Merge branch 'master' into bugfix/1309-implicit-h-for-query-in-json-l…

…oader
epam · Oct 17, 2023 · 7c24160 · 7c24160
2 parents 336abe4 + 6dbd10f
commit 7c24160
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diff --git a/.ci/version.txt b/.ci/version.txt
@@ -1,5 +1,5 @@
 1.15.0
 dev
-1
+2
 
-c063813402a30d41ab51d39f29ee9df32ca25a1bec8274a41a9f6474b9bc696d
+284f91159ae886214f74b856d19f5cfed089bb90fc85c038d90a40da588bf13a
diff --git a/api/dotnet/src/Indigo.Net.csproj b/api/dotnet/src/Indigo.Net.csproj
@@ -2,7 +2,7 @@
 
 	<PropertyGroup>
 		<TargetFrameworks>netstandard2.0</TargetFrameworks>
-		<Version>1.15.0-dev.1</Version>
+		<Version>1.15.0-dev.2</Version>
 		<Authors>EPAM Systems Life Science Department</Authors>
 		<Company>EPAM Systems</Company>
 		<Description>Universal cheminformatics toolkit</Description>

diff --git a/api/http/requirements.txt b/api/http/requirements.txt
@@ -1,7 +1,7 @@
 anyio==3.7.0
 asgiref==3.7.1
 click==8.1.3
-epam.indigo==1.15.0.dev1
+epam.indigo==1.15.0.dev2
 fastapi==0.95.2
 h11==0.14.0
 idna==3.4

diff --git a/api/http/setup.py b/api/http/setup.py
@@ -19,7 +19,7 @@
 
 setup_kwargs = {
     "name": "indigo-service",
-    "version": "1.15.0.dev1",
+    "version": "1.15.0.dev2",
     "description": "",
     "long_description": None,
     "author": "Ruslan Khyurri",

diff --git a/api/indigo-version.cmake b/api/indigo-version.cmake
@@ -1,4 +1,4 @@
-set(INDIGO_DEFAULT_VERSION "1.15.0-dev.1")
+set(INDIGO_DEFAULT_VERSION "1.15.0-dev.2")
 set(INDIGO_MAX_REVISION 1000)
 find_package(Git)
 if(GIT_EXECUTABLE)

diff --git a/api/java/pom.xml b/api/java/pom.xml
@@ -17,7 +17,7 @@
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
         <maven.compiler.source>1.8</maven.compiler.source>
         <maven.compiler.target>${maven.compiler.source}</maven.compiler.target>
-        <revision>1.15.0-dev.1</revision>
+        <revision>1.15.0-dev.2</revision>
     </properties>
 
     <licenses>

diff --git a/api/python/indigo/__init__.py b/api/python/indigo/__init__.py
@@ -3,4 +3,4 @@
 from .indigo.indigo_exception import IndigoException  # noqa
 from .indigo.indigo_object import IndigoObject  # noqa
 
-__version__ = "1.15.0.dev1"
+__version__ = "1.15.0.dev2"
diff --git a/api/python/setup.py b/api/python/setup.py
@@ -98,7 +98,7 @@
 
 setup(
     name="epam.indigo",
-    version="1.15.0.dev1",
+    version="1.15.0.dev2",
     description="Indigo universal cheminformatics toolkit",
     author="EPAM Systems Life Science Department",
     author_email="lifescience.opensource@epam.com",

diff --git a/api/r/DESCRIPTION b/api/r/DESCRIPTION
@@ -1,5 +1,5 @@
 Package: rindigo
-Version: 1.15.0-dev.1
+Version: 1.15.0-dev.2
 Date: 2020-12-10
 Title: R Package for Indigo Toolkit
 Authors@R: c(person(given = "Mikhail", family = "Kviatkovskii", role = c("cre"),

diff --git a/api/tests/integration/ref/formats/ket_to_mol.py.out b/api/tests/integration/ref/formats/ket_to_mol.py.out
@@ -1,4 +1,10 @@
 *** KET to MOL ***
+chem.ket:SUCCEED
+cysteine.ket:SUCCEED
+dala.ket:SUCCEED
+dcysteine.ket:SUCCEED
+dthymine.ket:SUCCEED
 suplabel.ket:SUCCEED
+thymine.ket:SUCCEED
 empty_apid.ket:SUCCEED
 ket-reaction-arrow.ket:SUCCEED
diff --git a/api/tests/integration/ref/formats/mol_to_ket.py.out b/api/tests/integration/ref/formats/mol_to_ket.py.out
@@ -3,5 +3,10 @@
 1046-imp_hydrogen.ket:SUCCEED
 SgroupDifferent.ket:SUCCEED
 atropisomer.ket:SUCCEED
+chem.ket:SUCCEED
+cysteine.ket:SUCCEED
+dcysteine.ket:SUCCEED
+dthymine.ket:SUCCEED
 non_atrop.ket:SUCCEED
 suplabel.ket:SUCCEED
+thymine.ket:SUCCEED
diff --git a/api/tests/integration/ref/formats/smarts.py.out b/api/tests/integration/ref/formats/smarts.py.out
@@ -27,3 +27,11 @@ CC[C+5]CCCCC
 [O;H] is ok. smarts_in==smarts_out
 [!O;H] is ok. smarts_in==smarts_out
 ([#6]1-[#6]-[#6]-1.[#6]) is ok. smarts_in==smarts_out
+[#9]/[#6]=[#6]/[#6]=[#6]/[#6] is ok. smarts_in==smarts_out
+[#9]\[#6]=[#6]\[#6]=[#6]\[#6] is ok. smarts_in==smarts_out
+[#9]/[#6]=[#6]/[#6]=[#6]/[#6] is ok. smarts_in==smarts_out
+[#9]/[#6]=[#6]/[#6]=[#6]/[#6] is ok. json_in==json_out
+[#9]/[#6]=[#6]/[#6]=[#6]/[#6] is ok. expected string found in json
+[#9]\[#6]=[#6]/[#6]=[#6]\[#6] is ok. smarts_in==smarts_out
+[#9]\[#6]=[#6]/[#6]=[#6]\[#6] is ok. json_in==json_out
+[#9]\[#6]=[#6]/[#6]=[#6]\[#6] is ok. expected string found in json
diff --git a/api/tests/integration/tests/formats/ket_to_mol.py b/api/tests/integration/tests/formats/ket_to_mol.py
@@ -24,11 +24,22 @@ def find_diff(a, b):
 ref_path = joinPathPy("ref/", __file__)
 root_rea = joinPathPy("reactions/", __file__)
 
-files = ["suplabel"]
+files = [
+    "suplabel",
+    "cysteine",
+    "dcysteine",
+    "thymine",
+    "dthymine",
+    "dala",
+    "chem",
+]
 
 files.sort()
 for filename in files:
     mol = indigo.loadMoleculeFromFile(os.path.join(root, filename + ".ket"))
+    # with open(os.path.join(ref_path, filename) + ".mol", "w") as file:
+    #     file.write(mol.molfile())
+
     with open(os.path.join(ref_path, filename) + ".mol", "r") as file:
         ket_ref = file.read()
     ket = mol.molfile()

diff --git a/api/tests/integration/tests/formats/mol_to_ket.py b/api/tests/integration/tests/formats/mol_to_ket.py
@@ -30,6 +30,11 @@ def find_diff(a, b):
     "suplabel",
     "atropisomer",
     "non_atrop",
+    "cysteine",
+    "dcysteine",
+    "thymine",
+    "dthymine",
+    "chem",
 ]
 
 files.sort()

diff --git a/api/tests/integration/tests/formats/molecules/chem.ket b/api/tests/integration/tests/formats/molecules/chem.ket
@@ -0,0 +1,183 @@
+{
+    "root": {
+        "nodes": [],
+        "templates": [
+            {
+                "$ref": "monomerTemplate-cch_3"
+            }
+        ]
+    },
+    "monomerTemplate-cch_3": {
+        "type": "monomerTemplate",
+        "id": "cch_3",
+        "class": "Chem",
+        "classHELM": "CHEM",
+        "alias": "cch",
+        "attachmentPoints": [
+            {
+                "type": "right",
+                "label": "R2",
+                "attachmentAtom": 8,
+                "leavingGroup": {
+                    "atoms": [
+                        1
+                    ]
+                }
+            },
+            {
+                "type": "side",
+                "label": "R3",
+                "attachmentAtom": 6,
+                "leavingGroup": {
+                    "atoms": [
+                        2
+                    ]
+                }
+            },
+            {
+                "type": "side",
+                "label": "R5",
+                "attachmentAtom": 3,
+                "leavingGroup": {
+                    "atoms": [
+                        0
+                    ]
+                }
+            }
+        ],
+        "atoms": [
+            {
+                "label": "H",
+                "location": [
+                    9.201199531555176,
+                    -7.158699989318848,
+                    0.0
+                ]
+            },
+            {
+                "label": "H",
+                "location": [
+                    8.374699592590332,
+                    -7.985400199890137,
+                    0.0
+                ]
+            },
+            {
+                "label": "O",
+                "location": [
+                    10.02810001373291,
+                    -7.985400199890137,
+                    0.0
+                ]
+            },
+            {
+                "label": "S",
+                "location": [
+                    9.718199729919434,
+                    -6.737199783325195,
+                    0.0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    9.194899559020996,
+                    -7.6427001953125,
+                    0.0
+                ],
+                "stereoLabel": "abs"
+            },
+            {
+                "label": "O",
+                "location": [
+                    9.698399543762207,
+                    -8.580300331115723,
+                    0.0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    9.698399543762207,
+                    -7.97629976272583,
+                    0.0
+                ]
+            },
+            {
+                "label": "C",
+                "location": [
+                    9.194899559020996,
+                    -7.03879976272583,
+                    0.0
+                ]
+            },
+            {
+                "label": "N",
+                "location": [
+                    8.704099655151368,
+                    -7.994699954986572,
+                    0.0
+                ]
+            }
+        ],
+        "bonds": [
+            {
+                "type": 1,
+                "atoms": [
+                    3,
+                    0
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    6,
+                    2
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    8,
+                    1
+                ]
+            },
+            {
+                "type": 2,
+                "atoms": [
+                    6,
+                    5
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    4,
+                    7
+                ],
+                "stereo": 1
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    7,
+                    3
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    4,
+                    6
+                ]
+            },
+            {
+                "type": 1,
+                "atoms": [
+                    8,
+                    4
+                ]
+            }
+        ]
+    }
+}
diff --git a/api/tests/integration/tests/formats/molecules/chem.mol b/api/tests/integration/tests/formats/molecules/chem.mol
@@ -0,0 +1,47 @@
+
+  -INDIGO-09062309442D
+
+  0  0  0  0  0  0  0  0  0  0  0 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 0 0 0 0 0
+M  V30 END CTAB
+M  V30 BEGIN TEMPLATE
+M  V30 TEMPLATE 3 CHEM/cch/cch
+M  V30 BEGIN CTAB
+M  V30 COUNTS 9 8 4 0 1
+M  V30 BEGIN ATOM
+M  V30 1 H 9.2012 -7.1587 0 0
+M  V30 2 H 8.3747 -7.9854 0 0
+M  V30 3 O 10.0281 -7.9854 0 0
+M  V30 4 S 9.7182 -6.7372 0 0
+M  V30 5 C 9.1949 -7.6427 0 0 CFG=2
+M  V30 6 O 9.6984 -8.5803 0 0
+M  V30 7 C 9.6984 -7.9763 0 0
+M  V30 8 C 9.1949 -7.0388 0 0
+M  V30 9 N 8.7041 -7.9947 0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 1 4 1
+M  V30 2 1 7 3
+M  V30 3 1 9 2
+M  V30 4 2 7 6
+M  V30 5 1 5 8 CFG=1
+M  V30 6 1 8 4
+M  V30 7 1 5 7
+M  V30 8 1 9 5
+M  V30 END BOND
+M  V30 BEGIN SGROUP
+M  V30 1 SUP 1 ATOMS=(1 2) XBONDS=(1 3) LABEL=H CSTATE=(4 3 0.8265 0 0) -
+M  V30 CLASS=LGRP
+M  V30 2 SUP 2 ATOMS=(1 3) XBONDS=(1 2) LABEL=OH CSTATE=(4 2 -0.825 0 0) -
+M  V30 CLASS=LGRP
+M  V30 3 SUP 3 ATOMS=(1 1) XBONDS=(1 1) LABEL=H CSTATE=(4 1 0 -0.8267 0) -
+M  V30 CLASS=LGRP
+M  V30 4 SUP 4 ATOMS=(6 4 5 6 7 8 9) XBONDS=(3 1 2 3) LABEL=cch CSTATE=(4 3 -
+M  V30 -0.8265 0 0) CSTATE=(4 2 0.825 0 0) CSTATE=(4 1 0 0.8267 0) CLASS=AA -
+M  V30 SAP=(3 9 2 Br) SAP=(3 7 3 Cx) SAP=(3 4 1 Ex)
+M  V30 END SGROUP
+M  V30 END CTAB
+M  V30 END TEMPLATE
+M  END
+