def test_addpatterns(self):
pdb_ligands = [
"CCS(=O)(=O)c1ccc(OC)c(Nc2ncc(-c3cccc(-c4ccccn4)c3)o2)c1",
"COc1ccc(S(=O)(=O)NCC2CC2)cc1Nc1ncc(-c2cccc(-c3cccnc3)c2)o1",
"COc1ccc(-c2oc3ncnc(N)c3c2-c2ccc(NC(=O)Nc3cc(C(F)(F)F)ccc3F)cc2)cc1",
"COC(=O)Nc1nc2ccc(Oc3ccc(NC(=O)Nc4cc(C(F)(F)F)ccc4F)cc3)cc2[nH]1",
"COc1cc(Nc2ncnc(-c3cccnc3Nc3ccccc3)n2)cc(OC)c1OC",
"O=C(Nc1ccc(Oc2ccccc2)cc1)c1cccnc1NCc1ccncc1",
"O=C(Nc1ccc(Oc2ccccc2)cc1)c1cccnc1NCc1ccncc1",
"CNC(=O)c1cc(Oc2ccc3[nH]c(Nc4ccc(Cl)c(C(F)(F)F)c4)nc3c2)ccn1",
"CNC(=O)c1cc(Oc2ccc3oc(Nc4ccc(Cl)c(OCC5CCC[NH+]5C)c4)nc3c2)ccn1",
"CNC(=O)c1cc(Oc2ccc3oc(Nc4ccc(Cl)c(OCC5CCC[NH+]5C)c4)nc3c2)ccn1",
"COc1cc2nccc(Oc3ccc4c(c3)OCCN4C(=O)Nc3ccc(Cl)cc3)c2cc1OC",
"CNC(=O)c1c(C)oc2cc(Oc3cc[nH+]c4cc(OCCN5CCOCC5)ccc34)ccc12",
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)Nc5ccc(Cl)cc5)cccc4c3)c2cc1OC",
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)Nc5ccc(Cl)cc5)cccc4c3)c2cc1OC",
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)NC5CC5)cccc4c3)c2cc1OC",
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)NC5CC5)cccc4c3)c2cc1OC",
"Cc1ccc(C(=O)Nc2cc(CCC[NH+](C)C)cc(C(F)(F)F)c2)cc1Nc1ncccc1-c1ccncn1",
"COc1cc(Nc2nccc(Nc3ccc4c(C)n[nH]c4c3)n2)cc(OC)c1OC",
"COc1cc(Nc2nccc(N(C)c3ccc4c(C)n[nH]c4c3)n2)cc(OC)c1OC",
"Cc1ccn(-c2ccc3c(c2)NCC3(C)C)c(=O)c1-c1ccc2nc(N)ncc2c1",
"Cc1ccn(-c2ccc3c(c2)NCC3(C)C)c(=O)c1-c1ccc2nc(N)ncc2c1",
"Cc1ccc(C(=O)NCCC2CCCC2)cc1C(=O)Nc1ccc(N)nc1",
"Cc1ccc(C(=O)NCCC2CCCC2)cc1C(=O)Nc1ccc(N)nc1",
"Cc1ccn(-c2cccc(C(F)(F)F)c2)c(=O)c1-c1ccc2nc(N)ncc2c1",
"Cc1ccn(-c2cccc(C(F)(F)F)c2)c(=O)c1-c1ccc2nc(N)ncc2c1",
"O=C(Nc1cncnc1)c1c(Cl)ccc2c(Nc3cccc(C(F)(F)F)c3)noc12",
"O=C(Nc1cncnc1)c1c(Cl)ccc2c(Nc3cccc(C(F)(F)F)c3)noc12",
"CC1(C)CNc2cc(NC(=O)c3cccnc3NCc3ccncc3)ccc21",
"CC1(C)CNc2cc(NC(=O)c3cccnc3NCc3ccncc3)ccc21"
]
for patterns in [
rdSubstructLibrary.PatternHolder(),
rdSubstructLibrary.TautomerPatternHolder()
]:
mols = [Chem.MolFromSmiles(smi) for smi in pdb_ligands]
holder = rdSubstructLibrary.CachedMolHolder()
slib_with_patterns = rdSubstructLibrary.SubstructLibrary(
holder, patterns)
for mol in mols:
slib_with_patterns.AddMol(mol)
for nthreads in [1, 2, 0]:
slib_without_patterns = rdSubstructLibrary.SubstructLibrary(
holder, None)
rdSubstructLibrary.AddPatterns(slib_without_patterns, nthreads)
# check for seg fault
# were the fingerprints really created
slib_without_patterns.GetFpHolder().GetFingerprint(0)
for mol in mols:
l1 = slib_with_patterns.CountMatches(mol)
l2 = slib_without_patterns.CountMatches(mol)
self.assertTrue(l1)
self.assertEqual(l1, l2)
def test_basic_addpatterns(self):
# add mols
pdb_ligands = [
"CCS(=O)(=O)c1ccc(OC)c(Nc2ncc(-c3cccc(-c4ccccn4)c3)o2)c1",
"COc1ccc(S(=O)(=O)NCC2CC2)cc1Nc1ncc(-c2cccc(-c3cccnc3)c2)o1",
"COc1ccc(-c2oc3ncnc(N)c3c2-c2ccc(NC(=O)Nc3cc(C(F)(F)F)ccc3F)cc2)cc1",
"COC(=O)Nc1nc2ccc(Oc3ccc(NC(=O)Nc4cc(C(F)(F)F)ccc4F)cc3)cc2[nH]1",
"COc1cc(Nc2ncnc(-c3cccnc3Nc3ccccc3)n2)cc(OC)c1OC",
"O=C(Nc1ccc(Oc2ccccc2)cc1)c1cccnc1NCc1ccncc1",
"O=C(Nc1ccc(Oc2ccccc2)cc1)c1cccnc1NCc1ccncc1",
"CNC(=O)c1cc(Oc2ccc3[nH]c(Nc4ccc(Cl)c(C(F)(F)F)c4)nc3c2)ccn1",
"CNC(=O)c1cc(Oc2ccc3oc(Nc4ccc(Cl)c(OCC5CCC[NH+]5C)c4)nc3c2)ccn1",
"CNC(=O)c1cc(Oc2ccc3oc(Nc4ccc(Cl)c(OCC5CCC[NH+]5C)c4)nc3c2)ccn1",
"COc1cc2nccc(Oc3ccc4c(c3)OCCN4C(=O)Nc3ccc(Cl)cc3)c2cc1OC",
"CNC(=O)c1c(C)oc2cc(Oc3cc[nH+]c4cc(OCCN5CCOCC5)ccc34)ccc12",
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)Nc5ccc(Cl)cc5)cccc4c3)c2cc1OC",
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)Nc5ccc(Cl)cc5)cccc4c3)c2cc1OC",
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)NC5CC5)cccc4c3)c2cc1OC",
"COc1cc2[nH+]ccc(Oc3ccc4c(C(=O)NC5CC5)cccc4c3)c2cc1OC",
"Cc1ccc(C(=O)Nc2cc(CCC[NH+](C)C)cc(C(F)(F)F)c2)cc1Nc1ncccc1-c1ccncn1",
"COc1cc(Nc2nccc(Nc3ccc4c(C)n[nH]c4c3)n2)cc(OC)c1OC",
"COc1cc(Nc2nccc(N(C)c3ccc4c(C)n[nH]c4c3)n2)cc(OC)c1OC",
"Cc1ccn(-c2ccc3c(c2)NCC3(C)C)c(=O)c1-c1ccc2nc(N)ncc2c1",
"Cc1ccn(-c2ccc3c(c2)NCC3(C)C)c(=O)c1-c1ccc2nc(N)ncc2c1",
"Cc1ccc(C(=O)NCCC2CCCC2)cc1C(=O)Nc1ccc(N)nc1",
"Cc1ccc(C(=O)NCCC2CCCC2)cc1C(=O)Nc1ccc(N)nc1",
"Cc1ccn(-c2cccc(C(F)(F)F)c2)c(=O)c1-c1ccc2nc(N)ncc2c1",
"Cc1ccn(-c2cccc(C(F)(F)F)c2)c(=O)c1-c1ccc2nc(N)ncc2c1",
"O=C(Nc1cncnc1)c1c(Cl)ccc2c(Nc3cccc(C(F)(F)F)c3)noc12",
"O=C(Nc1cncnc1)c1c(Cl)ccc2c(Nc3cccc(C(F)(F)F)c3)noc12",
"CC1(C)CNc2cc(NC(=O)c3cccnc3NCc3ccncc3)ccc21",
"CC1(C)CNc2cc(NC(=O)c3cccnc3NCc3ccncc3)ccc21"
]
for holder in [
rdSubstructLibrary.CachedSmilesMolHolder(),
rdSubstructLibrary.CachedTrustedSmilesMolHolder()
]:
for smi in pdb_ligands:
holder.AddSmiles(smi)
for patttern in [
None,
rdSubstructLibrary.PatternHolder(),
rdSubstructLibrary.TautomerPatternHolder()
]:
lib = rdSubstructLibrary.SubstructLibrary(holder)
rdSubstructLibrary.AddPatterns(lib, numThreads=-1)
self.assertEqual(len(lib.GetMolHolder()),
len(lib.GetFpHolder()))
for smi in pdb_ligands:
self.assertTrue(lib.CountMatches(Chem.MolFromSmiles(smi)))