import sys import unittest from rdkit import Chem from rdkit.Chem import rdFMCS class BondMatchOrderMatrix: def __init__(self, ignoreAromatization): self.MatchMatrix = [[False] * (Chem.BondType.ZERO + 1) for i in range(Chem.BondType.ZERO + 1)] for i in range(Chem.BondType.ZERO + 1): # fill cells of the same and unspecified type self.MatchMatrix[i][i] = True self.MatchMatrix[Chem.BondType.UNSPECIFIED][i] = \ self.MatchMatrix[i][Chem.BondType.UNSPECIFIED] = True self.MatchMatrix[Chem.BondType.ZERO][i] = \ self.MatchMatrix[i][Chem.BondType.ZERO] = True if ignoreAromatization: self.MatchMatrix[Chem.BondType.SINGLE][Chem.BondType.AROMATIC] = \ self.MatchMatrix[Chem.BondType.AROMATIC][Chem.BondType.SINGLE] = True self.MatchMatrix[Chem.BondType.DOUBLE][Chem.BondType.AROMATIC] = \ self.MatchMatrix[Chem.BondType.AROMATIC][Chem.BondType.DOUBLE] = True self.MatchMatrix[Chem.BondType.SINGLE][Chem.BondType.ONEANDAHALF] = \ self.MatchMatrix[Chem.BondType.ONEANDAHALF][Chem.BondType.SINGLE] = True self.MatchMatrix[Chem.BondType.DOUBLE][Chem.BondType.TWOANDAHALF] = \ self.MatchMatrix[Chem.BondType.TWOANDAHALF][Chem.BondType.DOUBLE] = True self.MatchMatrix[Chem.BondType.TRIPLE][Chem.BondType.THREEANDAHALF] = \ self.MatchMatrix[Chem.BondType.THREEANDAHALF][Chem.BondType.TRIPLE] = True self.MatchMatrix[Chem.BondType.QUADRUPLE][Chem.BondType.FOURANDAHALF] = \ self.MatchMatrix[Chem.BondType.FOURANDAHALF][Chem.BondType.QUADRUPLE] = True self.MatchMatrix[Chem.BondType.QUINTUPLE][Chem.BondType.FIVEANDAHALF] = \ self.MatchMatrix[Chem.BondType.FIVEANDAHALF][Chem.BondType.QUINTUPLE] = True def isEqual(self, i, j): return self.MatchMatrix[i][j] class CompareAny(rdFMCS.MCSAtomCompare): def __call__(self, p, mol1, atom1, mol2, atom2): if (p.MatchChiralTag and not self.CheckAtomChirality(p, mol1, atom1, mol2, atom2)): return False if (p.MatchFormalCharge and not self.CheckAtomCharge(p, mol1, atom1, mol2, atom2)): return False if (p.RingMatchesRingOnly): return self.CheckAtomRingMatch(p, mol1, atom1, mol2, atom2) return True class CompareAnyHeavyAtom(CompareAny): def __call__(self, p, mol1, atom1, mol2, atom2): a1 = mol1.GetAtomWithIdx(atom1) a2 = mol2.GetAtomWithIdx(atom2) # Any atom, including H, matches another atom of the same type, according to # the other flags if (a1.GetAtomicNum() == a2.GetAtomicNum() or (a1.GetAtomicNum() > 1 and a2.GetAtomicNum() > 1)): return CompareAny.__call__(self, p, mol1, atom1, mol2, atom2) return False class CompareElements(rdFMCS.MCSAtomCompare): def __call__(self, p, mol1, atom1, mol2, atom2): a1 = mol1.GetAtomWithIdx(atom1) a2 = mol2.GetAtomWithIdx(atom2) if (a1.GetAtomicNum() != a2.GetAtomicNum()): return False if (p.MatchValences and a1.GetTotalValence() != a2.GetTotalValence()): return False if (p.MatchChiralTag and not self.CheckAtomChirality(p, mol1, atom1, mol2, atom2)): return False if (p.MatchFormalCharge and not self.CheckAtomCharge(p, mol1, atom1, mol2, atom2)): return False if p.RingMatchesRingOnly: return self.CheckAtomRingMatch(p, mol1, atom1, mol2, atom2) return True class CompareIsotopes(rdFMCS.MCSAtomCompare): def __call__(self, p, mol1, atom1, mol2, atom2): a1 = mol1.GetAtomWithIdx(atom1) a2 = mol2.GetAtomWithIdx(atom2) if (a1.GetIsotope() != a2.GetIsotope()): return False if (p.MatchChiralTag and not self.CheckAtomChirality(p, mol1, atom1, mol2, atom2)): return False if (p.MatchFormalCharge and not self.CheckAtomCharge(p, mol1, atom1, mol2, atom2)): return False if p.RingMatchesRingOnly: return self.CheckAtomRingMatch(p, mol1, atom1, mol2, atom2) return True class CompareOrder(rdFMCS.MCSBondCompare): match = BondMatchOrderMatrix(True) # ignore Aromatization def __call__(self, p, mol1, bond1, mol2, bond2): b1 = mol1.GetBondWithIdx(bond1) b2 = mol2.GetBondWithIdx(bond2) t1 = b1.GetBondType() t2 = b2.GetBondType() if self.match.isEqual(t1, t2): if (p.MatchStereo and not self.CheckBondStereo(p, mol1, bond1, mol2, bond2)): return False if p.RingMatchesRingOnly: return self.CheckBondRingMatch(p, mol1, bond1, mol2, bond2) return True return False class AtomCompareCompareIsInt(rdFMCS.MCSAtomCompare): __call__ = 1 class AtomCompareNoCompare(rdFMCS.MCSAtomCompare): pass class AtomCompareUserData(rdFMCS.MCSAtomCompare): def __init__(self): super().__init__() self._matchAnyHet = False def setMatchAnyHet(self, v): self._matchAnyHet = v def __call__(self, p, mol1, atom1, mol2, atom2): a1 = mol1.GetAtomWithIdx(atom1) a2 = mol2.GetAtomWithIdx(atom2) if (a1.GetAtomicNum() != a2.GetAtomicNum() and ((not self._matchAnyHet) or a1.GetAtomicNum() == 6 or a2.GetAtomicNum() == 6)): return False if (p.MatchValences and a1.GetTotalValence() != a2.GetTotalValence()): return False if (p.MatchChiralTag and not self.CheckAtomChirality(p, mol1, atom1, mol2, atom2)): return False if (p.MatchFormalCharge and not self.CheckAtomCharge(p, mol1, atom1, mol2, atom2)): return False if p.RingMatchesRingOnly: return self.CheckAtomRingMatch(p, mol1, atom1, mol2, atom2) return True class BondCompareCompareIsInt(rdFMCS.MCSBondCompare): __call__ = 1 class BondCompareNoCompare(rdFMCS.MCSBondCompare): pass class BondCompareUserData(rdFMCS.MCSBondCompare): def __init__(self): super().__init__() self.match = None def setIgnoreAromatization(self, v): self.match = BondMatchOrderMatrix(v) def __call__(self, p, mol1, bond1, mol2, bond2): b1 = mol1.GetBondWithIdx(bond1) b2 = mol2.GetBondWithIdx(bond2) t1 = b1.GetBondType() t2 = b2.GetBondType() if self.match.isEqual(t1, t2): if (p.MatchStereo and not self.CheckBondStereo(p, mol1, bond1, mol2, bond2)): return False if p.RingMatchesRingOnly: return self.CheckBondRingMatch(p, mol1, bond1, mol2, bond2) return True return False class ProgressCallbackCallbackIsInt(rdFMCS.MCSProgress): __call__ = 1 class ProgressCallbackNoCallback(rdFMCS.MCSProgress): pass class ProgressCallback(rdFMCS.MCSProgress): def __init__(self, parent): super().__init__() self.parent = parent self.callCount = 0 def __call__(self, stat, params): self.callCount += 1 self.parent.assertTrue(isinstance(stat, rdFMCS.MCSProgressData)) self.parent.assertTrue(hasattr(stat, "numAtoms")) self.parent.assertTrue(isinstance(stat.numAtoms, int)) self.parent.assertTrue(hasattr(stat, "numBonds")) self.parent.assertTrue(isinstance(stat.numBonds, int)) self.parent.assertTrue(hasattr(stat, "seedProcessed")) self.parent.assertTrue(isinstance(stat.seedProcessed, int)) self.parent.assertTrue(isinstance(params, rdFMCS.MCSParameters)) self.parent.assertTrue(isinstance(params.AtomTyper, rdFMCS.MCSAtomCompare)) self.parent.assertTrue(isinstance(params.BondTyper, rdFMCS.BondCompare)) self.parent.assertEqual(params.ProgressCallback, self) return (self.callCount < 3) class Test21AcceptanceCallbackCallbackIsInt(rdFMCS.MCSAcceptance): __call__ = 1 class Test21AcceptanceCallbackNoCallback(rdFMCS.MCSAcceptance): pass class Test21AcceptanceCallback(rdFMCS.MCSAcceptance): def __init__(self, parent): super().__init__() self.parent = parent def __call__(self, query, target, atom_idx_match, bond_idx_match, params): self.parent.assertTrue(isinstance(query, Chem.Mol)) self.parent.assertTrue(isinstance(target, Chem.Mol)) self.parent.assertGreater(len(atom_idx_match), 0) self.parent.assertTrue(len(atom_idx_match) == 1 or len(bond_idx_match) > 0) self.parent.assertTrue(isinstance(params, rdFMCS.MCSParameters)) self.parent.assertTrue(isinstance(params.AtomTyper, rdFMCS.MCSAtomCompare)) self.parent.assertTrue(isinstance(params.BondTyper, rdFMCS.BondCompare)) self.parent.assertEqual(params.ShouldAcceptMCS, self) for query_atom_idx, target_atom_idx in atom_idx_match: if query.GetAtomWithIdx(query_atom_idx).GetAtomicNum() == 0: return True if target.GetAtomWithIdx(target_atom_idx).GetAtomicNum() == 0: return True for query_bond_idx, target_bond_idx in bond_idx_match: self.parent.assertIsNotNone(query.GetBondWithIdx(query_bond_idx)) self.parent.assertIsNotNone(target.GetBondWithIdx(target_bond_idx)) return False class Test21AtomCompare(rdFMCS.MCSAtomCompare): def __init__(self): super().__init__() def __call__(self, p, mol1, atom1, mol2, atom2): a1 = mol1.GetAtomWithIdx(atom1) a2 = mol2.GetAtomWithIdx(atom2) a1_is_dummy = (a1.GetAtomicNum() == 0) a2_is_dummy = (a2.GetAtomicNum() == 0) if a1_is_dummy ^ a2_is_dummy: atoms = (a1, a2) dummy_atom_idx = 0 if a1_is_dummy else 1 other_atom_idx = 1 - dummy_atom_idx return atoms[dummy_atom_idx].GetDegree() == 1 and atoms[other_atom_idx].GetDegree() > 1 if a1.GetAtomicNum() != a2.GetAtomicNum(): return False return self.CheckAtomRingMatch(p, mol1, atom1, mol2, atom2) class Test21ProgressCallback(rdFMCS.MCSProgress): def __init__(self, parent): super().__init__() self.parent = parent self.callCount = 0 def __call__(self, stat, params): self.callCount += 1 self.parent.assertTrue(isinstance(stat, rdFMCS.MCSProgressData)) self.parent.assertTrue(hasattr(stat, "numAtoms")) self.parent.assertTrue(isinstance(stat.numAtoms, int)) self.parent.assertTrue(hasattr(stat, "numBonds")) self.parent.assertTrue(isinstance(stat.numBonds, int)) self.parent.assertTrue(hasattr(stat, "seedProcessed")) self.parent.assertTrue(isinstance(stat.seedProcessed, int)) self.parent.assertTrue(isinstance(params, rdFMCS.MCSParameters)) self.parent.assertTrue(isinstance(params.AtomTyper, rdFMCS.MCSAtomCompare)) self.parent.assertTrue(isinstance(params.BondTyper, rdFMCS.BondCompare)) self.parent.assertEqual(params.ProgressCallback, self) return True class Test21FinalMatchCheckCallbackCallbackIsInt(rdFMCS.MCSFinalMatchCheck): __call__ = 1 class Test21FinalMatchCheckCallbackNoCallback(rdFMCS.MCSFinalMatchCheck): pass class Test21FinalMatchCheckCallback(rdFMCS.MCSFinalMatchCheck): def __init__(self, parent): super().__init__() self.parent = parent self.callCount = 0 def __call__(self, mol1, mol2, atom_idx_match, bond_idx_match, params): self.callCount += 1 self.parent.assertTrue(isinstance(mol1, Chem.Mol)) self.parent.assertTrue(isinstance(mol2, Chem.Mol)) self.parent.assertGreater(len(atom_idx_match), 0) self.parent.assertGreater(len(bond_idx_match), 0) self.parent.assertTrue(isinstance(params, rdFMCS.MCSParameters)) self.parent.assertTrue(isinstance(params.AtomTyper, rdFMCS.MCSAtomCompare)) self.parent.assertTrue(isinstance(params.BondTyper, rdFMCS.BondCompare)) self.parent.assertEqual(params.FinalMatchChecker, self) return True class Common: @staticmethod def getParams(**kwargs): params = rdFMCS.MCSParameters() for kw in ("AtomTyper", "BondTyper"): v = kwargs.get(kw, None) if v is not None: v_instance = v() setattr(params, kw, v_instance) return params @staticmethod def test1(self, **kwargs): 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:] if kwargs: params = Common.getParams(**kwargs) mcs = rdFMCS.FindMCS(ms, params) else: 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.assertTrue(qm is not None) for m in ms: self.assertTrue(m.HasSubstructMatch(qm)) if kwargs: params = Common.getParams(**kwargs) params.Threshold = 0.8 mcs = rdFMCS.FindMCS(ms, params) else: 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.assertTrue(qm is not None) for m in ms: self.assertTrue(m.HasSubstructMatch(qm)) def test2(self, **kwargs): 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:] if kwargs: params = Common.getParams(**kwargs) mcs = rdFMCS.FindMCS(ms, params) else: mcs = rdFMCS.FindMCS(ms) self.assertEqual(mcs.numBonds, 9) self.assertEqual(mcs.numAtoms, 10) qm = Chem.MolFromSmarts(mcs.smartsString) self.assertTrue(qm is not None) for m in ms: self.assertTrue(m.HasSubstructMatch(qm)) # smarts too hard to canonicalize this # self.assertEqual(mcs.smartsString,'[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6](-[#6]-[#8]-[#6]:,-[#6])-,:[#6]') if kwargs: params = Common.getParams(**kwargs) params.Threshold = 0.8 mcs = rdFMCS.FindMCS(ms, params) else: mcs = rdFMCS.FindMCS(ms, threshold=0.8) self.assertEqual(mcs.numBonds, 20) self.assertEqual(mcs.numAtoms, 19) qm = Chem.MolFromSmarts(mcs.smartsString) self.assertTrue(qm is not None) nHits = 0 for m in ms: if m.HasSubstructMatch(qm): nHits += 1 self.assertTrue(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, **kwargs): smis = ( "CC[14NH2]", "CC[14CH3]", ) ms = [Chem.MolFromSmiles(x) for x in smis] if kwargs: params = Common.getParams(**kwargs) mcs = rdFMCS.FindMCS(ms, params) else: mcs = rdFMCS.FindMCS(ms) self.assertEqual(mcs.numBonds, 1) self.assertEqual(mcs.numAtoms, 2) qm = Chem.MolFromSmarts(mcs.smartsString) if kwargs: params = Common.getParams(**kwargs) params.AtomTyper = CompareIsotopes() params.AtomCompareParameters.MatchIsotope = True mcs = rdFMCS.FindMCS(ms, params) else: mcs = rdFMCS.FindMCS(ms, atomCompare=rdFMCS.AtomCompare.CompareIsotopes) self.assertEqual(mcs.numBonds, 2) self.assertEqual(mcs.numAtoms, 3) qm = Chem.MolFromSmarts(mcs.smartsString) self.assertTrue(Chem.MolFromSmiles('CC[14CH3]').HasSubstructMatch(qm)) self.assertFalse(Chem.MolFromSmiles('CC[13CH3]').HasSubstructMatch(qm)) self.assertTrue(Chem.MolFromSmiles('OO[14CH3]').HasSubstructMatch(qm)) self.assertFalse(Chem.MolFromSmiles('O[13CH2][14CH3]').HasSubstructMatch(qm)) def test4RingMatches(self, **kwargs): smis = ['CCCCC', 'CCC1CCCCC1'] ms = [Chem.MolFromSmiles(x) for x in smis] if kwargs: params = Common.getParams(**kwargs) mcs = rdFMCS.FindMCS(ms, params) else: mcs = rdFMCS.FindMCS(ms) self.assertEqual(mcs.numBonds, 4) self.assertEqual(mcs.numAtoms, 5) self.assertEqual(mcs.smartsString, '[#6]-[#6]-[#6]-[#6]-[#6]') if kwargs: params = Common.getParams(**kwargs) params.BondCompareParameters.CompleteRingsOnly = True mcs = rdFMCS.FindMCS(ms, params) else: mcs = rdFMCS.FindMCS(ms, completeRingsOnly=True) self.assertEqual(mcs.numBonds, 2) self.assertEqual(mcs.numAtoms, 3) self.assertEqual(mcs.smartsString, '[#6]-&!@[#6]-&!@[#6]') if kwargs: params = Common.getParams(**kwargs) params.BondCompareParameters.CompleteRingsOnly = True params.BondCompareParameters.MatchFusedRings = True params.BondCompareParameters.MatchFusedRingsStrict = False mcs = rdFMCS.FindMCS(ms, params) else: mcs = rdFMCS.FindMCS(ms, completeRingsOnly=True, ringCompare=rdFMCS.RingCompare.PermissiveRingFusion) self.assertEqual(mcs.numBonds, 2) self.assertEqual(mcs.numAtoms, 3) self.assertEqual(mcs.smartsString, '[#6]-&!@[#6]-&!@[#6]') if kwargs: params = Common.getParams(**kwargs) params.BondCompareParameters.CompleteRingsOnly = True params.BondCompareParameters.MatchFusedRings = True params.BondCompareParameters.MatchFusedRingsStrict = True mcs = rdFMCS.FindMCS(ms, params) else: mcs = rdFMCS.FindMCS(ms, completeRingsOnly=True, ringCompare=rdFMCS.RingCompare.StrictRingFusion) self.assertEqual(mcs.numBonds, 2) self.assertEqual(mcs.numAtoms, 3) self.assertEqual(mcs.smartsString, '[#6]-&!@[#6]-&!@[#6]') if kwargs: params = Common.getParams(**kwargs) params.AtomCompareParameters.RingMatchesRingOnly = True params.BondCompareParameters.RingMatchesRingOnly = True mcs = rdFMCS.FindMCS(ms, params) else: mcs = rdFMCS.FindMCS(ms, ringMatchesRingOnly=True) self.assertEqual(mcs.numBonds, 1) self.assertEqual(mcs.numAtoms, 2) self.assertEqual(mcs.smartsString, '[#6&!R]-&!@[#6&!R]') smis = ['CC1CCC1', 'CCC1CCCCC1'] ms = [Chem.MolFromSmiles(x) for x in smis] if kwargs: params = Common.getParams(**kwargs) mcs = rdFMCS.FindMCS(ms, params) else: mcs = rdFMCS.FindMCS(ms) self.assertEqual(mcs.numBonds, 4) self.assertEqual(mcs.numAtoms, 5) self.assertEqual(mcs.smartsString, '[#6]-[#6](-[#6]-[#6])-[#6]') if kwargs: params = Common.getParams(**kwargs) params.BondCompareParameters.CompleteRingsOnly = True mcs = rdFMCS.FindMCS(ms, params) else: mcs = rdFMCS.FindMCS(ms, completeRingsOnly=True) self.assertEqual(mcs.numBonds, 1) self.assertEqual(mcs.numAtoms, 2) self.assertEqual(mcs.smartsString, '[#6]-&!@[#6]') if kwargs: params = Common.getParams(**kwargs) params.AtomCompareParameters.RingMatchesRingOnly = True params.BondCompareParameters.CompleteRingsOnly = True params.BondCompareParameters.RingMatchesRingOnly = True mcs = rdFMCS.FindMCS(ms, params) else: mcs = rdFMCS.FindMCS(ms, ringMatchesRingOnly=True, completeRingsOnly=True) self.assertEqual(mcs.numBonds, 1) self.assertEqual(mcs.numAtoms, 2) self.assertEqual(mcs.smartsString, '[#6&!R]-&!@[#6&R]') if kwargs: params = Common.getParams(**kwargs) params.AtomCompareParameters.RingMatchesRingOnly = True params.BondCompareParameters.CompleteRingsOnly = True params.BondCompareParameters.RingMatchesRingOnly = True params.BondCompareParameters.MatchFusedRings = True params.BondCompareParameters.MatchFusedRingsStrict = False mcs = rdFMCS.FindMCS(ms, params) else: mcs = rdFMCS.FindMCS(ms, ringMatchesRingOnly=True, completeRingsOnly=True, ringCompare=rdFMCS.RingCompare.PermissiveRingFusion) self.assertEqual(mcs.numBonds, 1) self.assertEqual(mcs.numAtoms, 2) self.assertEqual(mcs.smartsString, '[#6&!R]-&!@[#6&R]') if kwargs: params = Common.getParams(**kwargs) params.AtomCompareParameters.RingMatchesRingOnly = True params.BondCompareParameters.CompleteRingsOnly = True params.BondCompareParameters.RingMatchesRingOnly = True params.BondCompareParameters.MatchFusedRings = True params.BondCompareParameters.MatchFusedRingsStrict = True mcs = rdFMCS.FindMCS(ms, params) else: mcs = rdFMCS.FindMCS(ms, ringMatchesRingOnly=True, completeRingsOnly=True, ringCompare=rdFMCS.RingCompare.StrictRingFusion) self.assertEqual(mcs.numBonds, 1) self.assertEqual(mcs.numAtoms, 2) self.assertEqual(mcs.smartsString, '[#6&!R]-&!@[#6&R]') if kwargs: params = Common.getParams(**kwargs) params.AtomCompareParameters.RingMatchesRingOnly = True params.BondCompareParameters.RingMatchesRingOnly = True mcs = rdFMCS.FindMCS(ms, params) else: mcs = rdFMCS.FindMCS(ms, ringMatchesRingOnly=True) self.assertEqual(mcs.numBonds, 4) self.assertEqual(mcs.numAtoms, 5) self.assertEqual(mcs.smartsString, '[#6&!R]-&!@[#6&R](-&@[#6&R]-&@[#6&R])-&@[#6&R]') def test5AnyMatch(self, **kwargs): smis = ('c1ccccc1C', 'c1ccccc1O', 'c1ccccc1Cl') ms = [Chem.MolFromSmiles(x) for x in smis] if kwargs: params = Common.getParams(**kwargs) params.AtomTyper = CompareAny() mcs = rdFMCS.FindMCS(ms, params) else: 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] if kwargs: params = Common.getParams(**kwargs) params.AtomTyper = CompareAny() mcs = rdFMCS.FindMCS(ms, params) else: 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 testAtomCompareAnyHeavyAtom(self, **kwargs): # H matches H, O matches C smis = ('[H]c1ccccc1C', '[H]c1ccccc1O') ms = [Chem.MolFromSmiles(x, sanitize=False) for x in smis] if kwargs: params = Common.getParams(**kwargs) params.AtomTyper = CompareAnyHeavyAtom() mcs = rdFMCS.FindMCS(ms, params) else: mcs = rdFMCS.FindMCS(ms, atomCompare=rdFMCS.AtomCompare.CompareAnyHeavyAtom) self.assertEqual(mcs.numBonds, 8) self.assertEqual(mcs.numAtoms, 8) qm = Chem.MolFromSmarts(mcs.smartsString) for m in ms: self.assertTrue(m.HasSubstructMatch(qm)) def testAtomCompareAnyHeavyAtom1(self, **kwargs): # O matches C, H does not match O smis = ('[H]c1ccccc1C', 'Oc1ccccc1O') ms = [Chem.MolFromSmiles(x, sanitize=False) for x in smis] if kwargs: params = Common.getParams(**kwargs) params.AtomTyper = CompareAnyHeavyAtom() mcs = rdFMCS.FindMCS(ms, params) else: mcs = rdFMCS.FindMCS(ms, atomCompare=rdFMCS.AtomCompare.CompareAnyHeavyAtom) 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, **kwargs): ms = (Chem.MolFromSmiles('NC1OC1'), Chem.MolFromSmiles('C1OC1[N+](=O)[O-]')) if kwargs: params = Common.getParams(**kwargs) mcs = rdFMCS.FindMCS(ms, params) else: mcs = rdFMCS.FindMCS(ms) self.assertEqual(mcs.numBonds, 4) self.assertEqual(mcs.numAtoms, 4) if kwargs: params = Common.getParams(**kwargs) params.AtomCompareParameters.MatchValences = True mcs = rdFMCS.FindMCS(ms, params) else: mcs = rdFMCS.FindMCS(ms, matchValences=True) self.assertEqual(mcs.numBonds, 3) self.assertEqual(mcs.numAtoms, 3) def test7Seed(self, **kwargs): smis = ['C1CCC1CC1CC1', 'C1CCC1OC1CC1', 'C1CCC1NC1CC1', 'C1CCC1SC1CC1'] ms = [Chem.MolFromSmiles(x) for x in smis] if kwargs: params = Common.getParams(**kwargs) r = rdFMCS.FindMCS(ms, params) else: r = rdFMCS.FindMCS(ms) self.assertEqual(r.smartsString, "[#6]1-[#6]-[#6]-[#6]-1") if kwargs: params = Common.getParams(**kwargs) params.InitialSeed = 'C1CC1' r = rdFMCS.FindMCS(ms, params) else: r = rdFMCS.FindMCS(ms, seedSmarts='C1CC1') self.assertEqual(r.smartsString, "[#6]1-[#6]-[#6]-1") if kwargs: params = Common.getParams(**kwargs) params.InitialSeed = 'C1OC1' r = rdFMCS.FindMCS(ms, params) else: r = rdFMCS.FindMCS(ms, seedSmarts='C1OC1') self.assertEqual(r.smartsString, "[#6]1-[#6]-[#6]-[#6]-1") self.assertEqual(r.numAtoms, 4) self.assertEqual(r.numBonds, 4) if kwargs: params = Common.getParams(**kwargs) params.InitialSeed = 'C1OC1' params.AtomCompareParameters.RingMatchesRingOnly = True params.BondCompareParameters.RingMatchesRingOnly = True r = rdFMCS.FindMCS(ms, params) else: r = rdFMCS.FindMCS(ms, seedSmarts='C1OC1', ringMatchesRingOnly=True) self.assertEqual(r.smartsString, "[#6]1-&@[#6]-&@[#6]-&@[#6]-&@1") self.assertEqual(r.numAtoms, 4) self.assertEqual(r.numBonds, 4) if kwargs: params = Common.getParams(**kwargs) params.InitialSeed = 'C1OC1' params.BondCompareParameters.CompleteRingsOnly = True r = rdFMCS.FindMCS(ms, params) else: r = rdFMCS.FindMCS(ms, seedSmarts='C1OC1', completeRingsOnly=True) self.assertEqual(r.smartsString, "[#6]1-&@[#6]-&@[#6]-&@[#6]-&@1") self.assertEqual(r.numAtoms, 4) self.assertEqual(r.numBonds, 4) def test8MatchParams(self, **kwargs): smis = ("CCC1NC1", "CCC1N(C)C1", "CCC1OC1") ms = [Chem.MolFromSmiles(x) for x in smis] if kwargs: ps = Common.getParams(**kwargs) mcs = rdFMCS.FindMCS(ms, ps) else: mcs = rdFMCS.FindMCS(ms) self.assertEqual(mcs.numAtoms, 4) ps = Common.getParams(**kwargs) ps.BondCompareParameters.CompleteRingsOnly = True mcs = rdFMCS.FindMCS(ms, ps) self.assertEqual(mcs.numAtoms, 3) ps = Common.getParams(**kwargs) ps.BondCompareParameters.CompleteRingsOnly = True ps.BondCompareParameters.MatchFusedRings = True mcs = rdFMCS.FindMCS(ms, ps) self.assertEqual(mcs.numAtoms, 3) ps = Common.getParams(**kwargs) ps.BondCompareParameters.CompleteRingsOnly = True ps.BondCompareParameters.MatchFusedRingsStrict = True mcs = rdFMCS.FindMCS(ms, ps) self.assertEqual(mcs.numAtoms, 3) ps = Common.getParams(**kwargs) if kwargs: ps.AtomTyper = CompareAny() else: ps.AtomTyper = rdFMCS.AtomCompare.CompareAny mcs = rdFMCS.FindMCS(ms, ps) self.assertEqual(mcs.numAtoms, 5) def test9MatchCharge(self, **kwargs): smis = ("CCNC", "CCN(C)C", "CC[N+](C)C") ms = [Chem.MolFromSmiles(x) for x in smis] if kwargs: ps = Common.getParams(**kwargs) mcs = rdFMCS.FindMCS(ms, ps) else: mcs = rdFMCS.FindMCS(ms) self.assertEqual(mcs.numAtoms, 4) ps = Common.getParams(**kwargs) ps.AtomCompareParameters.MatchFormalCharge = True mcs = rdFMCS.FindMCS(ms, ps) self.assertEqual(mcs.numAtoms, 2) def test10MatchChargeAndParams(self, **kwargs): smis = ("CCNC", "CCN(C)C", "CC[N+](C)C", "CC[C+](C)C") ms = [Chem.MolFromSmiles(x) for x in smis] if kwargs: ps = Common.getParams(**kwargs) mcs = rdFMCS.FindMCS(ms, ps) else: mcs = rdFMCS.FindMCS(ms) self.assertEqual(mcs.numAtoms, 2) ps = Common.getParams(**kwargs) if kwargs: ps.AtomTyper = CompareAny() else: ps.AtomTyper = rdFMCS.AtomCompare.CompareAny mcs = rdFMCS.FindMCS(ms, ps) self.assertEqual(mcs.numAtoms, 4) ps = Common.getParams(**kwargs) ps.AtomCompareParameters.MatchFormalCharge = True mcs = rdFMCS.FindMCS(ms, ps) self.assertEqual(mcs.numAtoms, 2) def test11Github2034(self, **kwargs): smis = ("C1CC1N2CC2", "C1CC1N") ms = [Chem.MolFromSmiles(x) for x in smis] if kwargs: ps = Common.getParams(**kwargs) mcs = rdFMCS.FindMCS(ms, ps) else: mcs = rdFMCS.FindMCS(ms) self.assertEqual(mcs.numAtoms, 4) self.assertEqual(mcs.numBonds, 4) if kwargs: ps = Common.getParams(**kwargs) ps.AtomCompareParameters.RingMatchesRingOnly = True ps.BondCompareParameters.RingMatchesRingOnly = True mcs = rdFMCS.FindMCS(ms, ps) else: mcs = rdFMCS.FindMCS(ms, ringMatchesRingOnly=True) self.assertEqual(mcs.numAtoms, 3) self.assertEqual(mcs.numBonds, 3) ps = Common.getParams(**kwargs) ps.AtomCompareParameters.RingMatchesRingOnly = True mcs = rdFMCS.FindMCS(ms, ps) self.assertEqual(mcs.numAtoms, 3) self.assertEqual(mcs.numBonds, 3) def test19MCS3d(self, **kwargs): block1 = """ RDKit 3D 17 17 0 0 0 0 0 0 0 0999 V2000 0.1592 0.8577 0.8639 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9090 0.9385 -0.2218 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1866 -0.4482 -0.7339 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0705 -1.1345 -1.1348 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8460 -1.2511 -0.0884 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3508 0.1733 0.1788 C 0 0 1 0 0 0 0 0 0 0 0 0 1.6294 0.7269 -1.0491 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.2088 0.1739 1.6399 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4334 1.8588 1.2198 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8657 1.3295 0.1967 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.5185 1.5822 -1.0340 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7155 -1.0290 0.0396 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8809 -0.3833 -1.6049 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6828 -1.9159 -0.3875 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3276 -1.6370 0.8016 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2158 0.0912 0.8546 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6002 1.6926 -1.1014 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 6 1 1 0 1 8 1 0 1 9 1 0 2 10 1 0 2 11 1 0 3 12 1 0 3 13 1 0 5 14 1 0 5 15 1 0 6 16 1 1 7 17 1 0 M END """ block2 = """ RDKit 3D 17 17 0 0 0 0 0 0 0 0999 V2000 0.1592 0.8577 0.8639 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.9090 0.9385 -0.2218 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.1866 -0.4482 -0.7339 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.0705 -1.1345 -1.1348 O 0 0 0 0 0 0 0 0 0 0 0 0 0.8460 -1.2511 -0.0884 C 0 0 0 0 0 0 0 0 0 0 0 0 1.3508 0.1733 0.1788 C 0 0 2 0 0 0 0 0 0 0 0 0 2.4771 0.1924 0.9509 O 0 0 0 0 0 0 0 0 0 0 0 0 -0.1638 0.2755 1.7318 H 0 0 0 0 0 0 0 0 0 0 0 0 0.4849 1.8825 1.0902 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4598 1.5686 -1.0290 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8337 1.3595 0.1902 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.8991 -0.3820 -1.5700 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.6394 -1.0265 0.1178 H 0 0 0 0 0 0 0 0 0 0 0 0 1.6816 -1.9167 -0.3664 H 0 0 0 0 0 0 0 0 0 0 0 0 0.3727 -1.5979 0.8445 H 0 0 0 0 0 0 0 0 0 0 0 0 1.4834 0.6899 -0.7827 H 0 0 0 0 0 0 0 0 0 0 0 0 2.2370 0.0336 1.8861 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 4 1 0 4 5 1 0 5 6 1 0 6 7 1 0 6 1 1 0 1 8 1 0 1 9 1 0 2 10 1 0 2 11 1 0 3 12 1 0 3 13 1 0 5 14 1 0 5 15 1 0 6 16 1 6 7 17 1 0 M END """ m1 = Chem.MolFromMolBlock(block1, removeHs=False) m2 = Chem.MolFromMolBlock(block2, removeHs=False) ps = Common.getParams(**kwargs) ps.AtomCompareParameters.MaxDistance = 1.0 mcs = rdFMCS.FindMCS([m1, m2], ps) self.assertEqual(mcs.numAtoms, 14) self.assertEqual(mcs.numBonds, 14) class TestCase(unittest.TestCase): def setUp(self): pass def test1(self): Common.test1(self) def test1PythonImpl(self): Common.test1(self, AtomTyper=CompareElements, BondTyper=CompareOrder) def test2(self): Common.test2(self) def test2PythonImpl(self): Common.test2(self, AtomTyper=CompareElements, BondTyper=CompareOrder) def test2PythonImplAtomTyperOnly(self): Common.test2(self, AtomTyper=CompareElements) def test2PythonImplBondTyperOnly(self): Common.test2(self, BondTyper=CompareOrder) def test3IsotopeMatch(self): Common.test3IsotopeMatch(self) def test3IsotopeMatchPythonImpl(self): Common.test3IsotopeMatch(self, AtomTyper=CompareElements, BondTyper=CompareOrder) def test3IsotopeMatchPythonImplAtomTyperOnly(self): Common.test3IsotopeMatch(self, AtomTyper=CompareElements) def test3IsotopeMatchPythonImplBondTyperOnly(self): Common.test3IsotopeMatch(self, BondTyper=CompareOrder) def test4RingMatches(self): Common.test4RingMatches(self) def test4RingMatchesPythonImpl(self): Common.test4RingMatches(self, AtomTyper=CompareElements, BondTyper=CompareOrder) def test4RingMatchesPythonImplAtomTyperOnly(self): Common.test4RingMatches(self, AtomTyper=CompareElements) def test4RingMatchesPythonImplBondTyperOnly(self): Common.test4RingMatches(self, BondTyper=CompareOrder) def test5AnyMatch(self): Common.test5AnyMatch(self) def test5AnyMatchPythonImpl(self): Common.test5AnyMatch(self, AtomTyper=CompareElements, BondTyper=CompareOrder) def test5AnyMatchPythonImplAtomTyperOnly(self): Common.test5AnyMatch(self, AtomTyper=CompareElements) def test5AnyMatchPythonImplBondTyperOnly(self): Common.test5AnyMatch(self, BondTyper=CompareOrder) def testAtomCompareAnyHeavyAtom(self): Common.testAtomCompareAnyHeavyAtom(self) def testAtomCompareAnyHeavyAtomPythonImpl(self): Common.testAtomCompareAnyHeavyAtom(self, AtomTyper=CompareElements, BondTyper=CompareOrder) def testAtomCompareAnyHeavyAtomPythonImplAtomTyperOnly(self): Common.testAtomCompareAnyHeavyAtom(self, AtomTyper=CompareElements) def testAtomCompareAnyHeavyAtomPythonImplBondTyperOnly(self): Common.testAtomCompareAnyHeavyAtom(self, BondTyper=CompareOrder) def testAtomCompareAnyHeavyAtom1(self): Common.testAtomCompareAnyHeavyAtom1(self) def testAtomCompareAnyHeavyAtom1PythonImpl(self): Common.testAtomCompareAnyHeavyAtom1(self, AtomTyper=CompareElements, BondTyper=CompareOrder) def testAtomCompareAnyHeavyAtom1PythonImplAtomTyperOnly(self): Common.testAtomCompareAnyHeavyAtom1(self, AtomTyper=CompareElements) def testAtomCompareAnyHeavyAtom1PythonImplBondTyperOnly(self): Common.testAtomCompareAnyHeavyAtom1(self, BondTyper=CompareOrder) def test6MatchValences(self): Common.test6MatchValences(self) def test6MatchValencesPythonImpl(self): Common.test6MatchValences(self, AtomTyper=CompareElements, BondTyper=CompareOrder) def test6MatchValencesPythonImplAtomTyperOnly(self): Common.test6MatchValences(self, AtomTyper=CompareElements) def test6MatchValencesPythonImplBondTyperOnly(self): Common.test6MatchValences(self, BondTyper=CompareOrder) def test7Seed(self): Common.test7Seed(self) def test7SeedPythonImpl(self): Common.test7Seed(self, AtomTyper=CompareElements, BondTyper=CompareOrder) def test7SeedPythonImplAtomTyperOnly(self): Common.test7Seed(self, AtomTyper=CompareElements) def test7SeedPythonImplBondTyperOnly(self): Common.test7Seed(self, BondTyper=CompareOrder) def test8MatchParams(self): Common.test8MatchParams(self) def test8MatchParamsPythonImpl(self): Common.test8MatchParams(self, AtomTyper=CompareElements, BondTyper=CompareOrder) def test8MatchParamsPythonImplAtomTyperOnly(self): Common.test8MatchParams(self, AtomTyper=CompareElements) def test8MatchParamsPythonImplBondTyperOnly(self): Common.test8MatchParams(self, BondTyper=CompareOrder) def test9MatchCharge(self): Common.test9MatchCharge(self) def test9MatchChargePythonImpl(self): Common.test9MatchCharge(self, AtomTyper=CompareElements, BondTyper=CompareOrder) def test9MatchChargePythonImplAtomTyperOnly(self): Common.test9MatchCharge(self, AtomTyper=CompareElements) def test9MatchChargePythonImplBondTyperOnly(self): Common.test9MatchCharge(self, BondTyper=CompareOrder) def test10MatchChargeAndParams(self): Common.test10MatchChargeAndParams(self) def test10MatchChargeAndParamsPythonImpl(self): Common.test10MatchChargeAndParams(self, AtomTyper=CompareElements, BondTyper=CompareOrder) def test10MatchChargeAndParamsPythonImplAtomTyperOnly(self): Common.test10MatchChargeAndParams(self, AtomTyper=CompareElements) def test10MatchChargeAndParamsPythonImplBondTyperOnly(self): Common.test10MatchChargeAndParams(self, BondTyper=CompareOrder) def test11Github2034(self): Common.test11Github2034(self) def test11Github2034PythonImpl(self): Common.test11Github2034(self, AtomTyper=CompareElements, BondTyper=CompareOrder) def test11Github2034PythonImplAtomTyperOnly(self): Common.test11Github2034(self, AtomTyper=CompareElements) def test11Github2034PythonImplBondTyperOnly(self): Common.test11Github2034(self, BondTyper=CompareOrder) def test12MCSAtomCompareExceptions(self): ps = rdFMCS.MCSParameters() smis = ['CCCCC', 'CCC1CCCCC1'] ms = [Chem.MolFromSmiles(x) for x in smis] self.assertRaises(TypeError, lambda ps: setattr(ps, "AtomTyper", AtomCompareCompareIsInt())) self.assertRaises(TypeError, lambda ps: setattr(ps, "AtomTyper", AtomCompareNoCompare())) def test13MCSAtomCompareUserData(self): smis = ['CCOCCOC', 'CCNCCCC'] ms = [Chem.MolFromSmiles(x) for x in smis] ps = rdFMCS.MCSParameters() ps.AtomTyper = AtomCompareUserData() ps.AtomTyper.setMatchAnyHet(False) mcs = rdFMCS.FindMCS(ms, ps) self.assertEqual(mcs.numAtoms, 2) ps.AtomTyper.setMatchAnyHet(True) mcs = rdFMCS.FindMCS(ms, ps) self.assertEqual(mcs.numAtoms, 5) def test14MCSBondCompareExceptions(self): ps = rdFMCS.MCSParameters() smis = ['CCCCC', 'CCC1CCCCC1'] ms = [Chem.MolFromSmiles(x) for x in smis] self.assertRaises(TypeError, lambda ps: setattr(ps, "BondTyper", BondCompareCompareIsInt())) self.assertRaises(TypeError, lambda ps: setattr(ps, "BondTyper", BondCompareNoCompare())) def test15MCSBondCompareUserData(self): smis = ['C1CC=CCC1', 'c1ccccc1'] ms = [Chem.MolFromSmiles(x) for x in smis] ps = rdFMCS.MCSParameters() ps.BondTyper = BondCompareUserData() ps.BondCompareParameters.CompleteRingsOnly = True ps.BondTyper.setIgnoreAromatization(False) mcs = rdFMCS.FindMCS(ms, ps) self.assertEqual(mcs.numAtoms, 0) ps.BondTyper.setIgnoreAromatization(True) mcs = rdFMCS.FindMCS(ms, ps) self.assertEqual(mcs.numAtoms, 6) def test16MCSProgressCallbackExceptions(self): ps = rdFMCS.MCSParameters() smis = ['CCCC(C)CC(CC)CC', 'OC(N)CC(C)CC(CC)CC'] ms = [Chem.MolFromSmiles(x) for x in smis] self.assertRaises(TypeError, lambda ps: setattr(ps, "ProgressCallback", ProgressCallbackCallbackIsInt())) self.assertRaises(TypeError, lambda ps: setattr(ps, "ProgressCallback", ProgressCallbackNoCallback())) def test17MCSProgressCallbackCancel(self): ps = rdFMCS.MCSParameters() smis = ['CCCC(C)CC(CC)CC', 'OC(N)CC(C)CC(CC)CC'] ms = [Chem.MolFromSmiles(x) for x in smis] ps.AtomTyper = CompareElements() ps.ProgressCallback = ProgressCallback(self) mcs = rdFMCS.FindMCS(ms, ps) self.assertTrue(mcs.canceled) self.assertEqual(ps.ProgressCallback.callCount, 3) def test18GitHub3693(self): mols = [ Chem.MolFromSmiles(smi) for smi in ["Nc1ccc(O)cc1c1ccc2ccccc2c1", "Oc1cnc(NC2CCC2)c(c1)c1ccc2ccccc2c1"] ] params = rdFMCS.MCSParameters() res = rdFMCS.FindMCS(mols, params) self.assertEqual(res.numAtoms, 17) self.assertEqual(res.numBonds, 18) self.assertEqual( res.smartsString, "[#7]-,:[#6]:[#6](:[#6]:[#6](:[#6])-[#8])-[#6]1:[#6]:[#6]:[#6]2:[#6](:[#6]:1):[#6]:[#6]:[#6]:[#6]:2" ) params = rdFMCS.MCSParameters() params.BondCompareParameters.CompleteRingsOnly = True res = rdFMCS.FindMCS(mols, params) self.assertEqual(res.numAtoms, 11) self.assertEqual(res.numBonds, 12) self.assertEqual( res.smartsString, "[#6]-&!@[#6]1:&@[#6]:&@[#6]:&@[#6]2:&@[#6](:&@[#6]:&@1):&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@2") params = rdFMCS.MCSParameters() params.AtomCompareParameters.CompleteRingsOnly = True params.BondCompareParameters.CompleteRingsOnly = True res = rdFMCS.FindMCS(mols, params) self.assertEqual(res.numAtoms, 10) self.assertEqual(res.numBonds, 11) self.assertEqual( res.smartsString, "[#6]1:&@[#6]:&@[#6]:&@[#6]2:&@[#6](:&@[#6]:&@1):&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@2" ) params = rdFMCS.MCSParameters() params.AtomCompareParameters.CompleteRingsOnly = True # this will automatically be set to True params.BondCompareParameters.CompleteRingsOnly = False res = rdFMCS.FindMCS(mols, params) self.assertEqual(res.numAtoms, 10) self.assertEqual(res.numBonds, 11) self.assertEqual( res.smartsString, "[#6]1:&@[#6]:&@[#6]:&@[#6]2:&@[#6](:&@[#6]:&@1):&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@2" ) def test19MCS3d(self): Common.test19MCS3d(self) def Test21AtomCompareCompleteRingsOnly(self): mols = [Chem.MolFromSmiles(smi) for smi in ["C1CCCC1C", "C1CCCC1C1CCCCC1"]] params = rdFMCS.MCSParameters() params.AtomCompareParameters.CompleteRingsOnly = True res = rdFMCS.FindMCS(mols, params) self.assertEqual(res.numAtoms, 5) self.assertEqual(res.numBonds, 5) self.assertEqual(res.smartsString, "[#6&R]1-&@[#6&R]-&@[#6&R]-&@[#6&R]-&@[#6&R]-&@1") params = rdFMCS.MCSParameters() params.AtomCompareParameters.CompleteRingsOnly = True # this will automatically be set to True params.BondCompareParameters.CompleteRingsOnly = False res = rdFMCS.FindMCS(mols, params) self.assertEqual(res.numAtoms, 5) self.assertEqual(res.numBonds, 5) self.assertEqual(res.smartsString, "[#6&R]1-&@[#6&R]-&@[#6&R]-&@[#6&R]-&@[#6&R]-&@1") def test21ShouldAcceptMCS(self): mols1 = [ Chem.MolFromSmiles(smi) for smi in [ "OC(=O)CCc1c(C)ccc2ccccc12", "c1(C)cc(cccc2)c2c(*)c1" ] ] mols2 = [ Chem.MolFromSmiles(smi) for smi in [ "OC(=O)C(C1CC1)Cc1c(C)ccc2ccccc12", "c1(C)cc(cccc2)c2c(C2CC2*)c1" ] ] params = rdFMCS.MCSParameters() params.AtomTyper = Test21AtomCompare() params.BondTyper = rdFMCS.BondCompare.CompareAny self.assertRaises(TypeError, lambda params: setattr(params, "ShouldAcceptMCS", Test21AcceptanceCallbackCallbackIsInt())) self.assertRaises(TypeError, lambda params: setattr(params, "ShouldAcceptMCS", Test21AcceptanceCallbackNoCallback())) self.assertRaises(TypeError, lambda params: setattr(params, "FinalMatchChecker", Test21FinalMatchCheckCallbackCallbackIsInt())) self.assertRaises(TypeError, lambda params: setattr(params, "FinalMatchChecker", Test21FinalMatchCheckCallbackNoCallback())) params.ShouldAcceptMCS = Test21AcceptanceCallback(self) params.ProgressCallback = Test21ProgressCallback(self) params.FinalMatchChecker = Test21FinalMatchCheckCallback(self) params.AtomCompareParameters.RingMatchesRingOnly = False params.AtomCompareParameters.CompleteRingsOnly = False params.BondCompareParameters.RingMatchesRingOnly = True params.BondCompareParameters.CompleteRingsOnly = False mcs = rdFMCS.FindMCS(mols1, params) self.assertEqual(mcs.numAtoms, 11) self.assertEqual(mcs.numBonds, 12) self.assertEqual(mcs.smartsString, "[#6]1:&@[#6]:&@[#6]2:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@[#6]:&@2:&@[#6](:&@[#6]:&@1)-&!@[#0,#6]") self.assertGreater(params.ProgressCallback.callCount, 0) self.assertGreater(params.FinalMatchChecker.callCount, 0) params.AtomCompareParameters.RingMatchesRingOnly = True mcs = rdFMCS.FindMCS(mols2, params) self.assertEqual(mcs.numAtoms, 4) self.assertEqual(mcs.numBonds, 4) self.assertEqual(mcs.smartsString, "[#6]1-&@[#6]-&@[#6]-&@1-&!@[#0,#6;!R]") self.assertGreater(params.ProgressCallback.callCount, 0) self.assertGreater(params.FinalMatchChecker.callCount, 0) def test22DegenerateMCS(self): para = "CC1:C:C:C(N):C:C:1" ortho = "CC1:C:C:C:C:C:1N" if 1: mols1 = [Chem.MolFromSmiles(smi) for smi in [ "Nc1ccc(cc1)C-Cc1c(N)cccc1", "Nc1ccc(cc1)C=Cc1c(N)cccc1"] ] mols2 = [Chem.MolFromSmiles(smi) for smi in [ "Nc1ccccc1C-Cc1ccc(N)cc1", "Nc1ccccc1C=Cc1ccc(N)cc1"] ] p = rdFMCS.MCSParameters() mcs1 = rdFMCS.FindMCS(mols1) self.assertEqual(mcs1.numAtoms, 8) self.assertEqual(mcs1.numBonds, 8) self.assertNotEqual(mcs1.smartsString, "") self.assertIsNotNone(mcs1.queryMol) mcs1Smiles = Chem.MolToSmiles(Chem.MolFromSmarts(mcs1.smartsString)) self.assertEqual(mcs1Smiles, para) self.assertEqual(len(mcs1.degenerateSmartsQueryMolDict), 0) mcs2 = rdFMCS.FindMCS(mols2) self.assertEqual(mcs2.numAtoms, 8) self.assertEqual(mcs2.numBonds, 8) self.assertNotEqual(mcs2.smartsString, "") self.assertIsNotNone(mcs2.queryMol) mcs2Smiles = Chem.MolToSmiles(Chem.MolFromSmarts(mcs2.smartsString)) self.assertEqual(mcs2Smiles, ortho) self.assertEqual(len(mcs2.degenerateSmartsQueryMolDict), 0) self.assertNotEqual(mcs1Smiles, mcs2Smiles) self.assertEqual(Chem.MolToSmiles(mols1[0]), Chem.MolToSmiles(mols2[0])) self.assertEqual(Chem.MolToSmiles(mols1[1]), Chem.MolToSmiles(mols2[1])) p.StoreAll = True mcs1 = rdFMCS.FindMCS(mols1, p) self.assertEqual(mcs1.numAtoms, 8) self.assertEqual(mcs1.numBonds, 8) self.assertEqual(mcs1.smartsString, "") self.assertIsNone(mcs1.queryMol) self.assertEqual(len(mcs1.degenerateSmartsQueryMolDict), 2) mcs2 = rdFMCS.FindMCS(mols2, p) self.assertEqual(mcs2.numAtoms, 8) self.assertEqual(mcs2.numBonds, 8) self.assertEqual(mcs2.smartsString, "") self.assertIsNone(mcs2.queryMol) self.assertEqual(len(mcs2.degenerateSmartsQueryMolDict), 2) degSmiles1 = sorted(Chem.MolToSmiles(Chem.MolFromSmarts(sma)) for sma in mcs1.degenerateSmartsQueryMolDict.keys()) degSmiles2 = sorted(Chem.MolToSmiles(Chem.MolFromSmarts(sma)) for sma in mcs2.degenerateSmartsQueryMolDict.keys()) self.assertEqual(len(degSmiles1), 2) self.assertEqual(degSmiles1, degSmiles2) if 1: mols = [Chem.MolFromSmiles(smi) for smi in [ "Nc1ccc(cc1)C-C", "Nc1ccc(cc1)C=C"] ] p = rdFMCS.MCSParameters() mcs1 = rdFMCS.FindMCS(mols) self.assertEqual(mcs1.numAtoms, 8) self.assertEqual(mcs1.numBonds, 8) self.assertIsNotNone(mcs1.queryMol) self.assertNotEqual(mcs1.smartsString, "") self.assertEqual(Chem.MolToSmiles(Chem.MolFromSmarts(mcs1.smartsString)), para) self.assertEqual(len(mcs1.degenerateSmartsQueryMolDict), 0) p.StoreAll = True mcs2 = rdFMCS.FindMCS(mols, p) self.assertEqual(mcs2.numAtoms, 8) self.assertEqual(mcs2.numBonds, 8) self.assertIsNone(mcs2.queryMol) self.assertEqual(mcs2.smartsString, "") self.assertEqual(len(mcs2.degenerateSmartsQueryMolDict), 1) self.assertEqual(Chem.MolToSmiles(Chem.MolFromSmarts(tuple(mcs2.degenerateSmartsQueryMolDict.keys())[0])), para) if __name__ == "__main__": unittest.main()