- Fixed a few glitches which caused the build to fail on Windows

- added a few tests for ResonanceMolSupplier

Code/DistGeom/CMakeLists.txt

@@ -14,6 +14,6 @@ rdkit_headers(BoundsMatrix.h
               TriangleSmooth.h DEST DistGeom)
 
 rdkit_test(testDistGeom testDistGeom.cpp 
-LINK_LIBRARIES DistGeometry EigenSolvers ForceField Optimizer RDGeneral RDGeometryLib )
+LINK_LIBRARIES DistGeometry EigenSolvers ForceField ForceFieldHelpers Optimizer RDGeneral RDGeometryLib )
 
 add_subdirectory(Wrap)

Code/DistGeom/Wrap/CMakeLists.txt

@@ -1,6 +1,6 @@
 rdkit_python_extension(DistGeom DistGeom.cpp
                        DEST DistanceGeometry
-LINK_LIBRARIES DistGeometry EigenSolvers ForceField Optimizer RDGeneral RDGeometryLib RDBoost )
+LINK_LIBRARIES DistGeometry EigenSolvers ForceField ForceFieldHelpers Optimizer RDGeneral RDGeometryLib RDBoost )
 
 
 add_pytest(pyDistGeom ${CMAKE_CURRENT_SOURCE_DIR}/rough_test.py)

Code/GraphMol/FilterCatalog/filtercatalogtest.cpp

@@ -157,7 +157,7 @@ void testFilterCatalog() {
 void testFilterCatalogEntry() {
   SmartsMatcher *sm = new SmartsMatcher("Aromatic carbon chain");
   boost::shared_ptr<FilterMatcherBase> matcher(sm);
-  TEST_ASSERT(not matcher->isValid());
+  TEST_ASSERT(!matcher->isValid());
   const int debugParse = 0;
   const bool mergeHs = true;
   ROMOL_SPTR pattern(SmartsToMol("c:c:c:c:c", debugParse, mergeHs));

Code/GraphMol/ForceFieldHelpers/CrystalFF/TorsionPreferences.cpp

@@ -493,7 +493,7 @@ namespace ForceFields {
             Atom const *atom = (angle.dp_pattern.get())->getAtomWithIdx(i);
             int num;
             if (atom->getPropIfPresent("molAtomMapNumber", num)) {
-              if(num>0 and num<5) {
+              if(num>0 && num<5) {
                 angle.idx[num-1] = i;
               }
             }

Code/GraphMol/Wrap/rough_test.py

@@ -3147,23 +3147,50 @@ CAS<~>
       | Chem.UNCONSTRAINED_ANIONS, 10)
     self.assertEqual(len(resMolSuppl), 10)
     
-    resMolSuppl = Chem.ResonanceMolSupplier(mol,
-      Chem.ALLOW_INCOMPLETE_OCTETS \
-      | Chem.UNCONSTRAINED_CATIONS \
-      | Chem.UNCONSTRAINED_ANIONS, 0);
-    self.assertEqual(len(resMolSuppl), 0)
+    crambinPdb = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers',
+                                            'test_data','1CRN.pdb')
+    mol = Chem.MolFromPDBFile(crambinPdb)
+    resMolSuppl = Chem.ResonanceMolSupplier(mol)
+    self.assertEqual(len(resMolSuppl), 1)
+    resMolSuppl = Chem.ResonanceMolSupplier(mol, Chem.KEKULE_ALL)
+    self.assertEqual(len(resMolSuppl), 8)
 
   def testSubstructMatchAcetate(self):
     mol = Chem.MolFromSmiles('CC(=O)[O-]')
     query = Chem.MolFromSmarts('C(=O)[O-]')
     
     resMolSuppl = Chem.ResonanceMolSupplier(mol)
-    matches = mol.GetSubstructMatches(query,
-      False, False, False)
+    matches = mol.GetSubstructMatches(query)
     self.assertEqual(len(matches), 1)
-    matches = resMolSuppl.GetSubstructMatches(query,
-      False, False, False)
+    self.assertEqual(matches, ((1, 2, 3),))
+    matches = mol.GetSubstructMatches(query, uniquify = True)
+    self.assertEqual(len(matches), 1)
+    self.assertEqual(matches, ((1, 2, 3),))
+    matches = mol.GetSubstructMatches(query, uniquify = False)
+    self.assertEqual(len(matches), 1)
+    self.assertEqual(matches, ((1, 2, 3),))
+    matches = resMolSuppl.GetSubstructMatches(query)
     self.assertEqual(len(matches), 2)
+    self.assertEqual(matches, ((1, 2, 3), (1, 3, 2)))
+    matches = resMolSuppl.GetSubstructMatches(query, uniquify = True)
+    self.assertEqual(len(matches), 1)
+    self.assertEqual(matches, ((1, 2, 3),))
+    matches = resMolSuppl.GetSubstructMatches(query, uniquify = False)
+    self.assertEqual(len(matches), 2)
+    self.assertEqual(matches, ((1, 2, 3), (1, 3, 2)))
+    query = Chem.MolFromSmarts('C(~O)~O')
+    matches = mol.GetSubstructMatches(query, uniquify = False)
+    self.assertEqual(len(matches), 2)
+    self.assertEqual(matches, ((1, 2, 3), (1, 3, 2)))
+    matches = mol.GetSubstructMatches(query, uniquify = True)
+    self.assertEqual(len(matches), 1)
+    self.assertEqual(matches, ((1, 2, 3),))
+    matches = resMolSuppl.GetSubstructMatches(query, uniquify = False)
+    self.assertEqual(len(matches), 2)
+    self.assertEqual(matches, ((1, 2, 3), (1, 3, 2)))
+    matches = resMolSuppl.GetSubstructMatches(query, uniquify = True)
+    self.assertEqual(len(matches), 1)
+    self.assertEqual(matches, ((1, 2, 3),))
 
   def testSubstructMatchDMAP(self):
     mol = Chem.MolFromSmiles('C(C)Nc1cc[nH+]cc1')