Releases: LBC-LNBio/pyKVFinder
pyKVFinder v0.7.2
Python-C parallel KVFinder
The Python-C parallel KVFinder (pyKVFinder) detects and characterizes cavities (shape, volume, area, depth, openings [WIP], hydropathy, and interface residues and their frequencies) in target biomolecular structures using a dual-probe system. In addition to cavity detection, pyKVFinder also estimates the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES), and solvent accessible surface (SAS) to represent the molecular surface.
Python package
The pyKVFinder package is easily imported into Python scripts with a set of functions that enables full and standard workflows and step-by-step analysis.
Command-line interface
The integrated command-line interface performs cavity detection and characterization with a customizable set of parameters. The standard characterization includes shape, volume, area, and interface residues and their frequencies. The optional characterizations are depth (per cavity point, maximum and average) and hydropathy (per surface point and average) with six options of built-in hydrophobicity scales (EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, RadzickaWolfenden, WimleyWhite, and ZhaoLondon).
What's Changed
- Bump pytest-cov from 5.0.0 to 6.0.0 by @dependabot in #138
- Bump sphinx-rtd-theme from 3.0.1 to 3.0.2 by @dependabot in #140
- Bump sphinxcontrib-video from 0.2.1 to 0.3.2 by @dependabot in #144
- Bump pytest from 8.3.3 to 8.3.4 by @dependabot in #141
- Update matplotlib requirement from ~=3.9.2 to ~=3.10.0 by @dependabot in #143
- Update numpy requirement from ~=2.1.2 to ~=2.2.1 by 80bc7a2
- [MNT] Update pyKVFinder build with cibuildwheel by @jvsguerra in #145
Full Changelog: v0.7.1...v0.7.2
Contributors
Assets 3
pyKVFinder v0.7.1
Python-C parallel KVFinder
The Python-C parallel KVFinder (pyKVFinder) detects and characterizes cavities (shape, volume, area, depth, openings [WIP], hydropathy, and interface residues and their frequencies) in target biomolecular structures using a dual-probe system. In addition to cavity detection, pyKVFinder also estimates the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES), and solvent accessible surface (SAS) to represent the molecular surface.
Python package
The pyKVFinder package is easily imported into Python scripts with a set of functions that enables full and standard workflows and step-by-step analysis.
Command-line interface
The integrated command-line interface performs cavity detection and characterization with a customizable set of parameters. The standard characterization includes shape, volume, area, and interface residues and their frequencies. The optional characterizations are depth (per cavity point, maximum and average) and hydropathy (per surface point and average) with six options of built-in hydrophobicity scales (EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, RadzickaWolfenden, WimleyWhite, and ZhaoLondon).
What's Changed
- Bump black from 24.8.0 to 24.10.0 by @dependabot in #136
- Add compatibility for Python 3.13
Full Changelog: v0.7.0...v0.7.1
Contributors
Assets 3
pyKVFinder v0.7.0
Python-C parallel KVFinder
The Python-C parallel KVFinder (pyKVFinder) detects and characterizes cavities (shape, volume, area, depth, openings [WIP], hydropathy, and interface residues and their frequencies) in target biomolecular structures using a dual-probe system. In addition to cavity detection, pyKVFinder also estimates the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES), and solvent accessible surface (SAS) to represent the molecular surface.
Python package
The pyKVFinder package is easily imported into Python scripts with a set of functions that enables full and standard workflows and step-by-step analysis.
Command-line interface
The integrated command-line interface performs cavity detection and characterization with a customizable set of parameters. The standard characterization includes shape, volume, area, and interface residues and their frequencies. The optional characterizations are depth (per cavity point, maximum and average) and hydropathy (per surface point and average) with six options of built-in hydrophobicity scales (EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, RadzickaWolfenden, WimleyWhite, and ZhaoLondon).
What's Changed
- [ENH] Add PyMOL plugin for pyKVFinder by @jvsguerra and @wapablos in #132
Full Changelog: v0.6.16...v0.7.0
Contributors
Assets 3
pyKVFinder v0.6.16
Python-C parallel KVFinder
The Python-C parallel KVFinder (pyKVFinder) detects and characterizes cavities (shape, volume, area, depth, openings [WIP], hydropathy, and interface residues and their frequencies) in target biomolecular structures using a dual-probe system. In addition to cavity detection, pyKVFinder also estimates the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES), and solvent accessible surface (SAS) to represent the molecular surface.
Python package
The pyKVFinder package is easily imported into Python scripts with a set of functions that enables full and standard workflows and step-by-step analysis.
Command-line interface
The integrated command-line interface performs cavity detection and characterization with a customizable set of parameters. The standard characterization includes shape, volume, area, and interface residues and their frequencies. The optional characterizations are depth (per cavity point, maximum and average) and hydropathy (per surface point and average) with six options of built-in hydrophobicity scales (EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, RadzickaWolfenden, WimleyWhite, and ZhaoLondon).
What's Changed
- Bump flake8 from 7.1.0 to 7.1.1 by @dependabot in #123
- Bump black from 24.4.2 to 24.8.0 by @dependabot in #124
- Bump matplotlib from 3.9.1 to 3.9.2 by @dependabot in #126
- Bump pytest from 8.3.2 to 8.3.3 by @dependabot in #130
- Bump plotly from 5.23.0 to 5.24.1 by @dependabot in #131
Full Changelog: v0.6.15...v0.6.16
Contributors
Assets 2
pyKVFinder v0.6.15
Python-C parallel KVFinder
The Python-C parallel KVFinder (pyKVFinder) detects and characterizes cavities (shape, volume, area, depth, openings [WIP], hydropathy, and interface residues and their frequencies) in target biomolecular structures using a dual-probe system. In addition to cavity detection, pyKVFinder also estimates the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES), and solvent accessible surface (SAS) to represent the molecular surface.
Python package
The pyKVFinder package is easily imported into Python scripts with a set of functions that enables full and standard workflows and step-by-step analysis.
Command-line interface
The integrated command-line interface performs cavity detection and characterization with a customizable set of parameters. The standard characterization includes shape, volume, area, and interface residues and their frequencies. The optional characterizations are depth (per cavity point, maximum and average) and hydropathy (per surface point and average) with six options of built-in hydrophobicity scales (EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, RadzickaWolfenden, WimleyWhite, and ZhaoLondon).
What's Changed
- Bump flake8 from 7.0.0 to 7.1.0 by @dependabot in #114
- Bump matplotlib from 3.9.0 to 3.9.1 by @dependabot in #117
- Bump plotly from 5.22.0 to 5.23.0 by @dependabot in #120
- Bump pytest from 8.2.2 to 8.3.2 by @dependabot in #121
Full Changelog: v0.6.14...v0.6.15
Contributors
Assets 2
pyKVFinder v0.6.14
Python-C parallel KVFinder
The Python-C parallel KVFinder (pyKVFinder) detects and characterizes cavities (shape, volume, area, depth, openings [WIP], hydropathy, and interface residues and their frequencies) in target biomolecular structures using a dual-probe system. In addition to cavity detection, pyKVFinder also estimates the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES), and solvent accessible surface (SAS) to represent the molecular surface.
Python package
The pyKVFinder package is easily imported into Python scripts with a set of functions that enables full and standard workflows and step-by-step analysis.
Command-line interface
The integrated command-line interface performs cavity detection and characterization with a customizable set of parameters. The standard characterization includes shape, volume, area, and interface residues and their frequencies. The optional characterizations are depth (per cavity point, maximum and average) and hydropathy (per surface point and average) with six options of built-in hydrophobicity scales (EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, RadzickaWolfenden, WimleyWhite, and ZhaoLondon).
What's Changed
- Bump matplotlib from 3.8.4 to 3.9.0 by @dependabot in #108
- Bump pytest from 8.2.0 to 8.2.2 by @dependabot in #109 and #111
- Add option to return PDB as a raw string in pyKVFinder.export function by @jvsguerra in #113
Full Changelog: v0.6.13...v0.6.14
Contributors
Assets 2
pyKVFinder v0.6.13
Python-C parallel KVFinder
The Python-C parallel KVFinder (pyKVFinder) detects and characterizes cavities (shape, volume, area, depth, openings [WIP], hydropathy, and interface residues and their frequencies) in target biomolecular structures using a dual-probe system. In addition to cavity detection, pyKVFinder also estimates the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES), and solvent accessible surface (SAS) to represent the molecular surface.
Python package
The pyKVFinder package is easily imported into Python scripts with a set of functions that enables full and standard workflows and step-by-step analysis.
Command-line interface
The integrated command-line interface performs cavity detection and characterization with a customizable set of parameters. The standard characterization includes shape, volume, area, and interface residues and their frequencies. The optional characterizations are depth (per cavity point, maximum and average) and hydropathy (per surface point and average) with six options of built-in hydrophobicity scales (EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, RadzickaWolfenden, WimleyWhite, and ZhaoLondon).
What's Changed
- Bump matplotlib from 3.8.2 to 3.8.3 by @dependabot in #85
- Bump plotly from 5.18.0 to 5.19.0 by @dependabot in #86
- Bump pytest from 8.0.0 to 8.0.1 by @dependabot in #87
- Bump pytest from 8.0.1 to 8.0.2 by @dependabot in #88
- Bump pytest from 8.0.2 to 8.1.0 by @dependabot in #89
- Bump pytest from 8.1.0 to 8.1.1 by @dependabot in #90
- Bump plotly from 5.19.0 to 5.20.0 by @dependabot in #91
- Bump black from 24.2.0 to 24.3.0 by @dependabot in #92
- Bump pytest-cov from 4.1.0 to 5.0.0 by @dependabot in #96
- Bump matplotlib from 3.8.3 to 3.8.4 by @dependabot in #97
- Bump black from 24.3.0 to 24.4.0 by @dependabot in #98
- Bump plotly from 5.20.0 to 5.21.0 by @dependabot in #99
- Bump black from 24.4.0 to 24.4.1 by @dependabot in #100
- Bump black from 24.4.1 to 24.4.2 by @dependabot in #101
- Bump pytest from 8.1.1 to 8.2.0 by @dependabot in #102
- Bump plotly from 5.21.0 to 5.22.0 by @dependabot in #103
- [MNT] Additions for Project Documentation and Code Quality Workflows by @jvsguerra in #105
- [MNT] Update deployment workflow and simplify pylint workflow by @jvsguerra in #106
Full Changelog: v0.6.12...v0.6.13
Contributors
Assets 2
pyKVFinder v0.6.12
Python-C parallel KVFinder
The Python-C parallel KVFinder (pyKVFinder) detects and characterizes cavities (shape, volume, area, depth, openings [WIP], hydropathy, and interface residues and their frequencies) in target biomolecular structures using a dual-probe system. In addition to cavity detection, pyKVFinder also estimates the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES), and solvent accessible surface (SAS) to represent the molecular surface.
Python package
The pyKVFinder package is easily imported into Python scripts with a set of functions that enables full and standard workflows and step-by-step analysis.
Command-line interface
The integrated command-line interface performs cavity detection and characterization with a customizable set of parameters. The standard characterization includes shape, volume, area, and interface residues and their frequencies. The optional characterizations are depth (per cavity point, maximum and average) and hydropathy (per surface point and average) with six options of built-in hydrophobicity scales (EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, RadzickaWolfenden, WimleyWhite, and ZhaoLondon).
What's Changed
- Bump flake8 from 6.1.0 to 7.0.0 by @dependabot in #79
- Bump pytest from 7.4.4 to 8.0.0 by @dependabot in #81
- Bump black from 23.12.1 to 24.1.1 by @dependabot in #82
- Bump numpy from 1.26.3 to 1.26.4 by @dependabot in #83
- Bump black from 24.1.1 to 24.2.0 by @dependabot in #84
Full Changelog: v0.6.11...v0.6.12
Contributors
Assets 2
pyKVFinder v0.6.11
Python-C parallel KVFinder
The Python-C parallel KVFinder (pyKVFinder) detects and characterizes cavities (shape, volume, area, depth, openings [WIP], hydropathy, and interface residues and their frequencies) in target biomolecular structures using a dual-probe system. In addition to cavity detection, pyKVFinder also estimates the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES), and solvent accessible surface (SAS) to represent the molecular surface.
Python package
The pyKVFinder package is easily imported into Python scripts with a set of functions that enables full and standard workflows and step-by-step analysis.
Command-line interface
The integrated command-line interface performs cavity detection and characterization with a customizable set of parameters. The standard characterization includes shape, volume, area, and interface residues and their frequencies. The optional characterizations are depth (per cavity point, maximum and average) and hydropathy (per surface point and average) with six options of built-in hydrophobicity scales (EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, RadzickaWolfenden, WimleyWhite, and ZhaoLondon).
What's Changed
- Bump black from 23.11.0 to 23.12.1 by @dependabot in #76
- Bump pytest from 7.4.3 to 7.4.4 by @dependabot in #77
- Bump numpy from 1.26.2 to 1.26.3 by @dependabot in #78
Full Changelog: v0.6.10...v0.6.11
Contributors
Assets 2
pyKVFinder v0.6.10
Python-C parallel KVFinder
The Python-C parallel KVFinder (pyKVFinder) detects and characterizes cavities (shape, volume, area, depth, openings [WIP], hydropathy, and interface residues and their frequencies) in target biomolecular structures using a dual-probe system. In addition to cavity detection, pyKVFinder also estimates the molecular volume, using van der Waals (vdW) surface, solvent excluded surface (SES), and solvent accessible surface (SAS) to represent the molecular surface.
Python package
The pyKVFinder package is easily imported into Python scripts with a set of functions that enables full and standard workflows and step-by-step analysis.
Command-line interface
The integrated command-line interface performs cavity detection and characterization with a customizable set of parameters. The standard characterization includes shape, volume, area, and interface residues and their frequencies. The optional characterizations are depth (per cavity point, maximum and average) and hydropathy (per surface point and average) with six options of built-in hydrophobicity scales (EisenbergWeiss, HessaHeijne, KyteDoolittle, MoonFleming, RadzickaWolfenden, WimleyWhite, and ZhaoLondon).
What's Changed
- [MNT] Add Windows build support to pyKVFinder by @wapablos and @jvsguerra in #73
Full Changelog: v0.6.9...v0.6.10