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from rdkit import Chem
from rdkit import rdBase
from rdkit import RDConfig
import os
from rdkit.Chem import rdMolDescriptors as rdMD
from rdkit.Chem import AllChem
haveDescrs3D = hasattr(rdMD, 'CalcAUTOCORR3D')
import time, unittest
def _gen3D(m, is3d, calculator):
if not is3d:
m = Chem.AddHs(m)
ps = AllChem.ETKDG()
ps.randomSeed = 0xf00d
AllChem.EmbedMolecule(m, ps)
return calculator(m)
class TestCase(unittest.TestCase):
def setUp(self):
self.dataDir = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'Descriptors', 'test_data')
self.suppl = Chem.SDMolSupplier(os.path.join(self.dataDir, 'PBF_egfr.sdf'), removeHs=False)
@unittest.skipIf(not haveDescrs3D, "3d descriptors not present")
def test1AUTOCORR2D(self):
# not really a 3D descriptor, but this was added at the same time
with open(os.path.join(self.dataDir, 'auto2D.out')) as refFile:
for i, m in enumerate(self.suppl):
if i > 10:
break
nm = m.GetProp('_Name')
inl = refFile.readline()
split = inl.split('\t')
self.assertEqual(split[0], nm)
split.pop(0)
vs = rdMD.CalcAUTOCORR2D(m)
for rv, nv in zip(split, vs):
self.assertAlmostEqual(float(rv), nv, delta=0.05)
@unittest.skipIf(not haveDescrs3D, "3d descriptors not present")
def test2AUTOCORR3D(self):
with open(os.path.join(self.dataDir, 'auto3D_dragon.out')) as refFile:
for i, m in enumerate(self.suppl):
if i > 10:
break
nm = m.GetProp('_Name')
inl = refFile.readline()
split = inl.split('\t')
self.assertEqual(split[0], nm)
split.pop(0)
vs = _gen3D(m, True, rdMD.CalcAUTOCORR3D)
for rv, nv in zip(split, vs):
self.assertAlmostEqual(float(rv), nv, delta=0.05)
@unittest.skipIf(not haveDescrs3D, "3d descriptors not present")
def test3GETAWAY(self):
with open(os.path.join(self.dataDir, 'GETAWAY.new.out')) as refFile:
for i, m in enumerate(self.suppl):
if i > 10:
break
nm = m.GetProp('_Name')
inl = refFile.readline()
split = inl.split('\t')
self.assertEqual(split[0], nm)
split.pop(0)
vs = _gen3D(m, True, rdMD.CalcGETAWAY)
for rv, nv in zip(split, vs):
self.assertAlmostEqual(float(rv), nv, delta=0.05)
@unittest.skipIf(not haveDescrs3D, "3d descriptors not present")
def test4MORSE(self):
with open(os.path.join(self.dataDir, 'MORSE.out')) as refFile:
for i, m in enumerate(self.suppl):
if i > 10:
break
nm = m.GetProp('_Name')
inl = refFile.readline()
split = inl.split('\t')
self.assertEqual(split[0], nm)
split.pop(0)
vs = _gen3D(m, True, rdMD.CalcMORSE)
for rv, nv in zip(split, vs):
ref = float(rv)
self.assertTrue(ref < 1 or abs(ref - nv) / ref < 0.02)
@unittest.skipIf(not haveDescrs3D, "3d descriptors not present")
def test5RDF(self):
with open(os.path.join(self.dataDir, 'RDF.out')) as refFile:
for i, m in enumerate(self.suppl):
if i > 10:
break
nm = m.GetProp('_Name')
inl = refFile.readline()
split = inl.split('\t')
self.assertEqual(split[0], nm)
split.pop(0)
vs = _gen3D(m, True, rdMD.CalcRDF)
for rv, nv in zip(split, vs):
ref = float(rv)
self.assertTrue(ref < 0.5 or abs(ref - nv) / ref < 0.02)
@unittest.skipIf(not haveDescrs3D, "3d descriptors not present")
def test6WHIM(self):
with open(os.path.join(self.dataDir, 'whim.new.out')) as refFile:
for i, m in enumerate(self.suppl):
if i > 10:
break
nm = m.GetProp('_Name')
inl = refFile.readline()
split = inl.split('\t')
self.assertEqual(split[0], nm)
split.pop(0)
vs = _gen3D(m, True, lambda x: rdMD.CalcWHIM(x, thresh=0.01))
for rv, nv in zip(split, vs):
self.assertAlmostEqual(float(rv), nv, delta=0.01)
@unittest.skipIf(not haveDescrs3D, "3d descriptors not present")
def testGithub2037(self):
m = Chem.AddHs(Chem.MolFromSmiles("CCCCCCC"))
cids = AllChem.EmbedMultipleConfs(m, 10)
# start with defaults (which does not cache results):
npr1s = []
npr2s = []
for cid in cids:
npr1s.append(rdMD.CalcNPR1(m, confId=cid))
npr2s.append(rdMD.CalcNPR2(m, confId=cid))
for i in range(1, len(npr1s)):
self.assertNotAlmostEqual(npr1s[0], npr1s[i])
self.assertNotAlmostEqual(npr2s[0], npr2s[i])
# now ensure that we can cache:
npr1s = []
npr2s = []
for cid in cids:
npr1s.append(rdMD.CalcNPR1(m, confId=cid, force=False))
npr2s.append(rdMD.CalcNPR2(m, confId=cid, force=False))
for i in range(1, len(npr1s)):
self.assertAlmostEqual(npr1s[0], npr1s[i])
self.assertAlmostEqual(npr2s[0], npr2s[i])
if (__name__ == '__main__'):
unittest.main()
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