Merge pull request #108 from openforcefield/bannanc

Update ChemicalEnvironments SMIRKS parsing

.travis.yml

@@ -23,6 +23,8 @@ script:
   #- pip install $OPENEYE_CHANNEL openeye-toolkits && python -c "import openeye; print(openeye.__version__)"
   # Use beta version for partial bond orders
   - pip install --pre -i https://pypi.anaconda.org/openeye/simple openeye-toolkits && python -c "import openeye; print(openeye.__version__)"
+  # Install RDKit
+  - conda install --yes -c rdkit rdkit
   # Build the recipe
   - conda build devtools/conda-recipe
   # Use oeommtools for improper test
@@ -35,7 +37,6 @@ script:
 
 env:
   matrix:
-    - python=2.7  CONDA_PY=27
     - python=3.5  CONDA_PY=35
     - python=3.6  CONDA_PY=36
 

openforcefield/tests/test_chemicalenvironment.py

@@ -79,24 +79,30 @@ def test_parseSMIRKS(self):
                 ('ewg2', '[#7!-1,#8,#16]') ]
 
         smirksList = [ ["[#6](-[#1])-[#8]", None, ChemicalEnvironment],
-                ["[#6&X4&H0:1](-[#1])-[#6&X4]", 'VdW', AtomChemicalEnvironment],
+                ["[#6&X4&H0:1](-[#1])-[#6&X4]", 'Atom', AtomChemicalEnvironment],
                 [ "[#6&X4&H0:1](-[#1])-[#6&X4:2]", 'Bond', BondChemicalEnvironment],
                 [ "[*:1]-[*:2](-[#6&X4])-[*:3]", 'Angle', AngleChemicalEnvironment],
-                [ "[#6&X4&H0:1](-[#1])-[#6&X4:2]-[#6&X4&H0:3](-[#1])-[#6&X4:4]", 'Torsion', TorsionChemicalEnvironment],
-                [ "[#1:1]-[#6&X4:2](-[#8:3])-[#1:4]", 'Improper', ImproperChemicalEnvironment],
+                [ "[#6&X4&H0:1](-[#1])-[#6&X4:2]-[#6&X4&H0:3](-[#1])-[#6&X4:4]", 'ProperTorsion', TorsionChemicalEnvironment],
+                [ "[#1:1]-[#6&X4:2](-[#8:3])-[#1:4]", 'ImproperTorsion', ImproperChemicalEnvironment],
                 [ "[#1:1]-[#6&X4:2](-[#8:3])-[*:4](-[#6&H1])-[#8:5]", None, ChemicalEnvironment],
-                [ "[#6$(*~[#6]=[#8])$(*-,=$ewg2)]", None, ChemicalEnvironment],
+                [ "[#6$(*~[#6]=[#8])$(*-,=[$ewg2,#7])]", None, ChemicalEnvironment],
                 [ "CCC", None, ChemicalEnvironment],
-                [ "[#6:1]1(-;!@[#1,#6])=;@[#6]-;@[#6]1", 'VdW', ChemicalEnvironment],
+                [ "[#6:1]1(-;!@[#1,#6])=;@[#6]-;@[#6]1", 'Atom', ChemicalEnvironment],
                 [ "C(O-[#7,#8])CC=[*]", None, ChemicalEnvironment],
-                [ "[#6$([#6X4](~[$ewg1])(~[#8]~[#1])):1]-[#6X2H2;+0:2]-,=,:;!@;!#[$ewg2:3]-[#4:4]", 'Torsion', TorsionChemicalEnvironment],
-                [ "[#6$([#6X4](~[$ewg1])(~[#8]~[#1])):1]1=CCCC1", 'VdW', AtomChemicalEnvironment] ]
-
-        for [smirks, checkType, chemEnv] in smirksList:
-            env = chemEnv(smirks = smirks, replacements = replacements)
-            Type = env.getType()
-            self.assertEqual(Type,checkType,
-                    "SMIRKS (%s) clasified as %s instead of %s" % (smirks, Type, checkType))
+                [ "[#6$([#6X4](~[$ewg1])(~[#8]~[#1])):1]-[#6X2H2;+0:2]-,=,:;!@;!#[$ewg2:3]-[#4:4]", 'ProperTorsion', TorsionChemicalEnvironment],
+                [ "[#6$([#6X4](~[$ewg1])(~[#8]~[#1])):1]1=CCCC1", 'Atom', AtomChemicalEnvironment],
+                [ "[*:1]-[#7X3:2](-[#6a$(*1ccc(-[#8-1X1])cc1):3])-[*:4]", 'ImproperTorsion', ImproperChemicalEnvironment],
+                [ "[#6X4:1]1~[*:2]~[*$(*~[#1]):3]1", 'Angle', AngleChemicalEnvironment],
+                [ "[$([#7]1~[#6]-CC1)]", None, ChemicalEnvironment],
+                [ "[$(c1ccccc1)]", None, ChemicalEnvironment],
+                ]
+
+        for toolkit in ['openeye', 'rdkit']:
+            for [smirks, checkType, chemEnv] in smirksList:
+                env = chemEnv(smirks = smirks, replacements = replacements, toolkit=toolkit)
+                Type = env.getType()
+                self.assertEqual(Type,checkType,
+                        "SMIRKS (%s) clasified as %s instead of %s using %s toolkit" % (smirks, Type, checkType, toolkit))
 
     def test_environment_functions(self):
         """