New tests for specical query atoms and atropisomers (#7010)

* New tests for speical query atoms and atropisomers * fixed error, and used unique_ptrs * Removed test that makes GraphMol depend on GenericGroups * More to remove GraphMol dependency on GenericGroups
rdkit · Jan 11, 2024 · 73b4da2 · 73b4da2
1 parent d6e8e47
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diff --git a/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py b/Code/GraphMol/CIPLabeler/Wrap/pyCIPLabelWrapTest.py
@@ -59,6 +59,39 @@ def testLabelBondsList(self):
     self.assertFalse(bond1.HasProp("_CIPCode"))
     self.assertEqual(bond3.GetProp("_CIPCode"), "Z")
 
+  def doOneAtropIomerMandP(self,  inputSmiles , expected):
+
+    ps = Chem.SmilesParserParams()
+    ps.allowCXSMILES = True
+    ps.parseName = False
+    ps.sanitize = True
+    ps.removeHs = False
+    ps.explicit3dChirality = False
+
+    mol = Chem.MolFromSmiles(inputSmiles, ps)
+
+    self.assertIsNotNone(mol)
+    Chem.rdCIPLabeler.AssignCIPLabels(mol)
+
+    cipsCodes =""
+    for bondIndex in range(mol.GetNumBonds()):
+
+      bond = mol.GetBondWithIdx(bondIndex)
+
+      if (bond.HasProp("_CIPCode")):
+        cipsCodes += str(bondIndex) + bond.GetProp("_CIPCode") + ":" 
+
+    self.assertEqual(cipsCodes, expected)
+
+  def testAtropIsomer(self):
+    mol = "FC1=C(C2=C(C)C(N3C(=O)C4=C(N(C)C3=O)C(F)=CC=C4)=CC=C2)C2=C(NC3=C2CC[C@H](C(O)(C)C)C3)C(C(=O)N)=C1 |(2.1158,0.5489,;1.4029,0.9642,;0.6554,0.5402,;0.6459,-0.2846,;1.3556,-0.7053,;2.0747,-0.3011,;1.346,-1.5302,;2.3682,-1.8618,;2.9748,-1.3027,;2.794,-0.4978,;3.7623,-1.5486,;3.9431,-2.3535,;3.3364,-2.9126,;3.5173,-3.7175,;2.549,-2.6667,;1.9423,-3.2258,;4.7594,-2.6222,;4.9309,-3.4292,;5.3958,-2.0448,;5.2074,-1.2063,;4.3851,-0.9565,;0.6268,-1.9345,;-0.0827,-1.5137,;-0.0732,-0.6889,;-0.0819,0.9813,;-0.0819,1.8063,;-0.8665,2.0612,;-1.3515,1.3938,;-0.8665,0.7264,;-1.2039,-0.0639,;-2.0578,-0.1602,;-2.5629,0.5349,;-3.3837,0.4518,;-4.2045,0.3687,;-3.4668,1.2725,;-3.3006,-0.369,;-2.2074,1.3172,;0.6555,2.2474,;0.6459,3.0723,;-0.0731,3.4765,;1.3556,3.4931,;1.403,1.8235,),wU:7.14wD:31.35|"
+    self.doOneAtropIomerMandP(mol, "6P:")
+
+    mol = "C1(N2C(C)=CC=C2Br)=C(C)C(C)=C(N2C(C)=CC=C2Br)C(C)=C1C |(-0.0002,1.5403,;-0.0002,3.0805,;-1.334,3.8508,;-2.6678,3.0807,;-1.334,5.391,;1.3338,5.391,;1.3338,3.8508,;2.6676,3.0807,;-1.3338,0.7702,;-2.6678,1.5403,;-1.3338,-0.7702,;-2.6678,-1.5401,;-0.0002,-1.5403,;-0.0002,-3.0805,;1.3338,-3.8508,;2.6676,-3.0805,;1.3338,-5.391,;-1.334,-5.391,;-1.334,-3.8508,;-2.6678,-3.0805,;1.3338,-0.7702,;2.6678,-1.5403,;1.3338,0.7702,;2.6678,1.5404,),wU:1.6,13.14|"
+    self.doOneAtropIomerMandP(mol, "0m:12m:")
+
+    mol = "N1(n2c(C)ccc2Br)C(=O)[C@H](C)[C@H](C)C1=O |(-11.1517,1.8306,;-11.1517,3.3708,;-12.4855,4.1411,;-13.8193,3.371,;-12.4855,5.6813,;-9.8177,5.6813,;-9.8177,4.1411,;-8.4839,3.371,;-12.3975,0.9252,;-13.8622,1.4011,;-11.9217,-0.5394,;-12.8269,-1.7852,;-10.3817,-0.5394,;-9.4765,-1.7852,;-9.9059,0.9252,;-8.4413,1.4011,),wU:0.8,10.11,12.13|"
+    self.doOneAtropIomerMandP(mol, "0p:")
 
 if __name__ == '__main__':
   unittest.main()
diff --git a/Code/GraphMol/CMakeLists.txt b/Code/GraphMol/CMakeLists.txt
@@ -10,7 +10,7 @@ rdkit_library(GraphMol
               NontetrahedralStereo.cpp Atropisomers.cpp
               WedgeBonds.cpp
         SHARED
-              LINK_LIBRARIES RDGeometryLib RDGeneral  )
+              LINK_LIBRARIES RDGeometryLib RDGeneral )
 target_compile_definitions(GraphMol PRIVATE RDKIT_GRAPHMOL_BUILD)
 if (RDK_USE_URF)
     target_link_libraries(GraphMol PUBLIC ${RDK_URF_LIBS})

diff --git a/Code/GraphMol/FileParsers/test1.cpp b/Code/GraphMol/FileParsers/test1.cpp
@@ -5313,6 +5313,88 @@ void testGithub2000() {
   BOOST_LOG(rdInfoLog) << "done" << std::endl;
 }
 
+void testAtomQueries() {
+  BOOST_LOG(rdInfoLog) << "-------------------------------------" << std::endl;
+  BOOST_LOG(rdInfoLog) << "Testing atom queries contains HCOUNT, RBCOUNT, UNSAT"
+                       << std::endl;
+  {
+    std::string pathName = getenv("RDBASE");
+    pathName += "/Code/GraphMol/FileParsers/test_data/";
+    std::unique_ptr<RWMol> testQuery(
+        MolFileToMol(pathName + "AtomQuery1.mol", true, false, true));
+    TEST_ASSERT(testQuery);
+
+    std::unique_ptr<RWMol> testMol(
+        SmilesToMol("[H]C([H])([H])C1=CN=C(C=C)C(C2CCCCC2)=C1C"));
+    TEST_ASSERT(testMol);
+
+    MatchVectType mv;
+    SubstructMatch(*testMol, *testQuery, mv);
+    TEST_ASSERT(mv.size() > 0);
+
+    testMol.reset(SmilesToMol("[H]CC1=CN=C(C=C)C(C2CCCCC2)=C1C"));
+    TEST_ASSERT(testMol);
+
+    SubstructMatch(*testMol, *testQuery, mv);
+    TEST_ASSERT(mv.size() > 0);
+
+    testMol.reset(SmilesToMol("CCC1=CN=C(C=C)C(C2CCCCC2)=C1C"));
+    TEST_ASSERT(testMol);
+
+    SubstructMatch(*testMol, *testQuery, mv);
+    TEST_ASSERT(mv.size() == 0);  // search fails
+  }
+  {
+    std::string pathName = getenv("RDBASE");
+    pathName += "/Code/GraphMol/FileParsers/test_data/";
+    std::unique_ptr<RWMol> testQuery(
+        MolFileToMol(pathName + "AtomQuery2.mol", true, false, true));
+    TEST_ASSERT(testQuery);
+
+    std::unique_ptr<RWMol> testMol(SmilesToMol("C1(C)C(C)=CN=C(C)C=1C1CCCCC1"));
+    TEST_ASSERT(testMol);
+
+    MatchVectType mv;
+    SubstructMatch(*testMol, *testQuery, mv);
+    TEST_ASSERT(mv.size() > 0);
+
+    testMol.reset(SmilesToMol("C1(C)C(C)=CN=C(C)C=1C12CCC(CC1)CC2"));
+    TEST_ASSERT(testMol);
+
+    SubstructMatch(*testMol, *testQuery, mv);
+    TEST_ASSERT(mv.size() == 0);  // search fails
+  }
+  {
+    std::string pathName = getenv("RDBASE");
+    pathName += "/Code/GraphMol/FileParsers/test_data/";
+    std::unique_ptr<RWMol> testQuery(
+        MolFileToMol(pathName + "AtomQuery3.mol", true, false, true));
+    TEST_ASSERT(testQuery);
+
+    std::unique_ptr<RWMol> testMol(
+        SmilesToMol("CCC1=CN=C(C=C)C(C2CCCCC2)=C1C"));
+    TEST_ASSERT(testMol);
+
+    MatchVectType mv;
+    SubstructMatch(*testMol, *testQuery, mv);
+    TEST_ASSERT(mv.size() > 0);
+
+    testMol.reset(SmilesToMol("CCC1=CN=C(C3=CC=CC=C3)C(C2CCCCC2)=C1C"));
+    TEST_ASSERT(testMol);
+
+    SubstructMatch(*testMol, *testQuery, mv);
+    TEST_ASSERT(mv.size() > 0);
+
+    testMol.reset(SmilesToMol("CCC1=CN=C(C3CCCCC3)C(C2CCCCC2)=C1C"));
+    TEST_ASSERT(testMol);
+
+    SubstructMatch(*testMol, *testQuery, mv);
+    TEST_ASSERT(mv.size() == 0);
+  }
+
+  BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
+}
+
 void RunTests() {
 #if 1
   test1();
@@ -5411,6 +5493,7 @@ void RunTests() {
   testWedgeBondToDoublebond();
   testGithub1615();
   testGithub2000();
+  testAtomQueries();
 #endif
 }
 

diff --git a/Code/GraphMol/FileParsers/testAtropisomers.cpp b/Code/GraphMol/FileParsers/testAtropisomers.cpp
@@ -233,6 +233,64 @@ class MolAtropTest {
   }
 };
 
+void testLookForAtropisomersInSDdfFiles(std::string fileName,
+                                        unsigned int expectedHits,
+                                        unsigned int expectedMisses) {
+  BOOST_LOG(rdInfoLog) << "Looking for atropisomers in " << fileName
+                       << std::endl;
+
+  std::string rdbase = getenv("RDBASE");
+  std::string fName =
+      rdbase + "/Code/GraphMol/FileParsers/test_data/atropisomers/" + fileName;
+
+  std::ifstream in;
+  in.open(fName);
+  std::string line;
+  unsigned int foundCount = 0;
+  unsigned int notFoundCount = 0;
+  while (!in.eof()) {
+    std::string molBlock = "";
+    while (std::getline(in, line)) {
+      if (line.find("$$$$") != std::string::npos) {
+        break;
+      }
+
+      molBlock += line + "\n";
+    }
+
+    if (molBlock.length() < 10) {
+      continue;  // try for another;
+    }
+
+    std::unique_ptr<RWMol> mol(MolBlockToMol(molBlock, false, false, false));
+    TEST_ASSERT(mol != nullptr);
+
+    auto hasAtropisomers = RDKit::Atropisomers::doesMolHaveAtropisomers(*mol);
+
+    if (hasAtropisomers) {
+      BOOST_LOG(rdInfoLog) << "Found atropisomers in " << fileName << std::endl;
+      foundCount++;
+      printf("Atropisomers- %d hits   %d misses\r", foundCount, notFoundCount);
+      std::flush(std::cout);
+      std::ofstream out;
+      out.open(fName + "_" + std::to_string(foundCount) + ".sdf");
+      out << molBlock << std::endl;
+    } else {
+      notFoundCount++;
+      if (notFoundCount % 100 == 0) {
+        printf("Atropisomers- %d hits   %d misses\r", foundCount,
+               notFoundCount);
+        std::flush(std::cout);
+      }
+    }
+  }
+  printf("\nFinal results:\nFound atropisomers in %s - %d hits   %d misses\n",
+         fileName.c_str(), foundCount, notFoundCount);
+
+  TEST_ASSERT(foundCount == expectedHits);
+  TEST_ASSERT(notFoundCount == expectedMisses);
+}
+
 int main(int argc, char *argv[]) {
   (void)argc;
   (void)argv;
@@ -254,6 +312,7 @@ int main(int argc, char *argv[]) {
   BOOST_LOG(rdInfoLog) << " ---- Running with POSIX locale ----- " << std::endl;
 
   molAtropTest.RunTests();
+  testLookForAtropisomersInSDdfFiles("TestMultInSDF.sdf", 1, 4);
 
   return 0;
 }
diff --git a/Code/GraphMol/FileParsers/test_data/AtomQuery1.mol b/Code/GraphMol/FileParsers/test_data/AtomQuery1.mol
@@ -0,0 +1,32 @@
+
+  Mrv2308 06012316552D          
+
+  0  0  0     0  0            999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 10 10 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C -7.1459 4.3109 0 0
+M  V30 2 C -8.4795 3.5409 0 0
+M  V30 3 C -8.4795 2.0007 0 0
+M  V30 4 N -7.1459 1.2307 0 0
+M  V30 5 C -5.8122 2.0007 0 0
+M  V30 6 C -5.8122 3.5409 0 0
+M  V30 7 C -4.4785 4.3109 0 0 HCOUNT=3
+M  V30 8 C -7.146 5.8509 0 0
+M  V30 9 C -9.8132 4.3109 0 0
+M  V30 10 C -9.8132 1.2308 0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 2 1 2
+M  V30 2 1 2 3
+M  V30 3 2 5 6
+M  V30 4 1 6 1
+M  V30 5 1 6 7
+M  V30 6 1 1 8
+M  V30 7 1 2 9
+M  V30 8 1 3 10
+M  V30 9 2 3 4
+M  V30 10 1 4 5
+M  V30 END BOND
+M  V30 END CTAB
+M  END
diff --git a/Code/GraphMol/FileParsers/test_data/AtomQuery2.mol b/Code/GraphMol/FileParsers/test_data/AtomQuery2.mol
@@ -0,0 +1,32 @@
+
+  Mrv2308 06012316552D          
+
+  0  0  0     0  0            999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 10 10 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C -7.1459 4.3109 0 0
+M  V30 2 C -8.4795 3.5409 0 0
+M  V30 3 C -8.4795 2.0007 0 0
+M  V30 4 N -7.1459 1.2307 0 0
+M  V30 5 C -5.8122 2.0007 0 0
+M  V30 6 C -5.8122 3.5409 0 0
+M  V30 7 C -4.4785 4.3109 0 0
+M  V30 8 C -7.146 5.8509 0 0
+M  V30 9 C -9.8132 4.3109 0 0 RBCNT=2
+M  V30 10 C -9.8132 1.2308 0 0
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 2 1 2
+M  V30 2 1 2 3
+M  V30 3 2 5 6
+M  V30 4 1 6 1
+M  V30 5 1 6 7
+M  V30 6 1 1 8
+M  V30 7 1 2 9
+M  V30 8 1 3 10
+M  V30 9 2 3 4
+M  V30 10 1 4 5
+M  V30 END BOND
+M  V30 END CTAB
+M  END
diff --git a/Code/GraphMol/FileParsers/test_data/AtomQuery3.mol b/Code/GraphMol/FileParsers/test_data/AtomQuery3.mol
@@ -0,0 +1,32 @@
+
+  Mrv2308 06012316552D          
+
+  0  0  0     0  0            999 V3000
+M  V30 BEGIN CTAB
+M  V30 COUNTS 10 10 0 0 0
+M  V30 BEGIN ATOM
+M  V30 1 C -7.1459 4.3109 0 0
+M  V30 2 C -8.4795 3.5409 0 0
+M  V30 3 C -8.4795 2.0007 0 0
+M  V30 4 N -7.1459 1.2307 0 0
+M  V30 5 C -5.8122 2.0007 0 0
+M  V30 6 C -5.8122 3.5409 0 0
+M  V30 7 C -4.4785 4.3109 0 0
+M  V30 8 C -7.146 5.8509 0 0
+M  V30 9 C -9.8132 4.3109 0 0
+M  V30 10 C -9.8132 1.2308 0 0 UNSAT=1
+M  V30 END ATOM
+M  V30 BEGIN BOND
+M  V30 1 2 1 2
+M  V30 2 1 2 3
+M  V30 3 2 5 6
+M  V30 4 1 6 1
+M  V30 5 1 6 7
+M  V30 6 1 1 8
+M  V30 7 1 2 9
+M  V30 8 1 3 10
+M  V30 9 2 3 4
+M  V30 10 1 4 5
+M  V30 END BOND
+M  V30 END CTAB
+M  END
diff --git a/Code/GraphMol/FileParsers/test_data/cdk2_stereo.csv b/Code/GraphMol/FileParsers/test_data/cdk2_stereo.csv
@@ -1,2 +1,2 @@
-c1cc(Cl)ccc1c(n[o]2)nc2CSC/3=[NH+]/CCN3,mol_14069
-[C@@H]12/C=C\[C@@H](C(C(=O)O)C1C(=O)O)c3cccc(c23)[N+]([O-])=O,mol_12186,None,4.50,Scaffold_00,divscreen,0
+c1cc(Cl)ccc1c(n[o]2)nc2CSC/3=[NH+]/CCN3,mol_14069
+[C@@H]12/C=C\[C@@H](C(C(=O)O)C1C(=O)O)c3cccc(c23)[N+]([O-])=O,mol_12186,None,4.50,Scaffold_00,divscreen,0
diff --git a/Code/GraphMol/GenericGroups/CMakeLists.txt b/Code/GraphMol/GenericGroups/CMakeLists.txt
@@ -7,4 +7,4 @@ target_compile_definitions(GenericGroups PRIVATE RDKIT_GENERICGROUPS_BUILD)
 rdkit_headers(GenericGroups.h DEST GraphMol/GenericGroups)
 
 rdkit_catch_test(testGenericGroups generic_tests.cpp 
-    LINK_LIBRARIES GenericGroups FileParsers SmilesParse SubstructMatch)
+    LINK_LIBRARIES GenericGroups FileParsers MarvinParser SmilesParse SubstructMatch)
diff --git a/Code/GraphMol/GenericGroups/GenericGroups.h b/Code/GraphMol/GenericGroups/GenericGroups.h
@@ -592,13 +592,12 @@ const static std::map<
         {"NoCarbonRing", Matchers::NoCarbonRingAtomMatcher},
         {"CXX", Matchers::NoCarbonRingAtomMatcher},
         {"NoCarbonRingH", Matchers::NoCarbonRingHAtomMatcher},
-        {"CXH", Matchers::NoCarbonRingHAtomMatcher}
-};
+        {"CXH", Matchers::NoCarbonRingHAtomMatcher}};
 
-// This is an extension of adjustQueryProperties from GraphMol that allows the search of generic groups 
+// This is an extension of adjustQueryProperties from GraphMol that allows the
+// search of generic groups
 RDKIT_GENERICGROUPS_EXPORT ROMol *adjustQueryPropertiesWithGenericGroups(
-    const ROMol &mol,
-    const MolOps::AdjustQueryParameters *inParams=nullptr);
+    const ROMol &mol, const MolOps::AdjustQueryParameters *inParams = nullptr);
 
 //! returns false if any of the molecule's generic atoms are not satisfied in
 /// the current match