}
-		resolve();
-		return defer.promise( obj );
-	}
-} );
-var pnum = ( /[+-]?(?:\d*\.|)\d+(?:[eE][+-]?\d+|)/ ).source;
-
-var rcssNum = new RegExp( "^(?:([+-])=|)(" + pnum + ")([a-z%]*)$", "i" );
-
-
-var cssExpand = [ "Top", "Right", "Bottom", "Left" ];
-
-var documentElement = document.documentElement;
-
-
-
-	var isAttached = function( elem ) {
-			return jQuery.contains( elem.ownerDocument, elem );
-		},
-		composed = { composed: true };
-
-	// Support: IE 9 - 11+, Edge 12 - 18+, iOS 10.0 - 10.2 only
-	// Check attachment across shadow DOM boundaries when possible (gh-3504)
-	// Support: iOS 10.0-10.2 only
-	// Early iOS 10 versions support `attachShadow` but not `getRootNode`,
-	// leading to errors. We need to check for `getRootNode`.
-	if ( documentElement.getRootNode ) {
-		isAttached = function( elem ) {
-			return jQuery.contains( elem.ownerDocument, elem ) ||
-				elem.getRootNode( composed ) === elem.ownerDocument;
-		};
-	}
-var isHiddenWithinTree = function( elem, el ) {
-
-		// isHiddenWithinTree might be called from jQuery#filter function;
-		// in that case, element will be second argument
-		elem = el || elem;
-
-		// Inline style trumps all
-		return elem.style.display === "none" ||
-			elem.style.display === "" &&
-
-			// Otherwise, check computed style
-			// Support: Firefox <=43 - 45
-			// Disconnected elements can have computed display: none, so first confirm that elem is
-			// in the document.
-			isAttached( elem ) &&
-
-			jQuery.css( elem, "display" ) === "none";
-	};
-
-
-
-function adjustCSS( elem, prop, valueParts, tween ) {
-	var adjusted, scale,
-		maxIterations = 20,
-		currentValue = tween ?
-			function() {
-				return tween.cur();
-			} :
-			function() {
-				return jQuery.css( elem, prop, "" );
-			},
-		initial = currentValue(),
-		unit = valueParts && valueParts[ 3 ] || ( jQuery.cssNumber[ prop ] ? "" : "px" ),
-
-		// Starting value computation is required for potential unit mismatches
-		initialInUnit = elem.nodeType &&
-			( jQuery.cssNumber[ prop ] || unit !== "px" && +initial ) &&
-			rcssNum.exec( jQuery.css( elem, prop ) );
-
-	if ( initialInUnit && initialInUnit[ 3 ] !== unit ) {
-
-		// Support: Firefox <=54
-		// Halve the iteration target value to prevent interference from CSS upper bounds (gh-2144)
-		initial = initial / 2;
-
-		// Trust units reported by jQuery.css
-		unit = unit || initialInUnit[ 3 ];
-
-		// Iteratively approximate from a nonzero starting point
-		initialInUnit = +initial || 1;
-
-		while ( maxIterations-- ) {
-
-			// Evaluate and update our best guess (doubling guesses that zero out).
-			// Finish if the scale equals or crosses 1 (making the old*new product non-positive).
-			jQuery.style( elem, prop, initialInUnit + unit );
-			if ( ( 1 - scale ) * ( 1 - ( scale = currentValue() / initial || 0.5 ) ) <= 0 ) {
-				maxIterations = 0;
-			}
-			initialInUnit = initialInUnit / scale;
-
-		}
-
-		initialInUnit = initialInUnit * 2;
-		jQuery.style( elem, prop, initialInUnit + unit );
-
-		// Make sure we update the tween properties later on
-		valueParts = valueParts || [];
-	}
-
-	if ( valueParts ) {
-		initialInUnit = +initialInUnit || +initial || 0;
-
-		// Apply relative offset (+=/-=) if specified
-		adjusted = valueParts[ 1 ] ?
-			initialInUnit + ( valueParts[ 1 ] + 1 ) * valueParts[ 2 ] :
-			+valueParts[ 2 ];
-		if ( tween ) {
-			tween.unit = unit;
-			tween.start = initialInUnit;
-			tween.end = adjusted;
-		}
-	}
-	return adjusted;
-}
-
-
-var defaultDisplayMap = {};
-
-function getDefaultDisplay( elem ) {
-	var temp,
-		doc = elem.ownerDocument,
-		nodeName = elem.nodeName,
-		display = defaultDisplayMap[ nodeName ];
-
-	if ( display ) {
-		return display;
-	}
-
-	temp = doc.body.appendChild( doc.createElement( nodeName ) );
-	display = jQuery.css( temp, "display" );
-
-	temp.parentNode.removeChild( temp );
-
-	if ( display === "none" ) {
-		display = "block";
-	}
-	defaultDisplayMap[ nodeName ] = display;
-
-	return display;
-}
-
-function showHide( elements, show ) {
-	var display, elem,
-		values = [],
-		index = 0,
-		length = elements.length;
-
-	// Determine new display value for elements that need to change
-	for ( ; index < length; index++ ) {
-		elem = elements[ index ];
-		if ( !elem.style ) {
-			continue;
-		}
-
-		display = elem.style.display;
-		if ( show ) {
-
-			// Since we force visibility upon cascade-hidden elements, an immediate (and slow)
-			// check is required in this first loop unless we have a nonempty display value (either
-			// inline or about-to-be-restored)
-			if ( display === "none" ) {
-				values[ index ] = dataPriv.get( elem, "display" ) || null;
-				if ( !values[ index ] ) {
-					elem.style.display = "";
-				}
-			}
-			if ( elem.style.display === "" && isHiddenWithinTree( elem ) ) {
-				values[ index ] = getDefaultDisplay( elem );
-			}
-		} else {
-			if ( display !== "none" ) {
-				values[ index ] = "none";
-
-				// Remember what we're overwriting
-				dataPriv.set( elem, "display", display );
-			}
-		}
-	}
-
-	// Set the display of the elements in a second loop to avoid constant reflow
-	for ( index = 0; index < length; index++ ) {
-		if ( values[ index ] != null ) {
-			elements[ index ].style.display = values[ index ];
-		}
-	}
-
-	return elements;
-}
-
-jQuery.fn.extend( {
-	show: function() {
-		return showHide( this, true );
-	},
-	hide: function() {
-		return showHide( this );
-	},
-	toggle: function( state ) {
-		if ( typeof state === "boolean" ) {
-			return state ? this.show() : this.hide();
-		}
-
-		return this.each( function() {
-			if ( isHiddenWithinTree( this ) ) {
-				jQuery( this ).show();
-			} else {
-				jQuery( this ).hide();
-			}
-		} );
-	}
-} );
-var rcheckableType = ( /^(?:checkbox|radio)$/i );
-
-var rtagName = ( /<([a-z][^\/\0>\x20\t\r\n\f]*)/i );
-
-var rscriptType = ( /^$|^module$|\/(?:java|ecma)script/i );
-
-
-
-( function() {
-	var fragment = document.createDocumentFragment(),
-		div = fragment.appendChild( document.createElement( "div" ) ),
-		input = document.createElement( "input" );
-
-	// Support: Android 4.0 - 4.3 only
-	// Check state lost if the name is set (#11217)
-	// Support: Windows Web Apps (WWA)
-	// `name` and `type` must use .setAttribute for WWA (#14901)
-	input.setAttribute( "type", "radio" );
-	input.setAttribute( "checked", "checked" );
-	input.setAttribute( "name", "t" );
-
-	div.appendChild( input );
-
-	// Support: Android <=4.1 only
-	// Older WebKit doesn't clone checked state correctly in fragments
-	support.checkClone = div.cloneNode( true ).cloneNode( true ).lastChild.checked;
-
-	// Support: IE <=11 only
-	// Make sure textarea (and checkbox) defaultValue is properly cloned
-	div.innerHTML = "";
-	support.noCloneChecked = !!div.cloneNode( true ).lastChild.defaultValue;
-
-	// Support: IE <=9 only
-	// IE <=9 replaces ";
-	support.option = !!div.lastChild;
-} )();
-
-
-// We have to close these tags to support XHTML (#13200)
-var wrapMap = {
-
-	// XHTML parsers do not magically insert elements in the
-	// same way that tag soup parsers do. So we cannot shorten
-	// this by omitting  or other required elements.
-	thead: [ 1, "", "
          " ],
-	col: [ 2, "", "
          " ],
-	tr: [ 2, "", "
          " ],
-	td: [ 3, "", "
          " ],
-
-	_default: [ 0, "", "" ]
-};
-
-wrapMap.tbody = wrapMap.tfoot = wrapMap.colgroup = wrapMap.caption = wrapMap.thead;
-wrapMap.th = wrapMap.td;
-
-// Support: IE <=9 only
-if ( !support.option ) {
-	wrapMap.optgroup = wrapMap.option = [ 1, "" ];
-}
-
-
-function getAll( context, tag ) {
-
-	// Support: IE <=9 - 11 only
-	// Use typeof to avoid zero-argument method invocation on host objects (#15151)
-	var ret;
-
-	if ( typeof context.getElementsByTagName !== "undefined" ) {
-		ret = context.getElementsByTagName( tag || "*" );
-
-	} else if ( typeof context.querySelectorAll !== "undefined" ) {
-		ret = context.querySelectorAll( tag || "*" );
-
-	} else {
-		ret = [];
-	}
-
-	if ( tag === undefined || tag && nodeName( context, tag ) ) {
-		return jQuery.merge( [ context ], ret );
-	}
-
-	return ret;
-}
-
-
-// Mark scripts as having already been evaluated
-function setGlobalEval( elems, refElements ) {
-	var i = 0,
-		l = elems.length;
-
-	for ( ; i < l; i++ ) {
-		dataPriv.set(
-			elems[ i ],
-			"globalEval",
-			!refElements || dataPriv.get( refElements[ i ], "globalEval" )
-		);
-	}
-}
-
-
-var rhtml = /<|&#?\w+;/;
-
-function buildFragment( elems, context, scripts, selection, ignored ) {
-	var elem, tmp, tag, wrap, attached, j,
-		fragment = context.createDocumentFragment(),
-		nodes = [],
-		i = 0,
-		l = elems.length;
-
-	for ( ; i < l; i++ ) {
-		elem = elems[ i ];
-
-		if ( elem || elem === 0 ) {
-
-			// Add nodes directly
-			if ( toType( elem ) === "object" ) {
-
-				// Support: Android <=4.0 only, PhantomJS 1 only
-				// push.apply(_, arraylike) throws on ancient WebKit
-				jQuery.merge( nodes, elem.nodeType ? [ elem ] : elem );
-
-			// Convert non-html into a text node
-			} else if ( !rhtml.test( elem ) ) {
-				nodes.push( context.createTextNode( elem ) );
-
-			// Convert html into DOM nodes
-			} else {
-				tmp = tmp || fragment.appendChild( context.createElement( "div" ) );
-
-				// Deserialize a standard representation
-				tag = ( rtagName.exec( elem ) || [ "", "" ] )[ 1 ].toLowerCase();
-				wrap = wrapMap[ tag ] || wrapMap._default;
-				tmp.innerHTML = wrap[ 1 ] + jQuery.htmlPrefilter( elem ) + wrap[ 2 ];
-
-				// Descend through wrappers to the right content
-				j = wrap[ 0 ];
-				while ( j-- ) {
-					tmp = tmp.lastChild;
-				}
-
-				// Support: Android <=4.0 only, PhantomJS 1 only
-				// push.apply(_, arraylike) throws on ancient WebKit
-				jQuery.merge( nodes, tmp.childNodes );
-
-				// Remember the top-level container
-				tmp = fragment.firstChild;
-
-				// Ensure the created nodes are orphaned (#12392)
-				tmp.textContent = "";
-			}
-		}
-	}
-
-	// Remove wrapper from fragment
-	fragment.textContent = "";
-
-	i = 0;
-	while ( ( elem = nodes[ i++ ] ) ) {
-
-		// Skip elements already in the context collection (trac-4087)
-		if ( selection && jQuery.inArray( elem, selection ) > -1 ) {
-			if ( ignored ) {
-				ignored.push( elem );
-			}
-			continue;
-		}
-
-		attached = isAttached( elem );
-
-		// Append to fragment
-		tmp = getAll( fragment.appendChild( elem ), "script" );
-
-		// Preserve script evaluation history
-		if ( attached ) {
-			setGlobalEval( tmp );
-		}
-
-		// Capture executables
-		if ( scripts ) {
-			j = 0;
-			while ( ( elem = tmp[ j++ ] ) ) {
-				if ( rscriptType.test( elem.type || "" ) ) {
-					scripts.push( elem );
-				}
-			}
-		}
-	}
-
-	return fragment;
-}
-
-
-var rtypenamespace = /^([^.]*)(?:\.(.+)|)/;
-
-function returnTrue() {
-	return true;
-}
-
-function returnFalse() {
-	return false;
-}
-
-// Support: IE <=9 - 11+
-// focus() and blur() are asynchronous, except when they are no-op.
-// So expect focus to be synchronous when the element is already active,
-// and blur to be synchronous when the element is not already active.
-// (focus and blur are always synchronous in other supported browsers,
-// this just defines when we can count on it).
-function expectSync( elem, type ) {
-	return ( elem === safeActiveElement() ) === ( type === "focus" );
-}
-
-// Support: IE <=9 only
-// Accessing document.activeElement can throw unexpectedly
-// https://bugs.jquery.com/ticket/13393
-function safeActiveElement() {
-	try {
-		return document.activeElement;
-	} catch ( err ) { }
-}
-
-function on( elem, types, selector, data, fn, one ) {
-	var origFn, type;
-
-	// Types can be a map of types/handlers
-	if ( typeof types === "object" ) {
-
-		// ( types-Object, selector, data )
-		if ( typeof selector !== "string" ) {
-
-			// ( types-Object, data )
-			data = data || selector;
-			selector = undefined;
-		}
-		for ( type in types ) {
-			on( elem, type, selector, data, types[ type ], one );
-		}
-		return elem;
-	}
-
-	if ( data == null && fn == null ) {
-
-		// ( types, fn )
-		fn = selector;
-		data = selector = undefined;
-	} else if ( fn == null ) {
-		if ( typeof selector === "string" ) {
-
-			// ( types, selector, fn )
-			fn = data;
-			data = undefined;
-		} else {
-
-			// ( types, data, fn )
-			fn = data;
-			data = selector;
-			selector = undefined;
-		}
-	}
-	if ( fn === false ) {
-		fn = returnFalse;
-	} else if ( !fn ) {
-		return elem;
-	}
-
-	if ( one === 1 ) {
-		origFn = fn;
-		fn = function( event ) {
-
-			// Can use an empty set, since event contains the info
-			jQuery().off( event );
-			return origFn.apply( this, arguments );
-		};
-
-		// Use same guid so caller can remove using origFn
-		fn.guid = origFn.guid || ( origFn.guid = jQuery.guid++ );
-	}
-	return elem.each( function() {
-		jQuery.event.add( this, types, fn, data, selector );
-	} );
-}
-
-/*
- * Helper functions for managing events -- not part of the public interface.
- * Props to Dean Edwards' addEvent library for many of the ideas.
- */
-jQuery.event = {
-
-	global: {},
-
-	add: function( elem, types, handler, data, selector ) {
-
-		var handleObjIn, eventHandle, tmp,
-			events, t, handleObj,
-			special, handlers, type, namespaces, origType,
-			elemData = dataPriv.get( elem );
-
-		// Only attach events to objects that accept data
-		if ( !acceptData( elem ) ) {
-			return;
-		}
-
-		// Caller can pass in an object of custom data in lieu of the handler
-		if ( handler.handler ) {
-			handleObjIn = handler;
-			handler = handleObjIn.handler;
-			selector = handleObjIn.selector;
-		}
-
-		// Ensure that invalid selectors throw exceptions at attach time
-		// Evaluate against documentElement in case elem is a non-element node (e.g., document)
-		if ( selector ) {
-			jQuery.find.matchesSelector( documentElement, selector );
-		}
-
-		// Make sure that the handler has a unique ID, used to find/remove it later
-		if ( !handler.guid ) {
-			handler.guid = jQuery.guid++;
-		}
-
-		// Init the element's event structure and main handler, if this is the first
-		if ( !( events = elemData.events ) ) {
-			events = elemData.events = Object.create( null );
-		}
-		if ( !( eventHandle = elemData.handle ) ) {
-			eventHandle = elemData.handle = function( e ) {
-
-				// Discard the second event of a jQuery.event.trigger() and
-				// when an event is called after a page has unloaded
-				return typeof jQuery !== "undefined" && jQuery.event.triggered !== e.type ?
-					jQuery.event.dispatch.apply( elem, arguments ) : undefined;
-			};
-		}
-
-		// Handle multiple events separated by a space
-		types = ( types || "" ).match( rnothtmlwhite ) || [ "" ];
-		t = types.length;
-		while ( t-- ) {
-			tmp = rtypenamespace.exec( types[ t ] ) || [];
-			type = origType = tmp[ 1 ];
-			namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort();
-
-			// There *must* be a type, no attaching namespace-only handlers
-			if ( !type ) {
-				continue;
-			}
-
-			// If event changes its type, use the special event handlers for the changed type
-			special = jQuery.event.special[ type ] || {};
-
-			// If selector defined, determine special event api type, otherwise given type
-			type = ( selector ? special.delegateType : special.bindType ) || type;
-
-			// Update special based on newly reset type
-			special = jQuery.event.special[ type ] || {};
-
-			// handleObj is passed to all event handlers
-			handleObj = jQuery.extend( {
-				type: type,
-				origType: origType,
-				data: data,
-				handler: handler,
-				guid: handler.guid,
-				selector: selector,
-				needsContext: selector && jQuery.expr.match.needsContext.test( selector ),
-				namespace: namespaces.join( "." )
-			}, handleObjIn );
-
-			// Init the event handler queue if we're the first
-			if ( !( handlers = events[ type ] ) ) {
-				handlers = events[ type ] = [];
-				handlers.delegateCount = 0;
-
-				// Only use addEventListener if the special events handler returns false
-				if ( !special.setup ||
-					special.setup.call( elem, data, namespaces, eventHandle ) === false ) {
-
-					if ( elem.addEventListener ) {
-						elem.addEventListener( type, eventHandle );
-					}
-				}
-			}
-
-			if ( special.add ) {
-				special.add.call( elem, handleObj );
-
-				if ( !handleObj.handler.guid ) {
-					handleObj.handler.guid = handler.guid;
-				}
-			}
-
-			// Add to the element's handler list, delegates in front
-			if ( selector ) {
-				handlers.splice( handlers.delegateCount++, 0, handleObj );
-			} else {
-				handlers.push( handleObj );
-			}
-
-			// Keep track of which events have ever been used, for event optimization
-			jQuery.event.global[ type ] = true;
-		}
-
-	},
-
-	// Detach an event or set of events from an element
-	remove: function( elem, types, handler, selector, mappedTypes ) {
-
-		var j, origCount, tmp,
-			events, t, handleObj,
-			special, handlers, type, namespaces, origType,
-			elemData = dataPriv.hasData( elem ) && dataPriv.get( elem );
-
-		if ( !elemData || !( events = elemData.events ) ) {
-			return;
-		}
-
-		// Once for each type.namespace in types; type may be omitted
-		types = ( types || "" ).match( rnothtmlwhite ) || [ "" ];
-		t = types.length;
-		while ( t-- ) {
-			tmp = rtypenamespace.exec( types[ t ] ) || [];
-			type = origType = tmp[ 1 ];
-			namespaces = ( tmp[ 2 ] || "" ).split( "." ).sort();
-
-			// Unbind all events (on this namespace, if provided) for the element
-			if ( !type ) {
-				for ( type in events ) {
-					jQuery.event.remove( elem, type + types[ t ], handler, selector, true );
-				}
-				continue;
-			}
-
-			special = jQuery.event.special[ type ] || {};
-			type = ( selector ? special.delegateType : special.bindType ) || type;
-			handlers = events[ type ] || [];
-			tmp = tmp[ 2 ] &&
-				new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" );
-
-			// Remove matching events
-			origCount = j = handlers.length;
-			while ( j-- ) {
-				handleObj = handlers[ j ];
-
-				if ( ( mappedTypes || origType === handleObj.origType ) &&
-					( !handler || handler.guid === handleObj.guid ) &&
-					( !tmp || tmp.test( handleObj.namespace ) ) &&
-					( !selector || selector === handleObj.selector ||
-						selector === "**" && handleObj.selector ) ) {
-					handlers.splice( j, 1 );
-
-					if ( handleObj.selector ) {
-						handlers.delegateCount--;
-					}
-					if ( special.remove ) {
-						special.remove.call( elem, handleObj );
-					}
-				}
-			}
-
-			// Remove generic event handler if we removed something and no more handlers exist
-			// (avoids potential for endless recursion during removal of special event handlers)
-			if ( origCount && !handlers.length ) {
-				if ( !special.teardown ||
-					special.teardown.call( elem, namespaces, elemData.handle ) === false ) {
-
-					jQuery.removeEvent( elem, type, elemData.handle );
-				}
-
-				delete events[ type ];
-			}
-		}
-
-		// Remove data and the expando if it's no longer used
-		if ( jQuery.isEmptyObject( events ) ) {
-			dataPriv.remove( elem, "handle events" );
-		}
-	},
-
-	dispatch: function( nativeEvent ) {
-
-		var i, j, ret, matched, handleObj, handlerQueue,
-			args = new Array( arguments.length ),
-
-			// Make a writable jQuery.Event from the native event object
-			event = jQuery.event.fix( nativeEvent ),
-
-			handlers = (
-				dataPriv.get( this, "events" ) || Object.create( null )
-			)[ event.type ] || [],
-			special = jQuery.event.special[ event.type ] || {};
-
-		// Use the fix-ed jQuery.Event rather than the (read-only) native event
-		args[ 0 ] = event;
-
-		for ( i = 1; i < arguments.length; i++ ) {
-			args[ i ] = arguments[ i ];
-		}
-
-		event.delegateTarget = this;
-
-		// Call the preDispatch hook for the mapped type, and let it bail if desired
-		if ( special.preDispatch && special.preDispatch.call( this, event ) === false ) {
-			return;
-		}
-
-		// Determine handlers
-		handlerQueue = jQuery.event.handlers.call( this, event, handlers );
-
-		// Run delegates first; they may want to stop propagation beneath us
-		i = 0;
-		while ( ( matched = handlerQueue[ i++ ] ) && !event.isPropagationStopped() ) {
-			event.currentTarget = matched.elem;
-
-			j = 0;
-			while ( ( handleObj = matched.handlers[ j++ ] ) &&
-				!event.isImmediatePropagationStopped() ) {
-
-				// If the event is namespaced, then each handler is only invoked if it is
-				// specially universal or its namespaces are a superset of the event's.
-				if ( !event.rnamespace || handleObj.namespace === false ||
-					event.rnamespace.test( handleObj.namespace ) ) {
-
-					event.handleObj = handleObj;
-					event.data = handleObj.data;
-
-					ret = ( ( jQuery.event.special[ handleObj.origType ] || {} ).handle ||
-						handleObj.handler ).apply( matched.elem, args );
-
-					if ( ret !== undefined ) {
-						if ( ( event.result = ret ) === false ) {
-							event.preventDefault();
-							event.stopPropagation();
-						}
-					}
-				}
-			}
-		}
-
-		// Call the postDispatch hook for the mapped type
-		if ( special.postDispatch ) {
-			special.postDispatch.call( this, event );
-		}
-
-		return event.result;
-	},
-
-	handlers: function( event, handlers ) {
-		var i, handleObj, sel, matchedHandlers, matchedSelectors,
-			handlerQueue = [],
-			delegateCount = handlers.delegateCount,
-			cur = event.target;
-
-		// Find delegate handlers
-		if ( delegateCount &&
-
-			// Support: IE <=9
-			// Black-hole SVG  instance trees (trac-13180)
-			cur.nodeType &&
-
-			// Support: Firefox <=42
-			// Suppress spec-violating clicks indicating a non-primary pointer button (trac-3861)
-			// https://www.w3.org/TR/DOM-Level-3-Events/#event-type-click
-			// Support: IE 11 only
-			// ...but not arrow key "clicks" of radio inputs, which can have `button` -1 (gh-2343)
-			!( event.type === "click" && event.button >= 1 ) ) {
-
-			for ( ; cur !== this; cur = cur.parentNode || this ) {
-
-				// Don't check non-elements (#13208)
-				// Don't process clicks on disabled elements (#6911, #8165, #11382, #11764)
-				if ( cur.nodeType === 1 && !( event.type === "click" && cur.disabled === true ) ) {
-					matchedHandlers = [];
-					matchedSelectors = {};
-					for ( i = 0; i < delegateCount; i++ ) {
-						handleObj = handlers[ i ];
-
-						// Don't conflict with Object.prototype properties (#13203)
-						sel = handleObj.selector + " ";
-
-						if ( matchedSelectors[ sel ] === undefined ) {
-							matchedSelectors[ sel ] = handleObj.needsContext ?
-								jQuery( sel, this ).index( cur ) > -1 :
-								jQuery.find( sel, this, null, [ cur ] ).length;
-						}
-						if ( matchedSelectors[ sel ] ) {
-							matchedHandlers.push( handleObj );
-						}
-					}
-					if ( matchedHandlers.length ) {
-						handlerQueue.push( { elem: cur, handlers: matchedHandlers } );
-					}
-				}
-			}
-		}
-
-		// Add the remaining (directly-bound) handlers
-		cur = this;
-		if ( delegateCount < handlers.length ) {
-			handlerQueue.push( { elem: cur, handlers: handlers.slice( delegateCount ) } );
-		}
-
-		return handlerQueue;
-	},
-
-	addProp: function( name, hook ) {
-		Object.defineProperty( jQuery.Event.prototype, name, {
-			enumerable: true,
-			configurable: true,
-
-			get: isFunction( hook ) ?
-				function() {
-					if ( this.originalEvent ) {
-						return hook( this.originalEvent );
-					}
-				} :
-				function() {
-					if ( this.originalEvent ) {
-						return this.originalEvent[ name ];
-					}
-				},
-
-			set: function( value ) {
-				Object.defineProperty( this, name, {
-					enumerable: true,
-					configurable: true,
-					writable: true,
-					value: value
-				} );
-			}
-		} );
-	},
-
-	fix: function( originalEvent ) {
-		return originalEvent[ jQuery.expando ] ?
-			originalEvent :
-			new jQuery.Event( originalEvent );
-	},
-
-	special: {
-		load: {
-
-			// Prevent triggered image.load events from bubbling to window.load
-			noBubble: true
-		},
-		click: {
-
-			// Utilize native event to ensure correct state for checkable inputs
-			setup: function( data ) {
-
-				// For mutual compressibility with _default, replace `this` access with a local var.
-				// `|| data` is dead code meant only to preserve the variable through minification.
-				var el = this || data;
-
-				// Claim the first handler
-				if ( rcheckableType.test( el.type ) &&
-					el.click && nodeName( el, "input" ) ) {
-
-					// dataPriv.set( el, "click", ... )
-					leverageNative( el, "click", returnTrue );
-				}
-
-				// Return false to allow normal processing in the caller
-				return false;
-			},
-			trigger: function( data ) {
-
-				// For mutual compressibility with _default, replace `this` access with a local var.
-				// `|| data` is dead code meant only to preserve the variable through minification.
-				var el = this || data;
-
-				// Force setup before triggering a click
-				if ( rcheckableType.test( el.type ) &&
-					el.click && nodeName( el, "input" ) ) {
-
-					leverageNative( el, "click" );
-				}
-
-				// Return non-false to allow normal event-path propagation
-				return true;
-			},
-
-			// For cross-browser consistency, suppress native .click() on links
-			// Also prevent it if we're currently inside a leveraged native-event stack
-			_default: function( event ) {
-				var target = event.target;
-				return rcheckableType.test( target.type ) &&
-					target.click && nodeName( target, "input" ) &&
-					dataPriv.get( target, "click" ) ||
-					nodeName( target, "a" );
-			}
-		},
-
-		beforeunload: {
-			postDispatch: function( event ) {
-
-				// Support: Firefox 20+
-				// Firefox doesn't alert if the returnValue field is not set.
-				if ( event.result !== undefined && event.originalEvent ) {
-					event.originalEvent.returnValue = event.result;
-				}
-			}
-		}
-	}
-};
-
-// Ensure the presence of an event listener that handles manually-triggered
-// synthetic events by interrupting progress until reinvoked in response to
-// *native* events that it fires directly, ensuring that state changes have
-// already occurred before other listeners are invoked.
-function leverageNative( el, type, expectSync ) {
-
-	// Missing expectSync indicates a trigger call, which must force setup through jQuery.event.add
-	if ( !expectSync ) {
-		if ( dataPriv.get( el, type ) === undefined ) {
-			jQuery.event.add( el, type, returnTrue );
-		}
-		return;
-	}
-
-	// Register the controller as a special universal handler for all event namespaces
-	dataPriv.set( el, type, false );
-	jQuery.event.add( el, type, {
-		namespace: false,
-		handler: function( event ) {
-			var notAsync, result,
-				saved = dataPriv.get( this, type );
-
-			if ( ( event.isTrigger & 1 ) && this[ type ] ) {
-
-				// Interrupt processing of the outer synthetic .trigger()ed event
-				// Saved data should be false in such cases, but might be a leftover capture object
-				// from an async native handler (gh-4350)
-				if ( !saved.length ) {
-
-					// Store arguments for use when handling the inner native event
-					// There will always be at least one argument (an event object), so this array
-					// will not be confused with a leftover capture object.
-					saved = slice.call( arguments );
-					dataPriv.set( this, type, saved );
-
-					// Trigger the native event and capture its result
-					// Support: IE <=9 - 11+
-					// focus() and blur() are asynchronous
-					notAsync = expectSync( this, type );
-					this[ type ]();
-					result = dataPriv.get( this, type );
-					if ( saved !== result || notAsync ) {
-						dataPriv.set( this, type, false );
-					} else {
-						result = {};
-					}
-					if ( saved !== result ) {
-
-						// Cancel the outer synthetic event
-						event.stopImmediatePropagation();
-						event.preventDefault();
-
-						// Support: Chrome 86+
-						// In Chrome, if an element having a focusout handler is blurred by
-						// clicking outside of it, it invokes the handler synchronously. If
-						// that handler calls `.remove()` on the element, the data is cleared,
-						// leaving `result` undefined. We need to guard against this.
-						return result && result.value;
-					}
-
-				// If this is an inner synthetic event for an event with a bubbling surrogate
-				// (focus or blur), assume that the surrogate already propagated from triggering the
-				// native event and prevent that from happening again here.
-				// This technically gets the ordering wrong w.r.t. to `.trigger()` (in which the
-				// bubbling surrogate propagates *after* the non-bubbling base), but that seems
-				// less bad than duplication.
-				} else if ( ( jQuery.event.special[ type ] || {} ).delegateType ) {
-					event.stopPropagation();
-				}
-
-			// If this is a native event triggered above, everything is now in order
-			// Fire an inner synthetic event with the original arguments
-			} else if ( saved.length ) {
-
-				// ...and capture the result
-				dataPriv.set( this, type, {
-					value: jQuery.event.trigger(
-
-						// Support: IE <=9 - 11+
-						// Extend with the prototype to reset the above stopImmediatePropagation()
-						jQuery.extend( saved[ 0 ], jQuery.Event.prototype ),
-						saved.slice( 1 ),
-						this
-					)
-				} );
-
-				// Abort handling of the native event
-				event.stopImmediatePropagation();
-			}
-		}
-	} );
-}
-
-jQuery.removeEvent = function( elem, type, handle ) {
-
-	// This "if" is needed for plain objects
-	if ( elem.removeEventListener ) {
-		elem.removeEventListener( type, handle );
-	}
-};
-
-jQuery.Event = function( src, props ) {
-
-	// Allow instantiation without the 'new' keyword
-	if ( !( this instanceof jQuery.Event ) ) {
-		return new jQuery.Event( src, props );
-	}
-
-	// Event object
-	if ( src && src.type ) {
-		this.originalEvent = src;
-		this.type = src.type;
-
-		// Events bubbling up the document may have been marked as prevented
-		// by a handler lower down the tree; reflect the correct value.
-		this.isDefaultPrevented = src.defaultPrevented ||
-				src.defaultPrevented === undefined &&
-
-				// Support: Android <=2.3 only
-				src.returnValue === false ?
-			returnTrue :
-			returnFalse;
-
-		// Create target properties
-		// Support: Safari <=6 - 7 only
-		// Target should not be a text node (#504, #13143)
-		this.target = ( src.target && src.target.nodeType === 3 ) ?
-			src.target.parentNode :
-			src.target;
-
-		this.currentTarget = src.currentTarget;
-		this.relatedTarget = src.relatedTarget;
-
-	// Event type
-	} else {
-		this.type = src;
-	}
-
-	// Put explicitly provided properties onto the event object
-	if ( props ) {
-		jQuery.extend( this, props );
-	}
-
-	// Create a timestamp if incoming event doesn't have one
-	this.timeStamp = src && src.timeStamp || Date.now();
-
-	// Mark it as fixed
-	this[ jQuery.expando ] = true;
-};
-
-// jQuery.Event is based on DOM3 Events as specified by the ECMAScript Language Binding
-// https://www.w3.org/TR/2003/WD-DOM-Level-3-Events-20030331/ecma-script-binding.html
-jQuery.Event.prototype = {
-	constructor: jQuery.Event,
-	isDefaultPrevented: returnFalse,
-	isPropagationStopped: returnFalse,
-	isImmediatePropagationStopped: returnFalse,
-	isSimulated: false,
-
-	preventDefault: function() {
-		var e = this.originalEvent;
-
-		this.isDefaultPrevented = returnTrue;
-
-		if ( e && !this.isSimulated ) {
-			e.preventDefault();
-		}
-	},
-	stopPropagation: function() {
-		var e = this.originalEvent;
-
-		this.isPropagationStopped = returnTrue;
-
-		if ( e && !this.isSimulated ) {
-			e.stopPropagation();
-		}
-	},
-	stopImmediatePropagation: function() {
-		var e = this.originalEvent;
-
-		this.isImmediatePropagationStopped = returnTrue;
-
-		if ( e && !this.isSimulated ) {
-			e.stopImmediatePropagation();
-		}
-
-		this.stopPropagation();
-	}
-};
-
-// Includes all common event props including KeyEvent and MouseEvent specific props
-jQuery.each( {
-	altKey: true,
-	bubbles: true,
-	cancelable: true,
-	changedTouches: true,
-	ctrlKey: true,
-	detail: true,
-	eventPhase: true,
-	metaKey: true,
-	pageX: true,
-	pageY: true,
-	shiftKey: true,
-	view: true,
-	"char": true,
-	code: true,
-	charCode: true,
-	key: true,
-	keyCode: true,
-	button: true,
-	buttons: true,
-	clientX: true,
-	clientY: true,
-	offsetX: true,
-	offsetY: true,
-	pointerId: true,
-	pointerType: true,
-	screenX: true,
-	screenY: true,
-	targetTouches: true,
-	toElement: true,
-	touches: true,
-	which: true
-}, jQuery.event.addProp );
-
-jQuery.each( { focus: "focusin", blur: "focusout" }, function( type, delegateType ) {
-	jQuery.event.special[ type ] = {
-
-		// Utilize native event if possible so blur/focus sequence is correct
-		setup: function() {
-
-			// Claim the first handler
-			// dataPriv.set( this, "focus", ... )
-			// dataPriv.set( this, "blur", ... )
-			leverageNative( this, type, expectSync );
-
-			// Return false to allow normal processing in the caller
-			return false;
-		},
-		trigger: function() {
-
-			// Force setup before trigger
-			leverageNative( this, type );
-
-			// Return non-false to allow normal event-path propagation
-			return true;
-		},
-
-		// Suppress native focus or blur as it's already being fired
-		// in leverageNative.
-		_default: function() {
-			return true;
-		},
-
-		delegateType: delegateType
-	};
-} );
-
-// Create mouseenter/leave events using mouseover/out and event-time checks
-// so that event delegation works in jQuery.
-// Do the same for pointerenter/pointerleave and pointerover/pointerout
-//
-// Support: Safari 7 only
-// Safari sends mouseenter too often; see:
-// https://bugs.chromium.org/p/chromium/issues/detail?id=470258
-// for the description of the bug (it existed in older Chrome versions as well).
-jQuery.each( {
-	mouseenter: "mouseover",
-	mouseleave: "mouseout",
-	pointerenter: "pointerover",
-	pointerleave: "pointerout"
-}, function( orig, fix ) {
-	jQuery.event.special[ orig ] = {
-		delegateType: fix,
-		bindType: fix,
-
-		handle: function( event ) {
-			var ret,
-				target = this,
-				related = event.relatedTarget,
-				handleObj = event.handleObj;
-
-			// For mouseenter/leave call the handler if related is outside the target.
-			// NB: No relatedTarget if the mouse left/entered the browser window
-			if ( !related || ( related !== target && !jQuery.contains( target, related ) ) ) {
-				event.type = handleObj.origType;
-				ret = handleObj.handler.apply( this, arguments );
-				event.type = fix;
-			}
-			return ret;
-		}
-	};
-} );
-
-jQuery.fn.extend( {
-
-	on: function( types, selector, data, fn ) {
-		return on( this, types, selector, data, fn );
-	},
-	one: function( types, selector, data, fn ) {
-		return on( this, types, selector, data, fn, 1 );
-	},
-	off: function( types, selector, fn ) {
-		var handleObj, type;
-		if ( types && types.preventDefault && types.handleObj ) {
-
-			// ( event )  dispatched jQuery.Event
-			handleObj = types.handleObj;
-			jQuery( types.delegateTarget ).off(
-				handleObj.namespace ?
-					handleObj.origType + "." + handleObj.namespace :
-					handleObj.origType,
-				handleObj.selector,
-				handleObj.handler
-			);
-			return this;
-		}
-		if ( typeof types === "object" ) {
-
-			// ( types-object [, selector] )
-			for ( type in types ) {
-				this.off( type, selector, types[ type ] );
-			}
-			return this;
-		}
-		if ( selector === false || typeof selector === "function" ) {
-
-			// ( types [, fn] )
-			fn = selector;
-			selector = undefined;
-		}
-		if ( fn === false ) {
-			fn = returnFalse;
-		}
-		return this.each( function() {
-			jQuery.event.remove( this, types, fn, selector );
-		} );
-	}
-} );
-
-
-var
-
-	// Support: IE <=10 - 11, Edge 12 - 13 only
-	// In IE/Edge using regex groups here causes severe slowdowns.
-	// See https://connect.microsoft.com/IE/feedback/details/1736512/
-	rnoInnerhtml = /\s*$/g;
-
-// Prefer a tbody over its parent table for containing new rows
-function manipulationTarget( elem, content ) {
-	if ( nodeName( elem, "table" ) &&
-		nodeName( content.nodeType !== 11 ? content : content.firstChild, "tr" ) ) {
-
-		return jQuery( elem ).children( "tbody" )[ 0 ] || elem;
-	}
-
-	return elem;
-}
-
-// Replace/restore the type attribute of script elements for safe DOM manipulation
-function disableScript( elem ) {
-	elem.type = ( elem.getAttribute( "type" ) !== null ) + "/" + elem.type;
-	return elem;
-}
-function restoreScript( elem ) {
-	if ( ( elem.type || "" ).slice( 0, 5 ) === "true/" ) {
-		elem.type = elem.type.slice( 5 );
-	} else {
-		elem.removeAttribute( "type" );
-	}
-
-	return elem;
-}
-
-function cloneCopyEvent( src, dest ) {
-	var i, l, type, pdataOld, udataOld, udataCur, events;
-
-	if ( dest.nodeType !== 1 ) {
-		return;
-	}
-
-	// 1. Copy private data: events, handlers, etc.
-	if ( dataPriv.hasData( src ) ) {
-		pdataOld = dataPriv.get( src );
-		events = pdataOld.events;
-
-		if ( events ) {
-			dataPriv.remove( dest, "handle events" );
-
-			for ( type in events ) {
-				for ( i = 0, l = events[ type ].length; i < l; i++ ) {
-					jQuery.event.add( dest, type, events[ type ][ i ] );
-				}
-			}
-		}
-	}
-
-	// 2. Copy user data
-	if ( dataUser.hasData( src ) ) {
-		udataOld = dataUser.access( src );
-		udataCur = jQuery.extend( {}, udataOld );
-
-		dataUser.set( dest, udataCur );
-	}
-}
-
-// Fix IE bugs, see support tests
-function fixInput( src, dest ) {
-	var nodeName = dest.nodeName.toLowerCase();
-
-	// Fails to persist the checked state of a cloned checkbox or radio button.
-	if ( nodeName === "input" && rcheckableType.test( src.type ) ) {
-		dest.checked = src.checked;
-
-	// Fails to return the selected option to the default selected state when cloning options
-	} else if ( nodeName === "input" || nodeName === "textarea" ) {
-		dest.defaultValue = src.defaultValue;
-	}
-}
-
-function domManip( collection, args, callback, ignored ) {
-
-	// Flatten any nested arrays
-	args = flat( args );
-
-	var fragment, first, scripts, hasScripts, node, doc,
-		i = 0,
-		l = collection.length,
-		iNoClone = l - 1,
-		value = args[ 0 ],
-		valueIsFunction = isFunction( value );
-
-	// We can't cloneNode fragments that contain checked, in WebKit
-	if ( valueIsFunction ||
-			( l > 1 && typeof value === "string" &&
-				!support.checkClone && rchecked.test( value ) ) ) {
-		return collection.each( function( index ) {
-			var self = collection.eq( index );
-			if ( valueIsFunction ) {
-				args[ 0 ] = value.call( this, index, self.html() );
-			}
-			domManip( self, args, callback, ignored );
-		} );
-	}
-
-	if ( l ) {
-		fragment = buildFragment( args, collection[ 0 ].ownerDocument, false, collection, ignored );
-		first = fragment.firstChild;
-
-		if ( fragment.childNodes.length === 1 ) {
-			fragment = first;
-		}
-
-		// Require either new content or an interest in ignored elements to invoke the callback
-		if ( first || ignored ) {
-			scripts = jQuery.map( getAll( fragment, "script" ), disableScript );
-			hasScripts = scripts.length;
-
-			// Use the original fragment for the last item
-			// instead of the first because it can end up
-			// being emptied incorrectly in certain situations (#8070).
-			for ( ; i < l; i++ ) {
-				node = fragment;
-
-				if ( i !== iNoClone ) {
-					node = jQuery.clone( node, true, true );
-
-					// Keep references to cloned scripts for later restoration
-					if ( hasScripts ) {
-
-						// Support: Android <=4.0 only, PhantomJS 1 only
-						// push.apply(_, arraylike) throws on ancient WebKit
-						jQuery.merge( scripts, getAll( node, "script" ) );
-					}
-				}
-
-				callback.call( collection[ i ], node, i );
-			}
-
-			if ( hasScripts ) {
-				doc = scripts[ scripts.length - 1 ].ownerDocument;
-
-				// Reenable scripts
-				jQuery.map( scripts, restoreScript );
-
-				// Evaluate executable scripts on first document insertion
-				for ( i = 0; i < hasScripts; i++ ) {
-					node = scripts[ i ];
-					if ( rscriptType.test( node.type || "" ) &&
-						!dataPriv.access( node, "globalEval" ) &&
-						jQuery.contains( doc, node ) ) {
-
-						if ( node.src && ( node.type || "" ).toLowerCase()  !== "module" ) {
-
-							// Optional AJAX dependency, but won't run scripts if not present
-							if ( jQuery._evalUrl && !node.noModule ) {
-								jQuery._evalUrl( node.src, {
-									nonce: node.nonce || node.getAttribute( "nonce" )
-								}, doc );
-							}
-						} else {
-							DOMEval( node.textContent.replace( rcleanScript, "" ), node, doc );
-						}
-					}
-				}
-			}
-		}
-	}
-
-	return collection;
-}
-
-function remove( elem, selector, keepData ) {
-	var node,
-		nodes = selector ? jQuery.filter( selector, elem ) : elem,
-		i = 0;
-
-	for ( ; ( node = nodes[ i ] ) != null; i++ ) {
-		if ( !keepData && node.nodeType === 1 ) {
-			jQuery.cleanData( getAll( node ) );
-		}
-
-		if ( node.parentNode ) {
-			if ( keepData && isAttached( node ) ) {
-				setGlobalEval( getAll( node, "script" ) );
-			}
-			node.parentNode.removeChild( node );
-		}
-	}
-
-	return elem;
-}
-
-jQuery.extend( {
-	htmlPrefilter: function( html ) {
-		return html;
-	},
-
-	clone: function( elem, dataAndEvents, deepDataAndEvents ) {
-		var i, l, srcElements, destElements,
-			clone = elem.cloneNode( true ),
-			inPage = isAttached( elem );
-
-		// Fix IE cloning issues
-		if ( !support.noCloneChecked && ( elem.nodeType === 1 || elem.nodeType === 11 ) &&
-				!jQuery.isXMLDoc( elem ) ) {
-
-			// We eschew Sizzle here for performance reasons: https://jsperf.com/getall-vs-sizzle/2
-			destElements = getAll( clone );
-			srcElements = getAll( elem );
-
-			for ( i = 0, l = srcElements.length; i < l; i++ ) {
-				fixInput( srcElements[ i ], destElements[ i ] );
-			}
-		}
-
-		// Copy the events from the original to the clone
-		if ( dataAndEvents ) {
-			if ( deepDataAndEvents ) {
-				srcElements = srcElements || getAll( elem );
-				destElements = destElements || getAll( clone );
-
-				for ( i = 0, l = srcElements.length; i < l; i++ ) {
-					cloneCopyEvent( srcElements[ i ], destElements[ i ] );
-				}
-			} else {
-				cloneCopyEvent( elem, clone );
-			}
-		}
-
-		// Preserve script evaluation history
-		destElements = getAll( clone, "script" );
-		if ( destElements.length > 0 ) {
-			setGlobalEval( destElements, !inPage && getAll( elem, "script" ) );
-		}
-
-		// Return the cloned set
-		return clone;
-	},
-
-	cleanData: function( elems ) {
-		var data, elem, type,
-			special = jQuery.event.special,
-			i = 0;
-
-		for ( ; ( elem = elems[ i ] ) !== undefined; i++ ) {
-			if ( acceptData( elem ) ) {
-				if ( ( data = elem[ dataPriv.expando ] ) ) {
-					if ( data.events ) {
-						for ( type in data.events ) {
-							if ( special[ type ] ) {
-								jQuery.event.remove( elem, type );
-
-							// This is a shortcut to avoid jQuery.event.remove's overhead
-							} else {
-								jQuery.removeEvent( elem, type, data.handle );
-							}
-						}
-					}
-
-					// Support: Chrome <=35 - 45+
-					// Assign undefined instead of using delete, see Data#remove
-					elem[ dataPriv.expando ] = undefined;
-				}
-				if ( elem[ dataUser.expando ] ) {
-
-					// Support: Chrome <=35 - 45+
-					// Assign undefined instead of using delete, see Data#remove
-					elem[ dataUser.expando ] = undefined;
-				}
-			}
-		}
-	}
-} );
-
-jQuery.fn.extend( {
-	detach: function( selector ) {
-		return remove( this, selector, true );
-	},
-
-	remove: function( selector ) {
-		return remove( this, selector );
-	},
-
-	text: function( value ) {
-		return access( this, function( value ) {
-			return value === undefined ?
-				jQuery.text( this ) :
-				this.empty().each( function() {
-					if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
-						this.textContent = value;
-					}
-				} );
-		}, null, value, arguments.length );
-	},
-
-	append: function() {
-		return domManip( this, arguments, function( elem ) {
-			if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
-				var target = manipulationTarget( this, elem );
-				target.appendChild( elem );
-			}
-		} );
-	},
-
-	prepend: function() {
-		return domManip( this, arguments, function( elem ) {
-			if ( this.nodeType === 1 || this.nodeType === 11 || this.nodeType === 9 ) {
-				var target = manipulationTarget( this, elem );
-				target.insertBefore( elem, target.firstChild );
-			}
-		} );
-	},
-
-	before: function() {
-		return domManip( this, arguments, function( elem ) {
-			if ( this.parentNode ) {
-				this.parentNode.insertBefore( elem, this );
-			}
-		} );
-	},
-
-	after: function() {
-		return domManip( this, arguments, function( elem ) {
-			if ( this.parentNode ) {
-				this.parentNode.insertBefore( elem, this.nextSibling );
-			}
-		} );
-	},
-
-	empty: function() {
-		var elem,
-			i = 0;
-
-		for ( ; ( elem = this[ i ] ) != null; i++ ) {
-			if ( elem.nodeType === 1 ) {
-
-				// Prevent memory leaks
-				jQuery.cleanData( getAll( elem, false ) );
-
-				// Remove any remaining nodes
-				elem.textContent = "";
-			}
-		}
-
-		return this;
-	},
-
-	clone: function( dataAndEvents, deepDataAndEvents ) {
-		dataAndEvents = dataAndEvents == null ? false : dataAndEvents;
-		deepDataAndEvents = deepDataAndEvents == null ? dataAndEvents : deepDataAndEvents;
-
-		return this.map( function() {
-			return jQuery.clone( this, dataAndEvents, deepDataAndEvents );
-		} );
-	},
-
-	html: function( value ) {
-		return access( this, function( value ) {
-			var elem = this[ 0 ] || {},
-				i = 0,
-				l = this.length;
-
-			if ( value === undefined && elem.nodeType === 1 ) {
-				return elem.innerHTML;
-			}
-
-			// See if we can take a shortcut and just use innerHTML
-			if ( typeof value === "string" && !rnoInnerhtml.test( value ) &&
-				!wrapMap[ ( rtagName.exec( value ) || [ "", "" ] )[ 1 ].toLowerCase() ] ) {
-
-				value = jQuery.htmlPrefilter( value );
-
-				try {
-					for ( ; i < l; i++ ) {
-						elem = this[ i ] || {};
-
-						// Remove element nodes and prevent memory leaks
-						if ( elem.nodeType === 1 ) {
-							jQuery.cleanData( getAll( elem, false ) );
-							elem.innerHTML = value;
-						}
-					}
-
-					elem = 0;
-
-				// If using innerHTML throws an exception, use the fallback method
-				} catch ( e ) {}
-			}
-
-			if ( elem ) {
-				this.empty().append( value );
-			}
-		}, null, value, arguments.length );
-	},
-
-	replaceWith: function() {
-		var ignored = [];
-
-		// Make the changes, replacing each non-ignored context element with the new content
-		return domManip( this, arguments, function( elem ) {
-			var parent = this.parentNode;
-
-			if ( jQuery.inArray( this, ignored ) < 0 ) {
-				jQuery.cleanData( getAll( this ) );
-				if ( parent ) {
-					parent.replaceChild( elem, this );
-				}
-			}
-
-		// Force callback invocation
-		}, ignored );
-	}
-} );
-
-jQuery.each( {
-	appendTo: "append",
-	prependTo: "prepend",
-	insertBefore: "before",
-	insertAfter: "after",
-	replaceAll: "replaceWith"
-}, function( name, original ) {
-	jQuery.fn[ name ] = function( selector ) {
-		var elems,
-			ret = [],
-			insert = jQuery( selector ),
-			last = insert.length - 1,
-			i = 0;
-
-		for ( ; i <= last; i++ ) {
-			elems = i === last ? this : this.clone( true );
-			jQuery( insert[ i ] )[ original ]( elems );
-
-			// Support: Android <=4.0 only, PhantomJS 1 only
-			// .get() because push.apply(_, arraylike) throws on ancient WebKit
-			push.apply( ret, elems.get() );
-		}
-
-		return this.pushStack( ret );
-	};
-} );
-var rnumnonpx = new RegExp( "^(" + pnum + ")(?!px)[a-z%]+$", "i" );
-
-var getStyles = function( elem ) {
-
-		// Support: IE <=11 only, Firefox <=30 (#15098, #14150)
-		// IE throws on elements created in popups
-		// FF meanwhile throws on frame elements through "defaultView.getComputedStyle"
-		var view = elem.ownerDocument.defaultView;
-
-		if ( !view || !view.opener ) {
-			view = window;
-		}
-
-		return view.getComputedStyle( elem );
-	};
-
-var swap = function( elem, options, callback ) {
-	var ret, name,
-		old = {};
-
-	// Remember the old values, and insert the new ones
-	for ( name in options ) {
-		old[ name ] = elem.style[ name ];
-		elem.style[ name ] = options[ name ];
-	}
-
-	ret = callback.call( elem );
-
-	// Revert the old values
-	for ( name in options ) {
-		elem.style[ name ] = old[ name ];
-	}
-
-	return ret;
-};
-
-
-var rboxStyle = new RegExp( cssExpand.join( "|" ), "i" );
-
-
-
-( function() {
-
-	// Executing both pixelPosition & boxSizingReliable tests require only one layout
-	// so they're executed at the same time to save the second computation.
-	function computeStyleTests() {
-
-		// This is a singleton, we need to execute it only once
-		if ( !div ) {
-			return;
-		}
-
-		container.style.cssText = "position:absolute;left:-11111px;width:60px;" +
-			"margin-top:1px;padding:0;border:0";
-		div.style.cssText =
-			"position:relative;display:block;box-sizing:border-box;overflow:scroll;" +
-			"margin:auto;border:1px;padding:1px;" +
-			"width:60%;top:1%";
-		documentElement.appendChild( container ).appendChild( div );
-
-		var divStyle = window.getComputedStyle( div );
-		pixelPositionVal = divStyle.top !== "1%";
-
-		// Support: Android 4.0 - 4.3 only, Firefox <=3 - 44
-		reliableMarginLeftVal = roundPixelMeasures( divStyle.marginLeft ) === 12;
-
-		// Support: Android 4.0 - 4.3 only, Safari <=9.1 - 10.1, iOS <=7.0 - 9.3
-		// Some styles come back with percentage values, even though they shouldn't
-		div.style.right = "60%";
-		pixelBoxStylesVal = roundPixelMeasures( divStyle.right ) === 36;
-
-		// Support: IE 9 - 11 only
-		// Detect misreporting of content dimensions for box-sizing:border-box elements
-		boxSizingReliableVal = roundPixelMeasures( divStyle.width ) === 36;
-
-		// Support: IE 9 only
-		// Detect overflow:scroll screwiness (gh-3699)
-		// Support: Chrome <=64
-		// Don't get tricked when zoom affects offsetWidth (gh-4029)
-		div.style.position = "absolute";
-		scrollboxSizeVal = roundPixelMeasures( div.offsetWidth / 3 ) === 12;
-
-		documentElement.removeChild( container );
-
-		// Nullify the div so it wouldn't be stored in the memory and
-		// it will also be a sign that checks already performed
-		div = null;
-	}
-
-	function roundPixelMeasures( measure ) {
-		return Math.round( parseFloat( measure ) );
-	}
-
-	var pixelPositionVal, boxSizingReliableVal, scrollboxSizeVal, pixelBoxStylesVal,
-		reliableTrDimensionsVal, reliableMarginLeftVal,
-		container = document.createElement( "div" ),
-		div = document.createElement( "div" );
-
-	// Finish early in limited (non-browser) environments
-	if ( !div.style ) {
-		return;
-	}
-
-	// Support: IE <=9 - 11 only
-	// Style of cloned element affects source element cloned (#8908)
-	div.style.backgroundClip = "content-box";
-	div.cloneNode( true ).style.backgroundClip = "";
-	support.clearCloneStyle = div.style.backgroundClip === "content-box";
-
-	jQuery.extend( support, {
-		boxSizingReliable: function() {
-			computeStyleTests();
-			return boxSizingReliableVal;
-		},
-		pixelBoxStyles: function() {
-			computeStyleTests();
-			return pixelBoxStylesVal;
-		},
-		pixelPosition: function() {
-			computeStyleTests();
-			return pixelPositionVal;
-		},
-		reliableMarginLeft: function() {
-			computeStyleTests();
-			return reliableMarginLeftVal;
-		},
-		scrollboxSize: function() {
-			computeStyleTests();
-			return scrollboxSizeVal;
-		},
-
-		// Support: IE 9 - 11+, Edge 15 - 18+
-		// IE/Edge misreport `getComputedStyle` of table rows with width/height
-		// set in CSS while `offset*` properties report correct values.
-		// Behavior in IE 9 is more subtle than in newer versions & it passes
-		// some versions of this test; make sure not to make it pass there!
-		//
-		// Support: Firefox 70+
-		// Only Firefox includes border widths
-		// in computed dimensions. (gh-4529)
-		reliableTrDimensions: function() {
-			var table, tr, trChild, trStyle;
-			if ( reliableTrDimensionsVal == null ) {
-				table = document.createElement( "table" );
-				tr = document.createElement( "tr" );
-				trChild = document.createElement( "div" );
-
-				table.style.cssText = "position:absolute;left:-11111px;border-collapse:separate";
-				tr.style.cssText = "border:1px solid";
-
-				// Support: Chrome 86+
-				// Height set through cssText does not get applied.
-				// Computed height then comes back as 0.
-				tr.style.height = "1px";
-				trChild.style.height = "9px";
-
-				// Support: Android 8 Chrome 86+
-				// In our bodyBackground.html iframe,
-				// display for all div elements is set to "inline",
-				// which causes a problem only in Android 8 Chrome 86.
-				// Ensuring the div is display: block
-				// gets around this issue.
-				trChild.style.display = "block";
-
-				documentElement
-					.appendChild( table )
-					.appendChild( tr )
-					.appendChild( trChild );
-
-				trStyle = window.getComputedStyle( tr );
-				reliableTrDimensionsVal = ( parseInt( trStyle.height, 10 ) +
-					parseInt( trStyle.borderTopWidth, 10 ) +
-					parseInt( trStyle.borderBottomWidth, 10 ) ) === tr.offsetHeight;
-
-				documentElement.removeChild( table );
-			}
-			return reliableTrDimensionsVal;
-		}
-	} );
-} )();
-
-
-function curCSS( elem, name, computed ) {
-	var width, minWidth, maxWidth, ret,
-
-		// Support: Firefox 51+
-		// Retrieving style before computed somehow
-		// fixes an issue with getting wrong values
-		// on detached elements
-		style = elem.style;
-
-	computed = computed || getStyles( elem );
-
-	// getPropertyValue is needed for:
-	//   .css('filter') (IE 9 only, #12537)
-	//   .css('--customProperty) (#3144)
-	if ( computed ) {
-		ret = computed.getPropertyValue( name ) || computed[ name ];
-
-		if ( ret === "" && !isAttached( elem ) ) {
-			ret = jQuery.style( elem, name );
-		}
-
-		// A tribute to the "awesome hack by Dean Edwards"
-		// Android Browser returns percentage for some values,
-		// but width seems to be reliably pixels.
-		// This is against the CSSOM draft spec:
-		// https://drafts.csswg.org/cssom/#resolved-values
-		if ( !support.pixelBoxStyles() && rnumnonpx.test( ret ) && rboxStyle.test( name ) ) {
-
-			// Remember the original values
-			width = style.width;
-			minWidth = style.minWidth;
-			maxWidth = style.maxWidth;
-
-			// Put in the new values to get a computed value out
-			style.minWidth = style.maxWidth = style.width = ret;
-			ret = computed.width;
-
-			// Revert the changed values
-			style.width = width;
-			style.minWidth = minWidth;
-			style.maxWidth = maxWidth;
-		}
-	}
-
-	return ret !== undefined ?
-
-		// Support: IE <=9 - 11 only
-		// IE returns zIndex value as an integer.
-		ret + "" :
-		ret;
-}
-
-
-function addGetHookIf( conditionFn, hookFn ) {
-
-	// Define the hook, we'll check on the first run if it's really needed.
-	return {
-		get: function() {
-			if ( conditionFn() ) {
-
-				// Hook not needed (or it's not possible to use it due
-				// to missing dependency), remove it.
-				delete this.get;
-				return;
-			}
-
-			// Hook needed; redefine it so that the support test is not executed again.
-			return ( this.get = hookFn ).apply( this, arguments );
-		}
-	};
-}
-
-
-var cssPrefixes = [ "Webkit", "Moz", "ms" ],
-	emptyStyle = document.createElement( "div" ).style,
-	vendorProps = {};
-
-// Return a vendor-prefixed property or undefined
-function vendorPropName( name ) {
-
-	// Check for vendor prefixed names
-	var capName = name[ 0 ].toUpperCase() + name.slice( 1 ),
-		i = cssPrefixes.length;
-
-	while ( i-- ) {
-		name = cssPrefixes[ i ] + capName;
-		if ( name in emptyStyle ) {
-			return name;
-		}
-	}
-}
-
-// Return a potentially-mapped jQuery.cssProps or vendor prefixed property
-function finalPropName( name ) {
-	var final = jQuery.cssProps[ name ] || vendorProps[ name ];
-
-	if ( final ) {
-		return final;
-	}
-	if ( name in emptyStyle ) {
-		return name;
-	}
-	return vendorProps[ name ] = vendorPropName( name ) || name;
-}
-
-
-var
-
-	// Swappable if display is none or starts with table
-	// except "table", "table-cell", or "table-caption"
-	// See here for display values: https://developer.mozilla.org/en-US/docs/CSS/display
-	rdisplayswap = /^(none|table(?!-c[ea]).+)/,
-	rcustomProp = /^--/,
-	cssShow = { position: "absolute", visibility: "hidden", display: "block" },
-	cssNormalTransform = {
-		letterSpacing: "0",
-		fontWeight: "400"
-	};
-
-function setPositiveNumber( _elem, value, subtract ) {
-
-	// Any relative (+/-) values have already been
-	// normalized at this point
-	var matches = rcssNum.exec( value );
-	return matches ?
-
-		// Guard against undefined "subtract", e.g., when used as in cssHooks
-		Math.max( 0, matches[ 2 ] - ( subtract || 0 ) ) + ( matches[ 3 ] || "px" ) :
-		value;
-}
-
-function boxModelAdjustment( elem, dimension, box, isBorderBox, styles, computedVal ) {
-	var i = dimension === "width" ? 1 : 0,
-		extra = 0,
-		delta = 0;
-
-	// Adjustment may not be necessary
-	if ( box === ( isBorderBox ? "border" : "content" ) ) {
-		return 0;
-	}
-
-	for ( ; i < 4; i += 2 ) {
-
-		// Both box models exclude margin
-		if ( box === "margin" ) {
-			delta += jQuery.css( elem, box + cssExpand[ i ], true, styles );
-		}
-
-		// If we get here with a content-box, we're seeking "padding" or "border" or "margin"
-		if ( !isBorderBox ) {
-
-			// Add padding
-			delta += jQuery.css( elem, "padding" + cssExpand[ i ], true, styles );
-
-			// For "border" or "margin", add border
-			if ( box !== "padding" ) {
-				delta += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles );
-
-			// But still keep track of it otherwise
-			} else {
-				extra += jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles );
-			}
-
-		// If we get here with a border-box (content + padding + border), we're seeking "content" or
-		// "padding" or "margin"
-		} else {
-
-			// For "content", subtract padding
-			if ( box === "content" ) {
-				delta -= jQuery.css( elem, "padding" + cssExpand[ i ], true, styles );
-			}
-
-			// For "content" or "padding", subtract border
-			if ( box !== "margin" ) {
-				delta -= jQuery.css( elem, "border" + cssExpand[ i ] + "Width", true, styles );
-			}
-		}
-	}
-
-	// Account for positive content-box scroll gutter when requested by providing computedVal
-	if ( !isBorderBox && computedVal >= 0 ) {
-
-		// offsetWidth/offsetHeight is a rounded sum of content, padding, scroll gutter, and border
-		// Assuming integer scroll gutter, subtract the rest and round down
-		delta += Math.max( 0, Math.ceil(
-			elem[ "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ) ] -
-			computedVal -
-			delta -
-			extra -
-			0.5
-
-		// If offsetWidth/offsetHeight is unknown, then we can't determine content-box scroll gutter
-		// Use an explicit zero to avoid NaN (gh-3964)
-		) ) || 0;
-	}
-
-	return delta;
-}
-
-function getWidthOrHeight( elem, dimension, extra ) {
-
-	// Start with computed style
-	var styles = getStyles( elem ),
-
-		// To avoid forcing a reflow, only fetch boxSizing if we need it (gh-4322).
-		// Fake content-box until we know it's needed to know the true value.
-		boxSizingNeeded = !support.boxSizingReliable() || extra,
-		isBorderBox = boxSizingNeeded &&
-			jQuery.css( elem, "boxSizing", false, styles ) === "border-box",
-		valueIsBorderBox = isBorderBox,
-
-		val = curCSS( elem, dimension, styles ),
-		offsetProp = "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 );
-
-	// Support: Firefox <=54
-	// Return a confounding non-pixel value or feign ignorance, as appropriate.
-	if ( rnumnonpx.test( val ) ) {
-		if ( !extra ) {
-			return val;
-		}
-		val = "auto";
-	}
-
-
-	// Support: IE 9 - 11 only
-	// Use offsetWidth/offsetHeight for when box sizing is unreliable.
-	// In those cases, the computed value can be trusted to be border-box.
-	if ( ( !support.boxSizingReliable() && isBorderBox ||
-
-		// Support: IE 10 - 11+, Edge 15 - 18+
-		// IE/Edge misreport `getComputedStyle` of table rows with width/height
-		// set in CSS while `offset*` properties report correct values.
-		// Interestingly, in some cases IE 9 doesn't suffer from this issue.
-		!support.reliableTrDimensions() && nodeName( elem, "tr" ) ||
-
-		// Fall back to offsetWidth/offsetHeight when value is "auto"
-		// This happens for inline elements with no explicit setting (gh-3571)
-		val === "auto" ||
-
-		// Support: Android <=4.1 - 4.3 only
-		// Also use offsetWidth/offsetHeight for misreported inline dimensions (gh-3602)
-		!parseFloat( val ) && jQuery.css( elem, "display", false, styles ) === "inline" ) &&
-
-		// Make sure the element is visible & connected
-		elem.getClientRects().length ) {
-
-		isBorderBox = jQuery.css( elem, "boxSizing", false, styles ) === "border-box";
-
-		// Where available, offsetWidth/offsetHeight approximate border box dimensions.
-		// Where not available (e.g., SVG), assume unreliable box-sizing and interpret the
-		// retrieved value as a content box dimension.
-		valueIsBorderBox = offsetProp in elem;
-		if ( valueIsBorderBox ) {
-			val = elem[ offsetProp ];
-		}
-	}
-
-	// Normalize "" and auto
-	val = parseFloat( val ) || 0;
-
-	// Adjust for the element's box model
-	return ( val +
-		boxModelAdjustment(
-			elem,
-			dimension,
-			extra || ( isBorderBox ? "border" : "content" ),
-			valueIsBorderBox,
-			styles,
-
-			// Provide the current computed size to request scroll gutter calculation (gh-3589)
-			val
-		)
-	) + "px";
-}
-
-jQuery.extend( {
-
-	// Add in style property hooks for overriding the default
-	// behavior of getting and setting a style property
-	cssHooks: {
-		opacity: {
-			get: function( elem, computed ) {
-				if ( computed ) {
-
-					// We should always get a number back from opacity
-					var ret = curCSS( elem, "opacity" );
-					return ret === "" ? "1" : ret;
-				}
-			}
-		}
-	},
-
-	// Don't automatically add "px" to these possibly-unitless properties
-	cssNumber: {
-		"animationIterationCount": true,
-		"columnCount": true,
-		"fillOpacity": true,
-		"flexGrow": true,
-		"flexShrink": true,
-		"fontWeight": true,
-		"gridArea": true,
-		"gridColumn": true,
-		"gridColumnEnd": true,
-		"gridColumnStart": true,
-		"gridRow": true,
-		"gridRowEnd": true,
-		"gridRowStart": true,
-		"lineHeight": true,
-		"opacity": true,
-		"order": true,
-		"orphans": true,
-		"widows": true,
-		"zIndex": true,
-		"zoom": true
-	},
-
-	// Add in properties whose names you wish to fix before
-	// setting or getting the value
-	cssProps: {},
-
-	// Get and set the style property on a DOM Node
-	style: function( elem, name, value, extra ) {
-
-		// Don't set styles on text and comment nodes
-		if ( !elem || elem.nodeType === 3 || elem.nodeType === 8 || !elem.style ) {
-			return;
-		}
-
-		// Make sure that we're working with the right name
-		var ret, type, hooks,
-			origName = camelCase( name ),
-			isCustomProp = rcustomProp.test( name ),
-			style = elem.style;
-
-		// Make sure that we're working with the right name. We don't
-		// want to query the value if it is a CSS custom property
-		// since they are user-defined.
-		if ( !isCustomProp ) {
-			name = finalPropName( origName );
-		}
-
-		// Gets hook for the prefixed version, then unprefixed version
-		hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
-
-		// Check if we're setting a value
-		if ( value !== undefined ) {
-			type = typeof value;
-
-			// Convert "+=" or "-=" to relative numbers (#7345)
-			if ( type === "string" && ( ret = rcssNum.exec( value ) ) && ret[ 1 ] ) {
-				value = adjustCSS( elem, name, ret );
-
-				// Fixes bug #9237
-				type = "number";
-			}
-
-			// Make sure that null and NaN values aren't set (#7116)
-			if ( value == null || value !== value ) {
-				return;
-			}
-
-			// If a number was passed in, add the unit (except for certain CSS properties)
-			// The isCustomProp check can be removed in jQuery 4.0 when we only auto-append
-			// "px" to a few hardcoded values.
-			if ( type === "number" && !isCustomProp ) {
-				value += ret && ret[ 3 ] || ( jQuery.cssNumber[ origName ] ? "" : "px" );
-			}
-
-			// background-* props affect original clone's values
-			if ( !support.clearCloneStyle && value === "" && name.indexOf( "background" ) === 0 ) {
-				style[ name ] = "inherit";
-			}
-
-			// If a hook was provided, use that value, otherwise just set the specified value
-			if ( !hooks || !( "set" in hooks ) ||
-				( value = hooks.set( elem, value, extra ) ) !== undefined ) {
-
-				if ( isCustomProp ) {
-					style.setProperty( name, value );
-				} else {
-					style[ name ] = value;
-				}
-			}
-
-		} else {
-
-			// If a hook was provided get the non-computed value from there
-			if ( hooks && "get" in hooks &&
-				( ret = hooks.get( elem, false, extra ) ) !== undefined ) {
-
-				return ret;
-			}
-
-			// Otherwise just get the value from the style object
-			return style[ name ];
-		}
-	},
-
-	css: function( elem, name, extra, styles ) {
-		var val, num, hooks,
-			origName = camelCase( name ),
-			isCustomProp = rcustomProp.test( name );
-
-		// Make sure that we're working with the right name. We don't
-		// want to modify the value if it is a CSS custom property
-		// since they are user-defined.
-		if ( !isCustomProp ) {
-			name = finalPropName( origName );
-		}
-
-		// Try prefixed name followed by the unprefixed name
-		hooks = jQuery.cssHooks[ name ] || jQuery.cssHooks[ origName ];
-
-		// If a hook was provided get the computed value from there
-		if ( hooks && "get" in hooks ) {
-			val = hooks.get( elem, true, extra );
-		}
-
-		// Otherwise, if a way to get the computed value exists, use that
-		if ( val === undefined ) {
-			val = curCSS( elem, name, styles );
-		}
-
-		// Convert "normal" to computed value
-		if ( val === "normal" && name in cssNormalTransform ) {
-			val = cssNormalTransform[ name ];
-		}
-
-		// Make numeric if forced or a qualifier was provided and val looks numeric
-		if ( extra === "" || extra ) {
-			num = parseFloat( val );
-			return extra === true || isFinite( num ) ? num || 0 : val;
-		}
-
-		return val;
-	}
-} );
-
-jQuery.each( [ "height", "width" ], function( _i, dimension ) {
-	jQuery.cssHooks[ dimension ] = {
-		get: function( elem, computed, extra ) {
-			if ( computed ) {
-
-				// Certain elements can have dimension info if we invisibly show them
-				// but it must have a current display style that would benefit
-				return rdisplayswap.test( jQuery.css( elem, "display" ) ) &&
-
-					// Support: Safari 8+
-					// Table columns in Safari have non-zero offsetWidth & zero
-					// getBoundingClientRect().width unless display is changed.
-					// Support: IE <=11 only
-					// Running getBoundingClientRect on a disconnected node
-					// in IE throws an error.
-					( !elem.getClientRects().length || !elem.getBoundingClientRect().width ) ?
-					swap( elem, cssShow, function() {
-						return getWidthOrHeight( elem, dimension, extra );
-					} ) :
-					getWidthOrHeight( elem, dimension, extra );
-			}
-		},
-
-		set: function( elem, value, extra ) {
-			var matches,
-				styles = getStyles( elem ),
-
-				// Only read styles.position if the test has a chance to fail
-				// to avoid forcing a reflow.
-				scrollboxSizeBuggy = !support.scrollboxSize() &&
-					styles.position === "absolute",
-
-				// To avoid forcing a reflow, only fetch boxSizing if we need it (gh-3991)
-				boxSizingNeeded = scrollboxSizeBuggy || extra,
-				isBorderBox = boxSizingNeeded &&
-					jQuery.css( elem, "boxSizing", false, styles ) === "border-box",
-				subtract = extra ?
-					boxModelAdjustment(
-						elem,
-						dimension,
-						extra,
-						isBorderBox,
-						styles
-					) :
-					0;
-
-			// Account for unreliable border-box dimensions by comparing offset* to computed and
-			// faking a content-box to get border and padding (gh-3699)
-			if ( isBorderBox && scrollboxSizeBuggy ) {
-				subtract -= Math.ceil(
-					elem[ "offset" + dimension[ 0 ].toUpperCase() + dimension.slice( 1 ) ] -
-					parseFloat( styles[ dimension ] ) -
-					boxModelAdjustment( elem, dimension, "border", false, styles ) -
-					0.5
-				);
-			}
-
-			// Convert to pixels if value adjustment is needed
-			if ( subtract && ( matches = rcssNum.exec( value ) ) &&
-				( matches[ 3 ] || "px" ) !== "px" ) {
-
-				elem.style[ dimension ] = value;
-				value = jQuery.css( elem, dimension );
-			}
-
-			return setPositiveNumber( elem, value, subtract );
-		}
-	};
-} );
-
-jQuery.cssHooks.marginLeft = addGetHookIf( support.reliableMarginLeft,
-	function( elem, computed ) {
-		if ( computed ) {
-			return ( parseFloat( curCSS( elem, "marginLeft" ) ) ||
-				elem.getBoundingClientRect().left -
-					swap( elem, { marginLeft: 0 }, function() {
-						return elem.getBoundingClientRect().left;
-					} )
-			) + "px";
-		}
-	}
-);
-
-// These hooks are used by animate to expand properties
-jQuery.each( {
-	margin: "",
-	padding: "",
-	border: "Width"
-}, function( prefix, suffix ) {
-	jQuery.cssHooks[ prefix + suffix ] = {
-		expand: function( value ) {
-			var i = 0,
-				expanded = {},
-
-				// Assumes a single number if not a string
-				parts = typeof value === "string" ? value.split( " " ) : [ value ];
-
-			for ( ; i < 4; i++ ) {
-				expanded[ prefix + cssExpand[ i ] + suffix ] =
-					parts[ i ] || parts[ i - 2 ] || parts[ 0 ];
-			}
-
-			return expanded;
-		}
-	};
-
-	if ( prefix !== "margin" ) {
-		jQuery.cssHooks[ prefix + suffix ].set = setPositiveNumber;
-	}
-} );
-
-jQuery.fn.extend( {
-	css: function( name, value ) {
-		return access( this, function( elem, name, value ) {
-			var styles, len,
-				map = {},
-				i = 0;
-
-			if ( Array.isArray( name ) ) {
-				styles = getStyles( elem );
-				len = name.length;
-
-				for ( ; i < len; i++ ) {
-					map[ name[ i ] ] = jQuery.css( elem, name[ i ], false, styles );
-				}
-
-				return map;
-			}
-
-			return value !== undefined ?
-				jQuery.style( elem, name, value ) :
-				jQuery.css( elem, name );
-		}, name, value, arguments.length > 1 );
-	}
-} );
-
-
-function Tween( elem, options, prop, end, easing ) {
-	return new Tween.prototype.init( elem, options, prop, end, easing );
-}
-jQuery.Tween = Tween;
-
-Tween.prototype = {
-	constructor: Tween,
-	init: function( elem, options, prop, end, easing, unit ) {
-		this.elem = elem;
-		this.prop = prop;
-		this.easing = easing || jQuery.easing._default;
-		this.options = options;
-		this.start = this.now = this.cur();
-		this.end = end;
-		this.unit = unit || ( jQuery.cssNumber[ prop ] ? "" : "px" );
-	},
-	cur: function() {
-		var hooks = Tween.propHooks[ this.prop ];
-
-		return hooks && hooks.get ?
-			hooks.get( this ) :
-			Tween.propHooks._default.get( this );
-	},
-	run: function( percent ) {
-		var eased,
-			hooks = Tween.propHooks[ this.prop ];
-
-		if ( this.options.duration ) {
-			this.pos = eased = jQuery.easing[ this.easing ](
-				percent, this.options.duration * percent, 0, 1, this.options.duration
-			);
-		} else {
-			this.pos = eased = percent;
-		}
-		this.now = ( this.end - this.start ) * eased + this.start;
-
-		if ( this.options.step ) {
-			this.options.step.call( this.elem, this.now, this );
-		}
-
-		if ( hooks && hooks.set ) {
-			hooks.set( this );
-		} else {
-			Tween.propHooks._default.set( this );
-		}
-		return this;
-	}
-};
-
-Tween.prototype.init.prototype = Tween.prototype;
-
-Tween.propHooks = {
-	_default: {
-		get: function( tween ) {
-			var result;
-
-			// Use a property on the element directly when it is not a DOM element,
-			// or when there is no matching style property that exists.
-			if ( tween.elem.nodeType !== 1 ||
-				tween.elem[ tween.prop ] != null && tween.elem.style[ tween.prop ] == null ) {
-				return tween.elem[ tween.prop ];
-			}
-
-			// Passing an empty string as a 3rd parameter to .css will automatically
-			// attempt a parseFloat and fallback to a string if the parse fails.
-			// Simple values such as "10px" are parsed to Float;
-			// complex values such as "rotate(1rad)" are returned as-is.
-			result = jQuery.css( tween.elem, tween.prop, "" );
-
-			// Empty strings, null, undefined and "auto" are converted to 0.
-			return !result || result === "auto" ? 0 : result;
-		},
-		set: function( tween ) {
-
-			// Use step hook for back compat.
-			// Use cssHook if its there.
-			// Use .style if available and use plain properties where available.
-			if ( jQuery.fx.step[ tween.prop ] ) {
-				jQuery.fx.step[ tween.prop ]( tween );
-			} else if ( tween.elem.nodeType === 1 && (
-				jQuery.cssHooks[ tween.prop ] ||
-					tween.elem.style[ finalPropName( tween.prop ) ] != null ) ) {
-				jQuery.style( tween.elem, tween.prop, tween.now + tween.unit );
-			} else {
-				tween.elem[ tween.prop ] = tween.now;
-			}
-		}
-	}
-};
-
-// Support: IE <=9 only
-// Panic based approach to setting things on disconnected nodes
-Tween.propHooks.scrollTop = Tween.propHooks.scrollLeft = {
-	set: function( tween ) {
-		if ( tween.elem.nodeType && tween.elem.parentNode ) {
-			tween.elem[ tween.prop ] = tween.now;
-		}
-	}
-};
-
-jQuery.easing = {
-	linear: function( p ) {
-		return p;
-	},
-	swing: function( p ) {
-		return 0.5 - Math.cos( p * Math.PI ) / 2;
-	},
-	_default: "swing"
-};
-
-jQuery.fx = Tween.prototype.init;
-
-// Back compat <1.8 extension point
-jQuery.fx.step = {};
-
-
-
-
-var
-	fxNow, inProgress,
-	rfxtypes = /^(?:toggle|show|hide)$/,
-	rrun = /queueHooks$/;
-
-function schedule() {
-	if ( inProgress ) {
-		if ( document.hidden === false && window.requestAnimationFrame ) {
-			window.requestAnimationFrame( schedule );
-		} else {
-			window.setTimeout( schedule, jQuery.fx.interval );
-		}
-
-		jQuery.fx.tick();
-	}
-}
-
-// Animations created synchronously will run synchronously
-function createFxNow() {
-	window.setTimeout( function() {
-		fxNow = undefined;
-	} );
-	return ( fxNow = Date.now() );
-}
-
-// Generate parameters to create a standard animation
-function genFx( type, includeWidth ) {
-	var which,
-		i = 0,
-		attrs = { height: type };
-
-	// If we include width, step value is 1 to do all cssExpand values,
-	// otherwise step value is 2 to skip over Left and Right
-	includeWidth = includeWidth ? 1 : 0;
-	for ( ; i < 4; i += 2 - includeWidth ) {
-		which = cssExpand[ i ];
-		attrs[ "margin" + which ] = attrs[ "padding" + which ] = type;
-	}
-
-	if ( includeWidth ) {
-		attrs.opacity = attrs.width = type;
-	}
-
-	return attrs;
-}
-
-function createTween( value, prop, animation ) {
-	var tween,
-		collection = ( Animation.tweeners[ prop ] || [] ).concat( Animation.tweeners[ "*" ] ),
-		index = 0,
-		length = collection.length;
-	for ( ; index < length; index++ ) {
-		if ( ( tween = collection[ index ].call( animation, prop, value ) ) ) {
-
-			// We're done with this property
-			return tween;
-		}
-	}
-}
-
-function defaultPrefilter( elem, props, opts ) {
-	var prop, value, toggle, hooks, oldfire, propTween, restoreDisplay, display,
-		isBox = "width" in props || "height" in props,
-		anim = this,
-		orig = {},
-		style = elem.style,
-		hidden = elem.nodeType && isHiddenWithinTree( elem ),
-		dataShow = dataPriv.get( elem, "fxshow" );
-
-	// Queue-skipping animations hijack the fx hooks
-	if ( !opts.queue ) {
-		hooks = jQuery._queueHooks( elem, "fx" );
-		if ( hooks.unqueued == null ) {
-			hooks.unqueued = 0;
-			oldfire = hooks.empty.fire;
-			hooks.empty.fire = function() {
-				if ( !hooks.unqueued ) {
-					oldfire();
-				}
-			};
-		}
-		hooks.unqueued++;
-
-		anim.always( function() {
-
-			// Ensure the complete handler is called before this completes
-			anim.always( function() {
-				hooks.unqueued--;
-				if ( !jQuery.queue( elem, "fx" ).length ) {
-					hooks.empty.fire();
-				}
-			} );
-		} );
-	}
-
-	// Detect show/hide animations
-	for ( prop in props ) {
-		value = props[ prop ];
-		if ( rfxtypes.test( value ) ) {
-			delete props[ prop ];
-			toggle = toggle || value === "toggle";
-			if ( value === ( hidden ? "hide" : "show" ) ) {
-
-				// Pretend to be hidden if this is a "show" and
-				// there is still data from a stopped show/hide
-				if ( value === "show" && dataShow && dataShow[ prop ] !== undefined ) {
-					hidden = true;
-
-				// Ignore all other no-op show/hide data
-				} else {
-					continue;
-				}
-			}
-			orig[ prop ] = dataShow && dataShow[ prop ] || jQuery.style( elem, prop );
-		}
-	}
-
-	// Bail out if this is a no-op like .hide().hide()
-	propTween = !jQuery.isEmptyObject( props );
-	if ( !propTween && jQuery.isEmptyObject( orig ) ) {
-		return;
-	}
-
-	// Restrict "overflow" and "display" styles during box animations
-	if ( isBox && elem.nodeType === 1 ) {
-
-		// Support: IE <=9 - 11, Edge 12 - 15
-		// Record all 3 overflow attributes because IE does not infer the shorthand
-		// from identically-valued overflowX and overflowY and Edge just mirrors
-		// the overflowX value there.
-		opts.overflow = [ style.overflow, style.overflowX, style.overflowY ];
-
-		// Identify a display type, preferring old show/hide data over the CSS cascade
-		restoreDisplay = dataShow && dataShow.display;
-		if ( restoreDisplay == null ) {
-			restoreDisplay = dataPriv.get( elem, "display" );
-		}
-		display = jQuery.css( elem, "display" );
-		if ( display === "none" ) {
-			if ( restoreDisplay ) {
-				display = restoreDisplay;
-			} else {
-
-				// Get nonempty value(s) by temporarily forcing visibility
-				showHide( [ elem ], true );
-				restoreDisplay = elem.style.display || restoreDisplay;
-				display = jQuery.css( elem, "display" );
-				showHide( [ elem ] );
-			}
-		}
-
-		// Animate inline elements as inline-block
-		if ( display === "inline" || display === "inline-block" && restoreDisplay != null ) {
-			if ( jQuery.css( elem, "float" ) === "none" ) {
-
-				// Restore the original display value at the end of pure show/hide animations
-				if ( !propTween ) {
-					anim.done( function() {
-						style.display = restoreDisplay;
-					} );
-					if ( restoreDisplay == null ) {
-						display = style.display;
-						restoreDisplay = display === "none" ? "" : display;
-					}
-				}
-				style.display = "inline-block";
-			}
-		}
-	}
-
-	if ( opts.overflow ) {
-		style.overflow = "hidden";
-		anim.always( function() {
-			style.overflow = opts.overflow[ 0 ];
-			style.overflowX = opts.overflow[ 1 ];
-			style.overflowY = opts.overflow[ 2 ];
-		} );
-	}
-
-	// Implement show/hide animations
-	propTween = false;
-	for ( prop in orig ) {
-
-		// General show/hide setup for this element animation
-		if ( !propTween ) {
-			if ( dataShow ) {
-				if ( "hidden" in dataShow ) {
-					hidden = dataShow.hidden;
-				}
-			} else {
-				dataShow = dataPriv.access( elem, "fxshow", { display: restoreDisplay } );
-			}
-
-			// Store hidden/visible for toggle so `.stop().toggle()` "reverses"
-			if ( toggle ) {
-				dataShow.hidden = !hidden;
-			}
-
-			// Show elements before animating them
-			if ( hidden ) {
-				showHide( [ elem ], true );
-			}
-
-			/* eslint-disable no-loop-func */
-
-			anim.done( function() {
-
-				/* eslint-enable no-loop-func */
-
-				// The final step of a "hide" animation is actually hiding the element
-				if ( !hidden ) {
-					showHide( [ elem ] );
-				}
-				dataPriv.remove( elem, "fxshow" );
-				for ( prop in orig ) {
-					jQuery.style( elem, prop, orig[ prop ] );
-				}
-			} );
-		}
-
-		// Per-property setup
-		propTween = createTween( hidden ? dataShow[ prop ] : 0, prop, anim );
-		if ( !( prop in dataShow ) ) {
-			dataShow[ prop ] = propTween.start;
-			if ( hidden ) {
-				propTween.end = propTween.start;
-				propTween.start = 0;
-			}
-		}
-	}
-}
-
-function propFilter( props, specialEasing ) {
-	var index, name, easing, value, hooks;
-
-	// camelCase, specialEasing and expand cssHook pass
-	for ( index in props ) {
-		name = camelCase( index );
-		easing = specialEasing[ name ];
-		value = props[ index ];
-		if ( Array.isArray( value ) ) {
-			easing = value[ 1 ];
-			value = props[ index ] = value[ 0 ];
-		}
-
-		if ( index !== name ) {
-			props[ name ] = value;
-			delete props[ index ];
-		}
-
-		hooks = jQuery.cssHooks[ name ];
-		if ( hooks && "expand" in hooks ) {
-			value = hooks.expand( value );
-			delete props[ name ];
-
-			// Not quite $.extend, this won't overwrite existing keys.
-			// Reusing 'index' because we have the correct "name"
-			for ( index in value ) {
-				if ( !( index in props ) ) {
-					props[ index ] = value[ index ];
-					specialEasing[ index ] = easing;
-				}
-			}
-		} else {
-			specialEasing[ name ] = easing;
-		}
-	}
-}
-
-function Animation( elem, properties, options ) {
-	var result,
-		stopped,
-		index = 0,
-		length = Animation.prefilters.length,
-		deferred = jQuery.Deferred().always( function() {
-
-			// Don't match elem in the :animated selector
-			delete tick.elem;
-		} ),
-		tick = function() {
-			if ( stopped ) {
-				return false;
-			}
-			var currentTime = fxNow || createFxNow(),
-				remaining = Math.max( 0, animation.startTime + animation.duration - currentTime ),
-
-				// Support: Android 2.3 only
-				// Archaic crash bug won't allow us to use `1 - ( 0.5 || 0 )` (#12497)
-				temp = remaining / animation.duration || 0,
-				percent = 1 - temp,
-				index = 0,
-				length = animation.tweens.length;
-
-			for ( ; index < length; index++ ) {
-				animation.tweens[ index ].run( percent );
-			}
-
-			deferred.notifyWith( elem, [ animation, percent, remaining ] );
-
-			// If there's more to do, yield
-			if ( percent < 1 && length ) {
-				return remaining;
-			}
-
-			// If this was an empty animation, synthesize a final progress notification
-			if ( !length ) {
-				deferred.notifyWith( elem, [ animation, 1, 0 ] );
-			}
-
-			// Resolve the animation and report its conclusion
-			deferred.resolveWith( elem, [ animation ] );
-			return false;
-		},
-		animation = deferred.promise( {
-			elem: elem,
-			props: jQuery.extend( {}, properties ),
-			opts: jQuery.extend( true, {
-				specialEasing: {},
-				easing: jQuery.easing._default
-			}, options ),
-			originalProperties: properties,
-			originalOptions: options,
-			startTime: fxNow || createFxNow(),
-			duration: options.duration,
-			tweens: [],
-			createTween: function( prop, end ) {
-				var tween = jQuery.Tween( elem, animation.opts, prop, end,
-					animation.opts.specialEasing[ prop ] || animation.opts.easing );
-				animation.tweens.push( tween );
-				return tween;
-			},
-			stop: function( gotoEnd ) {
-				var index = 0,
-
-					// If we are going to the end, we want to run all the tweens
-					// otherwise we skip this part
-					length = gotoEnd ? animation.tweens.length : 0;
-				if ( stopped ) {
-					return this;
-				}
-				stopped = true;
-				for ( ; index < length; index++ ) {
-					animation.tweens[ index ].run( 1 );
-				}
-
-				// Resolve when we played the last frame; otherwise, reject
-				if ( gotoEnd ) {
-					deferred.notifyWith( elem, [ animation, 1, 0 ] );
-					deferred.resolveWith( elem, [ animation, gotoEnd ] );
-				} else {
-					deferred.rejectWith( elem, [ animation, gotoEnd ] );
-				}
-				return this;
-			}
-		} ),
-		props = animation.props;
-
-	propFilter( props, animation.opts.specialEasing );
-
-	for ( ; index < length; index++ ) {
-		result = Animation.prefilters[ index ].call( animation, elem, props, animation.opts );
-		if ( result ) {
-			if ( isFunction( result.stop ) ) {
-				jQuery._queueHooks( animation.elem, animation.opts.queue ).stop =
-					result.stop.bind( result );
-			}
-			return result;
-		}
-	}
-
-	jQuery.map( props, createTween, animation );
-
-	if ( isFunction( animation.opts.start ) ) {
-		animation.opts.start.call( elem, animation );
-	}
-
-	// Attach callbacks from options
-	animation
-		.progress( animation.opts.progress )
-		.done( animation.opts.done, animation.opts.complete )
-		.fail( animation.opts.fail )
-		.always( animation.opts.always );
-
-	jQuery.fx.timer(
-		jQuery.extend( tick, {
-			elem: elem,
-			anim: animation,
-			queue: animation.opts.queue
-		} )
-	);
-
-	return animation;
-}
-
-jQuery.Animation = jQuery.extend( Animation, {
-
-	tweeners: {
-		"*": [ function( prop, value ) {
-			var tween = this.createTween( prop, value );
-			adjustCSS( tween.elem, prop, rcssNum.exec( value ), tween );
-			return tween;
-		} ]
-	},
-
-	tweener: function( props, callback ) {
-		if ( isFunction( props ) ) {
-			callback = props;
-			props = [ "*" ];
-		} else {
-			props = props.match( rnothtmlwhite );
-		}
-
-		var prop,
-			index = 0,
-			length = props.length;
-
-		for ( ; index < length; index++ ) {
-			prop = props[ index ];
-			Animation.tweeners[ prop ] = Animation.tweeners[ prop ] || [];
-			Animation.tweeners[ prop ].unshift( callback );
-		}
-	},
-
-	prefilters: [ defaultPrefilter ],
-
-	prefilter: function( callback, prepend ) {
-		if ( prepend ) {
-			Animation.prefilters.unshift( callback );
-		} else {
-			Animation.prefilters.push( callback );
-		}
-	}
-} );
-
-jQuery.speed = function( speed, easing, fn ) {
-	var opt = speed && typeof speed === "object" ? jQuery.extend( {}, speed ) : {
-		complete: fn || !fn && easing ||
-			isFunction( speed ) && speed,
-		duration: speed,
-		easing: fn && easing || easing && !isFunction( easing ) && easing
-	};
-
-	// Go to the end state if fx are off
-	if ( jQuery.fx.off ) {
-		opt.duration = 0;
-
-	} else {
-		if ( typeof opt.duration !== "number" ) {
-			if ( opt.duration in jQuery.fx.speeds ) {
-				opt.duration = jQuery.fx.speeds[ opt.duration ];
-
-			} else {
-				opt.duration = jQuery.fx.speeds._default;
-			}
-		}
-	}
-
-	// Normalize opt.queue - true/undefined/null -> "fx"
-	if ( opt.queue == null || opt.queue === true ) {
-		opt.queue = "fx";
-	}
-
-	// Queueing
-	opt.old = opt.complete;
-
-	opt.complete = function() {
-		if ( isFunction( opt.old ) ) {
-			opt.old.call( this );
-		}
-
-		if ( opt.queue ) {
-			jQuery.dequeue( this, opt.queue );
-		}
-	};
-
-	return opt;
-};
-
-jQuery.fn.extend( {
-	fadeTo: function( speed, to, easing, callback ) {
-
-		// Show any hidden elements after setting opacity to 0
-		return this.filter( isHiddenWithinTree ).css( "opacity", 0 ).show()
-
-			// Animate to the value specified
-			.end().animate( { opacity: to }, speed, easing, callback );
-	},
-	animate: function( prop, speed, easing, callback ) {
-		var empty = jQuery.isEmptyObject( prop ),
-			optall = jQuery.speed( speed, easing, callback ),
-			doAnimation = function() {
-
-				// Operate on a copy of prop so per-property easing won't be lost
-				var anim = Animation( this, jQuery.extend( {}, prop ), optall );
-
-				// Empty animations, or finishing resolves immediately
-				if ( empty || dataPriv.get( this, "finish" ) ) {
-					anim.stop( true );
-				}
-			};
-
-		doAnimation.finish = doAnimation;
-
-		return empty || optall.queue === false ?
-			this.each( doAnimation ) :
-			this.queue( optall.queue, doAnimation );
-	},
-	stop: function( type, clearQueue, gotoEnd ) {
-		var stopQueue = function( hooks ) {
-			var stop = hooks.stop;
-			delete hooks.stop;
-			stop( gotoEnd );
-		};
-
-		if ( typeof type !== "string" ) {
-			gotoEnd = clearQueue;
-			clearQueue = type;
-			type = undefined;
-		}
-		if ( clearQueue ) {
-			this.queue( type || "fx", [] );
-		}
-
-		return this.each( function() {
-			var dequeue = true,
-				index = type != null && type + "queueHooks",
-				timers = jQuery.timers,
-				data = dataPriv.get( this );
-
-			if ( index ) {
-				if ( data[ index ] && data[ index ].stop ) {
-					stopQueue( data[ index ] );
-				}
-			} else {
-				for ( index in data ) {
-					if ( data[ index ] && data[ index ].stop && rrun.test( index ) ) {
-						stopQueue( data[ index ] );
-					}
-				}
-			}
-
-			for ( index = timers.length; index--; ) {
-				if ( timers[ index ].elem === this &&
-					( type == null || timers[ index ].queue === type ) ) {
-
-					timers[ index ].anim.stop( gotoEnd );
-					dequeue = false;
-					timers.splice( index, 1 );
-				}
-			}
-
-			// Start the next in the queue if the last step wasn't forced.
-			// Timers currently will call their complete callbacks, which
-			// will dequeue but only if they were gotoEnd.
-			if ( dequeue || !gotoEnd ) {
-				jQuery.dequeue( this, type );
-			}
-		} );
-	},
-	finish: function( type ) {
-		if ( type !== false ) {
-			type = type || "fx";
-		}
-		return this.each( function() {
-			var index,
-				data = dataPriv.get( this ),
-				queue = data[ type + "queue" ],
-				hooks = data[ type + "queueHooks" ],
-				timers = jQuery.timers,
-				length = queue ? queue.length : 0;
-
-			// Enable finishing flag on private data
-			data.finish = true;
-
-			// Empty the queue first
-			jQuery.queue( this, type, [] );
-
-			if ( hooks && hooks.stop ) {
-				hooks.stop.call( this, true );
-			}
-
-			// Look for any active animations, and finish them
-			for ( index = timers.length; index--; ) {
-				if ( timers[ index ].elem === this && timers[ index ].queue === type ) {
-					timers[ index ].anim.stop( true );
-					timers.splice( index, 1 );
-				}
-			}
-
-			// Look for any animations in the old queue and finish them
-			for ( index = 0; index < length; index++ ) {
-				if ( queue[ index ] && queue[ index ].finish ) {
-					queue[ index ].finish.call( this );
-				}
-			}
-
-			// Turn off finishing flag
-			delete data.finish;
-		} );
-	}
-} );
-
-jQuery.each( [ "toggle", "show", "hide" ], function( _i, name ) {
-	var cssFn = jQuery.fn[ name ];
-	jQuery.fn[ name ] = function( speed, easing, callback ) {
-		return speed == null || typeof speed === "boolean" ?
-			cssFn.apply( this, arguments ) :
-			this.animate( genFx( name, true ), speed, easing, callback );
-	};
-} );
-
-// Generate shortcuts for custom animations
-jQuery.each( {
-	slideDown: genFx( "show" ),
-	slideUp: genFx( "hide" ),
-	slideToggle: genFx( "toggle" ),
-	fadeIn: { opacity: "show" },
-	fadeOut: { opacity: "hide" },
-	fadeToggle: { opacity: "toggle" }
-}, function( name, props ) {
-	jQuery.fn[ name ] = function( speed, easing, callback ) {
-		return this.animate( props, speed, easing, callback );
-	};
-} );
-
-jQuery.timers = [];
-jQuery.fx.tick = function() {
-	var timer,
-		i = 0,
-		timers = jQuery.timers;
-
-	fxNow = Date.now();
-
-	for ( ; i < timers.length; i++ ) {
-		timer = timers[ i ];
-
-		// Run the timer and safely remove it when done (allowing for external removal)
-		if ( !timer() && timers[ i ] === timer ) {
-			timers.splice( i--, 1 );
-		}
-	}
-
-	if ( !timers.length ) {
-		jQuery.fx.stop();
-	}
-	fxNow = undefined;
-};
-
-jQuery.fx.timer = function( timer ) {
-	jQuery.timers.push( timer );
-	jQuery.fx.start();
-};
-
-jQuery.fx.interval = 13;
-jQuery.fx.start = function() {
-	if ( inProgress ) {
-		return;
-	}
-
-	inProgress = true;
-	schedule();
-};
-
-jQuery.fx.stop = function() {
-	inProgress = null;
-};
-
-jQuery.fx.speeds = {
-	slow: 600,
-	fast: 200,
-
-	// Default speed
-	_default: 400
-};
-
-
-// Based off of the plugin by Clint Helfers, with permission.
-// https://web.archive.org/web/20100324014747/http://blindsignals.com/index.php/2009/07/jquery-delay/
-jQuery.fn.delay = function( time, type ) {
-	time = jQuery.fx ? jQuery.fx.speeds[ time ] || time : time;
-	type = type || "fx";
-
-	return this.queue( type, function( next, hooks ) {
-		var timeout = window.setTimeout( next, time );
-		hooks.stop = function() {
-			window.clearTimeout( timeout );
-		};
-	} );
-};
-
-
-( function() {
-	var input = document.createElement( "input" ),
-		select = document.createElement( "select" ),
-		opt = select.appendChild( document.createElement( "option" ) );
-
-	input.type = "checkbox";
-
-	// Support: Android <=4.3 only
-	// Default value for a checkbox should be "on"
-	support.checkOn = input.value !== "";
-
-	// Support: IE <=11 only
-	// Must access selectedIndex to make default options select
-	support.optSelected = opt.selected;
-
-	// Support: IE <=11 only
-	// An input loses its value after becoming a radio
-	input = document.createElement( "input" );
-	input.value = "t";
-	input.type = "radio";
-	support.radioValue = input.value === "t";
-} )();
-
-
-var boolHook,
-	attrHandle = jQuery.expr.attrHandle;
-
-jQuery.fn.extend( {
-	attr: function( name, value ) {
-		return access( this, jQuery.attr, name, value, arguments.length > 1 );
-	},
-
-	removeAttr: function( name ) {
-		return this.each( function() {
-			jQuery.removeAttr( this, name );
-		} );
-	}
-} );
-
-jQuery.extend( {
-	attr: function( elem, name, value ) {
-		var ret, hooks,
-			nType = elem.nodeType;
-
-		// Don't get/set attributes on text, comment and attribute nodes
-		if ( nType === 3 || nType === 8 || nType === 2 ) {
-			return;
-		}
-
-		// Fallback to prop when attributes are not supported
-		if ( typeof elem.getAttribute === "undefined" ) {
-			return jQuery.prop( elem, name, value );
-		}
-
-		// Attribute hooks are determined by the lowercase version
-		// Grab necessary hook if one is defined
-		if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) {
-			hooks = jQuery.attrHooks[ name.toLowerCase() ] ||
-				( jQuery.expr.match.bool.test( name ) ? boolHook : undefined );
-		}
-
-		if ( value !== undefined ) {
-			if ( value === null ) {
-				jQuery.removeAttr( elem, name );
-				return;
-			}
-
-			if ( hooks && "set" in hooks &&
-				( ret = hooks.set( elem, value, name ) ) !== undefined ) {
-				return ret;
-			}
-
-			elem.setAttribute( name, value + "" );
-			return value;
-		}
-
-		if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) {
-			return ret;
-		}
-
-		ret = jQuery.find.attr( elem, name );
-
-		// Non-existent attributes return null, we normalize to undefined
-		return ret == null ? undefined : ret;
-	},
-
-	attrHooks: {
-		type: {
-			set: function( elem, value ) {
-				if ( !support.radioValue && value === "radio" &&
-					nodeName( elem, "input" ) ) {
-					var val = elem.value;
-					elem.setAttribute( "type", value );
-					if ( val ) {
-						elem.value = val;
-					}
-					return value;
-				}
-			}
-		}
-	},
-
-	removeAttr: function( elem, value ) {
-		var name,
-			i = 0,
-
-			// Attribute names can contain non-HTML whitespace characters
-			// https://html.spec.whatwg.org/multipage/syntax.html#attributes-2
-			attrNames = value && value.match( rnothtmlwhite );
-
-		if ( attrNames && elem.nodeType === 1 ) {
-			while ( ( name = attrNames[ i++ ] ) ) {
-				elem.removeAttribute( name );
-			}
-		}
-	}
-} );
-
-// Hooks for boolean attributes
-boolHook = {
-	set: function( elem, value, name ) {
-		if ( value === false ) {
-
-			// Remove boolean attributes when set to false
-			jQuery.removeAttr( elem, name );
-		} else {
-			elem.setAttribute( name, name );
-		}
-		return name;
-	}
-};
-
-jQuery.each( jQuery.expr.match.bool.source.match( /\w+/g ), function( _i, name ) {
-	var getter = attrHandle[ name ] || jQuery.find.attr;
-
-	attrHandle[ name ] = function( elem, name, isXML ) {
-		var ret, handle,
-			lowercaseName = name.toLowerCase();
-
-		if ( !isXML ) {
-
-			// Avoid an infinite loop by temporarily removing this function from the getter
-			handle = attrHandle[ lowercaseName ];
-			attrHandle[ lowercaseName ] = ret;
-			ret = getter( elem, name, isXML ) != null ?
-				lowercaseName :
-				null;
-			attrHandle[ lowercaseName ] = handle;
-		}
-		return ret;
-	};
-} );
-
-
-
-
-var rfocusable = /^(?:input|select|textarea|button)$/i,
-	rclickable = /^(?:a|area)$/i;
-
-jQuery.fn.extend( {
-	prop: function( name, value ) {
-		return access( this, jQuery.prop, name, value, arguments.length > 1 );
-	},
-
-	removeProp: function( name ) {
-		return this.each( function() {
-			delete this[ jQuery.propFix[ name ] || name ];
-		} );
-	}
-} );
-
-jQuery.extend( {
-	prop: function( elem, name, value ) {
-		var ret, hooks,
-			nType = elem.nodeType;
-
-		// Don't get/set properties on text, comment and attribute nodes
-		if ( nType === 3 || nType === 8 || nType === 2 ) {
-			return;
-		}
-
-		if ( nType !== 1 || !jQuery.isXMLDoc( elem ) ) {
-
-			// Fix name and attach hooks
-			name = jQuery.propFix[ name ] || name;
-			hooks = jQuery.propHooks[ name ];
-		}
-
-		if ( value !== undefined ) {
-			if ( hooks && "set" in hooks &&
-				( ret = hooks.set( elem, value, name ) ) !== undefined ) {
-				return ret;
-			}
-
-			return ( elem[ name ] = value );
-		}
-
-		if ( hooks && "get" in hooks && ( ret = hooks.get( elem, name ) ) !== null ) {
-			return ret;
-		}
-
-		return elem[ name ];
-	},
-
-	propHooks: {
-		tabIndex: {
-			get: function( elem ) {
-
-				// Support: IE <=9 - 11 only
-				// elem.tabIndex doesn't always return the
-				// correct value when it hasn't been explicitly set
-				// https://web.archive.org/web/20141116233347/http://fluidproject.org/blog/2008/01/09/getting-setting-and-removing-tabindex-values-with-javascript/
-				// Use proper attribute retrieval(#12072)
-				var tabindex = jQuery.find.attr( elem, "tabindex" );
-
-				if ( tabindex ) {
-					return parseInt( tabindex, 10 );
-				}
-
-				if (
-					rfocusable.test( elem.nodeName ) ||
-					rclickable.test( elem.nodeName ) &&
-					elem.href
-				) {
-					return 0;
-				}
-
-				return -1;
-			}
-		}
-	},
-
-	propFix: {
-		"for": "htmlFor",
-		"class": "className"
-	}
-} );
-
-// Support: IE <=11 only
-// Accessing the selectedIndex property
-// forces the browser to respect setting selected
-// on the option
-// The getter ensures a default option is selected
-// when in an optgroup
-// eslint rule "no-unused-expressions" is disabled for this code
-// since it considers such accessions noop
-if ( !support.optSelected ) {
-	jQuery.propHooks.selected = {
-		get: function( elem ) {
-
-			/* eslint no-unused-expressions: "off" */
-
-			var parent = elem.parentNode;
-			if ( parent && parent.parentNode ) {
-				parent.parentNode.selectedIndex;
-			}
-			return null;
-		},
-		set: function( elem ) {
-
-			/* eslint no-unused-expressions: "off" */
-
-			var parent = elem.parentNode;
-			if ( parent ) {
-				parent.selectedIndex;
-
-				if ( parent.parentNode ) {
-					parent.parentNode.selectedIndex;
-				}
-			}
-		}
-	};
-}
-
-jQuery.each( [
-	"tabIndex",
-	"readOnly",
-	"maxLength",
-	"cellSpacing",
-	"cellPadding",
-	"rowSpan",
-	"colSpan",
-	"useMap",
-	"frameBorder",
-	"contentEditable"
-], function() {
-	jQuery.propFix[ this.toLowerCase() ] = this;
-} );
-
-
-
-
-	// Strip and collapse whitespace according to HTML spec
-	// https://infra.spec.whatwg.org/#strip-and-collapse-ascii-whitespace
-	function stripAndCollapse( value ) {
-		var tokens = value.match( rnothtmlwhite ) || [];
-		return tokens.join( " " );
-	}
-
-
-function getClass( elem ) {
-	return elem.getAttribute && elem.getAttribute( "class" ) || "";
-}
-
-function classesToArray( value ) {
-	if ( Array.isArray( value ) ) {
-		return value;
-	}
-	if ( typeof value === "string" ) {
-		return value.match( rnothtmlwhite ) || [];
-	}
-	return [];
-}
-
-jQuery.fn.extend( {
-	addClass: function( value ) {
-		var classes, elem, cur, curValue, clazz, j, finalValue,
-			i = 0;
-
-		if ( isFunction( value ) ) {
-			return this.each( function( j ) {
-				jQuery( this ).addClass( value.call( this, j, getClass( this ) ) );
-			} );
-		}
-
-		classes = classesToArray( value );
-
-		if ( classes.length ) {
-			while ( ( elem = this[ i++ ] ) ) {
-				curValue = getClass( elem );
-				cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " );
-
-				if ( cur ) {
-					j = 0;
-					while ( ( clazz = classes[ j++ ] ) ) {
-						if ( cur.indexOf( " " + clazz + " " ) < 0 ) {
-							cur += clazz + " ";
-						}
-					}
-
-					// Only assign if different to avoid unneeded rendering.
-					finalValue = stripAndCollapse( cur );
-					if ( curValue !== finalValue ) {
-						elem.setAttribute( "class", finalValue );
-					}
-				}
-			}
-		}
-
-		return this;
-	},
-
-	removeClass: function( value ) {
-		var classes, elem, cur, curValue, clazz, j, finalValue,
-			i = 0;
-
-		if ( isFunction( value ) ) {
-			return this.each( function( j ) {
-				jQuery( this ).removeClass( value.call( this, j, getClass( this ) ) );
-			} );
-		}
-
-		if ( !arguments.length ) {
-			return this.attr( "class", "" );
-		}
-
-		classes = classesToArray( value );
-
-		if ( classes.length ) {
-			while ( ( elem = this[ i++ ] ) ) {
-				curValue = getClass( elem );
-
-				// This expression is here for better compressibility (see addClass)
-				cur = elem.nodeType === 1 && ( " " + stripAndCollapse( curValue ) + " " );
-
-				if ( cur ) {
-					j = 0;
-					while ( ( clazz = classes[ j++ ] ) ) {
-
-						// Remove *all* instances
-						while ( cur.indexOf( " " + clazz + " " ) > -1 ) {
-							cur = cur.replace( " " + clazz + " ", " " );
-						}
-					}
-
-					// Only assign if different to avoid unneeded rendering.
-					finalValue = stripAndCollapse( cur );
-					if ( curValue !== finalValue ) {
-						elem.setAttribute( "class", finalValue );
-					}
-				}
-			}
-		}
-
-		return this;
-	},
-
-	toggleClass: function( value, stateVal ) {
-		var type = typeof value,
-			isValidValue = type === "string" || Array.isArray( value );
-
-		if ( typeof stateVal === "boolean" && isValidValue ) {
-			return stateVal ? this.addClass( value ) : this.removeClass( value );
-		}
-
-		if ( isFunction( value ) ) {
-			return this.each( function( i ) {
-				jQuery( this ).toggleClass(
-					value.call( this, i, getClass( this ), stateVal ),
-					stateVal
-				);
-			} );
-		}
-
-		return this.each( function() {
-			var className, i, self, classNames;
-
-			if ( isValidValue ) {
-
-				// Toggle individual class names
-				i = 0;
-				self = jQuery( this );
-				classNames = classesToArray( value );
-
-				while ( ( className = classNames[ i++ ] ) ) {
-
-					// Check each className given, space separated list
-					if ( self.hasClass( className ) ) {
-						self.removeClass( className );
-					} else {
-						self.addClass( className );
-					}
-				}
-
-			// Toggle whole class name
-			} else if ( value === undefined || type === "boolean" ) {
-				className = getClass( this );
-				if ( className ) {
-
-					// Store className if set
-					dataPriv.set( this, "__className__", className );
-				}
-
-				// If the element has a class name or if we're passed `false`,
-				// then remove the whole classname (if there was one, the above saved it).
-				// Otherwise bring back whatever was previously saved (if anything),
-				// falling back to the empty string if nothing was stored.
-				if ( this.setAttribute ) {
-					this.setAttribute( "class",
-						className || value === false ?
-							"" :
-							dataPriv.get( this, "__className__" ) || ""
-					);
-				}
-			}
-		} );
-	},
-
-	hasClass: function( selector ) {
-		var className, elem,
-			i = 0;
-
-		className = " " + selector + " ";
-		while ( ( elem = this[ i++ ] ) ) {
-			if ( elem.nodeType === 1 &&
-				( " " + stripAndCollapse( getClass( elem ) ) + " " ).indexOf( className ) > -1 ) {
-				return true;
-			}
-		}
-
-		return false;
-	}
-} );
-
-
-
-
-var rreturn = /\r/g;
-
-jQuery.fn.extend( {
-	val: function( value ) {
-		var hooks, ret, valueIsFunction,
-			elem = this[ 0 ];
-
-		if ( !arguments.length ) {
-			if ( elem ) {
-				hooks = jQuery.valHooks[ elem.type ] ||
-					jQuery.valHooks[ elem.nodeName.toLowerCase() ];
-
-				if ( hooks &&
-					"get" in hooks &&
-					( ret = hooks.get( elem, "value" ) ) !== undefined
-				) {
-					return ret;
-				}
-
-				ret = elem.value;
-
-				// Handle most common string cases
-				if ( typeof ret === "string" ) {
-					return ret.replace( rreturn, "" );
-				}
-
-				// Handle cases where value is null/undef or number
-				return ret == null ? "" : ret;
-			}
-
-			return;
-		}
-
-		valueIsFunction = isFunction( value );
-
-		return this.each( function( i ) {
-			var val;
-
-			if ( this.nodeType !== 1 ) {
-				return;
-			}
-
-			if ( valueIsFunction ) {
-				val = value.call( this, i, jQuery( this ).val() );
-			} else {
-				val = value;
-			}
-
-			// Treat null/undefined as ""; convert numbers to string
-			if ( val == null ) {
-				val = "";
-
-			} else if ( typeof val === "number" ) {
-				val += "";
-
-			} else if ( Array.isArray( val ) ) {
-				val = jQuery.map( val, function( value ) {
-					return value == null ? "" : value + "";
-				} );
-			}
-
-			hooks = jQuery.valHooks[ this.type ] || jQuery.valHooks[ this.nodeName.toLowerCase() ];
-
-			// If set returns undefined, fall back to normal setting
-			if ( !hooks || !( "set" in hooks ) || hooks.set( this, val, "value" ) === undefined ) {
-				this.value = val;
-			}
-		} );
-	}
-} );
-
-jQuery.extend( {
-	valHooks: {
-		option: {
-			get: function( elem ) {
-
-				var val = jQuery.find.attr( elem, "value" );
-				return val != null ?
-					val :
-
-					// Support: IE <=10 - 11 only
-					// option.text throws exceptions (#14686, #14858)
-					// Strip and collapse whitespace
-					// https://html.spec.whatwg.org/#strip-and-collapse-whitespace
-					stripAndCollapse( jQuery.text( elem ) );
-			}
-		},
-		select: {
-			get: function( elem ) {
-				var value, option, i,
-					options = elem.options,
-					index = elem.selectedIndex,
-					one = elem.type === "select-one",
-					values = one ? null : [],
-					max = one ? index + 1 : options.length;
-
-				if ( index < 0 ) {
-					i = max;
-
-				} else {
-					i = one ? index : 0;
-				}
-
-				// Loop through all the selected options
-				for ( ; i < max; i++ ) {
-					option = options[ i ];
-
-					// Support: IE <=9 only
-					// IE8-9 doesn't update selected after form reset (#2551)
-					if ( ( option.selected || i === index ) &&
-
-							// Don't return options that are disabled or in a disabled optgroup
-							!option.disabled &&
-							( !option.parentNode.disabled ||
-								!nodeName( option.parentNode, "optgroup" ) ) ) {
-
-						// Get the specific value for the option
-						value = jQuery( option ).val();
-
-						// We don't need an array for one selects
-						if ( one ) {
-							return value;
-						}
-
-						// Multi-Selects return an array
-						values.push( value );
-					}
-				}
-
-				return values;
-			},
-
-			set: function( elem, value ) {
-				var optionSet, option,
-					options = elem.options,
-					values = jQuery.makeArray( value ),
-					i = options.length;
-
-				while ( i-- ) {
-					option = options[ i ];
-
-					/* eslint-disable no-cond-assign */
-
-					if ( option.selected =
-						jQuery.inArray( jQuery.valHooks.option.get( option ), values ) > -1
-					) {
-						optionSet = true;
-					}
-
-					/* eslint-enable no-cond-assign */
-				}
-
-				// Force browsers to behave consistently when non-matching value is set
-				if ( !optionSet ) {
-					elem.selectedIndex = -1;
-				}
-				return values;
-			}
-		}
-	}
-} );
-
-// Radios and checkboxes getter/setter
-jQuery.each( [ "radio", "checkbox" ], function() {
-	jQuery.valHooks[ this ] = {
-		set: function( elem, value ) {
-			if ( Array.isArray( value ) ) {
-				return ( elem.checked = jQuery.inArray( jQuery( elem ).val(), value ) > -1 );
-			}
-		}
-	};
-	if ( !support.checkOn ) {
-		jQuery.valHooks[ this ].get = function( elem ) {
-			return elem.getAttribute( "value" ) === null ? "on" : elem.value;
-		};
-	}
-} );
-
-
-
-
-// Return jQuery for attributes-only inclusion
-
-
-support.focusin = "onfocusin" in window;
-
-
-var rfocusMorph = /^(?:focusinfocus|focusoutblur)$/,
-	stopPropagationCallback = function( e ) {
-		e.stopPropagation();
-	};
-
-jQuery.extend( jQuery.event, {
-
-	trigger: function( event, data, elem, onlyHandlers ) {
-
-		var i, cur, tmp, bubbleType, ontype, handle, special, lastElement,
-			eventPath = [ elem || document ],
-			type = hasOwn.call( event, "type" ) ? event.type : event,
-			namespaces = hasOwn.call( event, "namespace" ) ? event.namespace.split( "." ) : [];
-
-		cur = lastElement = tmp = elem = elem || document;
-
-		// Don't do events on text and comment nodes
-		if ( elem.nodeType === 3 || elem.nodeType === 8 ) {
-			return;
-		}
-
-		// focus/blur morphs to focusin/out; ensure we're not firing them right now
-		if ( rfocusMorph.test( type + jQuery.event.triggered ) ) {
-			return;
-		}
-
-		if ( type.indexOf( "." ) > -1 ) {
-
-			// Namespaced trigger; create a regexp to match event type in handle()
-			namespaces = type.split( "." );
-			type = namespaces.shift();
-			namespaces.sort();
-		}
-		ontype = type.indexOf( ":" ) < 0 && "on" + type;
-
-		// Caller can pass in a jQuery.Event object, Object, or just an event type string
-		event = event[ jQuery.expando ] ?
-			event :
-			new jQuery.Event( type, typeof event === "object" && event );
-
-		// Trigger bitmask: & 1 for native handlers; & 2 for jQuery (always true)
-		event.isTrigger = onlyHandlers ? 2 : 3;
-		event.namespace = namespaces.join( "." );
-		event.rnamespace = event.namespace ?
-			new RegExp( "(^|\\.)" + namespaces.join( "\\.(?:.*\\.|)" ) + "(\\.|$)" ) :
-			null;
-
-		// Clean up the event in case it is being reused
-		event.result = undefined;
-		if ( !event.target ) {
-			event.target = elem;
-		}
-
-		// Clone any incoming data and prepend the event, creating the handler arg list
-		data = data == null ?
-			[ event ] :
-			jQuery.makeArray( data, [ event ] );
-
-		// Allow special events to draw outside the lines
-		special = jQuery.event.special[ type ] || {};
-		if ( !onlyHandlers && special.trigger && special.trigger.apply( elem, data ) === false ) {
-			return;
-		}
-
-		// Determine event propagation path in advance, per W3C events spec (#9951)
-		// Bubble up to document, then to window; watch for a global ownerDocument var (#9724)
-		if ( !onlyHandlers && !special.noBubble && !isWindow( elem ) ) {
-
-			bubbleType = special.delegateType || type;
-			if ( !rfocusMorph.test( bubbleType + type ) ) {
-				cur = cur.parentNode;
-			}
-			for ( ; cur; cur = cur.parentNode ) {
-				eventPath.push( cur );
-				tmp = cur;
-			}
-
-			// Only add window if we got to document (e.g., not plain obj or detached DOM)
-			if ( tmp === ( elem.ownerDocument || document ) ) {
-				eventPath.push( tmp.defaultView || tmp.parentWindow || window );
-			}
-		}
-
-		// Fire handlers on the event path
-		i = 0;
-		while ( ( cur = eventPath[ i++ ] ) && !event.isPropagationStopped() ) {
-			lastElement = cur;
-			event.type = i > 1 ?
-				bubbleType :
-				special.bindType || type;
-
-			// jQuery handler
-			handle = ( dataPriv.get( cur, "events" ) || Object.create( null ) )[ event.type ] &&
-				dataPriv.get( cur, "handle" );
-			if ( handle ) {
-				handle.apply( cur, data );
-			}
-
-			// Native handler
-			handle = ontype && cur[ ontype ];
-			if ( handle && handle.apply && acceptData( cur ) ) {
-				event.result = handle.apply( cur, data );
-				if ( event.result === false ) {
-					event.preventDefault();
-				}
-			}
-		}
-		event.type = type;
-
-		// If nobody prevented the default action, do it now
-		if ( !onlyHandlers && !event.isDefaultPrevented() ) {
-
-			if ( ( !special._default ||
-				special._default.apply( eventPath.pop(), data ) === false ) &&
-				acceptData( elem ) ) {
-
-				// Call a native DOM method on the target with the same name as the event.
-				// Don't do default actions on window, that's where global variables be (#6170)
-				if ( ontype && isFunction( elem[ type ] ) && !isWindow( elem ) ) {
-
-					// Don't re-trigger an onFOO event when we call its FOO() method
-					tmp = elem[ ontype ];
-
-					if ( tmp ) {
-						elem[ ontype ] = null;
-					}
-
-					// Prevent re-triggering of the same event, since we already bubbled it above
-					jQuery.event.triggered = type;
-
-					if ( event.isPropagationStopped() ) {
-						lastElement.addEventListener( type, stopPropagationCallback );
-					}
-
-					elem[ type ]();
-
-					if ( event.isPropagationStopped() ) {
-						lastElement.removeEventListener( type, stopPropagationCallback );
-					}
-
-					jQuery.event.triggered = undefined;
-
-					if ( tmp ) {
-						elem[ ontype ] = tmp;
-					}
-				}
-			}
-		}
-
-		return event.result;
-	},
-
-	// Piggyback on a donor event to simulate a different one
-	// Used only for `focus(in | out)` events
-	simulate: function( type, elem, event ) {
-		var e = jQuery.extend(
-			new jQuery.Event(),
-			event,
-			{
-				type: type,
-				isSimulated: true
-			}
-		);
-
-		jQuery.event.trigger( e, null, elem );
-	}
-
-} );
-
-jQuery.fn.extend( {
-
-	trigger: function( type, data ) {
-		return this.each( function() {
-			jQuery.event.trigger( type, data, this );
-		} );
-	},
-	triggerHandler: function( type, data ) {
-		var elem = this[ 0 ];
-		if ( elem ) {
-			return jQuery.event.trigger( type, data, elem, true );
-		}
-	}
-} );
-
-
-// Support: Firefox <=44
-// Firefox doesn't have focus(in | out) events
-// Related ticket - https://bugzilla.mozilla.org/show_bug.cgi?id=687787
-//
-// Support: Chrome <=48 - 49, Safari <=9.0 - 9.1
-// focus(in | out) events fire after focus & blur events,
-// which is spec violation - http://www.w3.org/TR/DOM-Level-3-Events/#events-focusevent-event-order
-// Related ticket - https://bugs.chromium.org/p/chromium/issues/detail?id=449857
-if ( !support.focusin ) {
-	jQuery.each( { focus: "focusin", blur: "focusout" }, function( orig, fix ) {
-
-		// Attach a single capturing handler on the document while someone wants focusin/focusout
-		var handler = function( event ) {
-			jQuery.event.simulate( fix, event.target, jQuery.event.fix( event ) );
-		};
-
-		jQuery.event.special[ fix ] = {
-			setup: function() {
-
-				// Handle: regular nodes (via `this.ownerDocument`), window
-				// (via `this.document`) & document (via `this`).
-				var doc = this.ownerDocument || this.document || this,
-					attaches = dataPriv.access( doc, fix );
-
-				if ( !attaches ) {
-					doc.addEventListener( orig, handler, true );
-				}
-				dataPriv.access( doc, fix, ( attaches || 0 ) + 1 );
-			},
-			teardown: function() {
-				var doc = this.ownerDocument || this.document || this,
-					attaches = dataPriv.access( doc, fix ) - 1;
-
-				if ( !attaches ) {
-					doc.removeEventListener( orig, handler, true );
-					dataPriv.remove( doc, fix );
-
-				} else {
-					dataPriv.access( doc, fix, attaches );
-				}
-			}
-		};
-	} );
-}
-var location = window.location;
-
-var nonce = { guid: Date.now() };
-
-var rquery = ( /\?/ );
-
-
-
-// Cross-browser xml parsing
-jQuery.parseXML = function( data ) {
-	var xml, parserErrorElem;
-	if ( !data || typeof data !== "string" ) {
-		return null;
-	}
-
-	// Support: IE 9 - 11 only
-	// IE throws on parseFromString with invalid input.
-	try {
-		xml = ( new window.DOMParser() ).parseFromString( data, "text/xml" );
-	} catch ( e ) {}
-
-	parserErrorElem = xml && xml.getElementsByTagName( "parsererror" )[ 0 ];
-	if ( !xml || parserErrorElem ) {
-		jQuery.error( "Invalid XML: " + (
-			parserErrorElem ?
-				jQuery.map( parserErrorElem.childNodes, function( el ) {
-					return el.textContent;
-				} ).join( "\n" ) :
-				data
-		) );
-	}
-	return xml;
-};
-
-
-var
-	rbracket = /\[\]$/,
-	rCRLF = /\r?\n/g,
-	rsubmitterTypes = /^(?:submit|button|image|reset|file)$/i,
-	rsubmittable = /^(?:input|select|textarea|keygen)/i;
-
-function buildParams( prefix, obj, traditional, add ) {
-	var name;
-
-	if ( Array.isArray( obj ) ) {
-
-		// Serialize array item.
-		jQuery.each( obj, function( i, v ) {
-			if ( traditional || rbracket.test( prefix ) ) {
-
-				// Treat each array item as a scalar.
-				add( prefix, v );
-
-			} else {
-
-				// Item is non-scalar (array or object), encode its numeric index.
-				buildParams(
-					prefix + "[" + ( typeof v === "object" && v != null ? i : "" ) + "]",
-					v,
-					traditional,
-					add
-				);
-			}
-		} );
-
-	} else if ( !traditional && toType( obj ) === "object" ) {
-
-		// Serialize object item.
-		for ( name in obj ) {
-			buildParams( prefix + "[" + name + "]", obj[ name ], traditional, add );
-		}
-
-	} else {
-
-		// Serialize scalar item.
-		add( prefix, obj );
-	}
-}
-
-// Serialize an array of form elements or a set of
-// key/values into a query string
-jQuery.param = function( a, traditional ) {
-	var prefix,
-		s = [],
-		add = function( key, valueOrFunction ) {
-
-			// If value is a function, invoke it and use its return value
-			var value = isFunction( valueOrFunction ) ?
-				valueOrFunction() :
-				valueOrFunction;
-
-			s[ s.length ] = encodeURIComponent( key ) + "=" +
-				encodeURIComponent( value == null ? "" : value );
-		};
-
-	if ( a == null ) {
-		return "";
-	}
-
-	// If an array was passed in, assume that it is an array of form elements.
-	if ( Array.isArray( a ) || ( a.jquery && !jQuery.isPlainObject( a ) ) ) {
-
-		// Serialize the form elements
-		jQuery.each( a, function() {
-			add( this.name, this.value );
-		} );
-
-	} else {
-
-		// If traditional, encode the "old" way (the way 1.3.2 or older
-		// did it), otherwise encode params recursively.
-		for ( prefix in a ) {
-			buildParams( prefix, a[ prefix ], traditional, add );
-		}
-	}
-
-	// Return the resulting serialization
-	return s.join( "&" );
-};
-
-jQuery.fn.extend( {
-	serialize: function() {
-		return jQuery.param( this.serializeArray() );
-	},
-	serializeArray: function() {
-		return this.map( function() {
-
-			// Can add propHook for "elements" to filter or add form elements
-			var elements = jQuery.prop( this, "elements" );
-			return elements ? jQuery.makeArray( elements ) : this;
-		} ).filter( function() {
-			var type = this.type;
-
-			// Use .is( ":disabled" ) so that fieldset[disabled] works
-			return this.name && !jQuery( this ).is( ":disabled" ) &&
-				rsubmittable.test( this.nodeName ) && !rsubmitterTypes.test( type ) &&
-				( this.checked || !rcheckableType.test( type ) );
-		} ).map( function( _i, elem ) {
-			var val = jQuery( this ).val();
-
-			if ( val == null ) {
-				return null;
-			}
-
-			if ( Array.isArray( val ) ) {
-				return jQuery.map( val, function( val ) {
-					return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
-				} );
-			}
-
-			return { name: elem.name, value: val.replace( rCRLF, "\r\n" ) };
-		} ).get();
-	}
-} );
-
-
-var
-	r20 = /%20/g,
-	rhash = /#.*$/,
-	rantiCache = /([?&])_=[^&]*/,
-	rheaders = /^(.*?):[ \t]*([^\r\n]*)$/mg,
-
-	// #7653, #8125, #8152: local protocol detection
-	rlocalProtocol = /^(?:about|app|app-storage|.+-extension|file|res|widget):$/,
-	rnoContent = /^(?:GET|HEAD)$/,
-	rprotocol = /^\/\//,
-
-	/* Prefilters
-	 * 1) They are useful to introduce custom dataTypes (see ajax/jsonp.js for an example)
-	 * 2) These are called:
-	 *    - BEFORE asking for a transport
-	 *    - AFTER param serialization (s.data is a string if s.processData is true)
-	 * 3) key is the dataType
-	 * 4) the catchall symbol "*" can be used
-	 * 5) execution will start with transport dataType and THEN continue down to "*" if needed
-	 */
-	prefilters = {},
-
-	/* Transports bindings
-	 * 1) key is the dataType
-	 * 2) the catchall symbol "*" can be used
-	 * 3) selection will start with transport dataType and THEN go to "*" if needed
-	 */
-	transports = {},
-
-	// Avoid comment-prolog char sequence (#10098); must appease lint and evade compression
-	allTypes = "*/".concat( "*" ),
-
-	// Anchor tag for parsing the document origin
-	originAnchor = document.createElement( "a" );
-
-originAnchor.href = location.href;
-
-// Base "constructor" for jQuery.ajaxPrefilter and jQuery.ajaxTransport
-function addToPrefiltersOrTransports( structure ) {
-
-	// dataTypeExpression is optional and defaults to "*"
-	return function( dataTypeExpression, func ) {
-
-		if ( typeof dataTypeExpression !== "string" ) {
-			func = dataTypeExpression;
-			dataTypeExpression = "*";
-		}
-
-		var dataType,
-			i = 0,
-			dataTypes = dataTypeExpression.toLowerCase().match( rnothtmlwhite ) || [];
-
-		if ( isFunction( func ) ) {
-
-			// For each dataType in the dataTypeExpression
-			while ( ( dataType = dataTypes[ i++ ] ) ) {
-
-				// Prepend if requested
-				if ( dataType[ 0 ] === "+" ) {
-					dataType = dataType.slice( 1 ) || "*";
-					( structure[ dataType ] = structure[ dataType ] || [] ).unshift( func );
-
-				// Otherwise append
-				} else {
-					( structure[ dataType ] = structure[ dataType ] || [] ).push( func );
-				}
-			}
-		}
-	};
-}
-
-// Base inspection function for prefilters and transports
-function inspectPrefiltersOrTransports( structure, options, originalOptions, jqXHR ) {
-
-	var inspected = {},
-		seekingTransport = ( structure === transports );
-
-	function inspect( dataType ) {
-		var selected;
-		inspected[ dataType ] = true;
-		jQuery.each( structure[ dataType ] || [], function( _, prefilterOrFactory ) {
-			var dataTypeOrTransport = prefilterOrFactory( options, originalOptions, jqXHR );
-			if ( typeof dataTypeOrTransport === "string" &&
-				!seekingTransport && !inspected[ dataTypeOrTransport ] ) {
-
-				options.dataTypes.unshift( dataTypeOrTransport );
-				inspect( dataTypeOrTransport );
-				return false;
-			} else if ( seekingTransport ) {
-				return !( selected = dataTypeOrTransport );
-			}
-		} );
-		return selected;
-	}
-
-	return inspect( options.dataTypes[ 0 ] ) || !inspected[ "*" ] && inspect( "*" );
-}
-
-// A special extend for ajax options
-// that takes "flat" options (not to be deep extended)
-// Fixes #9887
-function ajaxExtend( target, src ) {
-	var key, deep,
-		flatOptions = jQuery.ajaxSettings.flatOptions || {};
-
-	for ( key in src ) {
-		if ( src[ key ] !== undefined ) {
-			( flatOptions[ key ] ? target : ( deep || ( deep = {} ) ) )[ key ] = src[ key ];
-		}
-	}
-	if ( deep ) {
-		jQuery.extend( true, target, deep );
-	}
-
-	return target;
-}
-
-/* Handles responses to an ajax request:
- * - finds the right dataType (mediates between content-type and expected dataType)
- * - returns the corresponding response
- */
-function ajaxHandleResponses( s, jqXHR, responses ) {
-
-	var ct, type, finalDataType, firstDataType,
-		contents = s.contents,
-		dataTypes = s.dataTypes;
-
-	// Remove auto dataType and get content-type in the process
-	while ( dataTypes[ 0 ] === "*" ) {
-		dataTypes.shift();
-		if ( ct === undefined ) {
-			ct = s.mimeType || jqXHR.getResponseHeader( "Content-Type" );
-		}
-	}
-
-	// Check if we're dealing with a known content-type
-	if ( ct ) {
-		for ( type in contents ) {
-			if ( contents[ type ] && contents[ type ].test( ct ) ) {
-				dataTypes.unshift( type );
-				break;
-			}
-		}
-	}
-
-	// Check to see if we have a response for the expected dataType
-	if ( dataTypes[ 0 ] in responses ) {
-		finalDataType = dataTypes[ 0 ];
-	} else {
-
-		// Try convertible dataTypes
-		for ( type in responses ) {
-			if ( !dataTypes[ 0 ] || s.converters[ type + " " + dataTypes[ 0 ] ] ) {
-				finalDataType = type;
-				break;
-			}
-			if ( !firstDataType ) {
-				firstDataType = type;
-			}
-		}
-
-		// Or just use first one
-		finalDataType = finalDataType || firstDataType;
-	}
-
-	// If we found a dataType
-	// We add the dataType to the list if needed
-	// and return the corresponding response
-	if ( finalDataType ) {
-		if ( finalDataType !== dataTypes[ 0 ] ) {
-			dataTypes.unshift( finalDataType );
-		}
-		return responses[ finalDataType ];
-	}
-}
-
-/* Chain conversions given the request and the original response
- * Also sets the responseXXX fields on the jqXHR instance
- */
-function ajaxConvert( s, response, jqXHR, isSuccess ) {
-	var conv2, current, conv, tmp, prev,
-		converters = {},
-
-		// Work with a copy of dataTypes in case we need to modify it for conversion
-		dataTypes = s.dataTypes.slice();
-
-	// Create converters map with lowercased keys
-	if ( dataTypes[ 1 ] ) {
-		for ( conv in s.converters ) {
-			converters[ conv.toLowerCase() ] = s.converters[ conv ];
-		}
-	}
-
-	current = dataTypes.shift();
-
-	// Convert to each sequential dataType
-	while ( current ) {
-
-		if ( s.responseFields[ current ] ) {
-			jqXHR[ s.responseFields[ current ] ] = response;
-		}
-
-		// Apply the dataFilter if provided
-		if ( !prev && isSuccess && s.dataFilter ) {
-			response = s.dataFilter( response, s.dataType );
-		}
-
-		prev = current;
-		current = dataTypes.shift();
-
-		if ( current ) {
-
-			// There's only work to do if current dataType is non-auto
-			if ( current === "*" ) {
-
-				current = prev;
-
-			// Convert response if prev dataType is non-auto and differs from current
-			} else if ( prev !== "*" && prev !== current ) {
-
-				// Seek a direct converter
-				conv = converters[ prev + " " + current ] || converters[ "* " + current ];
-
-				// If none found, seek a pair
-				if ( !conv ) {
-					for ( conv2 in converters ) {
-
-						// If conv2 outputs current
-						tmp = conv2.split( " " );
-						if ( tmp[ 1 ] === current ) {
-
-							// If prev can be converted to accepted input
-							conv = converters[ prev + " " + tmp[ 0 ] ] ||
-								converters[ "* " + tmp[ 0 ] ];
-							if ( conv ) {
-
-								// Condense equivalence converters
-								if ( conv === true ) {
-									conv = converters[ conv2 ];
-
-								// Otherwise, insert the intermediate dataType
-								} else if ( converters[ conv2 ] !== true ) {
-									current = tmp[ 0 ];
-									dataTypes.unshift( tmp[ 1 ] );
-								}
-								break;
-							}
-						}
-					}
-				}
-
-				// Apply converter (if not an equivalence)
-				if ( conv !== true ) {
-
-					// Unless errors are allowed to bubble, catch and return them
-					if ( conv && s.throws ) {
-						response = conv( response );
-					} else {
-						try {
-							response = conv( response );
-						} catch ( e ) {
-							return {
-								state: "parsererror",
-								error: conv ? e : "No conversion from " + prev + " to " + current
-							};
-						}
-					}
-				}
-			}
-		}
-	}
-
-	return { state: "success", data: response };
-}
-
-jQuery.extend( {
-
-	// Counter for holding the number of active queries
-	active: 0,
-
-	// Last-Modified header cache for next request
-	lastModified: {},
-	etag: {},
-
-	ajaxSettings: {
-		url: location.href,
-		type: "GET",
-		isLocal: rlocalProtocol.test( location.protocol ),
-		global: true,
-		processData: true,
-		async: true,
-		contentType: "application/x-www-form-urlencoded; charset=UTF-8",
-
-		/*
-		timeout: 0,
-		data: null,
-		dataType: null,
-		username: null,
-		password: null,
-		cache: null,
-		throws: false,
-		traditional: false,
-		headers: {},
-		*/
-
-		accepts: {
-			"*": allTypes,
-			text: "text/plain",
-			html: "text/html",
-			xml: "application/xml, text/xml",
-			json: "application/json, text/javascript"
-		},
-
-		contents: {
-			xml: /\bxml\b/,
-			html: /\bhtml/,
-			json: /\bjson\b/
-		},
-
-		responseFields: {
-			xml: "responseXML",
-			text: "responseText",
-			json: "responseJSON"
-		},
-
-		// Data converters
-		// Keys separate source (or catchall "*") and destination types with a single space
-		converters: {
-
-			// Convert anything to text
-			"* text": String,
-
-			// Text to html (true = no transformation)
-			"text html": true,
-
-			// Evaluate text as a json expression
-			"text json": JSON.parse,
-
-			// Parse text as xml
-			"text xml": jQuery.parseXML
-		},
-
-		// For options that shouldn't be deep extended:
-		// you can add your own custom options here if
-		// and when you create one that shouldn't be
-		// deep extended (see ajaxExtend)
-		flatOptions: {
-			url: true,
-			context: true
-		}
-	},
-
-	// Creates a full fledged settings object into target
-	// with both ajaxSettings and settings fields.
-	// If target is omitted, writes into ajaxSettings.
-	ajaxSetup: function( target, settings ) {
-		return settings ?
-
-			// Building a settings object
-			ajaxExtend( ajaxExtend( target, jQuery.ajaxSettings ), settings ) :
-
-			// Extending ajaxSettings
-			ajaxExtend( jQuery.ajaxSettings, target );
-	},
-
-	ajaxPrefilter: addToPrefiltersOrTransports( prefilters ),
-	ajaxTransport: addToPrefiltersOrTransports( transports ),
-
-	// Main method
-	ajax: function( url, options ) {
-
-		// If url is an object, simulate pre-1.5 signature
-		if ( typeof url === "object" ) {
-			options = url;
-			url = undefined;
-		}
-
-		// Force options to be an object
-		options = options || {};
-
-		var transport,
-
-			// URL without anti-cache param
-			cacheURL,
-
-			// Response headers
-			responseHeadersString,
-			responseHeaders,
-
-			// timeout handle
-			timeoutTimer,
-
-			// Url cleanup var
-			urlAnchor,
-
-			// Request state (becomes false upon send and true upon completion)
-			completed,
-
-			// To know if global events are to be dispatched
-			fireGlobals,
-
-			// Loop variable
-			i,
-
-			// uncached part of the url
-			uncached,
-
-			// Create the final options object
-			s = jQuery.ajaxSetup( {}, options ),
-
-			// Callbacks context
-			callbackContext = s.context || s,
-
-			// Context for global events is callbackContext if it is a DOM node or jQuery collection
-			globalEventContext = s.context &&
-				( callbackContext.nodeType || callbackContext.jquery ) ?
-				jQuery( callbackContext ) :
-				jQuery.event,
-
-			// Deferreds
-			deferred = jQuery.Deferred(),
-			completeDeferred = jQuery.Callbacks( "once memory" ),
-
-			// Status-dependent callbacks
-			statusCode = s.statusCode || {},
-
-			// Headers (they are sent all at once)
-			requestHeaders = {},
-			requestHeadersNames = {},
-
-			// Default abort message
-			strAbort = "canceled",
-
-			// Fake xhr
-			jqXHR = {
-				readyState: 0,
-
-				// Builds headers hashtable if needed
-				getResponseHeader: function( key ) {
-					var match;
-					if ( completed ) {
-						if ( !responseHeaders ) {
-							responseHeaders = {};
-							while ( ( match = rheaders.exec( responseHeadersString ) ) ) {
-								responseHeaders[ match[ 1 ].toLowerCase() + " " ] =
-									( responseHeaders[ match[ 1 ].toLowerCase() + " " ] || [] )
-										.concat( match[ 2 ] );
-							}
-						}
-						match = responseHeaders[ key.toLowerCase() + " " ];
-					}
-					return match == null ? null : match.join( ", " );
-				},
-
-				// Raw string
-				getAllResponseHeaders: function() {
-					return completed ? responseHeadersString : null;
-				},
-
-				// Caches the header
-				setRequestHeader: function( name, value ) {
-					if ( completed == null ) {
-						name = requestHeadersNames[ name.toLowerCase() ] =
-							requestHeadersNames[ name.toLowerCase() ] || name;
-						requestHeaders[ name ] = value;
-					}
-					return this;
-				},
-
-				// Overrides response content-type header
-				overrideMimeType: function( type ) {
-					if ( completed == null ) {
-						s.mimeType = type;
-					}
-					return this;
-				},
-
-				// Status-dependent callbacks
-				statusCode: function( map ) {
-					var code;
-					if ( map ) {
-						if ( completed ) {
-
-							// Execute the appropriate callbacks
-							jqXHR.always( map[ jqXHR.status ] );
-						} else {
-
-							// Lazy-add the new callbacks in a way that preserves old ones
-							for ( code in map ) {
-								statusCode[ code ] = [ statusCode[ code ], map[ code ] ];
-							}
-						}
-					}
-					return this;
-				},
-
-				// Cancel the request
-				abort: function( statusText ) {
-					var finalText = statusText || strAbort;
-					if ( transport ) {
-						transport.abort( finalText );
-					}
-					done( 0, finalText );
-					return this;
-				}
-			};
-
-		// Attach deferreds
-		deferred.promise( jqXHR );
-
-		// Add protocol if not provided (prefilters might expect it)
-		// Handle falsy url in the settings object (#10093: consistency with old signature)
-		// We also use the url parameter if available
-		s.url = ( ( url || s.url || location.href ) + "" )
-			.replace( rprotocol, location.protocol + "//" );
-
-		// Alias method option to type as per ticket #12004
-		s.type = options.method || options.type || s.method || s.type;
-
-		// Extract dataTypes list
-		s.dataTypes = ( s.dataType || "*" ).toLowerCase().match( rnothtmlwhite ) || [ "" ];
-
-		// A cross-domain request is in order when the origin doesn't match the current origin.
-		if ( s.crossDomain == null ) {
-			urlAnchor = document.createElement( "a" );
-
-			// Support: IE <=8 - 11, Edge 12 - 15
-			// IE throws exception on accessing the href property if url is malformed,
-			// e.g. http://example.com:80x/
-			try {
-				urlAnchor.href = s.url;
-
-				// Support: IE <=8 - 11 only
-				// Anchor's host property isn't correctly set when s.url is relative
-				urlAnchor.href = urlAnchor.href;
-				s.crossDomain = originAnchor.protocol + "//" + originAnchor.host !==
-					urlAnchor.protocol + "//" + urlAnchor.host;
-			} catch ( e ) {
-
-				// If there is an error parsing the URL, assume it is crossDomain,
-				// it can be rejected by the transport if it is invalid
-				s.crossDomain = true;
-			}
-		}
-
-		// Convert data if not already a string
-		if ( s.data && s.processData && typeof s.data !== "string" ) {
-			s.data = jQuery.param( s.data, s.traditional );
-		}
-
-		// Apply prefilters
-		inspectPrefiltersOrTransports( prefilters, s, options, jqXHR );
-
-		// If request was aborted inside a prefilter, stop there
-		if ( completed ) {
-			return jqXHR;
-		}
-
-		// We can fire global events as of now if asked to
-		// Don't fire events if jQuery.event is undefined in an AMD-usage scenario (#15118)
-		fireGlobals = jQuery.event && s.global;
-
-		// Watch for a new set of requests
-		if ( fireGlobals && jQuery.active++ === 0 ) {
-			jQuery.event.trigger( "ajaxStart" );
-		}
-
-		// Uppercase the type
-		s.type = s.type.toUpperCase();
-
-		// Determine if request has content
-		s.hasContent = !rnoContent.test( s.type );
-
-		// Save the URL in case we're toying with the If-Modified-Since
-		// and/or If-None-Match header later on
-		// Remove hash to simplify url manipulation
-		cacheURL = s.url.replace( rhash, "" );
-
-		// More options handling for requests with no content
-		if ( !s.hasContent ) {
-
-			// Remember the hash so we can put it back
-			uncached = s.url.slice( cacheURL.length );
-
-			// If data is available and should be processed, append data to url
-			if ( s.data && ( s.processData || typeof s.data === "string" ) ) {
-				cacheURL += ( rquery.test( cacheURL ) ? "&" : "?" ) + s.data;
-
-				// #9682: remove data so that it's not used in an eventual retry
-				delete s.data;
-			}
-
-			// Add or update anti-cache param if needed
-			if ( s.cache === false ) {
-				cacheURL = cacheURL.replace( rantiCache, "$1" );
-				uncached = ( rquery.test( cacheURL ) ? "&" : "?" ) + "_=" + ( nonce.guid++ ) +
-					uncached;
-			}
-
-			// Put hash and anti-cache on the URL that will be requested (gh-1732)
-			s.url = cacheURL + uncached;
-
-		// Change '%20' to '+' if this is encoded form body content (gh-2658)
-		} else if ( s.data && s.processData &&
-			( s.contentType || "" ).indexOf( "application/x-www-form-urlencoded" ) === 0 ) {
-			s.data = s.data.replace( r20, "+" );
-		}
-
-		// Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
-		if ( s.ifModified ) {
-			if ( jQuery.lastModified[ cacheURL ] ) {
-				jqXHR.setRequestHeader( "If-Modified-Since", jQuery.lastModified[ cacheURL ] );
-			}
-			if ( jQuery.etag[ cacheURL ] ) {
-				jqXHR.setRequestHeader( "If-None-Match", jQuery.etag[ cacheURL ] );
-			}
-		}
-
-		// Set the correct header, if data is being sent
-		if ( s.data && s.hasContent && s.contentType !== false || options.contentType ) {
-			jqXHR.setRequestHeader( "Content-Type", s.contentType );
-		}
-
-		// Set the Accepts header for the server, depending on the dataType
-		jqXHR.setRequestHeader(
-			"Accept",
-			s.dataTypes[ 0 ] && s.accepts[ s.dataTypes[ 0 ] ] ?
-				s.accepts[ s.dataTypes[ 0 ] ] +
-					( s.dataTypes[ 0 ] !== "*" ? ", " + allTypes + "; q=0.01" : "" ) :
-				s.accepts[ "*" ]
-		);
-
-		// Check for headers option
-		for ( i in s.headers ) {
-			jqXHR.setRequestHeader( i, s.headers[ i ] );
-		}
-
-		// Allow custom headers/mimetypes and early abort
-		if ( s.beforeSend &&
-			( s.beforeSend.call( callbackContext, jqXHR, s ) === false || completed ) ) {
-
-			// Abort if not done already and return
-			return jqXHR.abort();
-		}
-
-		// Aborting is no longer a cancellation
-		strAbort = "abort";
-
-		// Install callbacks on deferreds
-		completeDeferred.add( s.complete );
-		jqXHR.done( s.success );
-		jqXHR.fail( s.error );
-
-		// Get transport
-		transport = inspectPrefiltersOrTransports( transports, s, options, jqXHR );
-
-		// If no transport, we auto-abort
-		if ( !transport ) {
-			done( -1, "No Transport" );
-		} else {
-			jqXHR.readyState = 1;
-
-			// Send global event
-			if ( fireGlobals ) {
-				globalEventContext.trigger( "ajaxSend", [ jqXHR, s ] );
-			}
-
-			// If request was aborted inside ajaxSend, stop there
-			if ( completed ) {
-				return jqXHR;
-			}
-
-			// Timeout
-			if ( s.async && s.timeout > 0 ) {
-				timeoutTimer = window.setTimeout( function() {
-					jqXHR.abort( "timeout" );
-				}, s.timeout );
-			}
-
-			try {
-				completed = false;
-				transport.send( requestHeaders, done );
-			} catch ( e ) {
-
-				// Rethrow post-completion exceptions
-				if ( completed ) {
-					throw e;
-				}
-
-				// Propagate others as results
-				done( -1, e );
-			}
-		}
-
-		// Callback for when everything is done
-		function done( status, nativeStatusText, responses, headers ) {
-			var isSuccess, success, error, response, modified,
-				statusText = nativeStatusText;
-
-			// Ignore repeat invocations
-			if ( completed ) {
-				return;
-			}
-
-			completed = true;
-
-			// Clear timeout if it exists
-			if ( timeoutTimer ) {
-				window.clearTimeout( timeoutTimer );
-			}
-
-			// Dereference transport for early garbage collection
-			// (no matter how long the jqXHR object will be used)
-			transport = undefined;
-
-			// Cache response headers
-			responseHeadersString = headers || "";
-
-			// Set readyState
-			jqXHR.readyState = status > 0 ? 4 : 0;
-
-			// Determine if successful
-			isSuccess = status >= 200 && status < 300 || status === 304;
-
-			// Get response data
-			if ( responses ) {
-				response = ajaxHandleResponses( s, jqXHR, responses );
-			}
-
-			// Use a noop converter for missing script but not if jsonp
-			if ( !isSuccess &&
-				jQuery.inArray( "script", s.dataTypes ) > -1 &&
-				jQuery.inArray( "json", s.dataTypes ) < 0 ) {
-				s.converters[ "text script" ] = function() {};
-			}
-
-			// Convert no matter what (that way responseXXX fields are always set)
-			response = ajaxConvert( s, response, jqXHR, isSuccess );
-
-			// If successful, handle type chaining
-			if ( isSuccess ) {
-
-				// Set the If-Modified-Since and/or If-None-Match header, if in ifModified mode.
-				if ( s.ifModified ) {
-					modified = jqXHR.getResponseHeader( "Last-Modified" );
-					if ( modified ) {
-						jQuery.lastModified[ cacheURL ] = modified;
-					}
-					modified = jqXHR.getResponseHeader( "etag" );
-					if ( modified ) {
-						jQuery.etag[ cacheURL ] = modified;
-					}
-				}
-
-				// if no content
-				if ( status === 204 || s.type === "HEAD" ) {
-					statusText = "nocontent";
-
-				// if not modified
-				} else if ( status === 304 ) {
-					statusText = "notmodified";
-
-				// If we have data, let's convert it
-				} else {
-					statusText = response.state;
-					success = response.data;
-					error = response.error;
-					isSuccess = !error;
-				}
-			} else {
-
-				// Extract error from statusText and normalize for non-aborts
-				error = statusText;
-				if ( status || !statusText ) {
-					statusText = "error";
-					if ( status < 0 ) {
-						status = 0;
-					}
-				}
-			}
-
-			// Set data for the fake xhr object
-			jqXHR.status = status;
-			jqXHR.statusText = ( nativeStatusText || statusText ) + "";
-
-			// Success/Error
-			if ( isSuccess ) {
-				deferred.resolveWith( callbackContext, [ success, statusText, jqXHR ] );
-			} else {
-				deferred.rejectWith( callbackContext, [ jqXHR, statusText, error ] );
-			}
-
-			// Status-dependent callbacks
-			jqXHR.statusCode( statusCode );
-			statusCode = undefined;
-
-			if ( fireGlobals ) {
-				globalEventContext.trigger( isSuccess ? "ajaxSuccess" : "ajaxError",
-					[ jqXHR, s, isSuccess ? success : error ] );
-			}
-
-			// Complete
-			completeDeferred.fireWith( callbackContext, [ jqXHR, statusText ] );
-
-			if ( fireGlobals ) {
-				globalEventContext.trigger( "ajaxComplete", [ jqXHR, s ] );
-
-				// Handle the global AJAX counter
-				if ( !( --jQuery.active ) ) {
-					jQuery.event.trigger( "ajaxStop" );
-				}
-			}
-		}
-
-		return jqXHR;
-	},
-
-	getJSON: function( url, data, callback ) {
-		return jQuery.get( url, data, callback, "json" );
-	},
-
-	getScript: function( url, callback ) {
-		return jQuery.get( url, undefined, callback, "script" );
-	}
-} );
-
-jQuery.each( [ "get", "post" ], function( _i, method ) {
-	jQuery[ method ] = function( url, data, callback, type ) {
-
-		// Shift arguments if data argument was omitted
-		if ( isFunction( data ) ) {
-			type = type || callback;
-			callback = data;
-			data = undefined;
-		}
-
-		// The url can be an options object (which then must have .url)
-		return jQuery.ajax( jQuery.extend( {
-			url: url,
-			type: method,
-			dataType: type,
-			data: data,
-			success: callback
-		}, jQuery.isPlainObject( url ) && url ) );
-	};
-} );
-
-jQuery.ajaxPrefilter( function( s ) {
-	var i;
-	for ( i in s.headers ) {
-		if ( i.toLowerCase() === "content-type" ) {
-			s.contentType = s.headers[ i ] || "";
-		}
-	}
-} );
-
-
-jQuery._evalUrl = function( url, options, doc ) {
-	return jQuery.ajax( {
-		url: url,
-
-		// Make this explicit, since user can override this through ajaxSetup (#11264)
-		type: "GET",
-		dataType: "script",
-		cache: true,
-		async: false,
-		global: false,
-
-		// Only evaluate the response if it is successful (gh-4126)
-		// dataFilter is not invoked for failure responses, so using it instead
-		// of the default converter is kludgy but it works.
-		converters: {
-			"text script": function() {}
-		},
-		dataFilter: function( response ) {
-			jQuery.globalEval( response, options, doc );
-		}
-	} );
-};
-
-
-jQuery.fn.extend( {
-	wrapAll: function( html ) {
-		var wrap;
-
-		if ( this[ 0 ] ) {
-			if ( isFunction( html ) ) {
-				html = html.call( this[ 0 ] );
-			}
-
-			// The elements to wrap the target around
-			wrap = jQuery( html, this[ 0 ].ownerDocument ).eq( 0 ).clone( true );
-
-			if ( this[ 0 ].parentNode ) {
-				wrap.insertBefore( this[ 0 ] );
-			}
-
-			wrap.map( function() {
-				var elem = this;
-
-				while ( elem.firstElementChild ) {
-					elem = elem.firstElementChild;
-				}
-
-				return elem;
-			} ).append( this );
-		}
-
-		return this;
-	},
-
-	wrapInner: function( html ) {
-		if ( isFunction( html ) ) {
-			return this.each( function( i ) {
-				jQuery( this ).wrapInner( html.call( this, i ) );
-			} );
-		}
-
-		return this.each( function() {
-			var self = jQuery( this ),
-				contents = self.contents();
-
-			if ( contents.length ) {
-				contents.wrapAll( html );
-
-			} else {
-				self.append( html );
-			}
-		} );
-	},
-
-	wrap: function( html ) {
-		var htmlIsFunction = isFunction( html );
-
-		return this.each( function( i ) {
-			jQuery( this ).wrapAll( htmlIsFunction ? html.call( this, i ) : html );
-		} );
-	},
-
-	unwrap: function( selector ) {
-		this.parent( selector ).not( "body" ).each( function() {
-			jQuery( this ).replaceWith( this.childNodes );
-		} );
-		return this;
-	}
-} );
-
-
-jQuery.expr.pseudos.hidden = function( elem ) {
-	return !jQuery.expr.pseudos.visible( elem );
-};
-jQuery.expr.pseudos.visible = function( elem ) {
-	return !!( elem.offsetWidth || elem.offsetHeight || elem.getClientRects().length );
-};
-
-
-
-
-jQuery.ajaxSettings.xhr = function() {
-	try {
-		return new window.XMLHttpRequest();
-	} catch ( e ) {}
-};
-
-var xhrSuccessStatus = {
-
-		// File protocol always yields status code 0, assume 200
-		0: 200,
-
-		// Support: IE <=9 only
-		// #1450: sometimes IE returns 1223 when it should be 204
-		1223: 204
-	},
-	xhrSupported = jQuery.ajaxSettings.xhr();
-
-support.cors = !!xhrSupported && ( "withCredentials" in xhrSupported );
-support.ajax = xhrSupported = !!xhrSupported;
-
-jQuery.ajaxTransport( function( options ) {
-	var callback, errorCallback;
-
-	// Cross domain only allowed if supported through XMLHttpRequest
-	if ( support.cors || xhrSupported && !options.crossDomain ) {
-		return {
-			send: function( headers, complete ) {
-				var i,
-					xhr = options.xhr();
-
-				xhr.open(
-					options.type,
-					options.url,
-					options.async,
-					options.username,
-					options.password
-				);
-
-				// Apply custom fields if provided
-				if ( options.xhrFields ) {
-					for ( i in options.xhrFields ) {
-						xhr[ i ] = options.xhrFields[ i ];
-					}
-				}
-
-				// Override mime type if needed
-				if ( options.mimeType && xhr.overrideMimeType ) {
-					xhr.overrideMimeType( options.mimeType );
-				}
-
-				// X-Requested-With header
-				// For cross-domain requests, seeing as conditions for a preflight are
-				// akin to a jigsaw puzzle, we simply never set it to be sure.
-				// (it can always be set on a per-request basis or even using ajaxSetup)
-				// For same-domain requests, won't change header if already provided.
-				if ( !options.crossDomain && !headers[ "X-Requested-With" ] ) {
-					headers[ "X-Requested-With" ] = "XMLHttpRequest";
-				}
-
-				// Set headers
-				for ( i in headers ) {
-					xhr.setRequestHeader( i, headers[ i ] );
-				}
-
-				// Callback
-				callback = function( type ) {
-					return function() {
-						if ( callback ) {
-							callback = errorCallback = xhr.onload =
-								xhr.onerror = xhr.onabort = xhr.ontimeout =
-									xhr.onreadystatechange = null;
-
-							if ( type === "abort" ) {
-								xhr.abort();
-							} else if ( type === "error" ) {
-
-								// Support: IE <=9 only
-								// On a manual native abort, IE9 throws
-								// errors on any property access that is not readyState
-								if ( typeof xhr.status !== "number" ) {
-									complete( 0, "error" );
-								} else {
-									complete(
-
-										// File: protocol always yields status 0; see #8605, #14207
-										xhr.status,
-										xhr.statusText
-									);
-								}
-							} else {
-								complete(
-									xhrSuccessStatus[ xhr.status ] || xhr.status,
-									xhr.statusText,
-
-									// Support: IE <=9 only
-									// IE9 has no XHR2 but throws on binary (trac-11426)
-									// For XHR2 non-text, let the caller handle it (gh-2498)
-									( xhr.responseType || "text" ) !== "text"  ||
-									typeof xhr.responseText !== "string" ?
-										{ binary: xhr.response } :
-										{ text: xhr.responseText },
-									xhr.getAllResponseHeaders()
-								);
-							}
-						}
-					};
-				};
-
-				// Listen to events
-				xhr.onload = callback();
-				errorCallback = xhr.onerror = xhr.ontimeout = callback( "error" );
-
-				// Support: IE 9 only
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          Tutorial
          This section is an introductory overview of pyKVFinder features. For detailed reference documentation of the functions and classes contained in the package, see the API reference.
          
-
          Before reading this section, you should know a bit of Python. If you would like to refresh your memory, refer to this Python tutorial.
          
-
          First of all, import pyKVFinder package on Python:
          
-
          >>> import pyKVFinder
-
          
-
          
-
          
-
          Cavity detection and characterization
          
-
          All files used on this tutorial can be found in our package and in our GitHub repository:
          
-
-
          In this tutorial, we will use pyKVFinder on a catalytic subunit of a cAMP-dependent protein kinase (cADK) to identify and characterize its cavities.
          
-
          pyKVFinder can be imported as a Python package in Python environment and users can decide to run the full pyKVFinder workflow through the single pyKVFinder function or run pyKVFinder functions in a stepwise fashion.
          
-
          
-
          Standard workflow
          
-
          The standard workflow for cavity detection with spatial and constitutional characterization (volume, area and interface residues) can be run at once with one command:
          
-
          >>> import os
->>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
->>> results = pyKVFinder.run_workflow(pdb)
->>> results
-<pyKVFinderResults object>
-
          
-
          
-
          Inside the pyKVFinderResults object, cavity and surface points, number of cavities, volume, area, and interface residues and their frequencies are stored as attributes. Below, we show how to access them:
          
-
          >>> results.cavities
-array([[[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]],
-
-      ...,
-
-      [[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
->>> results.surface
-array([[[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]],
-
-      ...,
-
-      [[-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        ...,
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1],
-        [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
->>> results.ncav
->>> 18
->>> results.volume
-{'KAA': 137.16, 'KAB': 47.52, 'KAC': 66.96, 'KAD': 8.21, 'KAE': 43.63, 'KAF': 12.53, 'KAG': 6.26, 'KAH': 520.13, 'KAI': 12.31, 'KAJ': 26.57, 'KAK': 12.31, 'KAL': 33.91, 'KAM': 23.11, 'KAN': 102.82, 'KAO': 6.05, 'KAP': 15.55, 'KAQ': 7.99, 'KAR': 7.78}
->>> results.area
-{'KAA': 126.41, 'KAB': 62.37, 'KAC': 74.57, 'KAD': 19.06, 'KAE': 57.08, 'KAF': 22.77, 'KAG': 15.38, 'KAH': 496.97, 'KAI': 30.58, 'KAJ': 45.64, 'KAK': 30.58, 'KAL': 45.58, 'KAM': 45.25, 'KAN': 129.77, 'KAO': 12.28, 'KAP': 25.04, 'KAQ': 13.46, 'KAR': 16.6}
->>> results.residues
-{'KAA': [['14', 'E', 'SER'], ['15', 'E', 'VAL'], ['18', 'E', 'PHE'], ['19', 'E', 'LEU'], ['100', 'E', 'PHE'], ['152', 'E', 'LEU'], ['155', 'E', 'GLU'], ['156', 'E', 'TYR'], ['292', 'E', 'LYS'], ['302', 'E', 'TRP'], ['303', 'E', 'ILE'], ['306', 'E', 'TYR']], 'KAB': [['18', 'E', 'PHE'], ['22', 'E', 'ALA'], ['25', 'E', 'ASP'], ['26', 'E', 'PHE'], ['29', 'E', 'LYS'], ['97', 'E', 'ALA'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['156', 'E', 'TYR']], 'KAC': [['141', 'E', 'PRO'], ['142', 'E', 'HIS'], ['144', 'E', 'ARG'], ['145', 'E', 'PHE'], ['148', 'E', 'ALA'], ['299', 'E', 'THR'], ['300', 'E', 'THR'], ['305', 'E', 'ILE'], ['310', 'E', 'VAL'], ['311', 'E', 'GLU'], ['313', 'E', 'PRO']], 'KAD': [['122', 'E', 'TYR'], ['124', 'E', 'ALA'], ['176', 'E', 'GLN'], ['318', 'E', 'PHE'], ['320', 'E', 'GLY'], ['321', 'E', 'PRO'], ['322', 'E', 'GLY'], ['323', 'E', 'ASP']], 'KAE': [['95', 'E', 'LEU'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['100', 'E', 'PHE'], ['103', 'E', 'LEU'], ['104', 'E', 'VAL'], ['105', 'E', 'LYS'], ['106', 'E', 'LEU']], 'KAF': [['123', 'E', 'VAL'], ['124', 'E', 'ALA'], ['175', 'E', 'ASP'], ['176', 'E', 'GLN'], ['181', 'E', 'GLN']], 'KAG': [['34', 'E', 'SER'], ['37', 'E', 'THR'], ['96', 'E', 'GLN'], ['106', 'E', 'LEU'], ['107', 'E', 'GLU'], ['108', 'E', 'PHE'], ['109', 'E', 'SER']], 'KAH': [['49', 'E', 'LEU'], ['50', 'E', 'GLY'], ['51', 'E', 'THR'], ['52', 'E', 'GLY'], ['53', 'E', 'SER'], ['54', 'E', 'PHE'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['72', 'E', 'LYS'], ['74', 'E', 'LEU'], ['84', 'E', 'GLN'], ['87', 'E', 'HIS'], ['88', 'E', 'THR'], ['91', 'E', 'GLU'], ['104', 'E', 'VAL'], ['120', 'E', 'MET'], ['121', 'E', 'GLU'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['166', 'E', 'ASP'], ['168', 'E', 'LYS'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['184', 'E', 'ASP'], ['186', 'E', 'GLY'], ['187', 'E', 'PHE'], ['201', 'E', 'THR'], ['327', 'E', 'PHE']], 'KAI': [['131', 'E', 'HIS'], ['138', 'E', 'PHE'], ['142', 'E', 'HIS'], ['146', 'E', 'TYR'], ['174', 'E', 'ILE'], ['314', 'E', 'PHE']], 'KAJ': [['33', 'E', 'PRO'], ['89', 'E', 'LEU'], ['92', 'E', 'LYS'], ['93', 'E', 'ARG'], ['96', 'E', 'GLN'], ['349', 'E', 'GLU'], ['350', 'E', 'PHE']], 'KAK': [['157', 'E', 'LEU'], ['162', 'E', 'LEU'], ['163', 'E', 'ILE'], ['164', 'E', 'TYR'], ['185', 'E', 'PHE'], ['188', 'E', 'ALA']], 'KAL': [['49', 'E', 'LEU'], ['127', 'E', 'GLU'], ['129', 'E', 'PHE'], ['130', 'E', 'SER'], ['326', 'E', 'ASN'], ['327', 'E', 'PHE'], ['328', 'E', 'ASP'], ['330', 'E', 'TYR']], 'KAM': [['51', 'E', 'THR'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['73', 'E', 'ILE'], ['74', 'E', 'LEU'], ['75', 'E', 'ASP'], ['115', 'E', 'ASN'], ['335', 'E', 'ILE'], ['336', 'E', 'ARG']], 'KAN': [['165', 'E', 'ARG'], ['166', 'E', 'ASP'], ['167', 'E', 'LEU'], ['199', 'E', 'CYS'], ['200', 'E', 'GLY'], ['201', 'E', 'THR'], ['204', 'E', 'TYR'], ['205', 'E', 'LEU'], ['206', 'E', 'ALA'], ['209', 'E', 'ILE'], ['219', 'E', 'VAL'], ['220', 'E', 'ASP'], ['223', 'E', 'ALA']], 'KAO': [['48', 'E', 'THR'], ['51', 'E', 'THR'], ['56', 'E', 'ARG'], ['330', 'E', 'TYR'], ['331', 'E', 'GLU']], 'KAP': [['222', 'E', 'TRP'], ['238', 'E', 'PHE'], ['253', 'E', 'GLY'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['273', 'E', 'LEU']], 'KAQ': [['207', 'E', 'PRO'], ['208', 'E', 'GLU'], ['211', 'E', 'LEU'], ['213', 'E', 'LYS'], ['275', 'E', 'VAL'], ['277', 'E', 'LEU']], 'KAR': [['237', 'E', 'PRO'], ['238', 'E', 'PHE'], ['249', 'E', 'LYS'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['256', 'E', 'ARG']]}
->>> results.frequencies
-{'KAA': {'RESIDUES': {'GLU': 1, 'ILE': 1, 'LEU': 2, 'LYS': 1, 'PHE': 2, 'SER': 1, 'TRP': 1, 'TYR': 2, 'VAL': 1}, 'CLASS': {'R1': 4, 'R2': 5, 'R3': 1, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAB': {'RESIDUES': {'ALA': 2, 'ASN': 1, 'ASP': 1, 'LYS': 1, 'PHE': 2, 'TYR': 1, 'VAL': 1}, 'CLASS': {'R1': 3, 'R2': 3, 'R3': 1, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAC': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'GLU': 1, 'HIS': 1, 'ILE': 1, 'PHE': 1, 'PRO': 2, 'THR': 2, 'VAL': 1}, 'CLASS': {'R1': 5, 'R2': 1, 'R3': 2, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAD': {'RESIDUES': {'ALA': 1, 'ASP': 1, 'GLN': 1, 'GLY': 2, 'PHE': 1, 'PRO': 1, 'TYR': 1}, 'CLASS': {'R1': 4, 'R2': 2, 'R3': 1, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAE': {'RESIDUES': {'ASN': 1, 'LEU': 3, 'LYS': 1, 'PHE': 1, 'VAL': 2}, 'CLASS': {'R1': 5, 'R2': 1, 'R3': 1, 'R4': 0, 'R5': 1, 'RX': 0}}, 'KAF': {'RESIDUES': {'ALA': 1, 'ASP': 1, 'GLN': 2, 'VAL': 1}, 'CLASS': {'R1': 2, 'R2': 0, 'R3': 2, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAG': {'RESIDUES': {'GLN': 1, 'GLU': 1, 'LEU': 1, 'PHE': 1, 'SER': 2, 'THR': 1}, 'CLASS': {'R1': 1, 'R2': 1, 'R3': 4, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAH': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'ASN': 1, 'ASP': 2, 'GLN': 1, 'GLU': 4, 'GLY': 4, 'HIS': 1, 'LEU': 3, 'LYS': 2, 'MET': 1, 'PHE': 3, 'SER': 1, 'THR': 4, 'TYR': 1, 'VAL': 3}, 'CLASS': {'R1': 11, 'R2': 4, 'R3': 8, 'R4': 6, 'R5': 4, 'RX': 0}}, 'KAI': {'RESIDUES': {'HIS': 2, 'ILE': 1, 'PHE': 2, 'TYR': 1}, 'CLASS': {'R1': 1, 'R2': 3, 'R3': 0, 'R4': 0, 'R5': 2, 'RX': 0}}, 'KAJ': {'RESIDUES': {'ARG': 1, 'GLN': 1, 'GLU': 1, 'LEU': 1, 'LYS': 1, 'PHE': 1, 'PRO': 1}, 'CLASS': {'R1': 2, 'R2': 1, 'R3': 1, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAK': {'RESIDUES': {'ALA': 1, 'ILE': 1, 'LEU': 2, 'PHE': 1, 'TYR': 1}, 'CLASS': {'R1': 4, 'R2': 2, 'R3': 0, 'R4': 0, 'R5': 0, 'RX': 0}}, 'KAL': {'RESIDUES': {'ASN': 1, 'ASP': 1, 'GLU': 1, 'LEU': 1, 'PHE': 2, 'SER': 1, 'TYR': 1}, 'CLASS': {'R1': 1, 'R2': 3, 'R3': 2, 'R4': 2, 'R5': 0, 'RX': 0}}, 'KAM': {'RESIDUES': {'ARG': 2, 'ASN': 1, 'ASP': 1, 'GLY': 1, 'ILE': 2, 'LEU': 1, 'THR': 1}, 'CLASS': {'R1': 4, 'R2': 0, 'R3': 2, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAN': {'RESIDUES': {'ALA': 2, 'ARG': 1, 'ASP': 2, 'CYS': 1, 'GLY': 1, 'ILE': 1, 'LEU': 2, 'THR': 1, 'TYR': 1, 'VAL': 1}, 'CLASS': {'R1': 7, 'R2': 1, 'R3': 2, 'R4': 2, 'R5': 1, 'RX': 0}}, 'KAO': {'RESIDUES': {'ARG': 1, 'GLU': 1, 'THR': 2, 'TYR': 1}, 'CLASS': {'R1': 0, 'R2': 1, 'R3': 2, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAP': {'RESIDUES': {'GLY': 1, 'LEU': 1, 'LYS': 1, 'PHE': 1, 'TRP': 1, 'VAL': 1}, 'CLASS': {'R1': 3, 'R2': 2, 'R3': 0, 'R4': 0, 'R5': 1, 'RX': 0}}, 'KAQ': {'RESIDUES': {'GLU': 1, 'LEU': 2, 'LYS': 1, 'PRO': 1, 'VAL': 1}, 'CLASS': {'R1': 4, 'R2': 0, 'R3': 0, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAR': {'RESIDUES': {'ARG': 1, 'LYS': 2, 'PHE': 1, 'PRO': 1, 'VAL': 1}, 'CLASS': {'R1': 2, 'R2': 1, 'R3': 0, 'R4': 0, 'R5': 3, 'RX': 0}}}
-
          
-
          
-
          
-
          Note
          
-
          The cavity nomenclature is based on the integer label. The cavity marked with 2, the first integer corresponding to a cavity, is KAA, the cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
          
-
          
-
          
-
          Note
          
-
          The cavity points belonging to the same cavity receive the same integer label in the grid. The code numbering is the following:
          
-
          
-
            
-
          • -1: bulk points.
            • 
-
          • 0: biomolecule points.
            • 
-
          • 1: empty space points.
            • 
-
          • >=2: cavity points.
            • 
-
          
-
          
-
          
-
          
-
          Note
          
-
          The surface points belonging to the same cavity receive the same integer label in the grid. The code numbering is the following:
          
-
          
-
            
-
          • -1: bulk points.
            • 
-
          • 0: biomolecule or empty space points.
            • 
-
          • >=2: cavity points.
            • 
-
          
-
          
-
          
-
          
-
          Note
          
-
          The pyKVFinder.run_workflow function uses default parameter specifications and therefore parameters can be adjusted to users’ needs.
          
-
          
-
          
-
          See also
          
-
-
          
-
          With these attributes, we can write the detected cavities and the characterization to files. Further, we can set a flag to plot the bar charts of the frequencies in a PDF file. Below, we illustrate the usage:
          
-
          >>> results.export_all(fn='results.toml', output='cavity.pdb', include_frequencies_pdf=True, pdf='barplots.pdf')
-
          
-
          
-
          
-
          Note
          
-
          The pyKVFinder.pyKVFinderResults.export_all methods uses default parameter specifications, except for include_frequencies_pdf parameter, and therefore parameters can be adjusted to users’ needs.
          
-
          
-
          
-
          See also
          
-
-
          
-
          
-
          
-
          Full workflow
          
-
          However, users may opt to perform the full workflow for cavity detection with spatial (volume and area), constitutional (interface residues), hydropathy and depth characterization. This full workflow can be run with one command by setting some parameters of pyKVFinder.run_workflow function:
          
-
          >>> results = pyKVFinder.run_workflow(pdb, include_depth=True, include_hydropathy=True, hydrophobicity_scale='EisenbergWeiss')
-
          
-
          
-
          Inside the pyKVFinderResults object, in addition to cavity and surface points, volume, area, and interface residues and their frequencies showed above, depth and hydropathy points, average depth, maximum depth and average hydropathy are also stored as attributes. Below, we show how to access them:
          
-
          >>> results.depths
-array([[[0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        ...,
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.]],
-
-      ...,
-
-      [[0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        ...,
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.]]])
->>> results.scales
-array([[[0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        ...,
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.]],
-
-      ...,
-
-      [[0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        ...,
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.],
-        [0., 0., 0., ..., 0., 0., 0.]]])
->>> results.avg_depth
-{'KAA': 1.35, 'KAB': 0.91, 'KAC': 0.68, 'KAD': 0.32, 'KAE': 0.99, 'KAF': 0.24, 'KAG': 0.1, 'KAH': 3.91, 'KAI': 0.0, 'KAJ': 0.96, 'KAK': 0.0, 'KAL': 1.07, 'KAM': 0.24, 'KAN': 0.0, 'KAO': 0.29, 'KAP': 0.7, 'KAQ': 0.22, 'KAR': 0.12}
->>> results.max_depth
-{'KAA': 3.79, 'KAB': 2.68, 'KAC': 2.62, 'KAD': 0.85, 'KAE': 3.0, 'KAF': 0.85, 'KAG': 0.6, 'KAH': 10.73, 'KAI': 0.0, 'KAJ': 2.24, 'KAK': 0.0, 'KAL': 3.0, 'KAM': 1.2, 'KAN': 0.0, 'KAO': 1.04, 'KAP': 2.08, 'KAQ': 0.85, 'KAR': 0.6}
->>> results.avg_hydropathy
-{'KAA': -0.73, 'KAB': -0.05, 'KAC': -0.07, 'KAD': -0.62, 'KAE': -0.81, 'KAF': -0.14, 'KAG': -0.33, 'KAH': -0.17, 'KAI': -0.4, 'KAJ': 0.62, 'KAK': -0.99, 'KAL': 0.36, 'KAM': -0.33, 'KAN': 0.18, 'KAO': 0.88, 'KAP': -0.96, 'KAQ': 0.48, 'KAR': 0.24, 'EisenbergWeiss': [-1.42, 2.6]}
-
          
-
          
-
          
-
          Note
          
-
          The cavity nomenclature is based on the integer label. The cavity marked with 2, the first integer corresponding to a cavity, is KAA, the cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
          
-
          
-
          
-
          Note
          
-
          The pyKVFinder.run_workflow function uses default parameter specifications, except for include_depth and include_hydropathy parameters, and therefore parameters can be adjusted to users’ needs.
          
-
          
-
          
-
          See also
          
-
-
          
-
          With these attributes, we can write the detected cavities with depth annotated on B-factor column, the surface cavity points with hydrophobicity scale annotated on B-factor column, and the characterization to files. Below, we illustrate the usage:
          
-
          >>> results.export_all(fn='results.toml', output='cavity.pdb', output_hydropathy='hydropathy.pdb', include_frequencies_pdf=False)
-
          
-
          
-
          
-
          Note
          
-
          The pyKVFinder.pyKVFinderResults.export_all methods uses default parameter specifications, and therefore parameters can be adjusted to users’ needs.
          
-
          
-
          
-
          See also
          
-
-
          
-
          
-
          
-
          Separated steps
          
-
          If users prefer, instead of running pyKVFinder.run_workflow function, you can apply the cavity detection and characterization in a step-by-step fashion. Below we describe each step in detail.
          
-
          
-
          1. Loading van der Waals radii dictionary
          
-
          The van der Waals radii file define the radius values for each residue and when not defined, it uses a generic value based on the atom type. pyKVFinder.read_vdw takes a vdW radii file (.dat) and returns a dictionary contaning radii values for each atom of each residue.
          
-
          >>> vdw = pyKVFinder.read_vdw()
->>> vdw
-{'ALA': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB1': 1.487, '1HB': 1.487, 'HB2': 1.487, '2HB': 1.487, 'HB3': 1.487, '3HB': 1.487, 'C': 1.908, 'O': 1.6612}, 'ARG': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG2': 1.487, '2HG': 1.487, 'HG3': 1.487, 'HG1': 1.487, '1HG': 1.487, 'CD': 1.908, 'HD2': 1.387, '1HD': 1.387, '2HD': 1.387, 'HD3': 1.387, 'HD1': 1.387, 'NE': 1.75, 'HE': 0.6, 'CZ': 1.908, 'NH1': 1.75, 'HH11': 0.6, '1HH1': 0.6, 'HH12': 0.6, '2HH1': 0.6, 'NH2': 1.75, 'HH21': 0.6, '2HH2': 0.6, 'HH22': 0.6, '1HH2': 0.6, 'C': 1.908, 'O': 1.6612}, 'ASH': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.908, 'OD1': 1.6612, 'OD2': 1.721, 'HD2': 0.0001, 'C': 1.908, 'O': 1.6612}, 'ASN': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'OD1': 1.6612, 'ND2': 1.824, 'HD21': 0.6, '1HD2': 0.6, 'HD22': 0.6, '2HD2': 0.6, 'C': 1.908, 'O': 1.6612}, 'ASP': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'OD1': 1.6612, 'OD2': 1.6612, 'C': 1.908, 'O': 1.6612}, 'CYM': {'N': 1.824, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB3': 1.387, 'HB2': 1.387, 'SG': 2.0, 'C': 1.908, 'O': 1.6612}, 'CYS': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.387, '2HB': 1.387, '1HB': 1.387, 'HB3': 1.387, 'HB1': 1.387, 'SG': 2.0, 'HG': 0.6, 'C': 1.908, 'O': 1.6612}, 'CYX': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.387, 'HB3': 1.387, 'SG': 2.0, 'C': 1.908, 'O': 1.6612}, 'GLH': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.908, 'HG2': 1.487, 'HG3': 1.487, 'CD': 1.908, 'OE1': 1.6612, 'OE2': 1.721, 'HE2': 0.0001, 'C': 1.908, 'O': 1.6612}, 'GLN': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG2': 1.487, '2HG': 1.487, 'HG3': 1.487, 'HG1': 1.487, '1HG': 1.487, 'CD': 1.908, 'OE1': 1.6612, 'NE2': 1.824, 'HE21': 0.6, '1HE2': 0.6, 'HE22': 0.6, '2HE2': 0.6, 'C': 1.908, 'O': 1.6612}, 'GLU': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG2': 1.487, '2HG': 1.487, 'HG3': 1.487, 'HG1': 1.487, '1HG': 1.487, 'CD': 1.908, 'OE1': 1.6612, 'OE2': 1.6612, 'C': 1.908, 'O': 1.6612}, 'GLY': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA2': 1.387, 'HA1': 1.387, '1HA': 1.387, '2HA': 1.387, 'HA3': 1.387, 'C': 1.908, 'O': 1.6612}, 'HID': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.85, 'ND1': 1.75, 'HD1': 0.6, 'CE1': 1.85, 'HE1': 1.359, 'NE2': 1.75, 'CD2': 2.0, 'HD2': 1.409, 'C': 1.908, 'O': 1.6612}, 'HIE': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.85, 'ND1': 1.75, 'CE1': 1.85, 'HE1': 1.359, 'NE2': 1.75, 'HE2': 0.6, 'CD2': 2.0, 'HD2': 1.409, 'C': 1.908, 'O': 1.6612}, 'HIP': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.85, 'ND1': 1.75, 'HD1': 0.6, 'CE1': 1.85, 'HE1': 1.359, 'NE2': 1.75, 'HE2': 0.6, 'CD2': 2.0, 'HD2': 1.409, 'C': 1.908, 'O': 1.6612}, 'ILE': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB': 1.487, 'CG2': 1.908, 'HG21': 1.487, '1HG2': 1.487, 'HG22': 1.487, '2HG2': 1.487, 'HG23': 1.487, '3HG2': 1.487, 'CG1': 1.908, 'HG12': 1.487, '2HG1': 1.487, 'HG13': 1.487, 'HG11': 1.487, '1HG1': 1.487, 'CD1': 1.908, 'HD11': 1.487, '1HD1': 1.487, 'HD12': 1.487, '2HD1': 1.487, 'HD13': 1.487, '3HD1': 1.487, 'C': 1.908, 'O': 1.6612}, 'LEU': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG': 1.487, 'CD1': 1.908, 'HD11': 1.487, '1HD1': 1.487, 'HD12': 1.487, '2HD1': 1.487, 'HD13': 1.487, '3HD1': 1.487, 'CD2': 1.908, 'HD21': 1.487, '1HD2': 1.487, 'HD22': 1.487, '2HD2': 1.487, 'HD23': 1.487, '3HD2': 1.487, 'C': 1.908, 'O': 1.6612}, 'LYN': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.908, 'HG2': 1.487, 'HG3': 1.487, 'CD': 1.908, 'HD2': 1.487, 'HD3': 1.487, 'CE': 1.908, 'HE2': 1.1, 'HE3': 1.1, 'NZ': 1.824, 'HZ2': 0.6, 'HZ3': 0.6, 'C': 1.908, 'O': 1.6612}, 'LYS': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG2': 1.487, '2HG': 1.487, 'HG3': 1.487, 'HG1': 1.487, '1HG': 1.487, 'CD': 1.908, 'HD2': 1.487, '1HD': 1.487, '2HD': 1.487, 'HD3': 1.487, 'HD1': 1.487, 'CE': 1.908, 'HE2': 1.1, '2HE': 1.1, 'HE3': 1.1, '1HE': 1.1, 'HE1': 1.1, 'NZ': 1.824, 'HZ1': 0.6, '1HZ': 0.6, 'HZ2': 0.6, '2HZ': 0.6, 'HZ3': 0.6, '3HZ': 0.6, 'C': 1.908, 'O': 1.6612}, 'MET': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'HG2': 1.387, '2HG': 1.387, 'HG3': 1.387, 'HG1': 1.387, '1HG': 1.387, 'SD': 2.0, 'CE': 1.908, 'HE1': 1.387, '1HE': 1.387, 'HE2': 1.387, '2HE': 1.387, 'HE3': 1.387, '3HE': 1.387, 'C': 1.908, 'O': 1.6612}, 'PHE': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'CD1': 1.908, 'HD1': 1.459, 'CE1': 1.908, 'HE1': 1.459, 'CZ': 1.908, 'HZ': 1.459, 'CE2': 1.908, 'HE2': 1.459, 'CD2': 1.908, 'HD2': 1.459, 'C': 1.908, 'O': 1.6612}, 'PRO': {'N': 1.824, 'CD': 1.908, 'HD2': 1.387, '1HD': 1.387, '2HD': 1.387, 'HD3': 1.387, 'HD1': 1.387, 'CG': 1.908, 'HG2': 1.487, '2HG': 1.487, 'HG3': 1.487, 'HG1': 1.487, '1HG': 1.487, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CA': 1.908, 'HA': 1.387, 'C': 1.908, 'O': 1.6612}, 'SER': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.387, '2HB': 1.387, '1HB': 1.387, 'HB3': 1.387, 'HB1': 1.387, 'OG': 1.721, 'HG': 0.0001, 'C': 1.908, 'O': 1.6612}, 'THR': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB': 1.387, 'CG2': 1.908, 'HG21': 1.487, '1HG2': 1.487, 'HG22': 1.487, '2HG2': 1.487, 'HG23': 1.487, '3HG2': 1.487, 'OG1': 1.721, 'HG1': 0.0001, 'C': 1.908, 'O': 1.6612}, 'TRP': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.85, 'CD1': 2.0, 'HD1': 1.409, 'NE1': 1.75, 'HE1': 0.6, 'CE2': 1.85, 'CZ2': 1.908, 'HZ2': 1.459, 'CH2': 1.908, 'HH2': 1.459, 'CZ3': 1.908, 'HZ3': 1.459, 'CE3': 1.908, 'HE3': 1.459, 'CD2': 1.85, 'C': 1.908, 'O': 1.6612}, 'TYR': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.908, 'CD1': 1.908, 'HD1': 1.459, 'CE1': 1.908, 'HE1': 1.459, 'CZ': 1.908, 'OH': 1.721, 'HH': 0.0001, 'CE2': 1.908, 'HE2': 1.459, 'CD2': 1.908, 'HD2': 1.459, 'C': 1.908, 'O': 1.6612}, 'VAL': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB': 1.487, 'CG1': 1.908, 'CG2': 1.908, 'HG11': 1.487, '1HG2': 1.487, '1HG1': 1.487, 'HG21': 1.487, 'HG12': 1.487, '2HG1': 1.487, 'HG22': 1.487, '2HG2': 1.487, 'HG13': 1.487, '3HG2': 1.487, '3HG1': 1.487, 'HG23': 1.487, 'C': 1.908, 'O': 1.6612}, 'HIS': {'N': 1.824, 'H': 0.6, 'HN': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, '2HB': 1.487, '1HB': 1.487, 'HB3': 1.487, 'HB1': 1.487, 'CG': 1.85, 'ND1': 1.75, 'HD1': 0.6, 'CE1': 1.85, 'HE1': 1.359, 'NE2': 1.75, 'CD2': 2.0, 'HD2': 1.409, 'C': 1.908, 'O': 1.6612}, 'PTR': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.908, 'CD1': 1.908, 'HD1': 1.459, 'CE1': 1.908, 'HE1': 1.459, 'CZ': 1.908, 'CE2': 1.908, 'HE2': 1.459, 'CD2': 1.908, 'HD2': 1.459, 'OH': 1.6837, 'P': 2.1, 'O1P': 1.85, 'O2P': 1.85, 'O3P': 1.85, 'C': 1.908, 'O': 1.6612}, 'SEP': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.387, 'HB3': 1.387, '1HB': 1.387, '2HB': 1.387, 'OG': 1.6837, 'P': 2.1, 'O1P': 1.85, 'O2P': 1.85, 'O3P': 1.85, 'C': 1.908, 'O': 1.6612}, 'TPO': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB': 1.387, 'CG2': 1.908, 'HG21': 1.487, 'HG22': 1.487, 'HG23': 1.487, '1HG2': 1.487, '2HG2': 1.487, '3HG2': 1.487, 'OG1': 1.6837, 'P': 2.1, 'O1P': 1.85, 'O2P': 1.85, 'O3P': 1.85, 'C': 1.908, 'O': 1.6612}, 'H2D': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.85, 'ND1': 1.75, 'CE1': 1.85, 'HE1': 1.359, 'NE2': 1.75, 'HE2': 0.6, 'CD2': 2.0, 'HD2': 1.409, 'P': 2.1, 'O1P': 1.85, 'O2P': 1.85, 'O3P': 1.85, 'C': 1.908, 'O': 1.6612}, 'Y1P': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.487, 'HB3': 1.487, 'CG': 1.908, 'CD1': 1.908, 'HD1': 1.459, 'CE1': 1.908, 'HE1': 1.459, 'CZ': 1.908, 'CE2': 1.908, 'HE2': 1.459, 'CD2': 1.908, 'HD2': 1.459, 'OG': 1.6837, 'P': 2.1, 'O1P': 1.721, 'O2P': 1.6612, 'O3P': 1.6612, 'H1P': 0.0001, 'C': 1.908, 'O': 1.6612}, 'T1P': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB': 1.387, 'CG2': 1.908, 'HG21': 1.487, 'HG22': 1.487, 'HG23': 1.487, 'OG': 1.6837, 'P': 2.1, 'O1P': 1.721, 'O2P': 1.6612, 'O3P': 1.6612, 'H1P': 0.0001, 'C': 1.908, 'O': 1.6612}, 'S1P': {'N': 1.824, 'H': 0.6, 'CA': 1.908, 'HA': 1.387, 'CB': 1.908, 'HB2': 1.387, 'HB3': 1.387, 'OG': 1.6837, 'P': 2.1, 'O1P': 1.721, 'O2P': 1.6612, 'O3P': 1.6612, 'H1P': 0.0001, 'C': 1.908, 'O': 1.6612}, 'GEN': {'AC': 2.0, 'AG': 1.72, 'AL': 2.0, 'AM': 2.0, 'AR': 1.88, 'AS': 1.85, 'AT': 2.0, 'AU': 1.66, 'B': 2.0, 'BA': 2.0, 'BE': 2.0, 'BH': 2.0, 'BI': 2.0, 'BK': 2.0, 'BR': 1.85, 'C': 1.66, 'CA': 2.0, 'CD': 1.58, 'CE': 2.0, 'CF': 2.0, 'CL': 1.75, 'CM': 2.0, 'CO': 2.0, 'CR': 2.0, 'CS': 2.0, 'CU': 1.4, 'DB': 2.0, 'DS': 2.0, 'DY': 2.0, 'ER': 2.0, 'ES': 2.0, 'EU': 2.0, 'F': 1.47, 'FE': 2.0, 'FM': 2.0, 'FR': 2.0, 'GA': 1.87, 'GD': 2.0, 'GE': 2.0, 'H': 0.91, 'HE': 1.4, 'HF': 2.0, 'HG': 1.55, 'HO': 2.0, 'HS': 2.0, 'I': 1.98, 'IN': 1.93, 'IR': 2.0, 'K': 2.75, 'KR': 2.02, 'LA': 2.0, 'LI': 1.82, 'LR': 2.0, 'LU': 2.0, 'MD': 2.0, 'MG': 1.73, 'MN': 2.0, 'MO': 2.0, 'MT': 2.0, 'N': 1.97, 'NA': 2.27, 'NB': 2.0, 'ND': 2.0, 'NE': 1.54, 'NI': 1.63, 'NO': 2.0, 'NP': 2.0, 'O': 1.69, 'OS': 2.0, 'P': 2.1, 'PA': 2.0, 'PB': 2.02, 'PD': 1.63, 'PM': 2.0, 'PO': 2.0, 'PR': 2.0, 'PT': 1.72, 'PU': 2.0, 'RA': 2.0, 'RB': 2.0, 'RE': 2.0, 'RF': 2.0, 'RH': 2.0, 'RN': 2.0, 'RU': 2.0, 'S': 2.09, 'SB': 2.0, 'SC': 2.0, 'SE': 1.9, 'SG': 2.0, 'SI': 2.1, 'SM': 2.0, 'SN': 2.17, 'SR': 2.0, 'TA': 2.0, 'TB': 2.0, 'TC': 2.0, 'TE': 2.06, 'TH': 2.0, 'TI': 2.0, 'TL': 1.96, 'TM': 2.0, 'U': 1.86, 'V': 2.0, 'W': 2.0, 'XE': 2.16, 'Y': 2.0, 'YB': 2.0, 'ZN': 1.39, 'ZR': 2.0}}
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          Note
          
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          The function takes the built-in dictionary when a .dat file is not specified. Otherwise, user must specify a .dat file following template of van der Waals radii file.
          
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          This step is only necessary if you are reading a custom van der Waals radii file to use in pyKVFinder.read_pdb.
          
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          See also
          
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          2. Loading data from target structure
          
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          pyKVFinder.read_pdb takes a target .pdb file and returns a NumPy array (atomic) with residue number, chain identifier, residue name, atom name, xyz coordinates and radius, considering a van der Waals radii dictionary, for each atom.
          
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          >>> import os
->>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
->>> atomic = pyKVFinder.read_pdb(pdb)
->>> atomic
-array([['13', 'E', 'GLU', ..., '-15.642', '-14.858', '1.824'],
-     ['13', 'E', 'GLU', ..., '-14.62', '-15.897', '1.908'],
-     ['13', 'E', 'GLU', ..., '-13.357', '-15.508', '1.908'],
-     ...,
-     ['350', 'E', 'PHE', ..., '18.878', '-9.885', '1.908'],
-     ['350', 'E', 'PHE', ..., '17.624', '-9.558', '1.908'],
-     ['350', 'E', 'PHE', ..., '19.234', '-13.442', '1.69']],
-    dtype='<U32')
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          Note
          
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          The function takes the built-in dictionary, when the vdw argument is not specified. If you wish to use a custom van der Waals radii file, you must read it with pyKVFinder.read_vdw as shown earlier and pass it as pyKVFinder.read_pdb(pdb, vdw=vdw).
          
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          Note
          
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          The structural data can be also read from a .xyz file with pyKVFinder.read_xyz function. However, XYZ format does not provide information about chain identifier and residue name, thus this fields will have A and UNK, respectively.
          
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          See also
          
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          3. Dimensioning the 3D grid
          
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          The pyKVFinder 3D grid must be calculated based on the target .pdb or .xyz file, the Probe Out diameter and the grid spacing.
          
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          pyKVFinder.get_vertices takes the NumPy array with residue number, chain identifier, residue name, atom name, xyz coordinates and radius for each atom, and the Probe Out (probe_out) and grid spacing (step) that will be applied in the detection, and returns a NumPy array with vertice coordinates (origin, X-axis, Y-axis, Z-axis) of the 3D grid.
          
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          >>> # Default Probe Out (probe_out): 4.0
->>> probe_out = 4.0
->>> # Default Grid Spacing (step): 0.6
->>> step = 0.6
->>> vertices = pyKVFinder.get_vertices(atomic, probe_out=probe_out, step=step)
->>> vertices
-array([[-19.911, -32.125, -30.806],
-     [ 40.188, -32.125, -30.806],
-     [-19.911,  43.446, -30.806],
-     [-19.911, -32.125,  27.352]])
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          Note
          
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          If the probe_out and step values are not defined, the function automatically sets them to the default values. So, you can call the function by pyKVFinder.get_vertices(atomic).
          
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          See also
          
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          4. Detecting biomolecular cavities
          
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          pyKVFinder.detect takes the NumPy array with residue number, chain identifier, residue name, atom name, xyz coordinates and radius for each atom, a NumPy array with vertices and a collection of detection parameters (step, probe_in, probe_out, removal_distance, volume_cutoff, surface), and returns a tuple with the number of detected cavities and a NumPy array with the cavity points in the 3D grid.
          
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          >>> # Default Grid Spacing (step): 0.6
->>> step = 0.6
->>> # Default Probe In (probe_in): 1.4
->>> probe_in = 1.4
->>> # Default Probe Out (probe_out): 4.0
->>> probe_out = 4.0
->>> # Default Removal Distance (removal_distance): 2.4
->>> removal_distance = 2.4
->>> # Default Volume Cutoff (volume_cutoff): 5.0
->>> volume_cutoff = 5.0
->>> # Default Surface Representation (surface): 'SES'
->>> surface = 'SES'
->>> ncav, cavities = pyKVFinder.detect(atomic, vertices, step=step, probe_in=probe_in, probe_out=probe_out, removal_distance=removal_distance, volume_cutoff=volume_cutoff, surface=surface)
->>> ncav
-18
->>> cavities
-array([[[-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      ...,
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1]],
-
-     ...,
-
-     [[-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      ...,
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
-
          
-
          
-
          
-
          Note
          
-
          If any of the detection parameters (step, probe_in, probe_out, removal_distance, volume_cutoff, surface) are not defined, the function automatically sets them to the default values. So, you can call the function by pyKVFinder.detect(atomic, vertices).
          
-
          
-
          
-
          Note
          
-
          The cavity points belonging to the same cavity receive the same integer label in the grid. The code numbering is the following:
          
-
          
-
            
-
          • -1: bulk points.
            • 
-
          • 0: biomolecule points.
            • 
-
          • 1: empty space points.
            • 
-
          • >=2: cavity points.
            • 
-
          
-
          
-
          
-
          
-
          See also
          
-
-
          
-
          
-
          4.1 Detecting biomolecular cavities with ligand adjustment
          
-
          The cavity detection can be limited around the target ligand(s), which will be passed to pyKVFinder through a .pdb or .xyz file. Thus, the detected cavities are limited within a radius (ligand_cutoff) of the target ligand(s).
          
-
          First, pyKVFinder.read_pdb takes an adenosine as the target ligand and returns the NumPy array with residue number, chain identifier, residue name, atom name, xyz coordinates and radius for each atom of the ligand.
          
-
          >>> ligand = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'ADN.pdb')
->>> latomic = pyKVFinder.read_pdb(ligand)
->>> latomic
-array([['351', 'E', 'ADN', "C5'", '11.087', '9.79', '2.052', '1.66'],
-     ['351', 'E', 'ADN', "O5'", '11.545', '8.52', '1.545', '1.69'],
-     ['351', 'E', 'ADN', "C4'", '10.688', '9.68', '3.523', '1.66'],
-     ['351', 'E', 'ADN', "O4'", '9.714', '10.725', '3.81', '1.69'],
-     ['351', 'E', 'ADN', "C3'", '9.973', '8.374', '3.903', '1.66'],
-     ['351', 'E', 'ADN', "O3'", '10.879', '7.361', '4.304', '1.69'],
-     ['351', 'E', 'ADN', "C2'", '9.115', '8.82', '5.059', '1.66'],
-     ['351', 'E', 'ADN', "O2'", '9.887', '9.034', '6.232', '1.69'],
-     ['351', 'E', 'ADN', "C1'", '8.625', '10.16', '4.5', '1.66'],
-     ['351', 'E', 'ADN', 'N1', '3.499', '10.104', '4.402', '1.97'],
-     ['351', 'E', 'ADN', 'C2', '4.376', '10.259', '5.387', '1.66'],
-     ['351', 'E', 'ADN', 'N3', '5.705', '10.249', '5.351', '1.97'],
-     ['351', 'E', 'ADN', 'C4', '6.136', '10.087', '4.094', '1.66'],
-     ['351', 'E', 'ADN', 'C5', '5.353', '9.952', '2.974', '1.66'],
-     ['351', 'E', 'ADN', 'C6', '3.957', '9.957', '3.146', '1.66'],
-     ['351', 'E', 'ADN', 'N6', '3.083', '9.826', '2.142', '1.97'],
-     ['351', 'E', 'ADN', 'N7', '6.146', '9.791', '1.843', '1.97'],
-     ['351', 'E', 'ADN', 'C8', '7.374', '9.872', '2.291', '1.66'],
-     ['351', 'E', 'ADN', 'N9', '7.444', '10.056', '3.646', '1.97']],
-    dtype='<U32')
-
          
-
          
-
          Afterwards, parKVFinder.detect takes the mandatory parameters (atomic and vertices) and a the ligand adjustment parameters (latomic and ligand_cutoff), and returns a tuple with the number of detected cavities and a NumPy array with the cavity points in the 3D grid.
          
-
          >>> # Default Ligand Cutoff (ligand_cutoff): 5.0
->>> ligand_cutoff = 5.0
->>> ncav_la, cavities_la = pyKVFinder.detect(atomic, vertices, latomic=latomic, ligand_cutoff=ligand_cutoff)
->>> ncav_la
-2
->>> cavities_la
-array([[[-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      ...,
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1]],
-
-     ...,
-
-     [[-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      ...,
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
-
          
-
          
-
          
-
          Note
          
-
          If the ligand_cutoff is not defined, the function automatically sets it to the default value. So, you can call the function by pyKVFinder.detect(atomic, vertices, latomic=latomic).
          
-
          The cavity points belonging to the same cavity receive the same integer label in the grid. The code numbering is the following:
          
-
          
-
            
-
          • -1: bulk points.
            • 
-
          • 0: biomolecule points.
            • 
-
          • 1: empty space points.
            • 
-
          • >=2: cavity points.
            • 
-
          
-
          
-
          
-
          
-
          See also
          
-
-
          
-
          
-
          
-
          
-
          5. Performing spatial characterization
          
-
          A spatial characterization, that includes volume, area and defining surface points, is performed on the detected cavities.
          
-
          pyKVFinder.spatial takes the detected cavities and the grid spacing (step) and and returns a tuple with a NumPy array with the surface points in the 3D grid, a dictionary with the volume of the detected cavities and a dictionary with the area of the detected cavities.
          
-
          >>> surface, volume, area = pyKVFinder.spatial(cavities, step=step)
->>> surface
-array([[[-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      ...,
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1]],
-
-     ...,
-
-     [[-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      ...,
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1],
-      [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
->>> volume
-{'KAA': 137.16, 'KAB': 47.52, 'KAC': 66.96, 'KAD': 8.21, 'KAE': 43.63, 'KAF': 12.53, 'KAG': 6.26, 'KAH': 520.13, 'KAI': 12.31, 'KAJ': 26.57, 'KAK': 12.31, 'KAL': 33.91, 'KAM': 23.11, 'KAN': 102.82, 'KAO': 6.05, 'KAP': 15.55, 'KAQ': 7.99, 'KAR': 7.78}
->>> area
-{'KAA': 126.41, 'KAB': 62.37, 'KAC': 74.57, 'KAD': 19.06, 'KAE': 57.08, 'KAF': 22.77, 'KAG': 15.38, 'KAH': 496.97, 'KAI': 30.58, 'KAJ': 45.64, 'KAK': 30.58, 'KAL': 45.58, 'KAM': 45.25, 'KAN': 129.77, 'KAO': 12.28, 'KAP': 25.04, 'KAQ': 13.46, 'KAR': 16.6}
-
          
-
          
-
          
-
          Note
          
-
          The cavity nomenclature is based on the integer label. The cavity marked with 2, the first integer corresponding to a cavity, is KAA, the cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
          
-
          
-
          
-
          Note
          
-
          The surface points belonging to the same cavity receive the same integer label in the grid. The code numbering is the following:
          
-
          
-
            
-
          • -1: bulk points.
            • 
-
          • 0: biomolecule or empty space points.
            • 
-
          • >=2: cavity points.
            • 
-
          
-
          
-
          
-
          
-
          Note
          
-
          If the step is not defined, the function automatically sets it to the default value. So, you can call the function by pyKVFinder.spatial(cavities).
          
-
          
-
          
-
          See also
          
-
-
          
-
          
-
          
-
          6. Performing constitutional characterization
          
-
          A constitutional characterization, that identifies the interface residues, is performed on the detected cavities.
          
-
          pyKVFinder.constitutional takes the detected cavities, the NumPy array with residue number, chain identifier, residue name, atom name, xyz coordinates and radius for each atom, the NumPy array with vertice coordinates (origin, X-axis, Y-axis, Z-axis) and a collection of detection parameters (step, probe_in, ignore_backbone), and returns a dictionary with interface residues of each cavity.
          
-
          >>> # Default ignore backbone contacts flag (ignore_backbone): False
->>> ignore_backbone = False
->>> residues = pyKVFinder.constitutional(cavities, atomic, vertices, step=step, probe_in=probe_in, ignore_backbone=ignore_backbone)
->>> residues
-{'KAA': [['14', 'E', 'SER'], ['15', 'E', 'VAL'], ['18', 'E', 'PHE'], ['19', 'E', 'LEU'], ['100', 'E', 'PHE'], ['152', 'E', 'LEU'], ['155', 'E', 'GLU'], ['156', 'E', 'TYR'], ['292', 'E', 'LYS'], ['302', 'E', 'TRP'], ['303', 'E', 'ILE'], ['306', 'E', 'TYR']], 'KAB': [['18', 'E', 'PHE'], ['22', 'E', 'ALA'], ['25', 'E', 'ASP'], ['26', 'E', 'PHE'], ['29', 'E', 'LYS'], ['97', 'E', 'ALA'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['156', 'E', 'TYR']], 'KAC': [['141', 'E', 'PRO'], ['142', 'E', 'HIS'], ['144', 'E', 'ARG'], ['145', 'E', 'PHE'], ['148', 'E', 'ALA'], ['299', 'E', 'THR'], ['300', 'E', 'THR'], ['305', 'E', 'ILE'], ['310', 'E', 'VAL'], ['311', 'E', 'GLU'], ['313', 'E', 'PRO']], 'KAD': [['122', 'E', 'TYR'], ['124', 'E', 'ALA'], ['176', 'E', 'GLN'], ['318', 'E', 'PHE'], ['320', 'E', 'GLY'], ['321', 'E', 'PRO'], ['322', 'E', 'GLY'], ['323', 'E', 'ASP']], 'KAE': [['95', 'E', 'LEU'], ['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['100', 'E', 'PHE'], ['103', 'E', 'LEU'], ['104', 'E', 'VAL'], ['105', 'E', 'LYS'], ['106', 'E', 'LEU']], 'KAF': [['123', 'E', 'VAL'], ['124', 'E', 'ALA'], ['175', 'E', 'ASP'], ['176', 'E', 'GLN'], ['181', 'E', 'GLN']], 'KAG': [['34', 'E', 'SER'], ['37', 'E', 'THR'], ['96', 'E', 'GLN'], ['106', 'E', 'LEU'], ['107', 'E', 'GLU'], ['108', 'E', 'PHE'], ['109', 'E', 'SER']], 'KAH': [['49', 'E', 'LEU'], ['50', 'E', 'GLY'], ['51', 'E', 'THR'], ['52', 'E', 'GLY'], ['53', 'E', 'SER'], ['54', 'E', 'PHE'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['72', 'E', 'LYS'], ['74', 'E', 'LEU'], ['84', 'E', 'GLN'], ['87', 'E', 'HIS'], ['88', 'E', 'THR'], ['91', 'E', 'GLU'], ['104', 'E', 'VAL'], ['120', 'E', 'MET'], ['121', 'E', 'GLU'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['166', 'E', 'ASP'], ['168', 'E', 'LYS'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['184', 'E', 'ASP'], ['186', 'E', 'GLY'], ['187', 'E', 'PHE'], ['201', 'E', 'THR'], ['327', 'E', 'PHE']], 'KAI': [['131', 'E', 'HIS'], ['138', 'E', 'PHE'], ['142', 'E', 'HIS'], ['146', 'E', 'TYR'], ['174', 'E', 'ILE'], ['314', 'E', 'PHE']], 'KAJ': [['33', 'E', 'PRO'], ['89', 'E', 'LEU'], ['92', 'E', 'LYS'], ['93', 'E', 'ARG'], ['96', 'E', 'GLN'], ['349', 'E', 'GLU'], ['350', 'E', 'PHE']], 'KAK': [['157', 'E', 'LEU'], ['162', 'E', 'LEU'], ['163', 'E', 'ILE'], ['164', 'E', 'TYR'], ['185', 'E', 'PHE'], ['188', 'E', 'ALA']], 'KAL': [['49', 'E', 'LEU'], ['127', 'E', 'GLU'], ['129', 'E', 'PHE'], ['130', 'E', 'SER'], ['326', 'E', 'ASN'], ['327', 'E', 'PHE'], ['328', 'E', 'ASP'], ['330', 'E', 'TYR']], 'KAM': [['51', 'E', 'THR'], ['55', 'E', 'GLY'], ['56', 'E', 'ARG'], ['73', 'E', 'ILE'], ['74', 'E', 'LEU'], ['75', 'E', 'ASP'], ['115', 'E', 'ASN'], ['335', 'E', 'ILE'], ['336', 'E', 'ARG']], 'KAN': [['165', 'E', 'ARG'], ['166', 'E', 'ASP'], ['167', 'E', 'LEU'], ['199', 'E', 'CYS'], ['200', 'E', 'GLY'], ['201', 'E', 'THR'], ['204', 'E', 'TYR'], ['205', 'E', 'LEU'], ['206', 'E', 'ALA'], ['209', 'E', 'ILE'], ['219', 'E', 'VAL'], ['220', 'E', 'ASP'], ['223', 'E', 'ALA']], 'KAO': [['48', 'E', 'THR'], ['51', 'E', 'THR'], ['56', 'E', 'ARG'], ['330', 'E', 'TYR'], ['331', 'E', 'GLU']], 'KAP': [['222', 'E', 'TRP'], ['238', 'E', 'PHE'], ['253', 'E', 'GLY'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['273', 'E', 'LEU']], 'KAQ': [['207', 'E', 'PRO'], ['208', 'E', 'GLU'], ['211', 'E', 'LEU'], ['213', 'E', 'LYS'], ['275', 'E', 'VAL'], ['277', 'E', 'LEU']], 'KAR': [['237', 'E', 'PRO'], ['238', 'E', 'PHE'], ['249', 'E', 'LYS'], ['254', 'E', 'LYS'], ['255', 'E', 'VAL'], ['256', 'E', 'ARG']]}
-
          
-
          
-
          If you wish to ignore backbones contacts (C, CA, N, O) with the cavity when defining interface residues, you must set ignore_backbone flag to True.
          
-
          >>> residues_ib = pyKVFinder.constitutional(cavities, atomic, vertices, step=step, probe_in=probe_in, ignore_backbone=True)
->>> residues_ib
-{'KAA': [['15', 'E', 'VAL'], ['18', 'E', 'PHE'], ['19', 'E', 'LEU'], ['100', 'E', 'PHE'], ['152', 'E', 'LEU'], ['155', 'E', 'GLU'], ['156', 'E', 'TYR'], ['292', 'E', 'LYS'], ['302', 'E', 'TRP'], ['303', 'E', 'ILE'], ['306', 'E', 'TYR']], 'KAB': [['18', 'E', 'PHE'], ['22', 'E', 'ALA'], ['25', 'E', 'ASP'], ['26', 'E', 'PHE'], ['29', 'E', 'LYS'], ['99', 'E', 'ASN'], ['156', 'E', 'TYR']], 'KAC': [['144', 'E', 'ARG'], ['145', 'E', 'PHE'], ['148', 'E', 'ALA'], ['299', 'E', 'THR'], ['300', 'E', 'THR'], ['305', 'E', 'ILE'], ['310', 'E', 'VAL'], ['311', 'E', 'GLU'], ['313', 'E', 'PRO']], 'KAD': [['122', 'E', 'TYR'], ['124', 'E', 'ALA'], ['176', 'E', 'GLN'], ['318', 'E', 'PHE']], 'KAE': [['98', 'E', 'VAL'], ['99', 'E', 'ASN'], ['103', 'E', 'LEU'], ['105', 'E', 'LYS'], ['106', 'E', 'LEU']], 'KAF': [['123', 'E', 'VAL'], ['175', 'E', 'ASP'], ['181', 'E', 'GLN']], 'KAG': [['34', 'E', 'SER'], ['37', 'E', 'THR'], ['96', 'E', 'GLN'], ['106', 'E', 'LEU'], ['109', 'E', 'SER']], 'KAH': [['49', 'E', 'LEU'], ['53', 'E', 'SER'], ['54', 'E', 'PHE'], ['57', 'E', 'VAL'], ['70', 'E', 'ALA'], ['72', 'E', 'LYS'], ['74', 'E', 'LEU'], ['84', 'E', 'GLN'], ['87', 'E', 'HIS'], ['88', 'E', 'THR'], ['91', 'E', 'GLU'], ['104', 'E', 'VAL'], ['120', 'E', 'MET'], ['122', 'E', 'TYR'], ['123', 'E', 'VAL'], ['127', 'E', 'GLU'], ['166', 'E', 'ASP'], ['168', 'E', 'LYS'], ['170', 'E', 'GLU'], ['171', 'E', 'ASN'], ['173', 'E', 'LEU'], ['183', 'E', 'THR'], ['184', 'E', 'ASP'], ['187', 'E', 'PHE'], ['201', 'E', 'THR'], ['327', 'E', 'PHE']], 'KAI': [['131', 'E', 'HIS'], ['138', 'E', 'PHE'], ['142', 'E', 'HIS'], ['146', 'E', 'TYR'], ['174', 'E', 'ILE'], ['314', 'E', 'PHE']], 'KAJ': [['33', 'E', 'PRO'], ['89', 'E', 'LEU'], ['92', 'E', 'LYS'], ['93', 'E', 'ARG'], ['96', 'E', 'GLN'], ['349', 'E', 'GLU'], ['350', 'E', 'PHE']], 'KAK': [['157', 'E', 'LEU'], ['162', 'E', 'LEU'], ['164', 'E', 'TYR'], ['185', 'E', 'PHE'], ['188', 'E', 'ALA']], 'KAL': [['127', 'E', 'GLU'], ['129', 'E', 'PHE'], ['130', 'E', 'SER'], ['327', 'E', 'PHE'], ['328', 'E', 'ASP'], ['330', 'E', 'TYR']], 'KAM': [['51', 'E', 'THR'], ['56', 'E', 'ARG'], ['73', 'E', 'ILE'], ['115', 'E', 'ASN'], ['335', 'E', 'ILE']], 'KAN': [['165', 'E', 'ARG'], ['166', 'E', 'ASP'], ['167', 'E', 'LEU'], ['201', 'E', 'THR'], ['204', 'E', 'TYR'], ['205', 'E', 'LEU'], ['206', 'E', 'ALA'], ['209', 'E', 'ILE'], ['219', 'E', 'VAL'], ['220', 'E', 'ASP'], ['223', 'E', 'ALA']], 'KAO': [['48', 'E', 'THR'], ['51', 'E', 'THR'], ['56', 'E', 'ARG'], ['330', 'E', 'TYR']], 'KAP': [['222', 'E', 'TRP'], ['238', 'E', 'PHE'], ['255', 'E', 'VAL'], ['273', 'E', 'LEU']], 'KAQ': [['207', 'E', 'PRO'], ['208', 'E', 'GLU'], ['211', 'E', 'LEU'], ['213', 'E', 'LYS'], ['277', 'E', 'LEU']], 'KAR': [['238', 'E', 'PHE'], ['249', 'E', 'LYS'], ['255', 'E', 'VAL'], ['256', 'E', 'ARG']]}
-
          
-
          
-
          
-
          Note
          
-
          The cavity nomenclature is based on the integer label. The cavity marked with 2, the first integer corresponding to a cavity, is KAA, the cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
          
-
          
-
          
-
          Note
          
-
          If the step, probe_in and ignore_backbone are not defined, the function automatically sets them to the default value. So, you can call the function by pyKVFinder.constitutional(cavities, atomic, vertices).
          
-
          
-
          
-
          See also
          
-
-
          
-
          
-
          6.1 Calculating and plotting frequencies
          
-
          With the interface residues defined, you can also calculate the frequencies of residues and classes of residues. The classes of residues are:
          
-
          
-
          R1:
          
-
          Alipathic apolar: Alanine, Glycine, Isoleucine, Leucine, Methionine, Valine
          
-
          
-
          R2:
          
-
          Aromatic: Phenylalanine, Tryptophan, Tyrosine
          
-
          
-
          R3:
          
-
          Polar uncharged: Asparagine, Cysteine, Glutamine, Proline, Serine, Threonine
          
-
          
-
          R4:
          
-
          Negatively charged: Aspartate, Glutamate
          
-
          
-
          R5:
          
-
          Positively charged: Arginine, Histidine, Lysine
          
-
          
-
          RX:
          
-
          Non-standard: Non-standard residues
          
-
          
-
          
-
          pyKVFinder.calculate_frequencies takes the dictionary of interface residues calculated above and returns a dictionary with the frequencies of residues and classes of residues of each detected cavity.
          
-
          >>> frequencies = pyKVFinder.calculate_frequencies(residues)
->>> frequencies
-{'KAA': {'RESIDUES': {'GLU': 1, 'ILE': 1, 'LEU': 2, 'LYS': 1, 'PHE': 2, 'SER': 1, 'TRP': 1, 'TYR': 2, 'VAL': 1}, 'CLASS': {'R1': 4, 'R2': 5, 'R3': 1, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAB': {'RESIDUES': {'ALA': 2, 'ASN': 1, 'ASP': 1, 'LYS': 1, 'PHE': 2, 'TYR': 1, 'VAL': 1}, 'CLASS': {'R1': 3, 'R2': 3, 'R3': 1, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAC': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'GLU': 1, 'HIS': 1, 'ILE': 1, 'PHE': 1, 'PRO': 2, 'THR': 2, 'VAL': 1}, 'CLASS': {'R1': 5, 'R2': 1, 'R3': 2, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAD': {'RESIDUES': {'ALA': 1, 'ASP': 1, 'GLN': 1, 'GLY': 2, 'PHE': 1, 'PRO': 1, 'TYR': 1}, 'CLASS': {'R1': 4, 'R2': 2, 'R3': 1, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAE': {'RESIDUES': {'ASN': 1, 'LEU': 3, 'LYS': 1, 'PHE': 1, 'VAL': 2}, 'CLASS': {'R1': 5, 'R2': 1, 'R3': 1, 'R4': 0, 'R5': 1, 'RX': 0}}, 'KAF': {'RESIDUES': {'ALA': 1, 'ASP': 1, 'GLN': 2, 'VAL': 1}, 'CLASS': {'R1': 2, 'R2': 0, 'R3': 2, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAG': {'RESIDUES': {'GLN': 1, 'GLU': 1, 'LEU': 1, 'PHE': 1, 'SER': 2, 'THR': 1}, 'CLASS': {'R1': 1, 'R2': 1, 'R3': 4, 'R4': 1, 'R5': 0, 'RX': 0}}, 'KAH': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'ASN': 1, 'ASP': 2, 'GLN': 1, 'GLU': 4, 'GLY': 4, 'HIS': 1, 'LEU': 3, 'LYS': 2, 'MET': 1, 'PHE': 3, 'SER': 1, 'THR': 4, 'TYR': 1, 'VAL': 3}, 'CLASS': {'R1': 11, 'R2': 4, 'R3': 8, 'R4': 6, 'R5': 4, 'RX': 0}}, 'KAI': {'RESIDUES': {'HIS': 2, 'ILE': 1, 'PHE': 2, 'TYR': 1}, 'CLASS': {'R1': 1, 'R2': 3, 'R3': 0, 'R4': 0, 'R5': 2, 'RX': 0}}, 'KAJ': {'RESIDUES': {'ARG': 1, 'GLN': 1, 'GLU': 1, 'LEU': 1, 'LYS': 1, 'PHE': 1, 'PRO': 1}, 'CLASS': {'R1': 2, 'R2': 1, 'R3': 1, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAK': {'RESIDUES': {'ALA': 1, 'ILE': 1, 'LEU': 2, 'PHE': 1, 'TYR': 1}, 'CLASS': {'R1': 4, 'R2': 2, 'R3': 0, 'R4': 0, 'R5': 0, 'RX': 0}}, 'KAL': {'RESIDUES': {'ASN': 1, 'ASP': 1, 'GLU': 1, 'LEU': 1, 'PHE': 2, 'SER': 1, 'TYR': 1}, 'CLASS': {'R1': 1, 'R2': 3, 'R3': 2, 'R4': 2, 'R5': 0, 'RX': 0}}, 'KAM': {'RESIDUES': {'ARG': 2, 'ASN': 1, 'ASP': 1, 'GLY': 1, 'ILE': 2, 'LEU': 1, 'THR': 1}, 'CLASS': {'R1': 4, 'R2': 0, 'R3': 2, 'R4': 1, 'R5': 2, 'RX': 0}}, 'KAN': {'RESIDUES': {'ALA': 2, 'ARG': 1, 'ASP': 2, 'CYS': 1, 'GLY': 1, 'ILE': 1, 'LEU': 2, 'THR': 1, 'TYR': 1, 'VAL': 1}, 'CLASS': {'R1': 7, 'R2': 1, 'R3': 2, 'R4': 2, 'R5': 1, 'RX': 0}}, 'KAO': {'RESIDUES': {'ARG': 1, 'GLU': 1, 'THR': 2, 'TYR': 1}, 'CLASS': {'R1': 0, 'R2': 1, 'R3': 2, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAP': {'RESIDUES': {'GLY': 1, 'LEU': 1, 'LYS': 1, 'PHE': 1, 'TRP': 1, 'VAL': 1}, 'CLASS': {'R1': 3, 'R2': 2, 'R3': 0, 'R4': 0, 'R5': 1, 'RX': 0}}, 'KAQ': {'RESIDUES': {'GLU': 1, 'LEU': 2, 'LYS': 1, 'PRO': 1, 'VAL': 1}, 'CLASS': {'R1': 4, 'R2': 0, 'R3': 0, 'R4': 1, 'R5': 1, 'RX': 0}}, 'KAR': {'RESIDUES': {'ARG': 1, 'LYS': 2, 'PHE': 1, 'PRO': 1, 'VAL': 1}, 'CLASS': {'R1': 2, 'R2': 1, 'R3': 0, 'R4': 0, 'R5': 3, 'RX': 0}}}
-
          
-
          
-
          
-
          Note
          
-
          The cavity nomenclature is based on the integer label. The cavity marked with 2, the first integer corresponding to a cavity, is KAA, the cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
          
-
          
-
          Afterwards, pyKVFinder.plot_frequencies takes the dictionary with the frequencies of residues and classes of residues of each detected cavity and a path to a PDF file, and plots the bar charts of calculated frequencies for each detected cavity in a PDF file.
          
-
          >>> fn = 'barplots.pdf'
->>> pyKVFinder.plot_frequencies(frequencies, fn=fn)
-
          
-
          
-
          
-
          Note
          
-
          If the fn is not defined, the function automatically sets it to the default value. So, you can call the function by pyKVFinder.plot_frequencies(frequencies).
          
-
          
-
          
-
          See also
          
-
-
          
-
          A sample barplot of pyKVFinder.plot_frequencies is shown below.
          
-../_images/plot-frequencies.png
-
          
-

          
-
          
-
          
-
          
-
          
-
          7. Performing hydropathy characterization
          
-
          A hydropathy characterization, that maps a target hydrophobicity scale on surface points and calculate the average hydropathy, is performed on the surface points of the detected cavities.
          
-
          pyKVFinder.hydropathy takes the surface points of the detected cavities, the NumPy array with residue number, chain identifier, residue name, atom name, xyz coordinates and radius for each atom, the NumPy array with vertice coordinates (origin, X-axis, Y-axis, Z-axis), a collection of detection parameters (step, probe_in) and a target hydrophobicity scale to be mapped on the surface points, and returns a tuple with a NumPy array with the hydropobicity scale mapped to the surface points in the 3D grid and a dictionary with the average hydrophobicity scale of the detected cavities and the range of the chosen hydrophobicity scale.
          
-
          >>> # Default Hydrophobicity Scale (hydropathy): 'EisenbergWeiss'
->>> hydrophobicity_scale = 'EisenbergWeiss'
->>> scales, avg_hydropathy = pyKVFinder.hydropathy(surface, atomic, vertices, step=step, probe_in=probe_in, hydrophobicity_scale=hydrophobicity_scale, ignore_backbone=ignore_backbone)
->>> scales
-array([[[0., 0., 0., ..., 0., 0., 0.],
-      [0., 0., 0., ..., 0., 0., 0.],
-      [0., 0., 0., ..., 0., 0., 0.],
-      ...,
-      [0., 0., 0., ..., 0., 0., 0.],
-      [0., 0., 0., ..., 0., 0., 0.],
-      [0., 0., 0., ..., 0., 0., 0.]],
-
-     ...,
-
-     [[0., 0., 0., ..., 0., 0., 0.],
-      [0., 0., 0., ..., 0., 0., 0.],
-      [0., 0., 0., ..., 0., 0., 0.],
-      ...,
-      [0., 0., 0., ..., 0., 0., 0.],
-      [0., 0., 0., ..., 0., 0., 0.],
-      [0., 0., 0., ..., 0., 0., 0.]]])
->>> avg_hydropathy
-{'KAA': -0.73, 'KAB': -0.05, 'KAC': -0.07, 'KAD': -0.62, 'KAE': -0.81, 'KAF': -0.14, 'KAG': -0.33, 'KAH': -0.16, 'KAI': -0.4, 'KAJ': 0.62, 'KAK': -0.99, 'KAL': 0.36, 'KAM': -0.33, 'KAN': 0.18, 'KAO': 0.88, 'KAP': -0.96, 'KAQ': 0.48, 'KAR': 0.24, 'EisenbergWeiss': [-1.42, 2.6]}
-
          
-
          
-
          
-
          Note
          
-
          The cavity nomenclature is based on the integer label. The cavity marked with 2, the first integer corresponding to a cavity, is KAA, the cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
          
-
          
-
          
-
          Note
          
-
          The pyKVFinder.hydropathy function accepts six built-in hydrophobicity scales:
          
-
          
-
          
-
          Otherwise, user must specify a .toml file following Hydrophobicity Scale File Template.
          
-
          
-
          
-
          Note
          
-
          If the step, probe_in, hydrophobicity_scale and ignore_backbone are not defined, the function automatically sets them to the default values. So, you can call the function by pyKVFinder.hydropathy(surface, atomic, vertices).
          
-
          
-
          
-
          See also
          
-
-
          
-
          
-
          
-
          8. Performing depth characterization
          
-
          A depth characterization identifies the degree of burial of the binding site. First, it identifies the cavity volume boundary. Subsequently, the depth of each cavity point is heuristically estimated by the shortest Euclidean distance between the cavity point and its respective boundary points. With this, the maximum and average depths for the detected cavities are calculated.
          
-
          pyKVFinder.depth takes the detected cavities and the grid spacing (step) and returns a tuple with a NumPy array with the depth of the cavity points in the 3D grid, a dictionary with the maximum depth of the detected cavities and a dictionary with the average depth of the detected cavities.
          
-
          >>> depths, max_depth, avg_depth = pyKVFinder.depth(cavities, step=step)
->>> depths
-array([[[0., 0., 0., ..., 0., 0., 0.],
-      [0., 0., 0., ..., 0., 0., 0.],
-      [0., 0., 0., ..., 0., 0., 0.],
-      ...,
-      [0., 0., 0., ..., 0., 0., 0.],
-      [0., 0., 0., ..., 0., 0., 0.],
-      [0., 0., 0., ..., 0., 0., 0.]],
-
-     ...,
-
-     [[0., 0., 0., ..., 0., 0., 0.],
-      [0., 0., 0., ..., 0., 0., 0.],
-      [0., 0., 0., ..., 0., 0., 0.],
-      ...,
-      [0., 0., 0., ..., 0., 0., 0.],
-      [0., 0., 0., ..., 0., 0., 0.],
-      [0., 0., 0., ..., 0., 0., 0.]]])
->>> max_depth
-{'KAA': 3.79, 'KAB': 2.68, 'KAC': 2.62, 'KAD': 0.85, 'KAE': 3.0, 'KAF': 0.85, 'KAG': 0.6, 'KAH': 10.73, 'KAI': 0.0, 'KAJ': 2.24, 'KAK': 0.0, 'KAL': 3.0, 'KAM': 1.2, 'KAN': 0.0, 'KAO': 1.04, 'KAP': 2.08, 'KAQ': 0.85, 'KAR': 0.6}
->>> avg_depth
-{'KAA': 1.35, 'KAB': 0.91, 'KAC': 0.68, 'KAD': 0.32, 'KAE': 0.99, 'KAF': 0.24, 'KAG': 0.1, 'KAH': 3.91, 'KAI': 0.0, 'KAJ': 0.96, 'KAK': 0.0, 'KAL': 1.07, 'KAM': 0.24, 'KAN': 0.0, 'KAO': 0.29, 'KAP': 0.7, 'KAQ': 0.22, 'KAR': 0.12}
-
          
-
          
-
          
-
          Note
          
-
          The cavity nomenclature is based on the integer label. The cavity marked with 2, the first integer corresponding to a cavity, is KAA, the cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
          
-
          
-
          
-
          Note
          
-
          If the step is not defined, the function automatically sets it to the default value. So, you can call the function by pyKVFinder.depth(cavities).
          
-
          
-
          
-
          See also
          
-
-
          
-
          
-
          
-
          9. Exporting cavities
          
-
          There are four different ways to export the detected cavities to PDB-formatted files.
          
-
          
-
          9.1 Exporting only cavity points
          
-
          >>> output_cavity = 'cavity_wo_surface.pdb'
->>> pyKVFinder.export(output_cavity, cavities, None, vertices, step=step)
-
          
-
          
-
          
-
          
-
          9.2 Exporting cavity and surface points
          
-
          >>> output_cavity = 'cavity.pdb'
->>> pyKVFinder.export(output_cavity, cavities, surface, vertices, step=step)
-
          
-
          
-
          
-
          
-
          9.3 Exporting cavity and surface points with depth mapped on B-factor
          
-
          >>> output_cavity = 'cavity_with_depth.pdb'
->>> pyKVFinder.export(output_cavity, cavities, surface, vertices, step=step, B=depths)
-
          
-
          
-
          
-
          
-
          9.4 Exporting cavity and surface points with depth mapped on B-factor and surface points with hydrophobicity scale mapped on B-factor
          
-
          >>> output_cavity = 'cavity_with_depth.pdb'
->>> output_hydropathy = 'hydropathy.pdb'
->>> pyKVFinder.export(output_cavity, cavities, surface, vertices, step=step, B=depths, output_hydropathy=output_hydropathy, scales=scales)
-
          
-
          
-
          
-
          Note
          
-
          The cavity nomenclature is based on the integer label. The cavity marked with 2, the first integer corresponding to a cavity, is KAA, the cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
          
-
          
-
          
-
          Note
          
-
          If the step, B, scales and output_hydropathy are not defined, the function automatically sets them to the default values. So, you can call the function by pyKVFinder.export(output_cavity, cavities, surface, vertices).
          
-
          
-
          
-
          See also
          
-
-
          
-
          
-
          
-
          
-
          10.  Writing results
          
-
          The function call depends on the characterizations performed on the detected cavities.
          
-
          
-
          10.1 Cavity detection only
          
-
          >>> output_results = 'results.toml'
->>> pyKVFinder.write_results(output_results, input=pdb, ligand=None, output=output_cavity, step=step)
-
          
-
          
-
          
-
          
-
          10.2 Spatial characterization
          
-
          >>> output_results = 'results.toml'
->>> pyKVFinder.write_results(output_results, input=pdb, ligand=None, output=output_cavity, volume=volume, area=area, step=step)
-
          
-
          
-
          
-
          
-
          10.3 Spatial and constitutional characterization
          
-
          >>> output_results = 'results.toml'
->>> pyKVFinder.write_results(output_results, input=pdb, ligand=None, output=output_cavity, volume=volume, area=area, residues=residues, frequencies=frequencies, step=step)
-
          
-
          
-
          
-
          
-
          10.4 Spatial, constitutional and depth characterization
          
-
          >>> output_results = 'results.toml'
->>> pyKVFinder.write_results(output_results, input=pdb, ligand=None, output=output_cavity, volume=volume, area=area, max_depth=max_depth, avg_depth=avg_depth, residues=residues, frequencies=frequencies, step=step)
-
          
-
          
-
          
-
          
-
          10.5 Spatial, constitutional, depth and hydropathy characterization
          
-
          >>> output_results = 'results.toml'
->>> pyKVFinder.write_results(output_results, input=pdb, ligand=None, output=output_cavity, output_hydropathy=output_hydropathy, volume=volume, area=area, max_depth=max_depth, avg_depth=avg_depth, avg_hydropathy=avg_hydropathy, residues=residues, frequencies=frequencies, step=step)
-
          
-
          
-
          
-
          Note
          
-
          The cavity nomenclature is based on the integer label. The cavity marked with 2, the first integer corresponding to a cavity, is KAA, the cavity marked with 3 is KAB, the cavity marked with 4 is KAC and so on.
          
-
          
-
          
-
          See also
          
-
-
          
-
          
-
          
-
          
-
          
-
          Steered detection
          
-
          All these steps showed so far were performed the detection on the whole target biomolecule; however, we can perform them on a custom 3D grid, where we can explore closed regions with a custom box, which can be defined by a .toml file.
          
-
          There are three methods to define a custom 3D grid as shown in Box configuration file template.
          
-
          First, we will create a box .toml file with:
          
-
            
-
          • Four vertices of the box (origin, X-axis, Y-axis and Z-axis):
            • 
-
          
-
          >>> import toml
->>> fn = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'custom-box.toml')
->>> box = toml.load(fn)
->>> box
-{'box': {'p1': [3.11, 7.34, 1.59], 'p2': [11.51, 7.34, 1.59], 'p3': [3.11, 10.74, 1.59], 'p4': [3.11, 7.34, 6.19]}}
-
          
-
          
-
          or
          
-
            
-
          • A list of residues and a padding:
            • 
-
          
-
          >>> fn = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'residues-box.toml')
->>> box = toml.load(fn)
->>> box
-{'box': {'residues': [['49', 'E', 'LEU'], ['50', 'E', 'GLY'], ['51', 'E', 'THR']], 'padding': 3.5}}
-
          
-
          
-
          A third way is to define a custom 3D grid with parKVFinder’s TOML-formatted parameters file.
          
-
          >>> fn = 'box.toml'
->>> box = """
-      [SETTINGS.visiblebox.p1]
-      x = 3.11
-      y = 7.34
-      z = 1.59
-
-      [SETTINGS.visiblebox.p2]
-      x = 11.51
-      y = 7.34
-      z = 1.59
-
-      [SETTINGS.visiblebox.p3]
-      x = 3.11
-      y = 10.74
-      z = 1.59
-
-      [SETTINGS.visiblebox.p4]
-      x = 3.11
-      y = 7.34
-      z = 6.19
-"""
->>> with open(fn, 'w') as f:
-...     toml.dump(toml.loads(box), f)
-
          
-
          
-
          
-
          Note
          
-
          Users can create this box with parKVFinder PyMOL plugin (PyMOL2 parKVFinder Tools) and save the parameters file from it.
          
-
          
-
          
-
          Workflows
          
-
          Then, you can explore the box adjustment mode with the standard and full workflows, defining the box parameter as the filepath of one box configuration file from above (custom-box.toml, residues-box.toml or box.toml).
          
-
          For instance, with custom-box.toml:
          
-
          >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', '1FMO.pdb')
->>> # Box configuration filepath
->>> fn = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'custom-box.toml')
->>> # Standard workflow
->>> results = pyKVFinder.run_workflow(pdb, box=fn)
->>> # Full workflow
->>> results = pyKVFinder.run_workflow(pdb, box=fn, include_depth=True, include_hydropathy=True, hydrophobicity_scale='EisenbergWeiss')
-
          
-
          
-
          
-
          See also
          
-
-
          
-
          
-
          
-
          Separated steps
          
-
          If you are running pyKVFinder package in a step-by-step fashion (Separated steps), the steps 3 and 4 are different than before.
          
-
            
-
          • Dimensioning the 3D grid: Instead of calling pyKVFinder.get_vertices, you call pyKVFinder.get_vertices_from_file.
            • 
-
          
-
          pyKVFinder.get_vertices_from_file takes .toml file with box configuration or parKVFinder parameters file, the NumPy array with residue number, chain identifier, residue name, atom name, xyz coordinates and radius for each atom, and a collection of detection parameters (step, probe_in and probe_out), and returns a tuple with a NumPy array with vertice coordinates (origin, X-axis, Y-axis, Z-axis) of the 3D grid and the NumPy array with residue number, chain identifier, residue name, atom name, xyz coordinates and radius for each atom inside the custom box.
          
-
          Users can define the box parameter as the filepath of one box configuration file from above (custom-box.toml, residues-box.toml or box.toml). For instance, with custom-box.toml:
          
-
          >>> vertices, atomic = pyKVFinder.get_vertices_from_file(fn, atomic, step=step, probe_in=probe_in, probe_out=probe_out)
-
          
-
          
-
          
-
          Note
          
-
          If the step, probe_in and probe_out are not defined, the function automatically sets them to the default value. So, you can call the function by pyKVFinder.get_vertices_from_file('box.toml', atomic).
          
-
          
-
            
-
          • Detecting biomolecular cavities: Now, you can explore this box adjustment mode, defining the box_adjustment parameter as True.
            • 
-
          
-
          >>> ncav, cavities = pyKVFinder.detect(atomic, vertices, step=step, probe_in=probe_in, probe_out=probe_out, removal_distance=removal_distance, volume_cutoff=volume_cutoff, box_adjustment=True, surface=surface)
->>> ncav
-1
->> cavities
-array([[[-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    ...,
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1]],
-
-    ...,
-
-    [[-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    ...,
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1],
-    [-1, -1, -1, ..., -1, -1, -1]]], dtype=int32)
-
          
-
          
-
          
-
          Note
          
-
          If any of the detection parameters (step, probe_in, probe_out, removal_distance, volume_cutoff, surface) are not defined, the function automatically sets them to the default value. So, you can call the function by pyKVFinder.detect(atomic, vertices, box_adjustment=True).
          
-
          
-
          
-
          Warning
          
-
          If you are using box adjusment mode, do not forget to set box_adjustment flag to True.
          
-
          
-
          
-
          See also
          
-
-
          
-
          
-
          
-
          
-
          
-
          Molecular volume
          
-
          All files used on this tutorial can be found in our package and in our GitHub repository:
          
-
-
          In this tutorial, we will use pyKVFinder on perchlorate (ClO4 ) to estimate the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES) and solvent accessible surface (SAS) to represent the molecular surface (see Figure below).
          
-
-
-
-
-
-
-
-
-
-
          ../_images/vdw.png
-
          
-(a) vdW
          		../_images/ses.png
-
          
-(b) SES
          		../_images/sas.png
-
          
-(c) SAS
          
-Molecular surface represenation
          
-
          First, we must load the target molecular structure (ClO4 )  into pyKVFinder.Molecule class.
          
-
          >>> pdb = os.path.join(os.path.dirname(pyKVFinder.__file__), 'data', 'tests', 'ClO4.pdb')
->>> molecule pyKVFinder.Molecule(pdb)
->>> molecule
-<pyKVFinder.main.Molecule object at 0x7f5ddacf2230>
-
          
-
          
-
          With the atomic information and vdW radii dictionary loaded, the molecule is inserted into a regular 3D grid, considering the vdW radii of any of the atoms. Natively, the vdW radii are taken from the built-in dictionary. In the 3D grid, each voxel corresponds to a molecule (0) or solvent (1) points. Here, we can model our molecule using the vdW surface, SES or SAS.
          
-
          
-
          1. vdW volume
          
-
          Molecule.vdw() takes a grid spacing and returns a NumPy array with the molecule points representing the vdW surface in the 3D grid.
          
-
          >>> # Grid Spacing (step): 0.1
->>> step = 0.1
->>> molecule.vdw(step=step)
->>> molecule.grid
-array([[[1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        ...,
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1]],
-
-        ...,
-
-      [[1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        ...,
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1]]], dtype=int32)
-
          
-
          
-
          
-
          Note
          
-
          If step is not defined, the function automatically sets it to the default value. So, you can call the function by molecule.vdw().
          
-
          
-
          We can preview our modelled molecule in the 3D grid by running:
          
-
          >>> molecule.export("vdw-model.pdb")
-
          
-
          
-../_images/vdw-grid.png
-
          We can also export our modelled molecule int the 3D grid by running:
          
-
          >>> molecule.preview()
-
          
-
          
-
          Now, we can estimate the vdW volume by running:
          
-
          >>> molecule.volume()
-83.64
-
          
-
          
-
          
-
          
-
          2. SES volume
          
-
          Molecule.surface() takes the grid spacing, the spherical probe size to model the surface, the SES representation and returns a NumPy array with the molecule points representing the SES in the 3D grid.
          
-
          >>> # Grid Spacing (step): 0.1
->>> step = 0.1
->>> # Spherical Probe (probe): 1.4
->>> probe = 1.4
->>> # Surface Representation: SES
->>> surface = 'SES'
->>> molecule.surface(step=step, probe=probe, surface=surface)
->>> molecule.grid
-array([[[1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        ...,
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1]],
-
-        ...,
-
-      [[1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        ...,
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1]]], dtype=int32)
-
          
-
          
-
          
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          Note
          
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          If any of the parameters (step, probe or surface) are not defined, the function automatically sets them to the default values. So, you can call the function by molecule.surface().
          
-
          
-
          We can preview our modelled molecule in the 3D grid by running:
          
-
          >>> molecule.preview()
-
          
-
          
-../_images/ses-grid.png
-
          Now, we can estimate the vdW volume by running:
          
-
          >>> molecule.volume()
-90.8
-
          
-
          
-
          
-
          
-
          3. SAS volume
          
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          Molecule.surface() takes a grid spacing, a spherical probe to model the surface, a SAS representation and returns a NumPy array with the molecule points representing the SES in the 3D grid.
          
-
          >>> # Grid Spacing (step): 0.1
->>> step = 0.1
->>> # Spherical Probe (probe): 1.4
->>> probe = 1.4
->>> # Surface Representation: SAS
->>> surface = 'SAS'
->>> molecule.surface(step=step, probe=probe, surface=surface)
->>> molecule.grid
-array([[[1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        ...,
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1]],
-
-        ...,
-
-      [[1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        ...,
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1],
-        [1, 1, 1, ..., 1, 1, 1]]], dtype=int32)
-
          
-
          
-
          
-
          Note
          
-
          If any of the parameters (step or probe) are not defined, the function automatically sets them to the default values. So, you can call the function by molecule.surface(surface='SAS').
          
-
          
-
          We can preview our modelled molecule in the 3D grid by running:
          
-
          >>> molecule.preview()
-
          
-
          
-../_images/sas-grid.png
-
          Now, we can estimate the vdW volume by running:
          
-
          >>> molecule.volume()
-340.28
-
          
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          Examples
          
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          Jupyter notebook examples are available for:
          
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-
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-  Index — pyKVFinder 0.5.0 documentation
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-
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-  Welcome to pyKVFinder’s documentation! — pyKVFinder 0.5.0 documentation
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          Welcome to pyKVFinder’s documentation!
          
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          Welcome to the Python-C parallel KVFinder (pyKVFinder) documentation, this page was built to help you get started with our cavity detection and characterization package.
          
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-  Search — pyKVFinder 0.5.0 documentation
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27, "provid": 27, "field": 27, "diamet": 27, "call": 27, "collect": 27, "distanc": 27, "adenosin": 27, "351": 27, "c5": 27, "087": 27, "052": 27, "o5": 27, "545": 27, "c4": 27, "688": 27, "523": 27, "o4": 27, "714": 27, "725": 27, "c3": 27, "973": 27, "374": 27, "903": 27, "o3": 27, "879": 27, "361": 27, "304": 27, "c2": 27, "059": 27, "o2": 27, "887": 27, "034": 27, "232": 27, "c1": 27, "625": 27, "n1": 27, "499": 27, "402": 27, "376": 27, "259": 27, "n3": 27, "705": 27, "136": 27, "094": 27, "353": 27, "952": 27, "974": 27, "c6": 27, "957": 27, "n6": 27, "083": 27, "826": 27, "n7": 27, "791": 27, "843": 27, "c8": 27, "872": 27, "291": 27, "n9": 27, "444": 27, "056": 27, "646": 27, "afterward": 27, "ncav_la": 27, "cavities_la": 27, "residues_ib": 27, "alipath": 27, "sampl": 27, "hydropob": 27, "accept": 27, "degre": 27, "burial": 27, "bind": 27, "site": 27, "boundari": 27, "subsequ": 27, "heurist": 27, "shortest": 27, "euclidean": 27, "between": 27, "wai": 27, "cavity_with_depth": 27, "output_result": 27, "far": 27, "were": 27, "dump": 27, "pymol2": 27, "tool": 27, "save": 27, "filepath": 27, "instanc": 27, "now": 27, "perchlor": 27, "clo": 27, "figur": 27, "represen": 27, "insert": 27, "regular": 27, "nativ": 27, "taken": 27, "here": 27, "340": 27, "jupyt": 27, "notebook": 27, "conserv": 27, "analysi": 27, "dynam": 27, "start": 28, "instal": 28}, "objects": {"pyKVFinder": [[1, 0, 1, "", "Molecule"], [2, 4, 1, "", "calculate_frequencies"], [3, 4, 1, "", "constitutional"], [4, 4, 1, "", "depth"], [5, 4, 1, "", "detect"], [6, 4, 1, "", "export"], [7, 4, 1, "", "export_openings"], [8, 4, 1, "", "get_vertices"], [9, 4, 1, "", "get_vertices_from_file"], [10, 4, 1, "", "hydropathy"], [12, 4, 1, "", "openings"], [13, 4, 1, "", "plot_frequencies"], [14, 0, 1, "", "pyKVFinderResults"], [15, 4, 1, "", "read_cavity"], [16, 4, 1, "", "read_pdb"], [17, 4, 1, "", "read_vdw"], [18, 4, 1, "", "read_xyz"], [19, 4, 1, "", "run_workflow"], [20, 4, 1, "", "spatial"], [21, 4, 1, "", "write_results"]], "pyKVFinder.Molecule": [[1, 1, 1, "", "_atomic"], [1, 1, 1, "", "_dim"], [1, 1, 1, "", "_grid"], [1, 1, 1, "", "_molecule"], [1, 1, 1, "", "_padding"], [1, 1, 1, "", "_probe"], [1, 1, 1, "", "_radii"], [1, 1, 1, "", "_representation"], [1, 1, 1, "", "_rotation"], [1, 1, 1, "", "_step"], [1, 1, 1, "", "_vertices"], [1, 2, 1, "", "atomic"], [1, 2, 1, "", "dim"], [1, 3, 1, "", "export"], [1, 2, 1, "", "grid"], [1, 2, 1, "", "molecule"], [1, 1, 1, "", "nthreads"], [1, 2, 1, "", "nx"], [1, 2, 1, "", "ny"], [1, 2, 1, "", "nz"], [1, 2, 1, "", "p1"], [1, 2, 1, "", "p2"], [1, 2, 1, "", "p3"], [1, 2, 1, "", "p4"], [1, 2, 1, "", "padding"], [1, 3, 1, "", "preview"], [1, 2, 1, "", "probe"], [1, 2, 1, "", "radii"], [1, 2, 1, "", "representation"], [1, 2, 1, "", "rotation"], [1, 2, 1, "", "step"], [1, 3, 1, "", "surface"], [1, 3, 1, "", "vdw"], [1, 1, 1, "", "verbose"], [1, 2, 1, "", "vertices"], [1, 3, 1, "", "volume"], [1, 2, 1, "", "xyzr"]], "pyKVFinder.pyKVFinderResults": [[14, 1, 1, "", "_input"], [14, 1, 1, "", "_ligand"], [14, 1, 1, "", "_step"], [14, 1, 1, "", "_vertices"], [14, 1, 1, "", "area"], [14, 1, 1, "", "avg_depth"], [14, 1, 1, "", "avg_hydropathy"], [14, 1, 1, "", "cavities"], [14, 1, 1, "", "depths"], [14, 3, 1, "", "export"], [14, 3, 1, "", "export_all"], [14, 1, 1, "", "frequencies"], [14, 1, 1, "", "max_depth"], [14, 1, 1, "", "ncav"], [14, 3, 1, "", "plot_frequencies"], [14, 1, 1, "", "residues"], [14, 1, 1, "", "scales"], [14, 1, 1, "", "surface"], [14, 1, 1, "", "volume"], [14, 3, 1, "", "write"]]}, "objtypes": {"0": "py:class", "1": "py:attribute", "2": "py:property", "3": "py:method", "4": "py:function"}, "objnames": {"0": ["py", "class", "Python class"], "1": ["py", "attribute", "Python attribute"], "2": ["py", "property", "Python property"], "3": ["py", "method", "Python method"], "4": ["py", "function", "Python function"]}, "titleterms": {"issu": 0, "scientif": 0, "team": 0, "cite": 0, "pykvfind": [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 28], "fund": 0, "licens": 0, "molecul": 1, "calculate_frequ": 2, "constitut": [3, 27], "depth": [4, 27], "detect": [5, 25, 27], "export": [6, 27], "export_open": 7, "get_vertic": 8, "get_vertices_from_fil": 9, "hydropathi": [10, 27], "function": 11, "class": 11, "open": 12, "plot_frequ": 13, "pykvfinderresult": 14, "read_cav": 15, "read_pdb": 16, "read_vdw": 17, "read_xyz": 18, "run_workflow": 19, "spatial": [20, 27], "write_result": 21, "box": [22, 25], "configur": 22, "file": [22, 23, 24], "templat": [22, 23, 24], "hydrophob": [23, 27], "scale": [23, 27], "van": [24, 27], "der": [24, 27], "waal": [24, 27], "radii": [24, 27], "posit": 25, "argument": 25, "option": 25, "character": [25, 27], "extra": 25, "adjus": 25, "ligand": [25, 27], "adjust": [25, 27], "requir": 26, "packag": 26, "manag": 26, "conda": 26, "instal": 26, "caviti": 27, "standard": 27, "workflow": 27, "full": 27, "separ": 27, "step": 27, "1": 27, "load": 27, "dictionari": 27, "2": 27, "data": 27, "from": 27, "target": 27, "structur": 27, "3": 27, "dimens": 27, "3d": 27, "grid": 27, "4": 27, "biomolecular": 27, "5": 27, "perform": 27, "6": 27, "calcul": 27, "plot": 27, "frequenc": 27, "7": 27, "8": 27, "9": 27, "onli": 27, "point": 27, "surfac": 27, "map": 27, "b": 27, "factor": 27, "10": 27, "write": 27, "result": 27, "steer": 27, "molecular": 27, "volum": 27, "vdw": 27, "se": 27, "sa": 27, "exampl": 27, "welcom": 28, "s": 28, "document": 28}, "envversion": {"sphinx.domains.c": 2, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 6, "sphinx.domains.index": 1, "sphinx.domains.javascript": 2, "sphinx.domains.math": 2, "sphinx.domains.python": 3, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.intersphinx": 1, "sphinx.ext.todo": 2, "sphinx.ext.viewcode": 1, "sphinx": 56}})
\ No newline at end of file
diff --git a/docs/source/_images/barplots.png b/docs/source/_images/barplots.png
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diff --git a/docs/source/_images/vdw-grid.png b/docs/source/_images/vdw-grid.png
deleted file mode 100644
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diff --git a/docs/source/_images/vdw.png b/docs/source/_images/vdw.png
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diff --git a/docs/source/_installation/index.rst b/docs/source/_installation/index.rst
deleted file mode 100644
index d4e7388d..00000000
--- a/docs/source/_installation/index.rst
+++ /dev/null
@@ -1,57 +0,0 @@
-Requirements
-============
-
-If you don’t have Python v3 and/or SWIG yet, the installation procedure differs depending on the operating system.
-
-Python and SWIG can be installed with conda, or with a package manager on Linux and macOS.
-
-Package managers
-----------------
-
-On Linux:
-
-.. code-block:: bash
-    
-  sudo apt install python3 swig
-
-On macOS:
-
-.. code-block:: bash
-    
-  brew install python3 swig
-
-.. note:: 
-
-  Users can use their preferred package manager to install SWIG and Python v3.
-
-Conda
------
-
-If you use conda, you can install Python v3 and SWIG from the defaults channel:
-
-.. code-block:: bash
-    
-  # Use an environment rather than install in base environement (recommended)
-  conda create -n myenv python=3
-  conda activate myenv
-  # The SWIG install command
-  conda install swig
-
-Installation
-============
-
-The prerequisites for installing pyKVFinder is Python v3 and SWIG. If you don’t have Python and/or SWIG yet, please refer to this `section `_.
-
-To install the latest release on `PyPI `_, 
-run:
-
-.. code-block:: bash
-
-  pip install pyKVFinder
-
-Or to install the latest developmental version, run:
-
-.. code-block:: bash
-
-  git clone https://github.com/LBC-LNBio/pyKVFinder.git
-  pip install pyKVFinder
diff --git a/docs/source/_about/index.rst b/docs/source/about/index.rst
similarity index 62%
rename from docs/source/_about/index.rst
rename to docs/source/about/index.rst
index 21113d3d..567861b0 100644
--- a/docs/source/_about/index.rst
+++ b/docs/source/about/index.rst
@@ -1,9 +1,6 @@
-.. raw:: html
-
-    
          About
          
-
+******
 Issues
-======
+******
 
 pyKVFinder package uses GitHub for project management. Please help us by reporting any problems or requests.
 
@@ -11,33 +8,40 @@ On `Issues `_ page, you can file
 
 .. toctree::
     
-    Bug Report 
-    Request for a new feature 
+    Bug Report 
+    Documentation 
+    Feature Request 
+    Maintenance 
+
 
 Only make sure the bug or request has not already been reported. Click on “Search” and enter some keywords to search.
 
 Thank you for helping us improve pyKVFinder!
 
+***************
 Scientific team
-===============
+***************
 
-pyKVFinder was developed by:
+pyKVFinder and PyMOL pyKVFinder Tools were developed by:
 
-- João Victor da Silva Guerra
-- Helder Veras Ribeiro Filho
-- Gabriel Ernesto Jara
-- Leandro Oliveira Bortot
-- José Geraldo de Carvalho Pereira
-- Paulo Sergio Lopes de Oliveira
+* João V. S. Guerra
+* Helder V. Ribeiro-Filho
+* Luiz F. G. Alves
+* Pablo W. A. Silva
+* Gabriel E. Jara
+* Leandro O. Bortot
+* José G. C. Pereira
+* Paulo S. Lopes-de-Oliveira
 
 Computational Biology Laboratory (`LBC `_), Brazilian Biosciences National Laboratory (`LNBio `_), Brazilian Center for Research in Energy and Materials (`CNPEM `_)
 
 If you have any further questions, inquires or if you wish to contribute to KVFinder project, please contact us at joao.guerra@lnbio.cnpem.br or paulo.oliveira@lnbio.cnpem.br.
 
+*****************
 Citing pyKVFinder
-=================
+*****************
 
-If you use pyKVFinder package, please cite:
+If you use `pyKVFinder package`, please cite:
 
 Guerra, J. V. S., Ribeiro-Filho, H. V., Jara, G. E., Bortot, L. O., Pereira, J. G. C., & Lopes-de-Oliveira, P. S. (2021). pyKVFinder: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science. BMC bioinformatics, 22(1), 607. ``_.
 
@@ -45,12 +49,18 @@ If you use `pyKVFinder.Molecule`, please also cite:
 
 Guerra, J. V. S., Alves, L. F. G., Bourissou, D., Lopes-de-Oliveira, P. S., & Szalóki, G. (2023). Cavity Characterization in Supramolecular Cages. Journal of chemical information and modeling, 63(12), 3772-3785. ``_.
 
+If you use `PyMOL pyKVFinder Tools`, please also cite:
+
+Guerra, J. V. da S., Ribeiro Filho, H. V., Bortot, L. O., Honorato, R. V., Pereira, J. G. de C., & Lopes-de-Oliveira, P. S. (2020). ParKVFinder: A thread-level parallel approach in biomolecular cavity detection. In SoftwareX (Vol. 12, p. 100606). Elsevier BV. https://doi.org/10.1016/j.softx.2020.100606.
+
+*******
 Funding
-=======
+*******
 
 This work was supported by the Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) [Grant Number 2018/00629-0], Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) [Grant Number 350244/2020-0], and Brazilian Center for Research in Energy and Materials (CNPEM).
 
+*******
 License
-=======
+*******
 
 The software is licensed under the terms of the GNU General Public License version 3 (GPL3) and is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
diff --git a/docs/source/conf.py b/docs/source/conf.py
index 0ee7744d..7aa6ff5e 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -195,7 +195,7 @@
 # -- Options for intersphinx extension ---------------------------------------
 
 # Example configuration for intersphinx: refer to the Python standard library.
-intersphinx_mapping = {"https://docs.python.org/": None}
+intersphinx_mapping = {'python': ('https://docs.python.org/3', None)}
 
 # -- Options for todo extension ----------------------------------------------
 
diff --git a/docs/source/index.rst b/docs/source/index.rst
index 0a6c3acf..21252c9d 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -1,60 +1,35 @@
+######################################
 Welcome to pyKVFinder's documentation!
-======================================
+######################################
 
 Welcome to the **Python-C parallel KVFinder (pyKVFinder)** documentation, this page was built to help you get started with our cavity detection and characterization package.
 
-* `Installation <_installation/index.html>`_
-* `Tutorial <_tutorial/index.html>`_
-* `API reference <_api_reference/index.html>`_
-* `Command-line interface <_cli/index.html>`_
-* `GitHub repository `_
-* `About <_about/index.html>`_
+.. Headings:
+..  # with overline, for parts
+..  * with overline, for chapters
+..  = for sections
+..  - for subsections
+..  ^ for subsubsections
+..  " for paragraphs
 
 .. toctree::
    :maxdepth: 1
-   :caption: Installation
-   :hidden:
+   :caption: Python Package
 
-   _installation/index
- 
-.. toctree::
-   :maxdepth: 1
-   :caption: Tutorial
-   :hidden:
-   
-   _tutorial/index
-   
-.. toctree::
-   :maxdepth: 1
-   :caption: API Reference
-   :hidden:
-
-   _api_reference/index
+   Installation 
+   Tutorial 
+   API Reference 
+   Examples 
 
 .. toctree::
    :maxdepth: 1
-   :caption: Command-line interface
-   :hidden:
-
-   _cli/index
+   :caption: Plugins
 
-.. toctree::
-    :maxdepth: 1
-    :caption: Configuration files
-    :hidden:
-
-    vdW radii <_cfg_files/vdw_file_template>
-    Custom grid <_cfg_files/box_file_template>
-    Hydrophobicity scale <_cfg_files/hydrophobicity_scale_file_template>
-
-.. toctree::
-   :maxdepth: 1
-   :caption: Citing pyKVFinder
-   :hidden:
+   Command-line interface 
+   PyMOL pyKVFinder Tools 
 
 .. toctree::
    :maxdepth: 1
    :caption: About
-   :hidden:
 
-   _about/index
+   about/index
diff --git a/docs/source/_api_reference/Molecule.rst b/docs/source/package/api_reference/Molecule.rst
similarity index 100%
rename from docs/source/_api_reference/Molecule.rst
rename to docs/source/package/api_reference/Molecule.rst
diff --git a/docs/source/_cfg_files/box_file_template.rst b/docs/source/package/api_reference/box_file_template.rst
similarity index 97%
rename from docs/source/_cfg_files/box_file_template.rst
rename to docs/source/package/api_reference/box_file_template.rst
index c0d5d330..103467b7 100644
--- a/docs/source/_cfg_files/box_file_template.rst
+++ b/docs/source/package/api_reference/box_file_template.rst
@@ -1,5 +1,5 @@
 Box configuration file template
-###############################
+===============================
 
 There are three methods for defining a custom 3D grid in pyKVFinder.
 
diff --git a/docs/source/_api_reference/calculate_frequencies.rst b/docs/source/package/api_reference/calculate_frequencies.rst
similarity index 100%
rename from docs/source/_api_reference/calculate_frequencies.rst
rename to docs/source/package/api_reference/calculate_frequencies.rst
diff --git a/docs/source/_api_reference/constitutional.rst b/docs/source/package/api_reference/constitutional.rst
similarity index 100%
rename from docs/source/_api_reference/constitutional.rst
rename to docs/source/package/api_reference/constitutional.rst
diff --git a/docs/source/_api_reference/depth.rst b/docs/source/package/api_reference/depth.rst
similarity index 100%
rename from docs/source/_api_reference/depth.rst
rename to docs/source/package/api_reference/depth.rst
diff --git a/docs/source/_api_reference/detect.rst b/docs/source/package/api_reference/detect.rst
similarity index 100%
rename from docs/source/_api_reference/detect.rst
rename to docs/source/package/api_reference/detect.rst
diff --git a/docs/source/_api_reference/export.rst b/docs/source/package/api_reference/export.rst
similarity index 100%
rename from docs/source/_api_reference/export.rst
rename to docs/source/package/api_reference/export.rst
diff --git a/docs/source/_api_reference/export_openings.rst b/docs/source/package/api_reference/export_openings.rst
similarity index 100%
rename from docs/source/_api_reference/export_openings.rst
rename to docs/source/package/api_reference/export_openings.rst
diff --git a/docs/source/_api_reference/get_vertices.rst b/docs/source/package/api_reference/get_vertices.rst
similarity index 100%
rename from docs/source/_api_reference/get_vertices.rst
rename to docs/source/package/api_reference/get_vertices.rst
diff --git a/docs/source/_api_reference/get_vertices_from_file.rst b/docs/source/package/api_reference/get_vertices_from_file.rst
similarity index 100%
rename from docs/source/_api_reference/get_vertices_from_file.rst
rename to docs/source/package/api_reference/get_vertices_from_file.rst
diff --git a/docs/source/_api_reference/hydropathy.rst b/docs/source/package/api_reference/hydropathy.rst
similarity index 100%
rename from docs/source/_api_reference/hydropathy.rst
rename to docs/source/package/api_reference/hydropathy.rst
diff --git a/docs/source/_cfg_files/hydrophobicity_scale_file_template.rst b/docs/source/package/api_reference/hydrophobicity_scale_file_template.rst
similarity index 98%
rename from docs/source/_cfg_files/hydrophobicity_scale_file_template.rst
rename to docs/source/package/api_reference/hydrophobicity_scale_file_template.rst
index 76b3c36d..4c4be074 100644
--- a/docs/source/_cfg_files/hydrophobicity_scale_file_template.rst
+++ b/docs/source/package/api_reference/hydrophobicity_scale_file_template.rst
@@ -1,5 +1,5 @@
 Hydrophobicity scale file template
-##################################
+==================================
 
 The hydrophobicity scale file defines the name of the scale and the hydrophobicity value for each residue and when not defined, it assigns zero to the missing residues. The package contains six built-in hydrophobicity scales: `Eisenberg & Weiss `_ [1], `Hessa & Heijne `_ [2], `Kyte & Doolittle `_ [3], `Moon & Fleming `_ [4], `Radzicka & Wolfenden `_ [5], `Wimley & White `_ [6] and `Zhao & London `_ [7]. However, the user can define its own file with a mandatory format and pass it to pyKVFinder. The format is shown below:
 
diff --git a/docs/source/_build/html/_images/barplots.png b/docs/source/package/api_reference/images/barplots.png
similarity index 100%
rename from docs/source/_build/html/_images/barplots.png
rename to docs/source/package/api_reference/images/barplots.png
diff --git a/docs/source/_api_reference/index.rst b/docs/source/package/api_reference/index.rst
similarity index 57%
rename from docs/source/_api_reference/index.rst
rename to docs/source/package/api_reference/index.rst
index 9d9325cd..5e390c36 100644
--- a/docs/source/_api_reference/index.rst
+++ b/docs/source/package/api_reference/index.rst
@@ -1,8 +1,8 @@
-.. raw:: html
+*************
+API Reference
+*************
 
-    
          API Reference
          
-
-The API of all pyKVFinder functions and classes with expected types and all parameters available.
+The API of all pyKVFinder functions, classes and configuration files with expected types and all parameters available.
 
 Functions
 =========
@@ -37,4 +37,13 @@ Classes
 
     Molecule
     pyKVFinderResults
-    
\ No newline at end of file
+
+Configuration Files
+===================
+
+.. toctree::
+    :maxdepth: 1
+
+    vdw_file_template
+    box_file_template
+    hydrophobicity_scale_file_template
diff --git a/docs/source/_api_reference/openings.rst b/docs/source/package/api_reference/openings.rst
similarity index 100%
rename from docs/source/_api_reference/openings.rst
rename to docs/source/package/api_reference/openings.rst
diff --git a/docs/source/_api_reference/plot_frequencies.rst b/docs/source/package/api_reference/plot_frequencies.rst
similarity index 100%
rename from docs/source/_api_reference/plot_frequencies.rst
rename to docs/source/package/api_reference/plot_frequencies.rst
diff --git a/docs/source/_api_reference/pyKVFinderResults.rst b/docs/source/package/api_reference/pyKVFinderResults.rst
similarity index 100%
rename from docs/source/_api_reference/pyKVFinderResults.rst
rename to docs/source/package/api_reference/pyKVFinderResults.rst
diff --git a/docs/source/_api_reference/read_cavity.rst b/docs/source/package/api_reference/read_cavity.rst
similarity index 100%
rename from docs/source/_api_reference/read_cavity.rst
rename to docs/source/package/api_reference/read_cavity.rst
diff --git a/docs/source/_api_reference/read_pdb.rst b/docs/source/package/api_reference/read_pdb.rst
similarity index 100%
rename from docs/source/_api_reference/read_pdb.rst
rename to docs/source/package/api_reference/read_pdb.rst
diff --git a/docs/source/_api_reference/read_vdw.rst b/docs/source/package/api_reference/read_vdw.rst
similarity index 100%
rename from docs/source/_api_reference/read_vdw.rst
rename to docs/source/package/api_reference/read_vdw.rst
diff --git a/docs/source/_api_reference/read_xyz.rst b/docs/source/package/api_reference/read_xyz.rst
similarity index 100%
rename from docs/source/_api_reference/read_xyz.rst
rename to docs/source/package/api_reference/read_xyz.rst
diff --git a/docs/source/_api_reference/run_workflow.rst b/docs/source/package/api_reference/run_workflow.rst
similarity index 100%
rename from docs/source/_api_reference/run_workflow.rst
rename to docs/source/package/api_reference/run_workflow.rst
diff --git a/docs/source/_api_reference/spatial.rst b/docs/source/package/api_reference/spatial.rst
similarity index 100%
rename from docs/source/_api_reference/spatial.rst
rename to docs/source/package/api_reference/spatial.rst
diff --git a/docs/source/_cfg_files/vdw_file_template.rst b/docs/source/package/api_reference/vdw_file_template.rst
similarity index 95%
rename from docs/source/_cfg_files/vdw_file_template.rst
rename to docs/source/package/api_reference/vdw_file_template.rst
index 84ac929f..45c7ad14 100644
--- a/docs/source/_cfg_files/vdw_file_template.rst
+++ b/docs/source/package/api_reference/vdw_file_template.rst
@@ -1,5 +1,5 @@
 Van der Waals radii file template
-#################################
+=================================
 
 The van der Waals radii file define the radius values for each atom by residue and when not defined, it uses a generic value based on the atom type. The package contains a built-in van der Waals radii file: `vdw.dat `_. However, the user can define its own file with a mandatory format and pass it to pyKVFinder. The format is shown below:
 
diff --git a/docs/source/_api_reference/write_results.rst b/docs/source/package/api_reference/write_results.rst
similarity index 100%
rename from docs/source/_api_reference/write_results.rst
rename to docs/source/package/api_reference/write_results.rst
diff --git a/docs/source/package/examples/index.rst b/docs/source/package/examples/index.rst
new file mode 100644
index 00000000..a4e8d731
--- /dev/null
+++ b/docs/source/package/examples/index.rst
@@ -0,0 +1,13 @@
+********
+Examples
+********
+
+Jupyter notebook `examples `_ are available for:
+
+.. toctree::
+  :maxdepth: 0
+
+  Conservation analysis 
+  Data visualization 
+  Molecular dynamics analysis 
+  Supramolecular cages analysis 
diff --git a/docs/source/package/installation/index.rst b/docs/source/package/installation/index.rst
new file mode 100644
index 00000000..94026957
--- /dev/null
+++ b/docs/source/package/installation/index.rst
@@ -0,0 +1,20 @@
+Installation
+============
+
+To install the latest release from `PyPI `_, 
+run:
+
+.. code-block:: bash
+
+  pip install pyKVFinder
+
+Or to install the latest developmental version from source, run:
+
+.. code-block:: bash
+
+  git clone https://github.com/LBC-LNBio/pyKVFinder.git
+  pip install -e pyKVFinder
+
+.. note:: 
+
+  SWIG is required for installing pyKVFinder from source, the installation procedure differs depending on the operating system. SWIG can be installed with conda (``conda install swig``), or with a package manager on Linux (``sudo apt install swig``) and macOS (``brew install swig``).
diff --git a/docs/source/_build/html/_images/plot-frequencies.png b/docs/source/package/tutorial/images/plot-frequencies.png
similarity index 100%
rename from docs/source/_build/html/_images/plot-frequencies.png
rename to docs/source/package/tutorial/images/plot-frequencies.png
diff --git a/docs/source/_build/html/_images/sas-grid.png b/docs/source/package/tutorial/images/sas-grid.png
similarity index 100%
rename from docs/source/_build/html/_images/sas-grid.png
rename to docs/source/package/tutorial/images/sas-grid.png
diff --git a/docs/source/_build/html/_images/sas.png b/docs/source/package/tutorial/images/sas.png
similarity index 100%
rename from docs/source/_build/html/_images/sas.png
rename to docs/source/package/tutorial/images/sas.png
diff --git a/docs/source/_build/html/_images/ses-grid.png b/docs/source/package/tutorial/images/ses-grid.png
similarity index 100%
rename from docs/source/_build/html/_images/ses-grid.png
rename to docs/source/package/tutorial/images/ses-grid.png
diff --git a/docs/source/_build/html/_images/ses.png b/docs/source/package/tutorial/images/ses.png
similarity index 100%
rename from docs/source/_build/html/_images/ses.png
rename to docs/source/package/tutorial/images/ses.png
diff --git a/docs/source/_build/html/_images/vdw-grid.png b/docs/source/package/tutorial/images/vdw-grid.png
similarity index 100%
rename from docs/source/_build/html/_images/vdw-grid.png
rename to docs/source/package/tutorial/images/vdw-grid.png
diff --git a/docs/source/_build/html/_images/vdw.png b/docs/source/package/tutorial/images/vdw.png
similarity index 100%
rename from docs/source/_build/html/_images/vdw.png
rename to docs/source/package/tutorial/images/vdw.png
diff --git a/docs/source/_tutorial/index.rst b/docs/source/package/tutorial/index.rst
similarity index 95%
rename from docs/source/_tutorial/index.rst
rename to docs/source/package/tutorial/index.rst
index 52efb1b1..b3d4c950 100644
--- a/docs/source/_tutorial/index.rst
+++ b/docs/source/package/tutorial/index.rst
@@ -1,19 +1,19 @@
-.. raw:: html
+********
+Tutorial
+********
 
-    
          Tutorial
          
-
-This section is an introductory overview of pyKVFinder features. For detailed reference documentation of the functions and classes contained in the package, see the `API reference <../_api_reference/index.html>`_.
+This section is an introductory overview of pyKVFinder features. For detailed reference documentation of the functions and classes contained in the package, see the `API reference <../api_reference/index.html>`_.
 
 Before reading this section, you should know a bit of Python. If you would like to refresh your memory, refer to this `Python tutorial `_.
 
 First of all, import pyKVFinder package on Python:
 
 .. code-block:: python
-
+  
   >>> import pyKVFinder
 
 Cavity detection and characterization
-#####################################
+=====================================
 
 All files used on this tutorial can be found in our package and in our `GitHub repository `_:
 
@@ -25,7 +25,7 @@ In this tutorial, we will use pyKVFinder on a catalytic subunit of a cAMP-depend
 pyKVFinder can be imported as a Python package in Python environment and users can decide to run the full pyKVFinder `workflow `_ through the single pyKVFinder function or run pyKVFinder functions in a `stepwise `_ fashion.
 
 Standard workflow
-*****************
+-----------------
 
 The **standard workflow** for cavity detection with spatial and constitutional characterization (volume, area and interface residues) can be run at once with one command:
 
@@ -115,7 +115,7 @@ Inside the *pyKVFinderResults object*, cavity and surface points, number of cavi
 
 .. seealso::
 
-  * `pyKVFinder.run_workflow <../_api_reference/run_workflow>`_
+  * `pyKVFinder.run_workflow <../api_reference/run_workflow>`_
 
 With these attributes, we can write the detected cavities and the characterization to files. Further, we can set a flag to plot the bar charts of the frequencies in a PDF file. Below, we illustrate the usage:
 
@@ -129,10 +129,10 @@ With these attributes, we can write the detected cavities and the characterizati
 
 .. seealso::
 
-  * `pyKVFinder.pyKVFinderResults <../_api_reference/pyKVFinderResults.html>`_
+  * `pyKVFinder.pyKVFinderResults <../api_reference/pyKVFinderResults.html>`_
 
 Full workflow
-*************
+-------------
 
 However, users may opt to perform the **full workflow** for cavity detection with spatial (volume and area), constitutional (interface residues), hydropathy and depth characterization. This full workflow can be run with one command by setting some parameters of ``pyKVFinder.run_workflow`` function:
 
@@ -197,7 +197,7 @@ Inside the *pyKVFinderResults object*, in addition to cavity and surface points,
 
 .. seealso::
 
-  * `pyKVFinder.run_workflow <../_api_reference/run_workflow>`_
+  * `pyKVFinder.run_workflow <../api_reference/run_workflow>`_
 
 With these attributes, we can write the detected cavities with depth annotated on B-factor column (temperature factor) and hydropathy annotated on Q-factor (occupancy) column, and the characterization to files. Below, we illustrate the usage:
 
@@ -211,15 +211,15 @@ With these attributes, we can write the detected cavities with depth annotated o
 
 .. seealso::
 
-  * `pyKVFinder.pyKVFinderResults <../_api_reference/pyKVFinderResults.html>`_
+  * `pyKVFinder.pyKVFinderResults <../api_reference/pyKVFinderResults.html>`_
 
 Separated steps
-***************
+---------------
 
 If users prefer, instead of running ``pyKVFinder.run_workflow`` function, you can apply the cavity detection and characterization in a step-by-step fashion. Below we describe each step in detail.
 
 1. Loading van der Waals radii dictionary
-=========================================
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The `van der Waals radii file <../_cfg_files/vdw_file_template.html>`_ define the radius values for each residue and when not defined, it uses a generic value based on the atom type. ``pyKVFinder.read_vdw`` takes a vdW radii file (*.dat*) and returns a dictionary contaning radii values for each atom of each residue.
 
@@ -237,10 +237,10 @@ The `van der Waals radii file <../_cfg_files/vdw_file_template.html>`_ define th
 
 .. seealso::
 
-  * `pyKVFinder.read_vdw <../_api_reference/read_vdw.html>`_
+  * `pyKVFinder.read_vdw <../api_reference/read_vdw.html>`_
 
 2. Loading data from target structure
-=====================================
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 ``pyKVFinder.read_pdb`` takes a target *.pdb* file and returns a NumPy array (``atomic``) with residue number, chain identifier, residue name, atom name, xyz coordinates and radius, considering a van der Waals radii dictionary, for each atom.
 
@@ -269,11 +269,11 @@ The `van der Waals radii file <../_cfg_files/vdw_file_template.html>`_ define th
 
 .. seealso::
 
-  * `pyKVFinder.read_pdb <../_api_reference/read_pdb.html>`_
-  * `pyKVFinder.read_xyz <../_api_reference/read_xyz.html>`_
+  * `pyKVFinder.read_pdb <../api_reference/read_pdb.html>`_
+  * `pyKVFinder.read_xyz <../api_reference/read_xyz.html>`_
 
 3. Dimensioning the 3D grid
-===========================
+^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The pyKVFinder 3D grid must be calculated based on the target *.pdb* or *.xyz* file, the Probe Out diameter and the grid spacing. 
 
@@ -298,10 +298,10 @@ The pyKVFinder 3D grid must be calculated based on the target *.pdb* or *.xyz* f
 
 .. seealso::
 
-  * `pyKVFinder.get_vertices <../_api_reference/get_vertices.html>`_
+  * `pyKVFinder.get_vertices <../api_reference/get_vertices.html>`_
 
 4. Detecting biomolecular cavities
-==================================
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 ``pyKVFinder.detect`` takes the NumPy array with residue number, chain identifier, residue name, atom name, xyz coordinates and radius for each atom, a NumPy array with vertices and a collection of detection parameters (``step``, ``probe_in``, ``probe_out``, ``removal_distance``, ``volume_cutoff``, ``surface``), and returns a tuple with the number of detected cavities and a NumPy array with the cavity points in the 3D grid.
 
@@ -356,10 +356,10 @@ The pyKVFinder 3D grid must be calculated based on the target *.pdb* or *.xyz* f
 
 .. seealso::
 
-  * `pyKVFinder.detect <../_api_reference/detect.html>`_
+  * `pyKVFinder.detect <../api_reference/detect.html>`_
 
 4.1 Detecting biomolecular cavities with ligand adjustment
-----------------------------------------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 The cavity detection can be limited around the target ligand(s), which will be passed to pyKVFinder through a *.pdb* or *.xyz* file. Thus, the detected cavities are limited within a radius (``ligand_cutoff``) of the target ligand(s).
 
@@ -432,12 +432,12 @@ Afterwards, ``parKVFinder.detect`` takes the mandatory parameters (``atomic`` an
 
 .. seealso::
 
-  * `pyKVFinder.read_pdb <../_api_reference/read_pdb.html>`_
-  * `pyKVFinder.read_xyz <../_api_reference/read_xyz.html>`_
-  * `pyKVFinder.detect <../_api_reference/detect.html>`_
+  * `pyKVFinder.read_pdb <../api_reference/read_pdb.html>`_
+  * `pyKVFinder.read_xyz <../api_reference/read_xyz.html>`_
+  * `pyKVFinder.detect <../api_reference/detect.html>`_
 
 5. Performing spatial characterization
-======================================
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 A spatial characterization, that includes volume, area and defining surface points, is performed on the detected cavities. 
 
@@ -487,10 +487,10 @@ A spatial characterization, that includes volume, area and defining surface poin
 
 .. seealso::
 
-  * `pyKVFinder.spatial <../_api_reference/spatial.html>`_  
+  * `pyKVFinder.spatial <../api_reference/spatial.html>`_
 
 6. Performing constitutional characterization
-=============================================
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 A constitutional characterization, that identifies the interface residues, is performed on the detected cavities.
 
@@ -522,10 +522,10 @@ If you wish to ignore backbones contacts (C, CA, N, O) with the cavity when defi
 
 .. seealso::
 
-  * `pyKVFinder.constitutional <../_api_reference/constitutional.html>`_  
+  * `pyKVFinder.constitutional <../api_reference/constitutional.html>`_  
 
 6.1 Calculating and plotting frequencies
-----------------------------------------
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 With the interface residues defined, you can also calculate the frequencies of residues and classes of residues. The classes of residues are:
 
@@ -561,19 +561,19 @@ Afterwards, ``pyKVFinder.plot_frequencies`` takes the dictionary with the freque
 
 .. seealso::
 
-  * `pyKVFinder.calculate_frequencies <../_api_reference/calculate_frequencies.html>`_  
-  * `pyKVFinder.plot_frequencies <../_api_reference/plot_frequencies.html>`_  
+  * `pyKVFinder.calculate_frequencies <../api_reference/calculate_frequencies.html>`_  
+  * `pyKVFinder.plot_frequencies <../api_reference/plot_frequencies.html>`_  
 
 A sample barplot of ``pyKVFinder.plot_frequencies`` is shown below.
 
-.. image:: ../_images/plot-frequencies.png
+.. image:: images/plot-frequencies.png
     :width: 600
     :align: center
 
 |
 
 7. Performing hydropathy characterization
-=========================================
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 A hydropathy characterization, that maps a target hydrophobicity scale on surface points and calculate the average hydropathy, is performed on the surface points of the detected cavities.
 
@@ -628,10 +628,10 @@ A hydropathy characterization, that maps a target hydrophobicity scale on surfac
 
 .. seealso::
 
-  * `pyKVFinder.hydropathy <../_api_reference/hydropathy.html>`_    
+  * `pyKVFinder.hydropathy <../api_reference/hydropathy.html>`_    
 
 8. Performing depth characterization
-====================================
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
 A depth characterization identifies the degree of burial of the binding site. First, it identifies the cavity volume boundary. Subsequently, the depth of each cavity point is heuristically estimated by the shortest Euclidean distance between the cavity point and its respective boundary points. With this, the maximum and average depths for the detected cavities are calculated.
 
@@ -673,15 +673,15 @@ A depth characterization identifies the degree of burial of the binding site. Fi
 
 .. seealso::
 
-  * `pyKVFinder.depth <../_api_reference/depth.html>`_  
+  * `pyKVFinder.depth <../api_reference/depth.html>`_  
 
 9. Exporting cavities
-=====================
+^^^^^^^^^^^^^^^^^^^^^
 
 There are four different ways to export the detected cavities to PDB-formatted files. 
 
 9.1 Exporting only cavity points
---------------------------------
+""""""""""""""""""""""""""""""""
 
 .. code-block:: python
 
@@ -689,7 +689,7 @@ There are four different ways to export the detected cavities to PDB-formatted f
   >>> pyKVFinder.export(output_cavity, cavities, None, vertices, step=step)
 
 9.2 Exporting cavity and surface points
----------------------------------------
+"""""""""""""""""""""""""""""""""""""""
 
 .. code-block:: python
 
@@ -697,7 +697,7 @@ There are four different ways to export the detected cavities to PDB-formatted f
   >>> pyKVFinder.export(output_cavity, cavities, surface, vertices, step=step)
 
 9.3 Exporting cavity and surface points with depth mapped on B-factor
----------------------------------------------------------------------
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 .. code-block:: python
 
@@ -705,7 +705,7 @@ There are four different ways to export the detected cavities to PDB-formatted f
   >>> pyKVFinder.export(output_cavity, cavities, surface, vertices, step=step, B=depths)
 
 9.4 Exporting cavity and surface points with depth mapped on B-factor and hydrophobicity scale mapped on Q-factor
------------------------------------------------------------------------------------------------------------------
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 .. code-block:: python
 
@@ -722,15 +722,15 @@ There are four different ways to export the detected cavities to PDB-formatted f
 
 .. seealso::
 
-  * `pyKVFinder.export <../_api_reference/export.html>`_  
+  * `pyKVFinder.export <../api_reference/export.html>`_  
 
-10.  Writing results
-====================
+10.   Writing results
+^^^^^^^^^^^^^^^^^^^^^
 
 The function call depends on the characterizations performed on the detected cavities.
 
 10.1 Cavity detection only
---------------------------
+""""""""""""""""""""""""""
 
 .. code-block:: python
 
@@ -738,7 +738,7 @@ The function call depends on the characterizations performed on the detected cav
   >>> pyKVFinder.write_results(output_results, input=pdb, ligand=None, output=output_cavity, step=step)
 
 10.2 Spatial characterization
------------------------------
+"""""""""""""""""""""""""""""
 
 .. code-block:: python
 
@@ -746,7 +746,7 @@ The function call depends on the characterizations performed on the detected cav
   >>> pyKVFinder.write_results(output_results, input=pdb, ligand=None, output=output_cavity, volume=volume, area=area, step=step)
 
 10.3 Spatial and constitutional characterization
-------------------------------------------------
+""""""""""""""""""""""""""""""""""""""""""""""""
 
 .. code-block:: python
 
@@ -754,7 +754,7 @@ The function call depends on the characterizations performed on the detected cav
   >>> pyKVFinder.write_results(output_results, input=pdb, ligand=None, output=output_cavity, volume=volume, area=area, residues=residues, frequencies=frequencies, step=step)
 
 10.4 Spatial, constitutional and depth characterization
--------------------------------------------------------
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 .. code-block:: python
 
@@ -762,7 +762,7 @@ The function call depends on the characterizations performed on the detected cav
   >>> pyKVFinder.write_results(output_results, input=pdb, ligand=None, output=output_cavity, volume=volume, area=area, max_depth=max_depth, avg_depth=avg_depth, residues=residues, frequencies=frequencies, step=step)
 
 10.5 Spatial, constitutional, depth and hydropathy characterization
--------------------------------------------------------------------
+"""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""""
 
 .. code-block:: python
 
@@ -775,10 +775,10 @@ The function call depends on the characterizations performed on the detected cav
 
 .. seealso::
 
-  * `pyKVFinder.write_results <../_api_reference/write_results.html>`_ 
+  * `pyKVFinder.write_results <../api_reference/write_results.html>`_ 
 
 Steered detection
-*****************
+-----------------
 
 All these steps showed so far were performed the detection on the whole target biomolecule; however, we can perform them on a custom 3D grid, where we can explore closed regions with a custom box, which can be defined by a *.toml* file.
 
@@ -841,7 +841,7 @@ A third way is to define a custom 3D grid with `parKVFinder `_ 
+  * `pyKVFinder.run_workflow <../api_reference/run_workflow>`_ 
 
 Separated steps
-===============
+^^^^^^^^^^^^^^^
 
 If you are running pyKVFinder package in a step-by-step fashion (`Separated steps `_), the steps `3 `_ and `4 `_ are different than before.
 
@@ -916,11 +916,11 @@ Users can define the ``box`` parameter as the filepath of one box configuration
 
 .. seealso::
 
-  * `pyKVFinder.get_vertices_from_file <../_api_reference/get_vertices_from_file.html>`_
-  * `pyKVFinder.detect <../_api_reference/detect.html>`_ 
+  * `pyKVFinder.get_vertices_from_file <../api_reference/get_vertices_from_file.html>`_
+  * `pyKVFinder.detect <../api_reference/detect.html>`_ 
 
 Molecular volume
-################
+================
 
 All files used on this tutorial can be found in our package and in our `GitHub repository `_:
 
@@ -929,7 +929,7 @@ All files used on this tutorial can be found in our package and in our `GitHub r
 In this tutorial, we will use pyKVFinder on perchlorate (ClO\ :sub:`4` \) to estimate the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES) and solvent accessible surface (SAS) to represent the molecular surface (see Figure below).
 
 +-------------------------------+--------------------------------+--------------------------------+
-| .. image:: ../_images/vdw.png | .. image:: ../_images/ses.png  | .. image:: ../_images/sas.png  |
+| .. image:: images/vdw.png     | .. image:: images/ses.png      | .. image:: images/sas.png      |
 |                               |                                |                                |
 | .. centered:: (a) vdW         | .. centered:: (b) SES          | .. centered:: (c) SAS          |
 +-------------------------------+--------------------------------+--------------------------------+
@@ -948,7 +948,7 @@ First, we must load the target molecular structure (ClO\ :sub:`4` \)  into ``pyK
 With the atomic information and vdW radii dictionary loaded, the molecule is inserted into a regular 3D grid, considering the vdW radii of any of the atoms. Natively, the vdW radii are taken from the `built-in dictionary `_. In the 3D grid, each voxel corresponds to a molecule (0) or solvent (1) points. Here, we can model our molecule using the vdW surface, SES or SAS.
 
 1. vdW volume
-*************
+-------------
 
 ``Molecule.vdw()`` takes a grid spacing and returns a NumPy array with the molecule points representing the vdW surface in the 3D grid. 
 
@@ -986,7 +986,7 @@ We can preview our modelled molecule in the 3D grid by running:
   
   >>> molecule.export("vdw-model.pdb")
 
-.. image:: ../_images/vdw-grid.png
+.. image:: images/vdw-grid.png
   :width: 500
   :align: center
 
@@ -1004,7 +1004,7 @@ Now, we can estimate the vdW volume by running:
   83.64
 
 2. SES volume
-*************
+-------------
 
 ``Molecule.surface()`` takes the grid spacing, the spherical probe size to model the surface, the SES representation and returns a NumPy array with the molecule points representing the SES in the 3D grid. 
 
@@ -1046,7 +1046,7 @@ We can preview our modelled molecule in the 3D grid by running:
   
   >>> molecule.preview()
 
-.. image:: ../_images/ses-grid.png
+.. image:: images/ses-grid.png
   :width: 500
   :align: center
 
@@ -1058,7 +1058,7 @@ Now, we can estimate the vdW volume by running:
   90.8
 
 3. SAS volume
-*************
+-------------
 
 ``Molecule.surface()`` takes a grid spacing, a spherical probe to model the surface, a SAS representation and returns a NumPy array with the molecule points representing the SES in the 3D grid. 
 
@@ -1100,7 +1100,7 @@ We can preview our modelled molecule in the 3D grid by running:
   
   >>> molecule.preview()
 
-.. image:: ../_images/sas-grid.png
+.. image:: images/sas-grid.png
   :width: 500
   :align: center
 
@@ -1110,16 +1110,3 @@ Now, we can estimate the vdW volume by running:
   
   >>> molecule.volume()
   340.28
-
-Examples
-########
-
-Jupyter notebook `examples `_ are available for:
-
-.. toctree::
-  :maxdepth: 0
-
-  Conservation analysis 
-  Data visualization 
-  Molecular dynamics analysis 
-  Supramolecular cages analysis 
diff --git a/docs/source/_cli/index.rst b/docs/source/plugins/cli/index.rst
similarity index 69%
rename from docs/source/_cli/index.rst
rename to docs/source/plugins/cli/index.rst
index ac8ad7ee..45e394a2 100644
--- a/docs/source/_cli/index.rst
+++ b/docs/source/plugins/cli/index.rst
@@ -1,6 +1,7 @@
-.. raw:: html
 
-    
          Command-line interface
          
+**********************
+Command-line interface
+**********************
 
 In addition to pyKVFinder package, a command-line interface (CLI) is available to ease cavity detection and characterization with the full set of customizable parameters.
 
@@ -17,7 +18,7 @@ In addition to pyKVFinder package, a command-line interface (CLI) is available t
                     (<.pdb> | <.xyz>)
 
 Positional arguments
---------------------
+====================
 
 The positional arguments are:
 
@@ -25,10 +26,10 @@ The positional arguments are:
   
   .. code-block:: bash
     
-    $ pyKVFinder <.pdb>
+    $ pyKVFinder (<.pdb> | <.xyz>)
 
 Optional arguments
-------------------
+==================
 
 The optional arguments are:
 
@@ -49,7 +50,7 @@ The optional arguments are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> --verbose
+    $ pyKVFinder (<.pdb> | <.xyz>) --verbose
 
   :Default: ``False``
 
@@ -57,17 +58,17 @@ The optional arguments are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -b 
-    $ pyKVFinder <.pdb> --base_name 
+    $ pyKVFinder (<.pdb> | <.xyz>) -b 
+    $ pyKVFinder (<.pdb> | <.xyz>) --base_name 
 
-  :Default: Prefix of target PDB file (<.pdb>)
+  :Default: Prefix of target PDB or XYZ file (<.pdb> | <.xyz>)
 
 * ``-O `` or ``--output_directory ``: A path to a directory for output files.
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -O 
-    $ pyKVFinder <.pdb> --output_directory 
+    $ pyKVFinder (<.pdb> | <.xyz>) -O 
+    $ pyKVFinder (<.pdb> | <.xyz>) --output_directory 
 
   :Default: Current working directory
 
@@ -75,12 +76,12 @@ The optional arguments are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> --nthreads 
+    $ pyKVFinder (<.pdb> | <.xyz>) --nthreads 
 
   :Default: ``os.cpu_count() - 1``
 
-Detection and characterization
-******************************
+Cavity detection
+----------------
 
 The arguments for adjusting biomolecular detection are:
 
@@ -88,8 +89,8 @@ The arguments for adjusting biomolecular detection are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -d 
-    $ pyKVFinder <.pdb> --dictionary 
+    $ pyKVFinder (<.pdb> | <.xyz>) -d 
+    $ pyKVFinder (<.pdb> | <.xyz>) --dictionary 
 
   :Default: ``vdw.dat``
 
@@ -97,8 +98,8 @@ The arguments for adjusting biomolecular detection are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -s 
-    $ pyKVFinder <.pdb> --step 
+    $ pyKVFinder (<.pdb> | <.xyz>) -s 
+    $ pyKVFinder (<.pdb> | <.xyz>) --step 
 
   :Default: ``0.6``
 
@@ -106,8 +107,8 @@ The arguments for adjusting biomolecular detection are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -i 
-    $ pyKVFinder <.pdb> --probe_in 
+    $ pyKVFinder (<.pdb> | <.xyz>) -i 
+    $ pyKVFinder (<.pdb> | <.xyz>) --probe_in 
 
   :Default: ``1.4``
 
@@ -115,8 +116,8 @@ The arguments for adjusting biomolecular detection are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -o 
-    $ pyKVFinder <.pdb> --probe_out 
+    $ pyKVFinder (<.pdb> | <.xyz>) -o 
+    $ pyKVFinder (<.pdb> | <.xyz>) --probe_out 
 
   :Default: ``4.0``
 
@@ -124,8 +125,8 @@ The arguments for adjusting biomolecular detection are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -V 
-    $ pyKVFinder <.pdb> --volume_cutoff 
+    $ pyKVFinder (<.pdb> | <.xyz>) -V 
+    $ pyKVFinder (<.pdb> | <.xyz>) --volume_cutoff 
 
   :Default: ``5.0``
 
@@ -133,8 +134,8 @@ The arguments for adjusting biomolecular detection are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -R 
-    $ pyKVFinder <.pdb> --removal_distance 
+    $ pyKVFinder (<.pdb> | <.xyz>) -R 
+    $ pyKVFinder (<.pdb> | <.xyz>) --removal_distance 
 
   :Default: ``2.4``
 
@@ -142,8 +143,8 @@ The arguments for adjusting biomolecular detection are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -S 
-    $ pyKVFinder <.pdb> --surface 
+    $ pyKVFinder (<.pdb> | <.xyz>) -S 
+    $ pyKVFinder (<.pdb> | <.xyz>) --surface 
 
   :Default: ``SES``
 
@@ -151,12 +152,12 @@ The arguments for adjusting biomolecular detection are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> --ignore_backbone
+    $ pyKVFinder (<.pdb> | <.xyz>) --ignore_backbone
 
   :Default: ``None``
 
-Extra characterization
-**********************
+Additional characterization
+---------------------------
 
 The parameters for additional characterization are:
 
@@ -164,8 +165,8 @@ The parameters for additional characterization are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -D
-    $ pyKVFinder <.pdb> --depth
+    $ pyKVFinder (<.pdb> | <.xyz>) -D
+    $ pyKVFinder (<.pdb> | <.xyz>) --depth
 
   :Default: ``None``
 
@@ -173,7 +174,7 @@ The parameters for additional characterization are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> --plot_frequencies
+    $ pyKVFinder (<.pdb> | <.xyz>) --plot_frequencies
 
   :Default: ``None``
 
@@ -181,31 +182,31 @@ The parameters for additional characterization are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> --hydropathy
+    $ pyKVFinder (<.pdb> | <.xyz>) --hydropathy
 
   In addition, the user can define one of the built-in hydrophobicity scale. The built-in hydrophobicity scales are: EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, RadzickaWolfenden, WimleyWhite and ZhaoLondon.
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> --hydropathy EisenbergWeiss
-    $ pyKVFinder <.pdb> --hydropathy HessaHeijne
-    $ pyKVFinder <.pdb> --hydropathy KyteDoolittle
-    $ pyKVFinder <.pdb> --hydropathy MoonFleming
-    $ pyKVFinder <.pdb> --hydropathy RadzickaWolfenden
-    $ pyKVFinder <.pdb> --hydropathy WimleyWhite
-    $ pyKVFinder <.pdb> --hydropathy ZhaoLondon
+    $ pyKVFinder (<.pdb> | <.xyz>) --hydropathy EisenbergWeiss
+    $ pyKVFinder (<.pdb> | <.xyz>) --hydropathy HessaHeijne
+    $ pyKVFinder (<.pdb> | <.xyz>) --hydropathy KyteDoolittle
+    $ pyKVFinder (<.pdb> | <.xyz>) --hydropathy MoonFleming
+    $ pyKVFinder (<.pdb> | <.xyz>) --hydropathy RadzickaWolfenden
+    $ pyKVFinder (<.pdb> | <.xyz>) --hydropathy WimleyWhite
+    $ pyKVFinder (<.pdb> | <.xyz>) --hydropathy ZhaoLondon
 
   Further, the user can also define a custom hydrophobicity scale file via a TOML-formatted file (see template).
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> --hydropathy <.toml>
+    $ pyKVFinder (<.pdb> | <.xyz>) --hydropathy <.toml>
 
   :Default: ``None``
   :Constant: ``EisenbergWeiss``
 
 Box adjusment
-*************
+-------------
 
 The box adjustment argument is:
 
@@ -213,13 +214,13 @@ The box adjustment argument is:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -B <.toml>
-    $ pyKVFinder <.pdb> --box <.toml>
+    $ pyKVFinder (<.pdb> | <.xyz>) -B <.toml>
+    $ pyKVFinder (<.pdb> | <.xyz>) --box <.toml>
 
   :Default: ``None``
 
 Ligand adjustment
-*****************
+-----------------
 
 The ligand adjustment arguments are:
 
@@ -227,8 +228,8 @@ The ligand adjustment arguments are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -L <.pdb>
-    $ pyKVFinder <.pdb> --ligand <.pdb>
+    $ pyKVFinder (<.pdb> | <.xyz>) -L (<.pdb> | <.xyz>)
+    $ pyKVFinder (<.pdb> | <.xyz>) --ligand (<.pdb> | <.xyz>)
 
   :Default: ``None``
 
@@ -236,6 +237,6 @@ The ligand adjustment arguments are:
 
   .. code-block:: bash
 
-    $ pyKVFinder <.pdb> -L <.pdb> --ligand_cutoff 
+    $ pyKVFinder (<.pdb> | <.xyz>) -L (<.pdb> | <.xyz>) --ligand_cutoff 
 
   :Default: ``5.0``
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new file mode 100644
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+++ b/docs/source/plugins/pymol/index.rst
@@ -0,0 +1,237 @@
+**********************
+PyMOL pyKVFinder Tools
+**********************
+
+If you wish to use pyKVFinder with a graphical user interface on [PyMOL](https://pymol.org/), PyMOL pyKVFinder Tools is available to use with PyMOL and has been been developed using Qt interface and Python3.
+
+Installation
+============
+
+First, you need to install PyMOL v2.x or v3.x on your computer. If you do not have it installed, please refer to PyMOL `website `_.
+
+After installing PyMOL, plug-in requires the installation of `pyKVFinder `_, `toml `_, and `pyqt5 `_ modules and PyMOL's native Python does not have it installed. So you need to install it:
+
+.. code-block:: bash
+
+    pip install pyKVFinder toml pyqt5
+
+
+.. note::
+    
+    `pip `_ package management system installation is required.
+
+Then, to install the `PyMOL pyKVFinder Tools` on PyMOL, download the latest `PyMOL-pyKVFinder-Tools.zip` from `here `_ and follow these steps:
+
+1. Open PyMOL.
+2. Go to **Plugin** menu, click on **Plugin Manager**.
+3. The **Plugin Manager** window will open, go to the **Install New Plugin** tab.
+4. Under **Install from local file** panel, click on **Choose file...**.
+5. The **Install Plugin** window will open, select the `PyMOL-pyKVFinder-Tools.zip` that you downloaded earliar.
+6. The **Select plugin directory** window will open, select
+   **/home/\/.pymol/startup** and click **OK**.
+7. The **Confirm** window will open, click **OK**.
+8. The **Sucess** window will appear, confirming that the plug-in has
+   been installed.
+9. Restart PyMOL.
+10. `PyMOL pyKVFinder Tools` is ready to use.
+
+Or, instead of selecting `PyMOL-pyKVFinder-Tools.zip` (Step 5), you can select `__init__.py` file on `pyKVFinder/plugins/PyMOL-pyKVFinder-Tools` directory tree.
+
+Tutorial
+========
+
+This tutorial will guide you through the steps to use PyMOL pyKVFinder Tools. All files used in this tutorial can be found our `GitHub repository `_:
+
+* `1FMO.pdb `_
+* `ADN.pdb `_
+
+In this tutorial, we will use pyKVFinder on a catalytic subunit of a cAMP-dependent protein kinase (cADK) to identify and characterize its cavities. First, load the `1FMO.pdb` and `ADN.pdb` file into PyMOL:
+
+.. image:: images/pymol_viewer_1.png
+    :width: 800
+    :align: center
+
+Whole biomolecule detection
+---------------------------
+
+The default parameters are designed to make a simple and fast whole biomolecule detection. 
+
+On PyMOL, open PyMOL pyKVFinder Tools under Plugin tab. The objects on the scene will be listed on the **Input PDB** combo box, on the **Main** tab. If not, press the **Refresh** button.
+
+The **Input PDB** selection sets which object will be analyzed by pyKVFinder. Select **1FMO** on the list box.
+
+.. image:: images/main_tab_1.png
+    :width: 800
+    :align: center
+
+To run pyKVFinder with the default parameters, just click **Run pyKVFinder** button.
+
+.. image:: images/main_tab_2.png
+    :width: 800
+    :align: center
+
+After execution is complete, cavities PDB is loaded into PyMOL viewer as \.KVFinder.output object and the results file is loaded on the **Results** tab. In addition, the focus automatically shifts to **Results** tab.
+
+.. image:: images/results_tab_1.png
+    :width: 800
+    :align: center
+
+We can select cavities in the **Volume** or **Surface Area** lists to highlight them on a new object called **cavities**, identifying each cavity. Additionally, we can select cavity tags in the **Interface Residues** list to highlight residues around the cavities on a new object named **residues**.
+
+.. image:: images/results_tab_2.png
+    :width: 800
+
+.. note::
+    
+    The interface residues surrounding the cavity KAH are colored in green (sticks), the surface points are colored in red (nb_spheres) and the remaining cavity points are colored in blue (non_bounded).
+
+We can visualize depth of the cavity points by clicking on **Depth** option on **Show descriptors**. We can select cavities in the **Average Depth** or **Maximum Depth** lists to highlight them on a new object called **depths**, identifying each cavity. 
+
+.. image:: images/results_tab_3.png
+    :width: 800
+
+.. note::
+    
+    The cavity points are colored using a gradient from blue to red to represent the depth of each point. The blue points correspond to the shallowest points on the cavity-bulk boundary, while the red points correspond to the deepest points. The depth scale ranges from 0.0 to the maximum depth of all cavities
+
+We can visualize hydropathy of the surface points by clicking on **Hydropathy** options on **Show descriptors**. We can select cavities in the **Average Hydropathy** list to highlight them on a new object called **hydropathy**, identifying each cavity. 
+
+.. image:: images/results_tab_4.png
+    :width: 800
+
+.. note::
+
+    The surface points are colored based on the closest amino acid to it. The Eisenberg & Weiss hydrophobicity scale ranges from -1.42 (highly hydrophobic) to 2.6 (highly hydrophilic).
+
+Changing cavity boundary
+^^^^^^^^^^^^^^^^^^^^^^^^
+
+pyKVFinder is all about parameter customization. One of pyKVFinder's most powerful assets is the ability to manually set the cavity boundary.
+
+pyKVFinder works with a double probe system to detect cavities. A smaller probe, called Probe In, and a bigger one, called Probe Out, that defines two molecular surfaces with different molecular accessibility. The space left between these surfaces is considered cavities.
+
+Let's show the effect of varying **Probe Out** and **Removal Distance** on the cavity boundary.
+
+First, we should copy the cavity KAH to a new object to compare cavity boundary from the previous execution.
+
+.. code-block:: bash
+
+    # Copy KAH
+    select resn KAH and output.KVFinder.output
+    create KAH, sele
+    delete sele
+    # Color KAH
+    color magenta, KAH
+
+Adjusting Probe Out
+"""""""""""""""""""
+
+As mentioned above, adjusting the Probe Out size changes the level of the cavity boundary. So let's go back on the **Main** tab and change the **Probe Out** size to 8.0 Å. Run pyKVFinder again.
+
+
+.. image:: images/pymol_viewer_2.png
+    :width: 800
+
+Again, copy the cavity KAF (same region of the previous detection) to a new object (KAF_PO).
+
+.. code-block:: bash
+
+    # Copy KAF
+    select resn KAF and output.KVFinder.output
+    create KAF_PO, sele
+    delete sele
+
+.. image:: images/pymol_viewer_3.png
+    :width: 800
+
+The cavity detected with the 4 Å Probe Out (magenta) has a lower boundary than that detected with the 8 Å probe (white). Therefore, by increasing the size of the Probe Out, the cavity boundary is also raised.
+
+Adjusting Removal Distance
+""""""""""""""""""""""""""
+
+Besides adjusting the Probe Out size, we can also adjust the Removal Distance to change the cavity boundary. So let's go back to the **Main** tab and change the **Removal Distance** to 1.2 Å and the size of Probe Out back to 4.0 Å. Run pyKVFinder again.
+
+.. image:: images/pymol_viewer_4.png
+    :width: 800
+
+Again, copy the cavity KAG (same region of the previous detections) to a new object (KAG_RD).
+
+.. code-block:: bash
+
+    # Copy KAG
+    select resn KAG and output.KVFinder.output
+    create KAG_RD, sele
+    delete sele
+
+.. image:: images/pymol_viewer_5.png
+    :width: 800
+
+|
+  
+The cavity KAH detected with the 2.4 Å Removal Distance (magenta) has a lower boundary than that detected with the 1.2 Å (KAG; white). Therefore, by decreasing the Removal Distance, the cavity boundary is also raised.
+
+Furthermore, changing the cavity boundary by varying Probe Out and Removal Distance also affects cavity segregation.
+
+.. note::
+
+    Usually the Removal Distance adjustment is less time-consuming than the Probe Out adjustment for similar effects.
+
+Steered detection
+-----------------
+
+An important feature of parKVFinder is the steered detection of cavities. We continue our tutorial illustrating two distinct methods of cavity segmentation.
+
+Box adjustment mode 
+^^^^^^^^^^^^^^^^^^^
+
+Box adjustment mode explores closed regions with a custom box, which can be drawn via the GUI.
+
+On the **Search Space** tab, select **Box Adjustment** check box. This will enable a **Box Adjustment** frame, which handles the custom box in PyMOL viewer
+
+.. image:: images/search_space_tab_1.png
+    :width: 800
+
+Then, select the adenosine ligand on ADN object. This can be made on the PyMOL viewer by clicking on the ligand structure or using ``select resn ADN`` PyMOL command.
+
+Click on **Draw Box** Button. This will create a custom box that limits the search space. It is fully customizable, but we will not change it for now.
+
+.. image:: images/pymol_viewer_6.png
+    :width: 800
+
+On the **Main** tab, change **Removal Distance** back to 2.4 Å. Run pyKVFinder again.
+
+.. image:: images/pymol_viewer_7.png
+    :width: 800
+
+Now, let's customize the box parameters to segment the binding site of our target protein.
+
+Each axis is associated with one color (red with X, green with Y and blue with Z). The adjustment is made by the arrows or directly setting the value in the entry on the **Search Space** tab in the **Box Adjustment** group. We can also adjust the box angles by the same procedure. After altering the values, just click on **Redraw** button to redraw the box object using the new values.
+
+Then, on the **Search Space** tab, reduce **Maximum X** to 1.0 Å and click **Redraw Box**. Run pyKVFinder again.
+
+.. image:: images/pymol_viewer_8.png
+    :width: 800
+
+Lastly, click on **Delete Box** button to delete the custom box.
+
+Ligand adjustment mode
+^^^^^^^^^^^^^^^^^^^^^^
+
+A last feature is to limit the search around a structure. In this last example, let's do a whole protein prospection again, but limiting the search space around ligands.
+
+First, on the **Search Space** tab, deselect **Box Adjustment** check box, which will disable the previous enabled **Box Adjustment** frame.
+
+Still on the **Search Space** tab, click on the check button **Ligand Adjustment**, which will enable the **Refresh** button, the **Ligand PDB** combo box and the **Ligand Cutoff** entry.
+
+.. image:: images/search_space_tab_2.png
+    :width: 800
+
+Click the **Refresh** button to display all objects in the scene in the Ligand PDB combo box. Select the **ADN** on the combo box and reduce Ligand Cutoff to 3.0 Å. Run pyKVFinder again.
+
+.. image:: images/pymol_viewer_9.png
+    :width: 800
+
+On the **Search Space** tab, increase **Ligand Cutoff** back to 5.0 Å. Back on the **Main** tab, increase **Probe Out** to 10.0 Å and reduce **Removal Distance** to 0.0 Å. Run pyKVFinder again.
+
+.. image:: images/pymol_viewer_10.png
+    :width: 800
diff --git a/plugins/PyMOL-pyKVFinder-Tools/INSTALLATION.md b/plugins/PyMOL-pyKVFinder-Tools/INSTALLATION.md
new file mode 100644
index 00000000..04a57c51
--- /dev/null
+++ b/plugins/PyMOL-pyKVFinder-Tools/INSTALLATION.md
@@ -0,0 +1,32 @@
+# Installation
+
+First, you need to install PyMOL v2.x or v3.x on your computer. If you do not have it installed, please refer to PyMOL [website](https://pymol.org/).
+
+_PyMOL pyKVFinder Tools_ is available to use with PyMOL and has been been developed using Qt interface and Python3.
+
+After installing PyMOL, plug-in requires the installation of [pyKVFinder](https://pypi.org/project/pyKVFinder/), [toml](https://pypi.org/project/toml/), and [pyqt5](https://pypi.org/project/PyQt5/) modules and PyMOL's native Python does not have it installed. So you need to install it:
+
+```bash
+# PyMOL v3 (python 3)
+$ pip3 install pyKVFinder toml pyqt5
+```
+
+_Note:_ [pip](https://pypi.org/project/pip/) package management system
+installation is required.
+
+Then, to install the _PyMOL pyKVFinder Tools_ on PyMOL, download the latest `PyMOL-pyKVFinder-Tools.zip` from [here](https://github.com/LBC-LNBio/pyKVFinder/releases/latest/download/PyMOL-pyKVFinder-Tools.zip) and follow these steps:
+
+1. Open PyMOL.
+2. Go to **Plugin** menu, click on **Plugin Manager**.
+3. The **Plugin Manager** window will open, go to the **Install New Plugin** tab.
+4. Under **Install from local file** panel, click on **Choose file...**.
+5. The **Install Plugin** window will open, select the `PyMOL-pyKVFinder-Tools.zip` that you downloaded earliar.
+6. The **Select plugin directory** window will open, select
+   **/home/\/.pymol/startup** and click **OK**.
+7. The **Confirm** window will open, click **OK**.
+8. The **Sucess** window will appear, confirming that the plug-in has
+   been installed.
+9. Restart PyMOL.
+10. _PyMOL pyKVFinder Tools_ is ready to use.
+
+Or, instead of selecting `PyMOL-pyKVFinder-Tools.zip` (Step 5), you can select `__init__.py` file on `pyKVFinder/plugins/PyMOL-pyKVFinder-Tools` directory tree.
diff --git a/plugins/PyMOL-pyKVFinder-Tools/PyMOL-pyKVFinder-Tools.ui b/plugins/PyMOL-pyKVFinder-Tools/PyMOL-pyKVFinder-Tools.ui
new file mode 100644
index 00000000..198b5514
--- /dev/null
+++ b/plugins/PyMOL-pyKVFinder-Tools/PyMOL-pyKVFinder-Tools.ui
@@ -0,0 +1,2432 @@
+
+
+ pyKVFinderGUI
+ 
+  
+   Qt::NonModal
+  
+  
+   
+    0
+    0
+    1026
+    774
+   
+  
+  
+   
+    10
+    50
+    false
+   
+  
+  
+   ArrowCursor
+  
+  
+   PyMOL pyKVFinder Tools
+  
+  
+   
+    pyKVFinder.icopyKVFinder.ico
+  
+  
+   
+    
+     10
+    
+    
+     10
+    
+    
+     10
+    
+    
+     10
+    
+    
+     10
+    
+    
+     
+      
+       true
+      
+      
+       
+        0
+        0
+       
+      
+      
+       
+        0
+        0
+       
+      
+      
+       
+        9
+        50
+        false
+       
+      
+      
+       Qt::LeftToRight
+      
+      
+       background-color: #d3d3d3;color:black; padding: 10px
+      
+      
+       QFrame::Box
+      
+      
+       QFrame::Sunken
+      
+      
+       Python-C parallel KVFinder (pyKVFinder) package identifies and describes cavities in a target biomolecular structure using a dual probe system.
+
+The description includes spatial, depth, constitutional and hydropathy characterization. The spatial description includes shape, volume, and area. The depth description defines depths for each cavity point, shown in the B-factor, and calculates the average and maximum depth per cavity. The constitutional description includes amino acids that form the identified cavities. The hydropathy description maps hydrophobicity scales at surface points, shown in the Q-factor, and estimates average hydropathy per cavity.
+      
+      
+       Qt::PlainText
+      
+      
+       false
+      
+      
+       Qt::AlignJustify|Qt::AlignVCenter
+      
+      
+       true
+      
+     
+    
+    
+     
+      
+       6
+      
+      
+       20
+      
+      
+       20
+      
+      
+       
+        
+         
+          0
+          0
+         
+        
+        
+         Run pyKVFinder
+        
+        
+         false
+        
+        
+         false
+        
+       
+      
+      
+       
+        
+         
+          0
+          0
+         
+        
+        
+         Model Surface
+        
+        
+         false
+        
+        
+         false
+        
+       
+      
+      
+       
+        
+         
+          0
+          0
+         
+        
+        
+         Restore Defaults
+        
+       
+      
+      
+       
+        
+         
+          0
+          0
+         
+        
+        
+         Exit
+        
+       
+      
+     
+    
+    
+     
+      
+       Qt::Horizontal
+      
+     
+    
+    
+     
+      
+       
+        0
+        0
+       
+      
+      
+       
+        10
+        50
+        false
+        false
+        true
+       
+      
+      
+       0
+      
+      
+       
+        Main
+       
+       
+        
+         
+          
+           
+            0
+            0
+           
+          
+          
+           
+            10
+            50
+            false
+            false
+            true
+           
+          
+          
+           Parameters
+          
+          
+           
+            3
+           
+           
+            
+             
+              
+               QLayout::SetNoConstraint
+              
+              
+               
+                
+                 
+                  0
+                  0
+                 
+                
+                
+                 
+                  10
+                  50
+                  false
+                  false
+                  true
+                 
+                
+                
+                 false
+                
+                
+                 QFrame::NoFrame
+                
+                
+                 Input PDB:
+                
+                
+                 Qt::PlainText
+                
+               
+              
+              
+               
+                
+                 
+                  0
+                  0
+                 
+                
+               
+              
+              
+               
+                
+                 
+                  0
+                  0
+                 
+                
+                
+                 
+                  10
+                  50
+                  false
+                  false
+                  true
+                 
+                
+                
+                 Refresh
+                
+               
+              
+              
+               
+                
+                 Qt::Horizontal
+                
+                
+                 
+                  40
+                  20
+                 
+                
+               
+              
+             
+            
+           
+           
+            
+             
+              
+               
+                
+                 QLayout::SetNoConstraint
+                
+                
+                 
+                  
+                   
+                  
+                  
+                   
+                  
+                  
+                   
+                  
+                  
+                   Step Size (Å):
+                  
+                 
+                
+                
+                 
+                  
+                   
+                    0
+                    0
+                   
+                  
+                  
+                   
+                    10
+                    50
+                    false
+                    false
+                    true
+                   
+                  
+                  
+                   Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter
+                  
+                  
+                   1
+                  
+                  
+                   0.100000000000000
+                  
+                  
+                   2.000000000000000
+                  
+                  
+                   0.100000000000000
+                  
+                  
+                   0.600000000000000
+                  
+                 
+                
+               
+              
+             
+             
+              
+               
+                
+                 QLayout::SetNoConstraint
+                
+                
+                 
+                  
+                   
+                    0
+                    0
+                   
+                  
+                  
+                   
+                    10
+                    50
+                    false
+                    false
+                    true
+                   
+                  
+                  
+                   true
+                  
+                  
+                   QFrame::NoFrame
+                  
+                  
+                   <html><head/><body><p>Probe In (Å):</p></body></html>
+                  
+                  
+                   Qt::RichText
+                  
+                 
+                
+                
+                 
+                  
+                   
+                    0
+                    0
+                   
+                  
+                  
+                   
+                    10
+                    50
+                    false
+                    false
+                    true
+                   
+                  
+                  
+                   1
+                  
+                  
+                   5.000000000000000
+                  
+                  
+                   0.100000000000000
+                  
+                  
+                   1.400000000000000
+                  
+                 
+                
+               
+              
+             
+             
+              
+               
+                
+                 QLayout::SetNoConstraint
+                
+                
+                 
+                  
+                   
+                    0
+                    0
+                   
+                  
+                  
+                   
+                    10
+                    50
+                    false
+                    false
+                    true
+                   
+                  
+                  
+                   true
+                  
+                  
+                   QFrame::NoFrame
+                  
+                  
+                   <html><head/><body><p>Probe Out (Å):</p></body></html>
+                  
+                  
+                   Qt::RichText
+                  
+                 
+                
+                
+                 
+                  
+                   
+                    0
+                    0
+                   
+                  
+                  
+                   
+                    10
+                    50
+                    false
+                    false
+                    true
+                   
+                  
+                  
+                   1
+                  
+                  
+                   50.000000000000000
+                  
+                  
+                   0.100000000000000
+                  
+                  
+                   4.000000000000000
+                  
+                 
+                
+               
+              
+             
+             
+              
+               
+                
+                 QLayout::SetNoConstraint
+                
+                
+                 
+                  
+                   
+                    0
+                    0
+                   
+                  
+                  
+                   
+                    10
+                    50
+                    false
+                    false
+                    true
+                   
+                  
+                  
+                   true
+                  
+                  
+                   QFrame::NoFrame
+                  
+                  
+                   <html><head/><body><p>Removal Distance (Å):</p></body></html>
+                  
+                  
+                   Qt::RichText
+                  
+                 
+                
+                
+                 
+                  
+                   
+                    0
+                    0
+                   
+                  
+                  
+                   
+                    10
+                    50
+                    false
+                    false
+                    true
+                   
+                  
+                  
+                   Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter
+                  
+                  
+                   1
+                  
+                  
+                   10.000000000000000
+                  
+                  
+                   0.100000000000000
+                  
+                  
+                   2.400000000000000
+                  
+                 
+                
+               
+              
+             
+             
+              
+               
+                
+                 QLayout::SetNoConstraint
+                
+                
+                 
+                  
+                   
+                    0
+                    0
+                   
+                  
+                  
+                   
+                    10
+                    50
+                    false
+                    false
+                    true
+                   
+                  
+                  
+                   true
+                  
+                  
+                   QFrame::NoFrame
+                  
+                  
+                   <html><head/><body><p>Volume Cutoff (ų):</p></body></html>
+                  
+                  
+                   Qt::RichText
+                  
+                 
+                
+                
+                 
+                  
+                   
+                    0
+                    0
+                   
+                  
+                  
+                   
+                    10
+                    50
+                    false
+                    false
+                    true
+                   
+                  
+                  
+                   1
+                  
+                  
+                   1000000000.000000000000000
+                  
+                  
+                   1.000000000000000
+                  
+                  
+                   5.000000000000000
+                  
+                 
+                
+               
+              
+             
+             
+              
+               
+                Qt::Horizontal
+               
+               
+                
+                 40
+                 20
+                
+               
+              
+             
+            
+           
+           
+            
+             
+              
+               
+                
+                 QLayout::SetNoConstraint
+                
+                
+                 
+                  
+                   
+                    0
+                    0
+                   
+                  
+                  
+                   
+                    10
+                    50
+                    false
+                    false
+                    true
+                   
+                  
+                  
+                   true
+                  
+                  
+                   QFrame::NoFrame
+                  
+                  
+                   <html><head/><body><p>Surface Representation:</p></body></html>
+                  
+                  
+                   Qt::RichText
+                  
+                 
+                
+                
+                 
+                  
+                   1
+                  
+                  
+                   
+                    van der Waals (vdW)
+                   
+                  
+                  
+                   
+                    Solvent Excluded Surface (SES)
+                   
+                  
+                  
+                   
+                    Solvent Accesible Surface (SAS)
+                   
+                  
+                 
+                
+               
+              
+             
+             
+              
+               
+                Qt::Horizontal
+               
+               
+                
+                 40
+                 20
+                
+               
+              
+             
+            
+           
+           
+            
+             
+              
+               QLayout::SetNoConstraint
+              
+              
+               9
+              
+              
+               9
+              
+              
+               9
+              
+              
+               9
+              
+              
+               
+                
+                 
+                  0
+                  0
+                 
+                
+                
+                 Hydropathy scale:
+                
+               
+              
+              
+               
+                
+                 
+                  0
+                  0
+                 
+                
+                
+                 
+                  200
+                  16777215
+                 
+                
+                
+                 QComboBox::AdjustToContents
+                
+                
+                 
+                  Eisenberg & Weiss
+                 
+                
+                
+                 
+                  Hessa & Heijne
+                 
+                
+                
+                 
+                  Kyte & Doolittle
+                 
+                
+                
+                 
+                  Radzicka & Wolfenden
+                 
+                
+                
+                 
+                  Moon & Fleming
+                 
+                
+                
+                 
+                  Wimley & White
+                 
+                
+                
+                 
+                  Zhao & London
+                 
+                
+               
+              
+              
+               
+                
+                 Ignore backbone
+                
+               
+              
+              
+               
+                
+                 Qt::Horizontal
+                
+                
+                 
+                  40
+                  20
+                 
+                
+               
+              
+             
+            
+           
+           
+            
+             
+              
+               QLayout::SetNoConstraint
+              
+              
+               
+                
+                 
+                  0
+                  0
+                 
+                
+                
+                 
+                  10
+                  50
+                  false
+                  false
+                  true
+                 
+                
+                
+                 false
+                
+                
+                 QFrame::NoFrame
+                
+                
+                 Output Base Name:
+                
+                
+                 Qt::PlainText
+                
+               
+              
+              
+               
+                
+                 
+                  10
+                  50
+                  false
+                  false
+                  true
+                 
+                
+                
+                 output
+                
+                
+                 Qt::VisualMoveStyle
+                
+                
+                 true
+                
+               
+              
+              
+               
+                
+                 Qt::Horizontal
+                
+                
+                 
+                  40
+                  20
+                 
+                
+               
+              
+             
+            
+           
+           
+            
+             
+              
+               QLayout::SetNoConstraint
+              
+              
+               
+                
+                 
+                  0
+                  0
+                 
+                
+                
+                 
+                  10
+                  50
+                  false
+                  false
+                  true
+                 
+                
+                
+                 false
+                
+                
+                 QFrame::NoFrame
+                
+                
+                 Output Directory:
+                
+                
+                 Qt::PlainText
+                
+               
+              
+              
+               
+                
+                 
+                  10
+                  50
+                  false
+                  false
+                  true
+                 
+                
+                
+                 
+                
+                
+                 QLineEdit::Normal
+                
+                
+                 true
+                
+                
+                 false
+                
+               
+              
+              
+               
+                
+                 
+                  10
+                  50
+                  false
+                  false
+                  true
+                 
+                
+                
+                 Browse...
+                
+               
+              
+             
+            
+           
+           
+            
+             
+              
+               QLayout::SetNoConstraint
+              
+              
+               
+                
+                 
+                  0
+                  0
+                 
+                
+                
+                 
+                  10
+                  50
+                  false
+                  false
+                  true
+                 
+                
+                
+                 false
+                
+                
+                 QFrame::NoFrame
+                
+                
+                 vdW dictionary:
+                
+                
+                 Qt::PlainText
+                
+               
+              
+              
+               
+                
+                 
+                  10
+                  50
+                  false
+                  false
+                  true
+                 
+                
+                
+                 
+                
+                
+                 QLineEdit::Normal
+                
+                
+                 true
+                
+                
+                 false
+                
+               
+              
+              
+               
+                
+                 
+                  10
+                  50
+                  false
+                  false
+                  true
+                 
+                
+                
+                 Browse...
+                
+               
+              
+             
+            
+           
+          
+         
+        
+        
+         
+          
+           Qt::Vertical
+          
+          
+           
+            20
+            40
+           
+          
+         
+        
+       
+      
+      
+       
+        Search Space
+       
+       
+        
+         
+          
+           Box Adjustment
+          
+          
+           true
+          
+          
+           true
+          
+          
+           
+            
+             
+              
+               
+                <html><head/><body><p>Minimum Y (Å):</p></body></html>
+               
+               
+                Qt::RichText
+               
+               
+                Qt::AlignCenter
+               
+              
+             
+             
+              
+               
+                false
+               
+               
+                1
+               
+               
+                50.000000000000000
+               
+               
+                0.100000000000000
+               
+              
+             
+            
+           
+           
+            
+             
+              
+               
+                <html><head/><body><p>Minimum Z (Å):</p></body></html>
+               
+               
+                Qt::RichText
+               
+               
+                Qt::AlignCenter
+               
+              
+             
+             
+              
+               
+                false
+               
+               
+                1
+               
+               
+                50.000000000000000
+               
+               
+                0.100000000000000
+               
+              
+             
+            
+           
+           
+            
+             
+              
+               
+                <html><head/><body><p>Angle 1 (°):</p></body></html>
+               
+               
+                Qt::RichText
+               
+               
+                Qt::AlignCenter
+               
+              
+             
+             
+              
+               
+                false
+               
+               
+                0
+               
+               
+                180.000000000000000
+               
+               
+                1.000000000000000
+               
+              
+             
+            
+           
+           
+            
+             
+              
+               
+                Draw Box
+               
+              
+             
+             
+              
+               
+                Delete Box
+               
+              
+             
+             
+              
+               
+                false
+               
+               
+                Redraw Box
+               
+              
+             
+            
+           
+           
+            
+             
+              
+               
+                
+                 10
+                 50
+                 false
+                 false
+                 true
+                
+               
+               
+                
+               
+               
+                <html><head/><body><p>Minimum X (Å):</p></body></html>
+               
+               
+                Qt::RichText
+               
+               
+                Qt::AlignCenter
+               
+              
+             
+             
+              
+               
+                false
+               
+               
+                
+                 10
+                 50
+                 false
+                 false
+                 true
+                
+               
+               
+                
+               
+               
+                1
+               
+               
+                50.000000000000000
+               
+               
+                0.100000000000000
+               
+              
+             
+            
+           
+           
+            
+             
+              
+               
+                true
+               
+               
+                
+                 0
+                 0
+                
+               
+               
+                
+                 10
+                 50
+                 false
+                 false
+                 true
+                
+               
+               
+                false
+               
+               
+                QFrame::NoFrame
+               
+               
+                Select residues and press Draw Box:
+               
+               
+                Qt::PlainText
+               
+               
+                Qt::AlignCenter
+               
+              
+             
+             
+              
+               
+                
+                 30
+                 26
+                
+               
+               
+                
+                 12
+                 75
+                 false
+                 true
+                 true
+                
+               
+               
+                WhatsThisCursor
+               
+               
+                Qt::NoFocus
+               
+               
+                ?
+               
+              
+             
+            
+           
+           
+            
+             
+              
+               
+                <html><head/><body><p>Angle 2 (°):</p></body></html>
+               
+               
+                Qt::RichText
+               
+               
+                Qt::AlignCenter
+               
+              
+             
+             
+              
+               
+                false
+               
+               
+                0
+               
+               
+                180.000000000000000
+               
+               
+                1.000000000000000
+               
+              
+             
+            
+           
+           
+            
+             
+              
+               
+                <html><head/><body><p>Maximum X (Å):</p></body></html>
+               
+               
+                Qt::RichText
+               
+               
+                Qt::AlignCenter
+               
+              
+             
+             
+              
+               
+                false
+               
+               
+                1
+               
+               
+                50.000000000000000
+               
+               
+                0.100000000000000
+               
+              
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+          
+          
+           <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
+<html><head><meta name="qrichtext" content="1" /><style type="text/css">
+p, li { white-space: pre-wrap; }
+</style></head><body style=" font-family:'Sans Serif'; font-size:10pt; font-weight:400; font-style:normal;">
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:12pt; font-weight:600;">How to run pyKVFinder</span></p>
+<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">To use PyMOL pyKVFinder Tools, follow these simple steps:</p>
+<ol style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li style=" margin-top:12px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Load a biomolecular structure</span> into PyMOL.</li>
+<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Start the PyMOL2 parKVFinder Tools plugin.</span></li>
+<li style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Select an input PDB file</span> from the 'Main' tab.</li>
+<li style=" margin-top:0px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Click the <span style=" font-weight:600;">&quot;Run pyKVFinder&quot;</span> button to begin the analysis.</li></ol>
+<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Once the run is complete, results can be found in the 'Results' tab. Here, users can review detailed information about the run, including the input file, ligand file, output directory, and step size, as well as cavity properties such as volume, area, depth, hydropathy and interface residues.</p>
+<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Additionally, users can load results from a previously generated file (.KVFinder.results.toml) by selecting the <span style=" font-weight:600;">'Results File'</span> using the <span style=" font-weight:600;">'Browse...'</span> button and clicking <span style=" font-weight:600;">'Load'</span>.</p>
+<h3 style=" margin-top:14px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:large; font-weight:600;">Search Space Adjustments</span></h3>
+<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">pyKVFinder offers two modes for adjusting the search space:</p>
+<ul style="margin-top: 0px; margin-bottom: 0px; margin-left: 0px; margin-right: 0px; -qt-list-indent: 1;"><li style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Box Adjustment:</span> This mode allows users to create a custom search box around a selection of interest. Click the <span style=" font-weight:600;">'Draw Box'</span> button to generate the box, which can be further refined by modifying one parameter (minimum and maximum XYZ, padding, or angles) at a time and clicking <span style=" font-weight:600;">'Redraw Box'</span>. For additional information, click the help button in the 'Box Adjustment' section.</li>
+<li style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-weight:600;">Ligand Adjustment:</span> This mode focuses on cavity points surrounding a specific ligand. Users can define the radius around the ligand using the <span style=" font-weight:600;">'Ligand Cutoff'</span> parameter.</li></ul>
+<hr />
+<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">For more detailed information, please refer to the <a href="https://lbc-lnbio.github.io/pyKVFinder/index.html"><span style=" text-decoration: underline; color:#0000ff;">pyKVFinder Documentation</span></a> and the <a href="https://lbc-lnbio.github.io/pyKVFinder/index.html"><span style=" text-decoration: underline; color:#0000ff;">Tutorial</span></a>.</p></body></html>
+          
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+           true
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+          
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+           background-color: #d3d3d3;color:black; padding: 20px; font: 10pt "Sans Serif";
+          
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+          
+          
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+          
+          
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+          
+          
+           QTextEdit::WidgetWidth
+          
+          
+           <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd">
+<html><head><meta name="qrichtext" content="1" /><style type="text/css">
+p, li { white-space: pre-wrap; }
+</style></head><body style=" font-family:'Sans Serif'; font-size:10pt; font-weight:400; font-style:normal;">
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Droid Sans Mono','monospace','monospace','Droid Sans Fallback'; color:#000000;">PyMOL pyKVFinder Tools integrates PyMOL (http://PyMOL.org/) with pyKVFinder (https://github.com/LBC-LNBio/pyKVFinder).</span></p>
+<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'Droid Sans Mono','monospace','monospace','Droid Sans Fallback'; color:#000000;"><br /></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Droid Sans Mono','monospace','monospace','Droid Sans Fallback'; font-weight:600; text-decoration: underline; color:#000000;">Scientific team</span></p>
+<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'Droid Sans Mono','monospace','monospace','Droid Sans Fallback'; color:#000000;"><br /></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Droid Sans Mono','monospace','monospace','Droid Sans Fallback'; color:#000000;">pyKVFinder and PyMOL pyKVFinder Tools was developed by:</span></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Droid Sans Mono','monospace','monospace','Droid Sans Fallback'; color:#000000;">- João V. S. Guerra</span></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Droid Sans Mono','monospace','monospace','Droid Sans Fallback'; color:#000000;">- Helder V. Ribeiro-Filho</span></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Droid Sans Mono','monospace','monospace','Droid Sans Fallback'; color:#000000;">- Luiz F. G. Alves</span></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Droid Sans Mono','monospace','monospace','Droid Sans Fallback'; color:#000000;">- Pablo W. A. Silva</span></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Droid Sans Mono','monospace','monospace','Droid Sans Fallback'; color:#000000;">- Leandro O. Bortot</span></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Droid Sans Mono','monospace','monospace','Droid Sans Fallback'; color:#000000;">- Rodrigo V. Honorato</span></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Droid Sans Mono','monospace','monospace','Droid Sans Fallback'; color:#000000;">- José G. C. Pereira</span></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Droid Sans Mono','monospace','monospace','Droid Sans Fallback'; color:#000000;">- Paulo S. Lopes-de-Oliveira (paulo.oliveira@lnbio.cnpem.br)</span></p>
+<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'Droid Sans Mono','monospace','monospace','Droid Sans Fallback'; color:#000000;"><br /></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Droid Sans Mono','monospace','monospace','Droid Sans Fallback'; color:#000000;">Brazilian Biosciences National Laboratory - LNBio</span></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Droid Sans Mono','monospace','monospace','Droid Sans Fallback'; color:#000000;">Brazilian Center for Research in Energy and Materials - CNPEM</span></p>
+<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><br /></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Droid Sans Mono','monospace','monospace','Droid Sans Fallback'; color:#000000;">Please refer and cite our papers if you use it in a publication.</span></p>
+<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'Droid Sans Mono','monospace','monospace','Droid Sans Fallback'; color:#000000;"><br /></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-family:'Droid Sans Mono','monospace','monospace','Droid Sans Fallback'; font-weight:600; text-decoration: underline; color:#000000;">Citing pyKVFinder</span></p>
+<p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-family:'Droid Sans Mono','monospace','monospace','Droid Sans Fallback'; color:#000000;"><br /></p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">If you use <span style=" text-decoration: underline;">pyKVFinder</span> package, please cite:</p>
+<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Guerra, J. V. S., Ribeiro-Filho, H. V., Jara, G. E., Bortot, L. O., Pereira, J. G. C., &amp; Lopes-de-Oliveira, P. S. (2021). pyKVFinder: an efficient and integrable Python package for biomolecular cavity detection and characterization in data science. BMC bioinformatics, 22(1), 607. <a href="https://doi.org/10.1186/s12859-021-04519-4"><span style=" text-decoration: underline; color:#0000ff;">https://doi.org/10.1186/s12859-021-04519-4</span></a>.</p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">If you use <span style=" text-decoration: underline;">pyKVFinder.Molecule</span>, please also cite:</p>
+<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Guerra, J. V. S., Alves, L. F. G., Bourissou, D., Lopes-de-Oliveira, P. S., &amp; Szalóki, G. (2023). Cavity Characterization in Supramolecular Cages. Journal of chemical information and modeling, 63(12), 3772-3785. <a href="https://doi.org/10.1021/acs.jcim.3c00328"><span style=" text-decoration: underline; color:#0000ff;">https://doi.org/10.1021/acs.jcim.3c00328</span></a>.</p>
+<p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">If you use <span style=" text-decoration: underline;">PyMOL pyKVFinder Tools</span>, please also cite:</p>
+<p style=" margin-top:12px; margin-bottom:12px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;">Guerra, J. V. da S., Ribeiro Filho, H. V., Bortot, L. O., Honorato, R. V., Pereira, J. G. de C., &amp; Lopes-de-Oliveira, P. S. (2020). ParKVFinder: A thread-level parallel approach in biomolecular cavity detection. In SoftwareX (Vol. 12, p. 100606). Elsevier BV. <a href="https://doi.org/10.1016/j.softx.2020.100606"><span style=" text-decoration: underline; color:#0000ff;">https://doi.org/10.1016/j.softx.2020.100606</span></a>.</p></body></html>
+          
+          
+           true
+          
+          
+           true
+          
+         
+        
+       
+      
+     
+    
+   
+  
+ 
+ 
+  tabs
+  button_run
+  button_restore
+  button_exit
+  input
+  refresh_input
+  probe_out
+  probe_in
+  volume_cutoff
+  removal_distance
+  basename
+  basedir
+  button_browse_basedir
+  box_adjustment
+  button_draw_box
+  button_delete_box
+  button_redraw_box
+  padding
+  min_x
+  max_x
+  min_y
+  max_y
+  min_z
+  max_z
+  angle1
+  angle2
+  ligand_adjustment
+  ligand
+  refresh_ligand
+  ligand_cutoff
+  results_file_entry
+  button_browse_results
+  button_load_results
+  volume_list
+  area_list
+  residues_list
+  about_text
+ 
+ 
+ 
+
diff --git a/plugins/PyMOL-pyKVFinder-Tools/__init__.py b/plugins/PyMOL-pyKVFinder-Tools/__init__.py
new file mode 100644
index 00000000..77a0ebe0
--- /dev/null
+++ b/plugins/PyMOL-pyKVFinder-Tools/__init__.py
@@ -0,0 +1,38 @@
+# This source code is part of the pyKVFinder package and is distributed
+# under the GNU GPL-3.0 license. Please see 'LICENSE' for further
+# information.
+
+"""
+This is the source code for PyMOL pyKVFinder Tools. It was developed using the
+PyMOL API, and is intended to be used as a plugin for PyMOL. The code is
+written in Python and uses the PyQt5 library for the graphical user interface.
+Changes in this file are not advised, as it controls all interactions with
+pyKVFinder.
+"""
+
+from .gui import PyMOLpyKVFinderTools
+
+# global reference to avoid garbage collection of our dialog
+dialog = None
+
+
+def __init_plugin__(app=None):
+    """
+    Add an entry to the PyMOL "Plugin" menu. This function is called when the
+    plugin is loaded by PyMOL.
+    """
+    from pymol.plugins import addmenuitemqt
+
+    addmenuitemqt("PyMOL pyKVFinder Tools", run_plugin_gui)
+
+
+def run_plugin_gui():
+    """
+    Open our custom dialog. If it is already open, bring it to the front.
+    """
+    global dialog
+
+    if dialog is None:
+        dialog = PyMOLpyKVFinderTools()
+
+    dialog.show()
diff --git a/plugins/PyMOL-pyKVFinder-Tools/actions.py b/plugins/PyMOL-pyKVFinder-Tools/actions.py
new file mode 100644
index 00000000..e62a8c6b
--- /dev/null
+++ b/plugins/PyMOL-pyKVFinder-Tools/actions.py
@@ -0,0 +1,249 @@
+# This source code is part of the pyKVFinder package and is distributed
+# under the GNU GPL-3.0 license. Please see 'LICENSE' for further
+# information.
+
+"""
+This is the source code for the actions performed by PyMOL pyKVFinder Tools.
+Changes in this file are not advised, as it controls interactions with
+pyKVFinder and PyQt5.
+"""
+
+import os
+
+from pymol import cmd
+from PyQt5.QtCore import QDir
+from PyQt5.QtWidgets import QComboBox, QFileDialog, QLineEdit, QListWidget
+
+
+def _load_area(results: dict, widget: QListWidget) -> None:
+    """
+    Load a area file into PyMOL.
+
+    Parameters
+    ----------
+    results : dict
+        The results from the pyKVFinder calculation.
+    widget : QListWidget
+        The widget to display the results.
+    """
+    # Get cavity indexes
+    indexes = sorted(results["RESULTS"]["AREA"].keys())
+    # Include Area
+    for index in indexes:
+        item = f"{index}: {results['RESULTS']['AREA'][index]}"
+        widget.addItem(item)
+
+
+def _load_avg_depth(results: dict, widget: QListWidget) -> None:
+    """
+    Load a avg_depth file into PyMOL.
+
+    Parameters
+    ----------
+    results : dict
+        The results from the pyKVFinder calculation.
+    widget : QListWidget
+        The widget to display the results.
+    """
+    # Get cavity indexes
+    indexes = sorted(results["RESULTS"]["AVG_DEPTH"].keys())
+    # Include Avg Depth
+    for index in indexes:
+        item = f"{index}: {results['RESULTS']['AVG_DEPTH'][index]}"
+        widget.addItem(item)
+
+
+def _load_avg_hydropathy(results: dict, widget: QListWidget) -> None:
+    """
+    Load a avg_hydropathy file into PyMOL.
+
+    Parameters
+    ----------
+    results : dict
+        The results from the pyKVFinder calculation.
+    widget : QListWidget
+        The widget to display the results.
+    """
+    # Get cavity indexes
+    indexes = sorted(results["RESULTS"]["AVG_HYDROPATHY"].keys())
+    # Include Avg Hydropathy
+    for index in indexes:
+        if not (
+            (index == "EisenbergWeiss")
+            or (index == "HessaHeijne")
+            or (index == "KyteDoolittle")
+            or (index == "RadzickaWolfenden")
+            or (index == "MoonFleming")
+            or (index == "WimleyWhite")
+            or (index == "ZhaoLondon")
+        ):
+            item = f"{index}: {results['RESULTS']['AVG_HYDROPATHY'][index]}"
+            widget.addItem(item)
+
+
+def _load_cavity_file(filename: str, pymolname: str) -> None:
+    """
+    Load a cavity file into PyMOL.
+
+    Parameters
+    ----------
+    filename : str
+        The path to the cavity file.
+    pymolname : str
+        The name to assign to the object in PyMOL.
+    """
+    # Remove previous results in objects with same cavity name
+    for obj in cmd.get_names("all"):
+        if pymolname == obj:
+            cmd.delete(obj)
+
+    # Load the cavity file
+    cmd.load(filename, pymolname, zoom=0)
+
+    # Hide and show to update the display
+    cmd.hide("everything", pymolname)
+    cmd.show("nonbonded", pymolname)
+
+
+def _load_max_depth(results: dict, widget: QListWidget) -> None:
+    """
+    Load a max_depth file into PyMOL.
+
+    Parameters
+    ----------
+    results : dict
+        The results from the pyKVFinder calculation.
+    widget : QListWidget
+        The widget to display the results.
+    """
+    # Get cavity indexes
+    indexes = sorted(results["RESULTS"]["MAX_DEPTH"].keys())
+    # Include Max Depth
+    for index in indexes:
+        item = f"{index}: {results['RESULTS']['MAX_DEPTH'][index]}"
+        widget.addItem(item)
+
+
+def _load_molecule_file(filename: str, pymolname: str) -> None:
+    """
+    Load a molecule file into PyMOL.
+
+    Parameters
+    ----------
+    filename : str
+        The path to the molecule file.
+    pymolname : str
+        The name to assign to the object in PyMOL.
+    """
+    # Remove previous results in objects with same cavity name
+    for obj in cmd.get_names("all"):
+        if pymolname == obj:
+            cmd.delete(obj)
+
+    # Load the molecule file
+    cmd.load(filename, pymolname, zoom=0)
+
+
+def _load_residues(results: dict, widget: QListWidget) -> None:
+    """
+    Load a residues file into PyMOL.
+
+    Parameters
+    ----------
+    results : dict
+        The results from the pyKVFinder calculation.
+    widget : QListWidget
+        The widget to display the results.
+    """
+    # Get cavity indexes
+    indexes = sorted(results["RESULTS"]["RESIDUES"].keys())
+    # Include Residues
+    for index in indexes:
+        widget.addItem(index)
+
+
+def _load_volume(results: dict, widget: QListWidget) -> None:
+    """
+    Load a volume file into PyMOL.
+
+    Parameters
+    ----------
+    results : dict
+        The results from the pyKVFinder calculation.
+    widget : QListWidget
+        The widget to display the results.
+    """
+    # Get cavity indexes
+    indexes = sorted(results["RESULTS"]["VOLUME"].keys())
+    # Include Volume
+    for index in indexes:
+        item = f"{index}: {results['RESULTS']['VOLUME'][index]}"
+        widget.addItem(item)
+
+
+def _refresh_list(widget: QComboBox) -> None:
+    """
+    Refresh the list of objects in the given widget.
+
+    Parameters
+    ----------
+    widget : QComboBox
+        The widget to refresh.
+    """
+    # Clear the current list
+    widget.clear()
+
+    # Get the list of objects in the PyMOL session
+    objects = cmd.get_names("all")
+    for obj in objects:
+        if (
+            (cmd.get_type(obj) == "object:molecule")  # molecules
+            and (obj != "box")  # custom grid
+            and (obj != "cavities")  # cavities highlight
+            and (obj != "residues")  # residues highlight
+            and (obj[-16:] != ".KVFinder.output")  # cavities output
+            and (obj != "target_exclusive")
+        ):
+            widget.addItem(obj)
+
+
+def _select_directory(widget: QLineEdit) -> None:
+    """
+    Open a dialog to select the base directory for the output files.
+    Callback |for the "Browse ..." button.
+    """
+    # Open the dialog
+    dirpath = QFileDialog.getExistingDirectory(
+        caption="Select Directory", directory=os.getcwd()
+    )
+
+    # Set the selected directory
+    if dirpath:
+        dirpath = QDir.toNativeSeparators(dirpath)
+        if os.path.isdir(dirpath):
+            widget.setText(dirpath)
+
+
+def _select_file(caption: str, filters: str, widget: QLineEdit) -> None:
+    """
+    Open a dialog to select a file. Callback for the "Browse ..." buttons.
+
+    Parameters
+    ----------
+    caption : str
+        The caption for the dialog.
+    entry : str
+        The entry to set the selected file.
+    filters : str
+        The filters for the dialog.
+    """
+    # Open the dialog
+    filepath, _ = QFileDialog.getOpenFileName(
+        caption=caption, filter=filters, directory=os.getcwd()
+    )
+
+    # Set the selected file
+    if filepath:
+        filepath = QDir.toNativeSeparators(filepath)
+        if os.path.isfile(filepath):
+            widget.setText(filepath)
diff --git a/plugins/PyMOL-pyKVFinder-Tools/box.py b/plugins/PyMOL-pyKVFinder-Tools/box.py
new file mode 100644
index 00000000..d37fe51c
--- /dev/null
+++ b/plugins/PyMOL-pyKVFinder-Tools/box.py
@@ -0,0 +1,719 @@
+# This source code is part of the pyKVFinder package and is distributed
+# under the GNU GPL-3.0 license. Please see 'LICENSE' for further
+# information.
+
+"""
+This is the source code for the custom box operations by PyMOL pyKVFinder Tools.
+Changes in this file are not advised, as it controls interactions with
+pyKVFinder and PyQt5.
+"""
+
+from math import cos, pi, sin
+
+import pymol
+import toml
+from pymol import cmd
+from PyQt5.QtCore import QCoreApplication
+from PyQt5.QtWidgets import QDoubleSpinBox, QMainWindow, QMessageBox, QPushButton
+
+
+class Box(object):
+
+    def __init__(self):
+        self.x = 0
+        self.y = 0
+        self.z = 0
+
+    def _set_box(
+        self,
+        button_draw_box: QPushButton,
+        button_redraw_box: QPushButton,
+        min_x: QDoubleSpinBox,
+        max_x: QDoubleSpinBox,
+        min_y: QDoubleSpinBox,
+        max_y: QDoubleSpinBox,
+        min_z: QDoubleSpinBox,
+        max_z: QDoubleSpinBox,
+        angle1: QDoubleSpinBox,
+        angle2: QDoubleSpinBox,
+        padding: QDoubleSpinBox,
+    ) -> None:
+        """
+        Create box coordinates, enable 'Delete Box' and 'Redraw Box' buttons
+        and call _draw_box function.
+
+        Parameters
+        ----------
+        button_draw_box : QPushButton
+            The button to draw the box.
+        button_redraw_box : QPushButton
+            The button to redraw the box.
+        min_x : QDoubleSpinBox
+            The minimum x value of the box.
+        max_x : QDoubleSpinBox
+            The maximum x value of the box.
+        min_y : QDoubleSpinBox
+            The minimum y value of the box.
+        max_y : QDoubleSpinBox
+        min_z : QDoubleSpinBox
+            The minimum z value of the box.
+        max_z : QDoubleSpinBox
+            The maximum z value of the box.
+        angle1 : QDoubleSpinBox
+            The first angle value of the box.
+        angle2 : QDoubleSpinBox
+            The second angle value of the box.
+        padding : QDoubleSpinBox
+            The padding value of the box.
+        """
+
+        # Delete Box object in PyMOL
+        if "box" in cmd.get_names("all"):
+            cmd.delete("box")
+        # Get dimensions of selected residues
+        selection = "sele"
+        if selection in cmd.get_names("selections"):
+            ([minx, miny, minz], [maxx, maxy, maxz]) = cmd.get_extent(selection)
+        else:
+            ([minx, miny, minz], [maxx, maxy, maxz]) = cmd.get_extent("")
+
+        # Get center of each dimension (x, y, z)
+        self.x = (minx + maxx) / 2
+        self.y = (miny + maxy) / 2
+        self.z = (minz + maxz) / 2
+
+        # Set Box variables in interface
+        min_x.setValue(round(self.x - (minx - padding.value()), 1))
+        max_x.setValue(round((maxx + padding.value()) - self.x, 1))
+        min_y.setValue(round(self.y - (miny - padding.value()), 1))
+        max_y.setValue(round((maxy + padding.value()) - self.y, 1))
+        min_z.setValue(round(self.z - (minz - padding.value()), 1))
+        max_z.setValue(round((maxz + padding.value()) - self.z, 1))
+        angle1.setValue(0)
+        angle2.setValue(0)
+
+        # Setting background box values
+        self.min_x_set = min_x.value()
+        self.max_x_set = max_x.value()
+        self.min_y_set = min_y.value()
+        self.max_y_set = max_y.value()
+        self.min_z_set = min_z.value()
+        self.max_z_set = max_z.value()
+        self.angle1_set = angle1.value()
+        self.angle2_set = angle2.value()
+        self.padding_set = padding.value()
+
+        # Draw box
+        self._draw_box(min_x, max_x, min_y, max_y, min_z, max_z, angle1, angle2)
+
+        # Enable/Disable buttons
+        button_draw_box.setEnabled(False)
+        button_redraw_box.setEnabled(True)
+        min_x.setEnabled(True)
+        min_y.setEnabled(True)
+        min_z.setEnabled(True)
+        max_x.setEnabled(True)
+        max_y.setEnabled(True)
+        max_z.setEnabled(True)
+        angle1.setEnabled(True)
+        angle2.setEnabled(True)
+
+    def _draw_box(
+        self,
+        min_x: QDoubleSpinBox,
+        max_x: QDoubleSpinBox,
+        min_y: QDoubleSpinBox,
+        max_y: QDoubleSpinBox,
+        min_z: QDoubleSpinBox,
+        max_z: QDoubleSpinBox,
+        angle1: QDoubleSpinBox,
+        angle2: QDoubleSpinBox,
+    ) -> None:
+        """
+        Draw box in PyMOL interface.
+
+        Parameters
+        ----------
+        min_x : QDoubleSpinBox
+            The minimum x value of the box.
+        max_x : QDoubleSpinBox
+            The maximum x value of the box.
+        min_y : QDoubleSpinBox
+            The minimum y value of the box.
+        max_y : QDoubleSpinBox
+        min_z : QDoubleSpinBox
+            The minimum z value of the box.
+        max_z : QDoubleSpinBox
+            The maximum z value of the box.
+        angle1 : QDoubleSpinBox
+            The first angle value of the box.
+        angle2 : QDoubleSpinBox
+            The second angle value of the box.
+        """
+        # Convert angle
+        a1 = (angle1.value() / 180.0) * pi
+        a2 = (angle2.value() / 180.0) * pi
+
+        # Get positions of box vertices
+        # P1
+        x1 = (
+            -min_x.value() * cos(a2)
+            - (-min_y.value()) * sin(a1) * sin(a2)
+            + (-min_z.value()) * cos(a1) * sin(a2)
+            + self.x
+        )
+
+        y1 = -min_y.value() * cos(a1) + (-min_z.value()) * sin(a1) + self.y
+
+        z1 = (
+            min_x.value() * sin(a2)
+            + min_y.value() * sin(a1) * cos(a2)
+            - min_z.value() * cos(a1) * cos(a2)
+            + self.z
+        )
+
+        # P2
+        x2 = (
+            max_x.value() * cos(a2)
+            - (-min_y.value()) * sin(a1) * sin(a2)
+            + (-min_z.value()) * cos(a1) * sin(a2)
+            + self.x
+        )
+
+        y2 = (-min_y.value()) * cos(a1) + (-min_z.value()) * sin(a1) + self.y
+
+        z2 = (
+            (-max_x.value()) * sin(a2)
+            - (-min_y.value()) * sin(a1) * cos(a2)
+            + (-min_z.value()) * cos(a1) * cos(a2)
+            + self.z
+        )
+
+        # P3
+        x3 = (
+            (-min_x.value()) * cos(a2)
+            - max_y.value() * sin(a1) * sin(a2)
+            + (-min_z.value()) * cos(a1) * sin(a2)
+            + self.x
+        )
+
+        y3 = max_y.value() * cos(a1) + (-min_z.value()) * sin(a1) + self.y
+
+        z3 = (
+            -(-min_x.value()) * sin(a2)
+            - max_y.value() * sin(a1) * cos(a2)
+            + (-min_z.value()) * cos(a1) * cos(a2)
+            + self.z
+        )
+
+        # P4
+        x4 = (
+            (-min_x.value()) * cos(a2)
+            - (-min_y.value()) * sin(a1) * sin(a2)
+            + max_z.value() * cos(a1) * sin(a2)
+            + self.x
+        )
+
+        y4 = (-min_y.value()) * cos(a1) + max_z.value() * sin(a1) + self.y
+
+        z4 = (
+            -(-min_x.value()) * sin(a2)
+            - (-min_y.value()) * sin(a1) * cos(a2)
+            + max_z.value() * cos(a1) * cos(a2)
+            + self.z
+        )
+
+        # P5
+        x5 = (
+            max_x.value() * cos(a2)
+            - max_y.value() * sin(a1) * sin(a2)
+            + (-min_z.value()) * cos(a1) * sin(a2)
+            + self.x
+        )
+
+        y5 = max_y.value() * cos(a1) + (-min_z.value()) * sin(a1) + self.y
+
+        z5 = (
+            (-max_x.value()) * sin(a2)
+            - max_y.value() * sin(a1) * cos(a2)
+            + (-min_z.value()) * cos(a1) * cos(a2)
+            + self.z
+        )
+
+        # P6
+        x6 = (
+            max_x.value() * cos(a2)
+            - (-min_y.value()) * sin(a1) * sin(a2)
+            + max_z.value() * cos(a1) * sin(a2)
+            + self.x
+        )
+
+        y6 = (-min_y.value()) * cos(a1) + max_z.value() * sin(a1) + self.y
+
+        z6 = (
+            (-max_x.value()) * sin(a2)
+            - (-min_y.value()) * sin(a1) * cos(a2)
+            + max_z.value() * cos(a1) * cos(a2)
+            + self.z
+        )
+
+        # P7
+        x7 = (
+            (-min_x.value()) * cos(a2)
+            - max_y.value() * sin(a1) * sin(a2)
+            + max_z.value() * cos(a1) * sin(a2)
+            + self.x
+        )
+
+        y7 = max_y.value() * cos(a1) + max_z.value() * sin(a1) + self.y
+
+        z7 = (
+            -(-min_x.value()) * sin(a2)
+            - max_y.value() * sin(a1) * cos(a2)
+            + max_z.value() * cos(a1) * cos(a2)
+            + self.z
+        )
+
+        # P8
+        x8 = (
+            max_x.value() * cos(a2)
+            - max_y.value() * sin(a1) * sin(a2)
+            + max_z.value() * cos(a1) * sin(a2)
+            + self.x
+        )
+
+        y8 = max_y.value() * cos(a1) + max_z.value() * sin(a1) + self.y
+
+        z8 = (
+            (-max_x.value()) * sin(a2)
+            - max_y.value() * sin(a1) * cos(a2)
+            + max_z.value() * cos(a1) * cos(a2)
+            + self.z
+        )
+
+        # Create box object
+        pymol.stored.list = []
+        if "box" in cmd.get_names("all"):
+            cmd.iterate("box", "stored.list.append((name, color))", quiet=1)
+        list_color = pymol.stored.list
+        cmd.delete("box")
+        if len(list_color) > 0:
+            for item in list_color:
+                at_name = item[0]
+                at_c = item[1]
+                cmd.set_color(at_name + "color", cmd.get_color_tuple(at_c))
+        else:
+            for at_name in [
+                "v2",
+                "v3",
+                "v4",
+                "v5",
+                "v6",
+                "v7",
+                "v8",
+                "v1x",
+                "v1y",
+                "v1z",
+                "v2x",
+                "v3y",
+                "v4z",
+            ]:
+                cmd.set_color(at_name + "color", [0.86, 0.86, 0.86])
+
+        # Create vertices
+        cmd.pseudoatom("box", name="v2", pos=[x2, y2, z2], color="v2color")
+        cmd.pseudoatom("box", name="v3", pos=[x3, y3, z3], color="v3color")
+        cmd.pseudoatom("box", name="v4", pos=[x4, y4, z4], color="v4color")
+        cmd.pseudoatom("box", name="v5", pos=[x5, y5, z5], color="v5color")
+        cmd.pseudoatom("box", name="v6", pos=[x6, y6, z6], color="v6color")
+        cmd.pseudoatom("box", name="v7", pos=[x7, y7, z7], color="v7color")
+        cmd.pseudoatom("box", name="v8", pos=[x8, y8, z8], color="v8color")
+
+        # Connect vertices
+        cmd.select("vertices", "(name v3,v7)")
+        cmd.bond("vertices", "vertices")
+        cmd.select("vertices", "(name v2,v6)")
+        cmd.bond("vertices", "vertices")
+        cmd.select("vertices", "(name v5,v8)")
+        cmd.bond("vertices", "vertices")
+        cmd.select("vertices", "(name v2,v5)")
+        cmd.bond("vertices", "vertices")
+        cmd.select("vertices", "(name v4,v6)")
+        cmd.bond("vertices", "vertices")
+        cmd.select("vertices", "(name v4,v7)")
+        cmd.bond("vertices", "vertices")
+        cmd.select("vertices", "(name v3,v5)")
+        cmd.bond("vertices", "vertices")
+        cmd.select("vertices", "(name v6,v8)")
+        cmd.bond("vertices", "vertices")
+        cmd.select("vertices", "(name v7,v8)")
+        cmd.bond("vertices", "vertices")
+        cmd.pseudoatom("box", name="v1x", pos=[x1, y1, z1], color="red")
+        cmd.pseudoatom("box", name="v2x", pos=[x2, y2, z2], color="red")
+        cmd.select("vertices", "(name v1x,v2x)")
+        cmd.bond("vertices", "vertices")
+        cmd.pseudoatom("box", name="v1y", pos=[x1, y1, z1], color="forest")
+        cmd.pseudoatom("box", name="v3y", pos=[x3, y3, z3], color="forest")
+        cmd.select("vertices", "(name v1y,v3y)")
+        cmd.bond("vertices", "vertices")
+        cmd.pseudoatom("box", name="v4z", pos=[x4, y4, z4], color="blue")
+        cmd.pseudoatom("box", name="v1z", pos=[x1, y1, z1], color="blue")
+        cmd.select("vertices", "(name v1z,v4z)")
+        cmd.bond("vertices", "vertices")
+        cmd.delete("vertices")
+
+    def _delete_box(
+        self,
+        button_draw_box: QPushButton,
+        button_redraw_box: QPushButton,
+        min_x: QDoubleSpinBox,
+        max_x: QDoubleSpinBox,
+        min_y: QDoubleSpinBox,
+        max_y: QDoubleSpinBox,
+        min_z: QDoubleSpinBox,
+        max_z: QDoubleSpinBox,
+        angle1: QDoubleSpinBox,
+        angle2: QDoubleSpinBox,
+    ) -> None:
+        """
+        Delete box object, disable 'Delete Box' and 'Redraw Box' buttons and
+        enable 'Draw Box' button.
+
+        Parameters
+        ----------
+        button_draw_box : QPushButton
+            The button to draw the box.
+        button_redraw_box : QPushButton
+            The button to redraw the box.
+        min_x : QDoubleSpinBox
+            The minimum x value of the box.
+        max_x : QDoubleSpinBox
+            The maximum x value of the box.
+        min_y : QDoubleSpinBox
+            The minimum y value of the box.
+        max_y : QDoubleSpinBox
+        min_z : QDoubleSpinBox
+            The minimum z value of the box.
+        max_z : QDoubleSpinBox
+            The maximum z value of the box.
+        angle1 : QDoubleSpinBox
+            The first angle value of the box.
+        angle2 : QDoubleSpinBox
+            The second angle value of the box.
+        """
+        from pymol import cmd
+
+        # Reset all box variables
+        self.x = 0
+        self.y = 0
+        self.z = 0
+
+        # Delete Box and Vertices objects in PyMOL
+        cmd.delete("vertices")
+        cmd.delete("box")
+
+        # Set Box variables in the interface
+        min_x.setValue(0.0)
+        max_x.setValue(0.0)
+        min_y.setValue(0.0)
+        max_y.setValue(0.0)
+        min_z.setValue(0.0)
+        max_z.setValue(0.0)
+        angle1.setValue(0)
+        angle2.setValue(0)
+
+        # Change state of buttons in the interface
+        button_draw_box.setEnabled(True)
+        button_redraw_box.setEnabled(False)
+        min_x.setEnabled(False)
+        min_y.setEnabled(False)
+        min_z.setEnabled(False)
+        max_x.setEnabled(False)
+        max_y.setEnabled(False)
+        max_z.setEnabled(False)
+        angle1.setEnabled(False)
+        angle2.setEnabled(False)
+
+    def _redraw_box(
+        self,
+        min_x: QDoubleSpinBox,
+        max_x: QDoubleSpinBox,
+        min_y: QDoubleSpinBox,
+        max_y: QDoubleSpinBox,
+        min_z: QDoubleSpinBox,
+        max_z: QDoubleSpinBox,
+        angle1: QDoubleSpinBox,
+        angle2: QDoubleSpinBox,
+        padding: QDoubleSpinBox,
+    ) -> None:
+        """
+        Redraw box in PyMOL interface. If selection is provided, the box will
+        be drawn around the selected residues. If no selection is provided,
+        the box will be drawn around the entire structure.
+
+        Parameters
+        ----------
+        button_draw_box : QPushButton
+            The button to draw the box.
+        button_redraw_box : QPushButton
+            The button to redraw the box.
+        min_x : QDoubleSpinBox
+            The minimum x value of the box.
+        max_x : QDoubleSpinBox
+            The maximum x value of the box.
+        min_y : QDoubleSpinBox
+            The minimum y value of the box.
+        max_y : QDoubleSpinBox
+        min_z : QDoubleSpinBox
+            The minimum z value of the box.
+        max_z : QDoubleSpinBox
+            The maximum z value of the box.
+        angle1 : QDoubleSpinBox
+            The first angle value of the box.
+        angle2 : QDoubleSpinBox
+            The second angle value of the box.
+        padding : QDoubleSpinBox
+            The padding value of the box.
+        """
+
+        # Provided a selection
+        if "sele" in cmd.get_names("selections"):
+            # Get dimensions of selected residues
+            ([minx, miny, minz], [maxx, maxy, maxz]) = cmd.get_extent("sele")
+
+            if (
+                min_x.value() != self.min_x_set
+                or max_x.value() != self.max_x_set
+                or min_y.value() != self.min_y_set
+                or max_y.value() != self.max_y_set
+                or min_z.value() != self.min_z_set
+                or max_z.value() != self.max_z_set
+                or angle1.value() != self.angle1_set
+                or angle2.value() != self.angle2_set
+            ):
+                self.min_x_set = min_x.value()
+                self.max_x_set = max_x.value()
+                self.min_y_set = min_y.value()
+                self.max_y_set = max_y.value()
+                self.min_z_set = min_z.value()
+                self.max_z_set = max_z.value()
+                self.angle1_set = angle1.value()
+                self.angle2_set = angle2.value()
+            # Padding or selection altered
+            else:
+                # Get center of each dimension (x, y, z)
+                self.x = (minx + maxx) / 2
+                self.y = (miny + maxy) / 2
+                self.z = (minz + maxz) / 2
+
+                # Set background box values
+                self.min_x_set = (
+                    round(self.x - (minx - padding.value()), 1)
+                    + min_x.value()
+                    - self.min_x_set
+                )
+                self.max_x_set = (
+                    round((maxx + padding.value()) - self.x, 1)
+                    + max_x.value()
+                    - self.max_x_set
+                )
+                self.min_y_set = (
+                    round(self.y - (miny - padding.value()), 1)
+                    + min_y.value()
+                    - self.min_y_set
+                )
+                self.max_y_set = (
+                    round((maxy + padding.value()) - self.y, 1)
+                    + max_y.value()
+                    - self.max_y_set
+                )
+                self.min_z_set = (
+                    round(self.z - (minz - padding.value()), 1)
+                    + min_z.value()
+                    - self.min_z_set
+                )
+                self.max_z_set = (
+                    round((maxz + padding.value()) - self.z, 1)
+                    + max_z.value()
+                    - self.max_z_set
+                )
+                self.angle1_set = 0 + angle1.value()
+                self.angle2_set = 0 + angle2.value()
+                self.padding_set = padding.value()
+        # Not provided a selection
+        else:
+            if (
+                min_x.value() != self.min_x_set
+                or max_x.value() != self.max_x_set
+                or min_y.value() != self.min_y_set
+                or max_y.value() != self.max_y_set
+                or min_z.value() != self.min_z_set
+                or max_z.value() != self.max_z_set
+                or angle1.value() != self.angle1_set
+                or angle2.value() != self.angle2_set
+            ):
+                self.min_x_set = min_x.value()
+                self.max_x_set = max_x.value()
+                self.min_y_set = min_y.value()
+                self.max_y_set = max_y.value()
+                self.min_z_set = min_z.value()
+                self.max_z_set = max_z.value()
+                self.angle1_set = angle1.value()
+                self.angle2_set = angle2.value()
+
+            if self.padding_set != padding.value():
+                # Prepare dimensions without old padding
+                minx = self.padding_set - self.min_x_set
+                maxx = self.max_x_set - self.padding_set
+                miny = self.padding_set - self.min_y_set
+                maxy = self.max_y_set - self.padding_set
+                minz = self.padding_set - self.min_z_set
+                maxz = self.max_z_set - self.padding_set
+
+                # Get center of each dimension (x, y, z)
+                self.x = (minx + maxx) / 2
+                self.y = (miny + maxy) / 2
+                self.z = (minz + maxz) / 2
+
+                # Set background box values
+                self.min_x_set = round(self.x - (minx - padding.value()), 1)
+                self.max_x_set = round((maxx + padding.value()) - self.x, 1)
+                self.min_y_set = round(self.y - (miny - padding.value()), 1)
+                self.max_y_set = round((maxy + self.padding.value()) - self.y, 1)
+                self.min_z_set = round(self.z - (min_z - padding.value()), 1)
+                self.max_z_set = round((maxz + padding.value()) - self.z, 1)
+                self.angle1_set = angle1.value()
+                self.angle2_set = angle2.value()
+                self.padding_set = padding.value()
+
+        # Set Box variables in the interface
+        min_x.setValue(self.min_x_set)
+        max_x.setValue(self.max_x_set)
+        min_y.setValue(self.min_y_set)
+        max_y.setValue(self.max_y_set)
+        min_z.setValue(self.min_z_set)
+        max_z.setValue(self.max_z_set)
+        angle1.setValue(self.angle1_set)
+        angle2.setValue(self.angle2_set)
+
+        # Redraw box
+        self._draw_box(min_x, max_x, min_y, max_y, min_z, max_z, angle1, angle2)
+
+    def _create_box_file(self, filename: str) -> dict:
+        """
+        Create a box file (box..pdb) with the parameters from the GUI.
+
+        Returns
+        -------
+        dict
+            The box parameters.
+        """
+        # Get box parameters
+        min_x = self.min_x_set
+        max_x = self.max_x_set
+        min_y = self.min_y_set
+        max_y = self.max_y_set
+        min_z = self.min_z_set
+        max_z = self.max_z_set
+        angle1 = self.angle1_set
+        angle2 = self.angle2_set
+
+        # Convert angle
+        angle1 = (angle1 / 180.0) * pi
+        angle2 = (angle2 / 180.0) * pi
+
+        # Get positions of box vertices
+        # P1
+        x1 = (
+            -min_x * cos(angle2)
+            - (-min_y) * sin(angle1) * sin(angle2)
+            + (-min_z) * cos(angle1) * sin(angle2)
+            + self.x
+        )
+
+        y1 = -min_y * cos(angle1) + (-min_z) * sin(angle1) + self.y
+
+        z1 = (
+            min_x * sin(angle2)
+            + min_y * sin(angle1) * cos(angle2)
+            - min_z * cos(angle1) * cos(angle2)
+            + self.z
+        )
+
+        # P2
+        x2 = (
+            max_x * cos(angle2)
+            - (-min_y) * sin(angle1) * sin(angle2)
+            + (-min_z) * cos(angle1) * sin(angle2)
+            + self.x
+        )
+
+        y2 = (-min_y) * cos(angle1) + (-min_z) * sin(angle1) + self.y
+
+        z2 = (
+            (-max_x) * sin(angle2)
+            - (-min_y) * sin(angle1) * cos(angle2)
+            + (-min_z) * cos(angle1) * cos(angle2)
+            + self.z
+        )
+
+        # P3
+        x3 = (
+            (-min_x) * cos(angle2)
+            - max_y * sin(angle1) * sin(angle2)
+            + (-min_z) * cos(angle1) * sin(angle2)
+            + self.x
+        )
+
+        y3 = max_y * cos(angle1) + (-min_z) * sin(angle1) + self.y
+
+        z3 = (
+            -(-min_x) * sin(angle2)
+            - max_y * sin(angle1) * cos(angle2)
+            + (-min_z) * cos(angle1) * cos(angle2)
+            + self.z
+        )
+
+        # P4
+        x4 = (
+            (-min_x) * cos(angle2)
+            - (-min_y) * sin(angle1) * sin(angle2)
+            + max_z * cos(angle1) * sin(angle2)
+            + self.x
+        )
+
+        y4 = (-min_y) * cos(angle1) + max_z * sin(angle1) + self.y
+
+        z4 = (
+            -(-min_x) * sin(angle2)
+            - (-min_y) * sin(angle1) * cos(angle2)
+            + max_z * cos(angle1) * cos(angle2)
+            + self.z
+        )
+
+        # Create points
+        p1 = [x1, y1, z1]
+        p2 = [x2, y2, z2]
+        p3 = [x3, y3, z3]
+        p4 = [x4, y4, z4]
+        box = {"p1": p1, "p2": p2, "p3": p3, "p4": p4}
+
+        with open(filename, "w") as f:
+            toml.dump(box, f)
+
+        return filename
+
+    def _help(self, mainwindow: QMainWindow) -> None:
+        """
+        Display help information about the box operations.
+        """
+        text = QCoreApplication.translate(
+            "pyKVFinder",
+            '
          Box Adjustment mode:
          - Create a selection (optional);
          - Define a Padding (optional);
          - Click on Draw Box button.

          Customize your box:
          - Change one item at a time (e.g. Padding, Minimum X, Maximum X, ...);
          - Click on Redraw Box button.
          Delete box:
          - Click on Delete Box button.
          Colors of the box object:
          - Red corresponds to X axis;
          - Green corresponds to Y axis;
          - Blue corresponds to Z axis.
          ',
+            None,
+        )
+        help_information = QMessageBox(mainwindow)
+        help_information.setText(text)
+        help_information.setWindowTitle("Help")
+        help_information.setStyleSheet("QLabel{min-width:500 px;}")
+        help_information.exec_()
diff --git a/plugins/PyMOL-pyKVFinder-Tools/gui.py b/plugins/PyMOL-pyKVFinder-Tools/gui.py
new file mode 100644
index 00000000..857a9dea
--- /dev/null
+++ b/plugins/PyMOL-pyKVFinder-Tools/gui.py
@@ -0,0 +1,674 @@
+# This source code is part of the pyKVFinder package and is distributed
+# under the GNU GPL-3.0 license. Please see 'LICENSE' for further
+# information.
+
+"""
+This is the source code for the graphical user interface of PyMOL pyKVFinder
+Tools. The code is written in Python and uses the PyQt5 library for the
+graphical user interface. Changes in this file are not advised, as it
+controls all interactions with pyKVFinder.
+"""
+
+import os
+import time
+
+import toml
+from pymol import cmd
+from PyQt5.QtWidgets import QCheckBox, QMainWindow, QMessageBox, QScrollBar
+from PyQt5.uic import loadUi
+
+import pyKVFinder
+
+from .actions import (
+    _load_area,
+    _load_avg_depth,
+    _load_avg_hydropathy,
+    _load_cavity_file,
+    _load_max_depth,
+    _load_molecule_file,
+    _load_residues,
+    _load_volume,
+    _refresh_list,
+    _select_directory,
+    _select_file,
+)
+from .box import Box
+from .visualization import (
+    _show_cavities,
+    _show_depth,
+    _show_descriptors,
+    _show_hydropathy,
+    _show_residues,
+)
+
+
+class PyMOLpyKVFinderTools(QMainWindow):
+    """
+    PyMOL pyKVFinder Tools. This class is the main window for the pyKVFinder
+    plugin. It contains all the widgets and methods to interact with the
+    plugin.
+    """
+
+    def __init__(self) -> None:
+        super().__init__()
+        # Initialize GUI
+        self._initialize_gui()
+
+        # Restore default values
+        self._startup()
+
+        # Startup custom grid
+        self.box = Box()
+
+        # Results
+        global results
+        results = None
+        self.pyKVFindeResults = None
+        self.input_pdb = None
+        self.ligand_pdb = None
+        self.cavity_pdb = None
+
+    def _initialize_gui(self) -> None:
+        """
+        Initialize the graphical user interface of the plugin.
+        """
+        # populate the QMainWindow from our *.ui file
+        uifile = os.path.join(os.path.dirname(__file__), "PyMOL-pyKVFinder-Tools.ui")
+        loadUi(uifile, self)
+
+        # Dialog buttons binds
+        self.button_run.clicked.connect(self.run)
+        self.button_exit.clicked.connect(self.close)
+        self.button_surface.clicked.connect(self.model_surface)
+        self.button_restore.clicked.connect(self.restore)
+
+        # ScrollBars binded to QListWidgets in Descriptors
+        scroll_bar_volume = QScrollBar(self)
+        self.volume_list.setVerticalScrollBar(scroll_bar_volume)
+        scroll_bar_area = QScrollBar(self)
+        self.area_list.setVerticalScrollBar(scroll_bar_area)
+        scroll_bar_residues = QScrollBar(self)
+        self.residues_list.setVerticalScrollBar(scroll_bar_residues)
+
+        # Browse buttons
+        self.button_browse_basedir.clicked.connect(
+            lambda: _select_directory(self.basedir)
+        )
+        self.button_browse_vdw.clicked.connect(
+            lambda: _select_file("Choose van der Waals radii dictionary", "*", self.vdw)
+        )
+        self.button_browse_results.clicked.connect(
+            lambda: _select_file(
+                "Choose KVFinder Results File",
+                "KVFinder Results File (*.toml);;All files (*)",
+                self.results_file_entry,
+            )
+        )
+
+        # Surface representation bindings in Main Tab
+        self.surface.currentIndexChanged.connect(self._surface_selection)
+
+        # Box Adjustment
+        self.button_draw_box.clicked.connect(
+            lambda: self.box._set_box(
+                self.button_draw_box,
+                self.button_redraw_box,
+                self.min_x,
+                self.max_x,
+                self.min_y,
+                self.max_y,
+                self.min_z,
+                self.max_z,
+                self.angle1,
+                self.angle2,
+                self.padding,
+            )
+        )
+        self.button_delete_box.clicked.connect(
+            lambda: self.box._delete_box(
+                self.button_draw_box,
+                self.button_redraw_box,
+                self.min_x,
+                self.max_x,
+                self.min_y,
+                self.max_y,
+                self.min_z,
+                self.max_z,
+                self.angle1,
+                self.angle2,
+            )
+        )
+        self.button_redraw_box.clicked.connect(
+            lambda: self.box._redraw_box(
+                self.min_x,
+                self.max_x,
+                self.min_y,
+                self.max_y,
+                self.min_z,
+                self.max_z,
+                self.angle1,
+                self.angle2,
+                self.padding,
+            )
+        )
+        self.button_box_adjustment_help.clicked.connect(lambda: self.box._help(self))
+
+        # Refresh the list of objects in the input and ligand widgets
+        self.refresh_input.clicked.connect(lambda: _refresh_list(self.input))
+        self.refresh_ligand.clicked.connect(lambda: _refresh_list(self.ligand))
+
+        # Visualization in results tab
+        self.button_load_results.clicked.connect(self._load_run)
+        self.volume_list.itemSelectionChanged.connect(
+            lambda: _show_cavities(self.volume_list, self.area_list, self.cavity_pdb)
+        )
+        self.area_list.itemSelectionChanged.connect(
+            lambda: _show_cavities(self.area_list, self.volume_list, self.cavity_pdb)
+        )
+        self.residues_list.itemSelectionChanged.connect(
+            lambda: _show_residues(results, self.residues_list, self.input_pdb)
+        )
+        self.avg_depth_list.itemSelectionChanged.connect(
+            lambda: _show_depth(
+                self.avg_depth_list, self.max_depth_list, self.cavity_pdb
+            )
+        )
+        self.max_depth_list.itemSelectionChanged.connect(
+            lambda: _show_depth(
+                self.max_depth_list, self.avg_depth_list, self.cavity_pdb
+            )
+        )
+        self.avg_hydropathy_list.itemSelectionChanged.connect(
+            lambda: _show_hydropathy(results, self.avg_hydropathy_list, self.cavity_pdb)
+        )
+        self.default_view.toggled.connect(
+            lambda: _show_descriptors(self.cavity_pdb, "default")
+        )
+        self.depth_view.toggled.connect(
+            lambda: _show_descriptors(self.cavity_pdb, "depth")
+        )
+        self.hydropathy_view.toggled.connect(
+            lambda: _show_descriptors(self.cavity_pdb, "hydropathy", results)
+        )
+
+    def _surface_selection(self) -> None:
+        """
+        Get the surface selection from the GUI. This method is called when the
+        user selects a surface type in the GUI.
+        """
+        # Get the surface type
+        surface = self.surface.currentText()[:-1][-3:]
+        if surface == "vdW":
+            self.probe_in.setValue(0.0)
+            self.probe_in.setEnabled(False)
+        elif surface == "SES":
+            self.probe_in.setValue(1.4)
+            self.probe_in.setEnabled(True)
+        elif surface == "SAS":
+            self.probe_in.setValue(1.4)
+            self.probe_in.setEnabled(True)
+
+    def _restore_results(self, remove_inputs: bool) -> None:
+        """
+        Restore the results tab to the default values. This method is called
+        when the user clicks the 'Restore Defaults' button in the GUI.
+        """
+        # Remove cavities, residues and pdbs (input, ligand, cavity)
+        cmd.delete("cavities")
+        cmd.delete("residues")
+        if self.input_pdb and remove_inputs:
+            cmd.delete(self.input_pdb)
+        if self.ligand_pdb and remove_inputs:
+            cmd.delete(self.ligand_pdb)
+        if self.cavity_pdb:
+            cmd.delete(self.cavity_pdb)
+        results = self.input_pdb = self.ligand_pdb = self.cavity_pdb = None
+        cmd.frame(1)
+
+        # Clean results
+        self._clean_results_tab()
+        self.results_file_entry.clear()
+
+    def _startup(self) -> None:
+        """
+        Set the default values for the widgets in the GUI. This method is
+        called when the plugin is started.
+        """
+        # Startup Main tab
+        _refresh_list(self.input)
+        self.step_size.setValue(0.6)
+        self.probe_in.setValue(1.4)
+        self.probe_out.setValue(4.0)
+        self.removal_distance.setValue(2.4)
+        self.volume_cutoff.setValue(5.0)
+        self.surface.setCurrentIndex(1)  # 0: vdW, 1: SES, 2: SAS
+        self.basename.setText("output")
+        self.basedir.setText(os.getcwd())
+        self.vdw.setText(
+            os.path.join(os.path.dirname(pyKVFinder.__file__), "data", "vdw.dat")
+        )
+
+        # Startup Box Adjustment tab
+        self.box_adjustment.setChecked(False)
+        self.padding.setValue(3.5)
+        # self._delete_box() # TODO: Implement this method
+
+        # Startup Ligand Adjustment tab
+        self.ligand_adjustment.setChecked(False)
+        self.ligand.clear()
+        self.ligand_cutoff.setValue(5.0)
+
+    def closeEvent(self, event) -> None:
+        """
+        Exit the plugin. This method is called when the user clicks the 'Exit'
+        button in the GUI.
+        """
+        global dialog
+        dialog = None
+
+    def restore(self) -> None:
+        """
+        Restore the default values for the widgets in the GUI. This method is
+        called when the user clicks the 'Restore Defaults' button in the GUI.
+        """
+        # Restore to startup values
+        self._startup()
+
+        # Restore results tab
+        reply = QMessageBox(self)
+        reply.setText("Also restore Results Visualization tab?")
+        reply.setWindowTitle("Restore Values")
+        reply.setStandardButtons(QMessageBox.Yes | QMessageBox.No)
+        reply.setIcon(QMessageBox.Information)
+        reply.checkbox = QCheckBox("Also remove input and ligand PDBs?")
+        reply.layout = reply.layout()
+        reply.layout.addWidget(reply.checkbox, 1, 2)
+        if reply.exec_() == QMessageBox.Yes:
+            self._restore_results(reply.checkbox.isChecked())
+
+    def _get_parameters(self) -> dict:
+        """
+        Get the parameters from the GUI. This method is called when the user
+        clicks the 'Run pyKVFinder' button in the GUI. It will return a
+        dictionary with the parameters to run pyKVFinder.
+
+        Returns
+        -------
+        dict
+            The parameters to run pyKVFinder.
+        """
+        # TODO: Add box parameters. Fix me.
+        # Get the parameters from the GUI
+        parameters = {
+            "input": os.path.join(
+                self.basedir.text(),
+                self.basename.text(),
+                f"{self.input.currentText()}.pdb",
+            ),
+            "ligand": (
+                os.path.join(
+                    self.basedir.text(),
+                    self.basename.text(),
+                    f"{self.ligand.currentText()}.pdb",
+                )
+                if self.ligand.currentText() != ""
+                else None
+            ),
+            "step": self.step_size.value(),
+            "probe_in": self.probe_in.value(),
+            "probe_out": self.probe_out.value(),
+            "removal_distance": self.removal_distance.value(),
+            "volume_cutoff": self.volume_cutoff.value(),
+            "surface": (
+                "SES"
+                if self.surface.currentText()[:-1][-3:] == "vdW"
+                else self.surface.currentText()[:-1][-3:]
+            ),
+            "basename": self.basename.text(),
+            "basedir": os.path.join(self.basedir.text(), self.basename.text()),
+            "vdw": self.vdw.text(),
+            "box": (
+                self.box._create_box_file(
+                    os.path.join(
+                        self.basedir.text(),
+                        self.basename.text(),
+                        f"box.{self.basename.text()}.toml",
+                    )
+                )
+                if self.box_adjustment.isChecked()
+                else None
+            ),
+            "padding": self.padding.value(),
+            "ligand_adjustment": self.ligand_adjustment.isChecked(),
+            "ligand_cutoff": self.ligand_cutoff.value(),
+            "hydrophobicity_scale": self.hscale.currentText().replace(" & ", ""),
+            "ignore_backbone": self.ignore_backbone.isChecked(),
+        }
+
+        return parameters
+
+    def _prepare_run(self, parameters: dict) -> bool:
+        """
+        Prepare the plugin to run pyKVFinder. This method is called when the
+        user clicks the 'Run pyKVFinder' button in the GUI. It will check if
+        the input files are valid and if the output directory is writable.
+
+        Parameters
+        ----------
+        parameters : dict
+            The parameters to run pyKVFinder.
+        """
+        # Create basedir if it does not exist
+        os.makedirs(parameters["basedir"], exist_ok=True)
+
+        # Save input pdb file
+        if self.input.currentText() != "":
+            for obj in cmd.get_names("all"):
+                if obj == self.input.currentText():
+                    cmd.save(parameters["input"], self.input.currentText(), 0, "pdb")
+        else:
+            QMessageBox.critical(
+                self, "Error", "Please select an input.", QMessageBox.Ok
+            )
+            return False
+
+        # Save ligand pdb file
+        if self.ligand_adjustment.isChecked():
+            if self.ligand.currentText() != "":
+                for obj in cmd.get_names("all"):
+                    if obj == self.ligand.currentText():
+                        cmd.save(
+                            parameters["ligand"], self.ligand.currentText(), 0, "pdb"
+                        )
+            else:
+                QMessageBox.critical(
+                    self, "Error", "Please select a ligand.", QMessageBox.Ok
+                )
+                return False
+
+        # Check box adjustment mode
+        if self.box_adjustment.isChecked():
+            if "box" not in cmd.get_names("all"):
+                QMessageBox.critical(self, "Error", "Draw a box in PyMOL!")
+                return False
+
+        # Save parameters file
+        with open(
+            os.path.join(
+                parameters["basedir"], f'{parameters["basename"]}.parameters.toml'
+            ),
+            "w",
+        ) as f:
+            toml.dump(parameters, f)
+
+        return True
+
+    def _load_run(self) -> None:
+        """
+        Load the results of pyKVFinder into PyMOL. This method is called after
+        running pyKVFinder. It will load the cavities and the results into
+        PyMOL.
+        """
+        # Get results file
+        results_file = self.results_file_entry.text()
+
+        # Check if results file exist
+        if os.path.exists(results_file) and results_file.endswith(".toml"):
+            print(f"> Loading results from: {results_file}")
+        else:
+            QMessageBox.critical(
+                self, "Error", "Results file cannot be opened! Check results file path."
+            )
+
+        # Create global variable for results
+        global results
+
+        # Read results (Ubuntu/macOS)
+        results = toml.load(results_file)
+
+        # Clean results tab
+        self._clean_results_tab()
+
+        # Load file information
+        self._load_file_information()
+
+        # Load characterization (volume, area, depth, residues and hydropathy)
+        _load_volume(results, self.volume_list)
+        _load_area(results, self.area_list)
+        _load_avg_depth(results, self.avg_depth_list)
+        _load_max_depth(results, self.max_depth_list)
+        _load_avg_hydropathy(results, self.avg_hydropathy_list)
+        _load_residues(results, self.residues_list)
+
+        # Set default view in results
+        self.default_view.setChecked(True)
+
+        # Remove previous objects from PyMOL
+        objects = cmd.get_names("all")
+        for obj in ["cavities", "residues", "depth", "hydropathy"]:
+            if obj in objects:
+                cmd.delete(obj)
+        cmd.frame(1)
+
+        # Load input file
+        if "INPUT" in results["FILES"].keys():
+            self.input_pdb = os.path.basename(results["FILES"]["INPUT"]).replace(
+                ".pdb", ""
+            )
+            _load_molecule_file(results["FILES"]["INPUT"], self.input_pdb)
+        else:
+            self.input_pdb = None
+
+        # Load ligand file
+        if "LIGAND" in results["FILES"].keys():
+            self.ligand_pdb = os.path.basename(results["FILES"]["LIGAND"]).replace(
+                ".pdb", ""
+            )
+            _load_molecule_file(results["FILES"]["LIGAND"], self.ligand_pdb)
+        else:
+            self.ligand_pdb = None
+
+        # Load cavities file
+        self.cavity_pdb = os.path.basename(results["FILES"]["OUTPUT"]).replace(
+            ".pdb", ""
+        )
+        _load_cavity_file(results["FILES"]["OUTPUT"], self.cavity_pdb)
+
+    def _load_file_information(self) -> None:
+        """
+        Load the file information into the results tab. This method is called
+        after running pyKVFinder. It will load the file information into the
+        results tab.
+        """
+        if "INPUT" in results["FILES"].keys():
+            self.input_file_entry.setText(f"{results['FILES']['INPUT']}")
+        else:
+            self.input_file_entry.setText(f"")
+
+        # Ligand File
+        if "LIGAND" in results["FILES"].keys():
+            self.ligand_file_entry.setText(f"{results['FILES']['LIGAND']}")
+        else:
+            self.ligand_file_entry.setText(f"")
+
+        # Cavities File
+        self.cavities_file_entry.setText(f"{results['FILES']['OUTPUT']}")
+
+        # Step Size
+        if "PARAMETERS" in results.keys():
+            if "STEP" in results["PARAMETERS"].keys():
+                self.step_size_entry.setText(f"{results['PARAMETERS']['STEP']:.2f}")
+
+    def _clean_results_tab(self) -> None:
+        """
+        Clean the results tab. This method is called before loading the results
+        of pyKVFinder into PyMOL. It will clear the lists in the results tab.
+        """
+        # Input File
+        self.input_file_entry.setText(f"")
+
+        # Ligand File
+        self.ligand_file_entry.setText(f"")
+
+        # Cavities File
+        self.cavities_file_entry.setText(f"")
+
+        # Step Size
+        self.step_size_entry.setText(f"")
+
+        # Volume
+        self.volume_list.clear()
+
+        # Area
+        self.area_list.clear()
+
+        # Depth
+        self.avg_depth_list.clear()
+        self.max_depth_list.clear()
+
+        # Hydropathy
+        self.avg_hydropathy_list.clear()
+
+        # Residues
+        self.residues_list.clear()
+
+    def model_surface(self) -> None:
+        """
+        Model the surface of the input. This method is called when the user
+        clicks the 'Model Surface' button in the GUI. It will model the surface
+        of the input structure in PyMOL.
+        """
+        # Get parameters from the GUI
+        parameters = self._get_parameters()
+
+        # Save input pdb file
+        if self.input.currentText() != "":
+            for obj in cmd.get_names("all"):
+                if obj == self.input.currentText():
+                    cmd.save(parameters["input"], self.input.currentText(), 0, "pdb")
+        else:
+            QMessageBox.critical(
+                self, "Error", "Please select an input.", QMessageBox.Ok
+            )
+            return False
+
+        # Load molecule
+        surface = pyKVFinder.Molecule(
+            molecule=parameters["input"], radii=parameters["vdw"]
+        )
+
+        # Model the surface
+        if parameters["surface"] == "vdW":
+            surface.vdw(step=parameters["step"])
+        elif parameters["surface"] == "SES":
+            surface.surface(
+                step=parameters["step"],
+                probe=parameters["probe_in"],
+                surface=parameters["surface"],
+            )
+        elif parameters["surface"] == "SAS":
+            surface.surface(
+                step=parameters["step"],
+                probe=parameters["probe_in"],
+                surface=parameters["surface"],
+            )
+
+        # Save surface file
+        pymolname = f"{parameters['basename']}.KVFinder.surface"
+        filename = os.path.join(parameters["basedir"], f"{pymolname}.pdb")
+        surface.export(filename)
+
+        # Remove previous results in objects with same cavity name
+        for obj in cmd.get_names("all"):
+            if pymolname == obj:
+                cmd.delete(obj)
+
+        # Load the cavity file
+        cmd.load(filename, pymolname, zoom=0)
+
+        # Hide and show to update the display
+        cmd.hide("everything", pymolname)
+        cmd.show("sphere", pymolname)
+        cmd.alter(pymolname, f"vdw={parameters['step'] / 2}")
+        cmd.rebuild()
+
+    def run(self) -> bool:
+        """
+        Run pyKVFinder with the current parameters. This method is called when
+        the user clicks the 'Run pyKVFinder' button in the GUI. After
+        completion, it will display the results in the GUI.
+        """
+        # Get parameters from the GUI
+        parameters = self._get_parameters()
+
+        # Prepare parameters to run pyKVFinder
+        if not self._prepare_run(parameters):
+            QMessageBox.critical(
+                self,
+                "Error!",
+                "An error occurred while preparing the run. Please check the \
+parameters.",
+                QMessageBox.Ok,
+            )
+            return False
+
+        # Print the current status for users
+        print(f"[==> Running pyKVFinder for {self.input.currentText()} ...")
+        start_time = time.time()
+
+        # Run pyKVFinder
+        self.pyKVFindeResults = pyKVFinder.run_workflow(
+            input=parameters["input"],
+            ligand=parameters["ligand"],
+            vdw=parameters["vdw"],
+            box=parameters["box"],
+            step=parameters["step"],
+            probe_in=parameters["probe_in"],
+            probe_out=parameters["probe_out"],
+            removal_distance=parameters["removal_distance"],
+            volume_cutoff=parameters["volume_cutoff"],
+            ligand_cutoff=parameters["ligand_cutoff"],
+            include_depth=True,
+            include_hydropathy=True,
+            hydrophobicity_scale=parameters["hydrophobicity_scale"],
+            surface=parameters["surface"],
+            ignore_backbone=parameters["ignore_backbone"],
+        )
+
+        # Export results and cavities to file
+        results_file = os.path.join(
+            parameters["basedir"],
+            f"{parameters['basename']}.KVFinder.results.toml",
+        )
+        cavity_file = os.path.join(
+            parameters["basedir"],
+            f"{parameters['basename']}.KVFinder.output.pdb",
+        )
+        self.pyKVFindeResults.export_all(
+            fn=results_file,
+            output=cavity_file,
+            include_frequencies_pdf=False,
+        )
+
+        # Elapsed time
+        elapsed_time = time.time() - start_time
+        print(f"> Cavities detected: {self.pyKVFindeResults.ncav}")
+        print(f"> Elapsed time: {elapsed_time:.2f} seconds")
+
+        # Set the results filename in the GUI
+        self.results_file_entry.setText(results_file)
+        self.tabs.setCurrentIndex(2)
+
+        # Sucessful run
+        if self.pyKVFindeResults.ncav > 0:
+            self._load_run()
+        # Unsucessful run
+        elif self.pyKVFindeResults.ncav == 0:
+            QMessageBox.warning(
+                self,
+                "Warning",
+                "No cavities were detected. Please check the parameters.",
+                QMessageBox.Ok,
+            )
+
+        return True
diff --git a/plugins/PyMOL-pyKVFinder-Tools/pyKVFinder.ico b/plugins/PyMOL-pyKVFinder-Tools/pyKVFinder.ico
new file mode 100644
index 00000000..6e6d1131
Binary files /dev/null and b/plugins/PyMOL-pyKVFinder-Tools/pyKVFinder.ico differ
diff --git a/plugins/PyMOL-pyKVFinder-Tools/visualization.py b/plugins/PyMOL-pyKVFinder-Tools/visualization.py
new file mode 100644
index 00000000..c9e3bb11
--- /dev/null
+++ b/plugins/PyMOL-pyKVFinder-Tools/visualization.py
@@ -0,0 +1,348 @@
+# This source code is part of the pyKVFinder package and is distributed
+# under the GNU GPL-3.0 license. Please see 'LICENSE' for further
+# information.
+
+"""
+This is the source code for the visualization embedded in PyMOL 
+pyKVFinder Tools. Changes in this file are not advised, as it controls
+interactions with pyKVFinder and PyQt5.
+"""
+
+from pymol import cmd
+from PyQt5.QtWidgets import QListWidget
+
+
+def _show_residues(results: dict, widget: QListWidget, input_pdb: str) -> None:
+    """
+    Show the residues for the selected cavity.
+
+    Parameters
+    ----------
+    results : dict
+        The results from the pyKVFinder calculation.
+    widget : QListWidget
+        The widget to display the results.
+    """
+
+    # Get the selected cavity
+    indexes = [item.text() for item in widget.selectedItems()]
+
+    # Clean objects
+    cmd.set("auto_zoom", 0)
+    cmd.delete("res")
+    cmd.delete("residues")
+
+    # Return if no cavity is selected
+    if len(indexes) < 1:
+        return
+
+    # Get residues from selected cavities
+    residues = []
+    for index in indexes:
+        for residue in results["RESULTS"]["RESIDUES"][index]:
+            if residue not in residues:
+                residues.append(residue)
+
+    # Check if input pdb is loaded
+    control = 0
+    for item in cmd.get_names("all"):
+        if item == input_pdb:
+            control = 1
+            break
+    if control == 0:
+        return
+
+    # Select residues
+    command = ""
+    while len(residues) > 0:
+        res, chain, _ = residues.pop(0)
+        command = f"{command} (resid {res} and chain {chain}) or"
+    command = f"obj {input_pdb} and ({command[:-3]})"
+    cmd.select("res", command)
+
+    # Create residues object and show
+    cmd.create("residues", "res")
+    cmd.delete("res")
+    cmd.hide("everything", "residues")
+    cmd.show("sticks", "residues")
+    cmd.set("auto_zoom", 1)
+
+
+def _show_cavities(widget1: QListWidget, widget2: QListWidget, cavity_pdb: str):
+    """
+    Show the selected cavities in Volume and Area lists. Surface cavity points are
+    colored in red and remaining points are colored in blue.
+
+    Parameters
+    ----------
+    widget1 : QListWidget
+        The widget 1.
+    widget2 : QListWidget
+        The widget 2.
+    cavity_pdb : str
+        The name of the cavity pdb.
+    """
+    # Get items from widget1
+    indexes = [item.text()[0:3] for item in widget1.selectedItems()]
+
+    # Select items from widget2
+    for index in range(widget1.count()):
+        if widget2.item(index).text()[0:3] in indexes:
+            widget2.item(index).setSelected(True)
+        else:
+            widget2.item(index).setSelected(False)
+
+    # Clean objects
+    cmd.set("auto_zoom", 0)
+    cmd.delete("cavs")
+    cmd.delete("cavities")
+
+    # Return if no cavity is selected
+    if len(indexes) < 1:
+        return
+
+    # Check if cavity file is loaded
+    control = 0
+    for item in cmd.get_names("all"):
+        if item == cavity_pdb:
+            control = 1
+            break
+    if control == 0:
+        return
+
+    # Color filling cavity points as blue nonbonded
+    command = f"obj {cavity_pdb} and (resname "
+    while len(indexes) > 0:
+        command = f"{command}{indexes.pop(0)},"
+    command = f"{command[:-1]})"
+    cmd.select("cavs", command)
+
+    # Create cavities object with blue nonbonded
+    cmd.create("cavities", "cavs")
+    cmd.delete("cavs")
+    cmd.color("blue", "cavities")
+    cmd.show("nonbonded", "cavities")
+
+    # Color surface cavity points as red nb_spheres
+    cmd.select("cavs", "cavities and name HA")
+    cmd.color("red", "cavs")
+    cmd.show("nb_spheres", "cavs")
+    cmd.delete("cavs")
+
+    # Reset cavities output object
+    cmd.disable(cavity_pdb)
+    cmd.enable(cavity_pdb)
+    for item in cmd.get_names("all"):
+        if item == "hydropathy":
+            cmd.disable("hydropathy")
+            cmd.enable("hydropathy")
+        if item == "depths":
+            cmd.disable("depths")
+            cmd.enable("depths")
+    cmd.set("auto_zoom", 1)
+
+
+def _show_depth(widget1: QListWidget, widget2: QListWidget, cavity_pdb: str) -> None:
+    """
+    Show the selected cavities colored by depth in Max Depth and Avg Depth lists.
+
+    Parameters
+    ----------
+    widget1 : QListWidget
+        The widget 1.
+    widget2 : QListWidget
+        The widget 2.
+    cavity_pdb : str
+        The name of the cavity pdb.
+    """
+    # Get items from widget1
+    indexes = [item.text()[0:3] for item in widget1.selectedItems()]
+
+    # Select items from widget2
+    for index in range(widget1.count()):
+        if widget2.item(index).text()[0:3] in indexes:
+            widget2.item(index).setSelected(True)
+        else:
+            widget2.item(index).setSelected(False)
+
+    # Clean objects
+    cmd.set("auto_zoom", 0)
+    cmd.delete("deps")
+    cmd.delete("depths")
+
+    # Return if no cavity is selected
+    if len(indexes) < 1:
+        return
+
+    # Check if cavity file is loaded
+    control = 0
+    for item in cmd.get_names("all"):
+        if item == cavity_pdb:
+            control = 1
+            break
+    if control == 0:
+        return
+
+    # Color filling cavity points as blue nonbonded
+    command = f"obj {cavity_pdb} and (resname "
+    while len(indexes) > 0:
+        command = f"{command}{indexes.pop(0)},"
+    command = f"{command[:-1]})"
+    cmd.select("deps", command)
+
+    # Create cavities object with blue nonbonded
+    cmd.create("depths", "deps")
+    cmd.delete("deps")
+    cmd.spectrum("b", "rainbow", "depths")
+    cmd.show("nb_spheres", "depths")
+
+    # Reset cavities output object
+    cmd.disable(cavity_pdb)
+    for item in cmd.get_names("all"):
+        if item == "cavities":
+            cmd.disable("cavities")
+            cmd.enable("cavities")
+        if item == "depths":
+            cmd.disable("hydropathy")
+            cmd.enable("hydropathy")
+    cmd.enable(cavity_pdb)
+    cmd.set("auto_zoom", 1)
+
+
+def _show_hydropathy(results: dict, widget: QListWidget, cavity_pdb: str) -> None:
+    """
+    Show the selected cavities colored by hydropathy in Avg Hydropathy list.
+
+    Parameters
+    ----------
+    results : dict
+        The results from the pyKVFinder calculation.
+    widget1 : QListWidget
+        The widget 1.
+    widget2 : QListWidget
+        The widget 2.
+    cavity_pdb : str
+        The name of the cavity pdb.
+    """
+    # Get items from list1
+    indexes = [item.text()[0:3] for item in widget.selectedItems()]
+
+    # Clean objects
+    cmd.set("auto_zoom", 0)
+    cmd.delete("hyd")
+    cmd.delete("hydropathy")
+
+    # Return if no cavity is selected
+    if len(indexes) < 1:
+        return
+
+    # Check if cavity file is loaded
+    control = 0
+    for item in cmd.get_names("all"):
+        if item == cavity_pdb:
+            control = 1
+            break
+    if control == 0:
+        return
+
+    # Color filling cavity points as blue nonbonded
+    command = f"obj {cavity_pdb} and (resname "
+    while len(indexes) > 0:
+        command = f"{command}{indexes.pop(0)},"
+    command = f"{command[:-1]}) and (name HA+HS)"
+    cmd.select("hyd", command)
+
+    # Get minimum and maximum of hydropathy scale
+    hydropathy_scales = [
+        "EisenbergWeiss",
+        "HessaHeijne",
+        "KyteDoolittle",
+        "RadzickaWolfenden",
+        "MoonFleming",
+        "WimleyWhite",
+        "ZhaoLondon",
+    ]
+    minimum, maximum = None, None
+    for hscale in hydropathy_scales:
+        if hscale in results["RESULTS"]["AVG_HYDROPATHY"]:
+            minimum, maximum = results["RESULTS"]["AVG_HYDROPATHY"][hscale]
+            break
+
+    # Create cavities object with blue nonbonded
+    cmd.create("hydropathy", "hyd")
+    cmd.delete("hyd")
+    cmd.spectrum(
+        "q", "yellow_white_blue", "hydropathy", minimum=minimum, maximum=maximum
+    )
+    cmd.show("nb_spheres", "hydropathy")
+
+    # Reset cavities output object
+    cmd.disable(cavity_pdb)
+    for item in cmd.get_names("all"):
+        if item == "cavities":
+            cmd.disable("cavities")
+            cmd.enable("cavities")
+        if item == "depths":
+            cmd.disable("depths")
+            cmd.enable("depths")
+    cmd.enable(cavity_pdb)
+    cmd.set("auto_zoom", 1)
+
+
+def _show_descriptors(cavity_pdb: str, view: str, results: dict = None) -> None:
+    """
+    Show the cavity file colored by descriptors (default, depth, hydropathy).
+
+    Parameters
+    ----------
+    cavity_pdb : str
+        The name of the cavity pdb.
+    view : str
+        The type of view to display ('default', 'depth', 'hydropathy').
+    results : dict, optional
+        The results from the pyKVFinder calculation, required for hydropathy view.
+    """
+    # Clean objects
+    cmd.set("auto_zoom", 0)
+    cmd.delete("view")
+
+    # Check if cavity file is loaded
+    control = 0
+    for item in cmd.get_names("all"):
+        if item == cavity_pdb:
+            control = 1
+    if control == 0:
+        return
+
+    # Color filling cavity points as blue nonbonded
+    command = f"obj {cavity_pdb} and (name H+HA)"
+    command = f"{command[:-1]})"
+    cmd.select("view", command)
+
+    if view == "default":
+        cmd.show("nonbonded", "view")
+        cmd.color("white", "view")
+    elif view == "depth":
+        cmd.show("nonbonded", "view")
+        cmd.spectrum("b", "rainbow", "view")
+    elif view == "hydropathy" and results is not None:
+        # Get minimum and maximum of hydropathy scale
+        hydropathy_scales = [
+            "EisenbergWeiss",
+            "HessaHeijne",
+            "KyteDoolittle",
+            "RadzickaWolfenden",
+            "MoonFleming",
+            "WimleyWhite",
+            "ZhaoLondon",
+        ]
+        minimum, maximum = None, None
+        for hscale in hydropathy_scales:
+            if hscale in results["RESULTS"]["AVG_HYDROPATHY"]:
+                minimum, maximum = results["RESULTS"]["AVG_HYDROPATHY"][hscale]
+                break
+
+        cmd.show("nonbonded", "view")
+        cmd.spectrum("q", "yellow_white_blue", "view", minimum=minimum, maximum=maximum)
+
+    cmd.delete("view")
diff --git a/pyKVFinder/__init__.py b/pyKVFinder/__init__.py
index d1b0684d..3730a5b9 100644
--- a/pyKVFinder/__init__.py
+++ b/pyKVFinder/__init__.py
@@ -31,7 +31,7 @@
 """
 
 __name__ = "pyKVFinder"
-__version__ = "0.6.16"
+__version__ = "0.7.0"
 license = "GNU GPL-3.0 License"
 
 from .utils import *
diff --git a/pyKVFinder/utils.py b/pyKVFinder/utils.py
index 56798bb0..27f8d778 100644
--- a/pyKVFinder/utils.py
+++ b/pyKVFinder/utils.py
@@ -945,7 +945,7 @@ def plot_frequencies(
     {'KAA': {'RESIDUES': {'ALA': 1, 'ARG': 1, 'ASN': 1, 'ASP': 2, 'GLN': 1, 'GLU': 4, 'GLY': 4, 'HIS': 1, 'LEU': 3, 'LYS': 2, 'MET': 1, 'PHE': 3, 'SER': 1, 'THR': 4, 'TYR': 1, 'VAL': 3}, 'CLASS': {'R1': 11, 'R2': 4, 'R3': 8, 'R4': 6, 'R5': 4, 'RX': 0}}}
     >>> plot_frequencies(frequencies, fn='barplots.pdf')
 
-    .. image:: ../_images/barplots.png
+    .. image:: images/barplots.png
         :width: 600
         :align: center
     """
diff --git a/pyproject.toml b/pyproject.toml
index be262fa6..f6e21873 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -23,7 +23,7 @@ authors = [
 maintainers = [{ name = "João V. S. Guerra", email = "jvsguerra@gmail.com" }]
 license = { file = "LICENSE" }
 readme = { file = "README.md", content-type = "text/markdown" }
-requires-python = ">=3.9"
+requires-python = ">=3.10"
 keywords = [
     "structural biology",
     "proteins",
@@ -40,7 +40,6 @@ classifiers = [
     'Programming Language :: Python',
     'Programming Language :: Python :: 3',
     "Programming Language :: Python :: 3",
-    "Programming Language :: Python :: 3.9",
     "Programming Language :: Python :: 3.10",
     "Programming Language :: Python :: 3.11",
     "Programming Language :: Python :: 3.12",
@@ -64,6 +63,8 @@ dynamic = ["version"]
 
 [project.optional-dependencies]
 dev = ["pytest==8.3.3", "pytest-cov==5.0.0", "black==24.8.0", "flake8==7.1.1"]
+docs = ["sphinx==7.4.7", "sphinx-rtd-theme==2.0.0"]
+plugins = ["pyqt5~=5.15", "toml==0.10.2"]
 
 [project.urls]
 homepage = "https://github.com/LBC-LNBio/pyKVFinder/"
@@ -95,7 +96,7 @@ before-build = [
     "pip3 install certifi",
     "git clean -fxd build",
 ]
-build = ["cp39-*", "cp310-*", "cp311-*", "cp312-*"]
+build = ["cp310-*", "cp311-*", "cp312-*"]
 
 [tool.cibuildwheel.linux]
 archs = ["native"]