from rdkit import RDConfig import os,sys import unittest from rdkit import Chem from rdkit.Chem import rdFMCS class TestCase(unittest.TestCase): def setUp(self) : pass def test1(self): smis=( "Cc1nc(CN(C(C)c2ncccc2)CCCCN)ccc1 CHEMBL1682991", #-- QUERY "Cc1ccc(CN(C(C)c2ccccn2)CCCCN)nc1 CHEMBL1682990", "Cc1cccnc1CN(C(C)c1ccccn1)CCCCN CHEMBL1682998", "CC(N(CCCCN)Cc1c(N)cccn1)c1ccccn1 CHEMBL1682987", "Cc1cc(C)c(CN(C(C)c2ccccn2)CCCCN)nc1 CHEMBL1682992", "Cc1cc(C(C)N(CCCCN)Cc2c(C)cccn2)ncc1 CHEMBL1682993", "Cc1nc(C(C)N(CCCCN)Cc2nc3c([nH]2)cccc3)ccc1 CHEMBL1682878", "CC(c1ncccc1)N(CCCCN)Cc1nc2c([nH]1)cccc2 CHEMBL1682867", "CC(N(CCCCN)Cc1c(C(C)(C)C)cccn1)c1ccccn1 CHEMBL1682989", "CC(N(CCCCN)Cc1c(C(F)(F)F)cccn1)c1ccccn1 CHEMBL1682988", ) ms = [Chem.MolFromSmiles(x.split()[0]) for x in smis] qm = ms[0] ms = ms[1:] mcs = rdFMCS.FindMCS(ms) self.assertEqual(mcs.numBonds,21) self.assertEqual(mcs.numAtoms,21) self.assertEqual(mcs.smartsString,'[#6](:[#6]:[#6]):[#6]:[#7]:[#6]-[#6]-[#7](-[#6](-[#6])-[#6]1:[#6]:[#6]:[#6]:[#6]:[#7]:1)-[#6]-[#6]-[#6]-[#6]-[#7]') qm = Chem.MolFromSmarts(mcs.smartsString) self.failUnless(qm is not None) for m in ms: self.failUnless(m.HasSubstructMatch(qm)) mcs = rdFMCS.FindMCS(ms,threshold=0.8) self.assertEqual(mcs.numBonds,21) self.assertEqual(mcs.numAtoms,21) self.assertEqual(mcs.smartsString,'[#6](:[#6]:[#6]):[#6]:[#7]:[#6]-[#6]-[#7](-[#6](-[#6])-[#6]1:[#6]:[#6]:[#6]:[#6]:[#7]:1)-[#6]-[#6]-[#6]-[#6]-[#7]') qm = Chem.MolFromSmarts(mcs.smartsString) self.failUnless(qm is not None) for m in ms: self.failUnless(m.HasSubstructMatch(qm)) def test2(self): smis=( "CHEMBL122452 CN(CCCN(C)CCc1ccccc1)CCOC(c1ccccc1)c1ccccc1", "CHEMBL123252 CN(CCCc1ccccc1)CCCN(C)CCOC(c1ccccc1)c1ccccc1", "CHEMBL121611 Fc1ccc(C(OCCNCCCNCCc2ccccc2)c2ccc(F)cc2)cc1", "CHEMBL121050 O=C(Cc1ccccc1)NCCCCNCCOC(c1ccc(F)cc1)c1ccc(F)cc1", "CHEMBL333667 O=C(Cc1ccccc1)NCCNCCOC(c1ccc(F)cc1)c1ccc(F)cc1", "CHEMBL121486 O=C(Cc1ccc(Br)cc1)NC=CNCCOC(c1ccc(F)cc1)c1ccc(F)cc1", "CHEMBL123830 O=C(Cc1ccc(F)cc1)NCCNCCOC(c1ccc(F)cc1)c1ccc(F)cc1", "CHEMBL420900 O=C(Cc1ccccc1)NCCCNCCOC(c1ccc(F)cc1)c1ccc(F)cc1", "CHEMBL121460 CN(CCOC(c1ccc(F)cc1)c1ccc(F)cc1)CCN(C)CCOC(c1ccc(F)cc1)c1ccc(F)cc1", "CHEMBL120901 COC(=O)C1C2CCC(CC1C(=O)Oc1ccccc1)N2C", "CHEMBL122859 O=C1CN(CCc2ccccc2)CCN1CCOC(c1ccc(F)cc1)c1ccc(F)cc1", "CHEMBL121027 CN(CCOC(c1ccccc1)c1ccccc1)CCN(C)CCc1ccc(F)cc1", ) ms = [Chem.MolFromSmiles(x.split()[1]) for x in smis] qm = ms[0] ms = ms[1:] mcs = rdFMCS.FindMCS(ms) self.assertEqual(mcs.numBonds,9) self.assertEqual(mcs.numAtoms,10) qm = Chem.MolFromSmarts(mcs.smartsString) self.failUnless(qm is not None) for m in ms: self.failUnless(m.HasSubstructMatch(qm)) # smarts too hard to canonicalize this #self.assertEqual(mcs.smartsString,'[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6](-[#6]-[#8]-[#6]:,-[#6])-,:[#6]') mcs = rdFMCS.FindMCS(ms,threshold=0.8) self.assertEqual(mcs.numBonds,20) self.assertEqual(mcs.numAtoms,19) qm = Chem.MolFromSmarts(mcs.smartsString) self.failUnless(qm is not None) nHits=0 for m in ms: if m.HasSubstructMatch(qm): nHits+=1 self.failUnless(nHits>=int(0.8*len(smis))) # smarts too hard to canonicalize this #self.assertEqual(mcs.smartsString,'[#6]1:[#6]:[#6]:[#6](:[#6]:[#6]:1)-[#6](-[#8]-[#6]-[#6]-[#7]-[#6]-[#6])-[#6]2:[#6]:[#6]:[#6]:[#6]:[#6]:2') def test3IsotopeMatch(self): smis=( "CC[14NH2]", "CC[14CH3]", ) ms = [Chem.MolFromSmiles(x) for x in smis] mcs = rdFMCS.FindMCS(ms) self.assertEqual(mcs.numBonds,1) self.assertEqual(mcs.numAtoms,2) qm = Chem.MolFromSmarts(mcs.smartsString) mcs = rdFMCS.FindMCS(ms,atomCompare=rdFMCS.AtomCompare.CompareIsotopes) self.assertEqual(mcs.numBonds,2) self.assertEqual(mcs.numAtoms,3) qm = Chem.MolFromSmarts(mcs.smartsString) self.failUnless(Chem.MolFromSmiles('CC[14CH3]').HasSubstructMatch(qm)) self.failIf(Chem.MolFromSmiles('CC[13CH3]').HasSubstructMatch(qm)) self.failUnless(Chem.MolFromSmiles('OO[14CH3]').HasSubstructMatch(qm)) self.failIf(Chem.MolFromSmiles('O[13CH2][14CH3]').HasSubstructMatch(qm)) def test4RingMatches(self): smis = ['CCCCC','CCC1CCCCC1'] ms = [Chem.MolFromSmiles(x) for x in smis] mcs = rdFMCS.FindMCS(ms) self.assertEqual(mcs.numBonds,4) self.assertEqual(mcs.numAtoms,5) self.assertEqual(mcs.smartsString,'[#6]-[#6]-[#6]-[#6]-[#6]') mcs = rdFMCS.FindMCS(ms,completeRingsOnly=True) self.assertEqual(mcs.numBonds,2) self.assertEqual(mcs.numAtoms,3) self.assertEqual(mcs.smartsString,'[#6]-[#6]-[#6]') mcs = rdFMCS.FindMCS(ms,ringMatchesRingOnly=True) self.assertEqual(mcs.numBonds,2) self.assertEqual(mcs.numAtoms,3) self.assertEqual(mcs.smartsString,'[#6]-[#6]-[#6]') smis = ['CC1CCC1','CCC1CCCCC1'] ms = [Chem.MolFromSmiles(x) for x in smis] mcs = rdFMCS.FindMCS(ms) self.assertEqual(mcs.numBonds,4) self.assertEqual(mcs.numAtoms,5) self.assertEqual(mcs.smartsString,'[#6]-[#6](-[#6]-[#6])-[#6]') mcs = rdFMCS.FindMCS(ms,completeRingsOnly=True) self.assertEqual(mcs.numBonds,1) self.assertEqual(mcs.numAtoms,2) self.assertEqual(mcs.smartsString,'[#6]-[#6]') mcs = rdFMCS.FindMCS(ms,ringMatchesRingOnly=True) self.assertEqual(mcs.numBonds,4) self.assertEqual(mcs.numAtoms,5) self.assertEqual(mcs.smartsString,'[#6]-[#6](-[#6]-[#6])-[#6]') def test5AnyMatch(self): smis=('c1ccccc1C', 'c1ccccc1O', 'c1ccccc1Cl' ) ms = [Chem.MolFromSmiles(x) for x in smis] mcs = rdFMCS.FindMCS(ms,atomCompare=rdFMCS.AtomCompare.CompareAny) self.assertEqual(mcs.numBonds,7) self.assertEqual(mcs.numAtoms,7) qm = Chem.MolFromSmarts(mcs.smartsString) for m in ms: self.assertTrue(m.HasSubstructMatch(qm)) smis=('c1cccnc1C', 'c1cnncc1O', 'c1cccnc1Cl' ) ms = [Chem.MolFromSmiles(x) for x in smis] mcs = rdFMCS.FindMCS(ms,atomCompare=rdFMCS.AtomCompare.CompareAny) self.assertEqual(mcs.numBonds,7) self.assertEqual(mcs.numAtoms,7) qm = Chem.MolFromSmarts(mcs.smartsString) for m in ms: self.assertTrue(m.HasSubstructMatch(qm)) def test6MatchValences(self): ms = (Chem.MolFromSmiles('NC1OC1'),Chem.MolFromSmiles('C1OC1[N+](=O)[O-]')) mcs = rdFMCS.FindMCS(ms) self.assertEqual(mcs.numBonds,4) self.assertEqual(mcs.numAtoms,4) mcs = rdFMCS.FindMCS(ms,matchValences=True) self.assertEqual(mcs.numBonds,3) self.assertEqual(mcs.numAtoms,3) def test7Seed(self): smis = ['C1CCC1CC1CC1','C1CCC1OC1CC1','C1CCC1NC1CC1','C1CCC1SC1CC1'] ms = [Chem.MolFromSmiles(x) for x in smis] r = rdFMCS.FindMCS(ms) self.assertEqual(r.smartsString,"[#6]1-[#6]-[#6]-[#6]-1") r = rdFMCS.FindMCS(ms,seedSmarts='C1CC1') self.assertEqual(r.smartsString,"[#6]1-[#6]-[#6]-1") r = rdFMCS.FindMCS(ms,seedSmarts='C1OC1') self.assertEqual(r.smartsString,"") if __name__=="__main__": unittest.main()