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import os
import unittest
from rdkit import Chem, DataStructs, Geometry, RDConfig
from rdkit.Chem import AllChem, ChemicalFeatures, rdDistGeom
def lstFeq(l1, l2, tol=1.e-4):
if (len(list(l1)) != len(list(l2))):
return 0
for i in range(len(list(l1))):
if not feq(l1[i], l2[i], tol):
return 0
return 1
def feq(v1, v2, tol2=1e-4):
return abs(v1 - v2) <= tol2
class TestCase(unittest.TestCase):
def setUp(self):
pass
def testBasic(self):
cfac = ChemicalFeatures.BuildFeatureFactory(
os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'MolChemicalFeatures', 'test_data',
'featDef.txt'))
self.assertTrue(cfac.GetNumFeatureDefs() == 2)
fNames = cfac.GetFeatureFamilies()
self.assertTrue(len(fNames) == 2)
self.assertTrue(fNames[0] == 'HBondDonor')
self.assertTrue(fNames[1] == 'HBondAcceptor')
mol = Chem.MolFromSmiles("COCN")
rdDistGeom.EmbedMolecule(mol, 30, 100, useExpTorsionAnglePrefs=False, useBasicKnowledge=False)
self.assertTrue(cfac.GetNumMolFeatures(mol) == 3)
for i in range(cfac.GetNumMolFeatures(mol)):
self.assertTrue(cfac.GetMolFeature(mol, i))
# check that the recompute argument works:
self.assertTrue(cfac.GetMolFeature(mol, 0))
for i in range(cfac.GetNumMolFeatures(mol)):
self.assertTrue(cfac.GetMolFeature(mol, i, "", False))
self.assertRaises(IndexError, lambda: cfac.GetMolFeature(mol, 3))
feats = cfac.GetFeaturesForMol(mol)
self.assertTrue(len(feats) == 3)
fTypes = ['HBondDonor', 'HBondAcceptor', 'HBondAcceptor']
positions = [[1.3041, -0.6079, 0.0924], [-0.7066, 0.5994, 0.1824], [1.3041, -0.6079, 0.0924]]
targetAids = [[3], [1], [3]]
for i, feat in enumerate(feats):
self.assertEqual(feat.GetFamily(), fTypes[i])
pos = list(feat.GetPos())
aids = list(feat.GetAtomIds())
self.assertEqual(aids, targetAids[i])
self.assertTrue(lstFeq(pos, positions[i]))
nmol = feat.GetMol()
self.assertEqual(Chem.MolToSmiles(nmol), "COCN")
ncfac = feat.GetFactory()
self.assertEqual(ncfac.GetNumFeatureDefs(), 2)
self.assertEqual(feat.GetActiveConformer(), -1)
def testIncludeOnly(self):
cfac = ChemicalFeatures.BuildFeatureFactory(
os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'MolChemicalFeatures', 'test_data',
'featDef.txt'))
self.assertTrue(cfac.GetNumFeatureDefs() == 2)
mol = Chem.MolFromSmiles("COCN")
rdDistGeom.EmbedMolecule(mol)
self.assertTrue(cfac.GetNumMolFeatures(mol, includeOnly="HBondAcceptor") == 2)
self.assertTrue(cfac.GetNumMolFeatures(mol, includeOnly="HBondDonor") == 1)
self.assertTrue(cfac.GetNumMolFeatures(mol, includeOnly="Bogus") == 0)
self.assertRaises(IndexError, lambda: cfac.GetMolFeature(mol, 1, includeOnly="HBondDonor"))
self.assertRaises(IndexError,
lambda: cfac.GetMolFeature(mol, 2, includeOnly="HBondAcceptor"))
f = cfac.GetMolFeature(mol, 0, includeOnly="HBondDonor")
self.assertTrue(f.GetFamily() == 'HBondDonor')
feats = cfac.GetFeaturesForMol(mol, includeOnly="HBondAcceptor")
self.assertTrue(len(feats) == 2)
feats = cfac.GetFeaturesForMol(mol, includeOnly="HBondDonor")
self.assertTrue(len(feats) == 1)
feats = cfac.GetFeaturesForMol(mol, includeOnly="Bogus")
self.assertTrue(len(feats) == 0)
def testStringParse(self):
fdefBlock = \
"""DefineFeature HDonor1 [N,O;!H0]
Family HBondDonor
Weights 1.0
EndFeature
DefineFeature HAcceptor1 [N,O;H0]
Family HBondAcceptor
Weights 1.0
EndFeature
"""
cfac = ChemicalFeatures.BuildFeatureFactoryFromString(fdefBlock)
self.assertTrue(cfac.GetNumFeatureDefs() == 2)
def testStringParse2(self):
fdefBlock = \
"""DefineFeature HDonor1 [N,O;!H0]\r
Family HBondDonor\r
Weights 1.0\r
EndFeature\r
DefineFeature HAcceptor1 [N,O;H0]\r
Family HBondAcceptor\r
Weights 1.0\r
EndFeature\r
"""
cfac = ChemicalFeatures.BuildFeatureFactoryFromString(fdefBlock)
self.assertTrue(cfac.GetNumFeatureDefs() == 2)
def testParseErrorHandling(self):
fdefBlock = \
"""DefineFeature HDonor1 [N,O;!HQ]
Family HBondDonor
Weights 1.0
EndFeature
"""
self.assertRaises(ValueError,
lambda: ChemicalFeatures.BuildFeatureFactoryFromString(fdefBlock))
fdefBlock = \
"""DefineFeature HDonor1 [N,O;!H0]
Family HBondDonor
Weights 1.0
"""
self.assertRaises(ValueError,
lambda: ChemicalFeatures.BuildFeatureFactoryFromString(fdefBlock))
self.assertRaises(IOError, lambda: ChemicalFeatures.BuildFeatureFactory('noSuchFile.txt'))
def testAtomMatch(self):
fdefBlock = \
"""
DefineFeature HAcceptor1 [#7,#8]
Family HBondAcceptor
Weights 1.0
EndFeature
DefineFeature Arom1 a1aaaaa1
Family Aromatic
Weights 1.0,1.0,1.0,1.0,1.0,1.0
EndFeature
"""
cfac = ChemicalFeatures.BuildFeatureFactoryFromString(fdefBlock)
self.assertTrue(cfac.GetNumFeatureDefs() == 2)
mol = Chem.MolFromSmiles('n1ccccc1')
feats = cfac.GetFeaturesForMol(mol)
self.assertTrue(len(feats) == 2)
m = ChemicalFeatures.GetAtomMatch(feats)
self.assertFalse(m)
mol = Chem.MolFromSmiles('c1ccccc1N')
feats = cfac.GetFeaturesForMol(mol)
self.assertTrue(len(feats) == 2)
m = ChemicalFeatures.GetAtomMatch(feats)
self.assertTrue(len(m) == 2)
def testIssue231(self):
fdefs = """
DefineFeature HDonor1 [N,O;!H0]
Family HBondDonor
Weights 1.0
EndFeature
DefineFeature HAcceptor1 [N,O;H0]
Family HBondAcceptor
Weights 1.0
EndFeature
"""
cfac = ChemicalFeatures.BuildFeatureFactoryFromString(fdefs)
m = Chem.MolFromSmiles('O=CCCN')
rdDistGeom.EmbedMolecule(m)
feats = cfac.GetFeaturesForMol(m)
for feat in feats:
feat.GetPos()
m = None
for feat in feats:
feat.GetPos()
def testGithub2603(self):
cfac = ChemicalFeatures.BuildFeatureFactory(
os.path.join(RDConfig.RDDataDir, "BaseFeatures.fdef"))
m = Chem.MolFromSmiles('OCc1ccccc1CN')
feats = cfac.GetFeaturesForMol(m)
self.assertEqual(feats[0].GetFamily(), 'Donor')
cfac = None
self.assertEqual(feats[0].GetFamily(), 'Donor')
def testGithub2530(self):
cfac = ChemicalFeatures.BuildFeatureFactory(
os.path.join(RDConfig.RDDataDir, "BaseFeatures.fdef"))
m = Chem.MolFromSmiles('C1CCC1OC')
rdDistGeom.EmbedMolecule(m)
feats = cfac.GetFeaturesForMol(m)
feat_pos = feats[0].GetPos(-1)
feat_pos_default = feats[0].GetPos()
self.assertEqual(feat_pos[0], feat_pos_default[0])
self.assertEqual(feat_pos[1], feat_pos_default[1])
self.assertEqual(feat_pos[2], feat_pos_default[2])
# Conformers generation:
m2 = Chem.AddHs(m)
AllChem.EmbedMultipleConfs(m2, numConfs=10, params=AllChem.ETKDG())
feats_0 = cfac.GetFeaturesForMol(m2, confId=-1)
feats_5 = cfac.GetFeaturesForMol(m2, confId=5)
self.assertNotEqual(feats_5[0], feats_0[0])
self.assertNotEqual(feats_5[1], feats_0[1])
self.assertNotEqual(feats_5[2], feats_0[2])
if __name__ == '__main__':
unittest.main()
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