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4db0bade46
Fixes #2420 Tests updated to reflect changes. The existing CompleteRingsOnly code wasn't actually guaranteeing CompleteRingsOnly at all, it was just causing #2420. The updated code actually makes sure that bonds that were ring bonds in one of the queries are ring bonds in the final MCS. This is done via a relatively simple DFS.
259 lines
9.8 KiB
Python
259 lines
9.8 KiB
Python
from rdkit import RDConfig
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import os
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import sys
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import unittest
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from rdkit import Chem
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from rdkit.Chem import rdFMCS
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class TestCase(unittest.TestCase):
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def setUp(self):
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pass
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def test1(self):
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smis = (
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"Cc1nc(CN(C(C)c2ncccc2)CCCCN)ccc1 CHEMBL1682991", # -- QUERY
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"Cc1ccc(CN(C(C)c2ccccn2)CCCCN)nc1 CHEMBL1682990",
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"Cc1cccnc1CN(C(C)c1ccccn1)CCCCN CHEMBL1682998",
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"CC(N(CCCCN)Cc1c(N)cccn1)c1ccccn1 CHEMBL1682987",
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"Cc1cc(C)c(CN(C(C)c2ccccn2)CCCCN)nc1 CHEMBL1682992",
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"Cc1cc(C(C)N(CCCCN)Cc2c(C)cccn2)ncc1 CHEMBL1682993",
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"Cc1nc(C(C)N(CCCCN)Cc2nc3c([nH]2)cccc3)ccc1 CHEMBL1682878",
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"CC(c1ncccc1)N(CCCCN)Cc1nc2c([nH]1)cccc2 CHEMBL1682867",
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"CC(N(CCCCN)Cc1c(C(C)(C)C)cccn1)c1ccccn1 CHEMBL1682989",
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"CC(N(CCCCN)Cc1c(C(F)(F)F)cccn1)c1ccccn1 CHEMBL1682988",
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)
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ms = [Chem.MolFromSmiles(x.split()[0]) for x in smis]
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qm = ms[0]
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ms = ms[1:]
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mcs = rdFMCS.FindMCS(ms)
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self.assertEqual(mcs.numBonds, 21)
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self.assertEqual(mcs.numAtoms, 21)
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self.assertEqual(
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mcs.smartsString,
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'[#6](:[#6]:[#6]):[#6]:[#7]:[#6]-[#6]-[#7](-[#6](-[#6])-[#6]1:[#6]:[#6]:[#6]:[#6]:[#7]:1)-[#6]-[#6]-[#6]-[#6]-[#7]'
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)
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qm = Chem.MolFromSmarts(mcs.smartsString)
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self.assertTrue(qm is not None)
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for m in ms:
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self.assertTrue(m.HasSubstructMatch(qm))
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mcs = rdFMCS.FindMCS(ms, threshold=0.8)
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self.assertEqual(mcs.numBonds, 21)
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self.assertEqual(mcs.numAtoms, 21)
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self.assertEqual(
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mcs.smartsString,
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'[#6](:[#6]:[#6]):[#6]:[#7]:[#6]-[#6]-[#7](-[#6](-[#6])-[#6]1:[#6]:[#6]:[#6]:[#6]:[#7]:1)-[#6]-[#6]-[#6]-[#6]-[#7]'
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)
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qm = Chem.MolFromSmarts(mcs.smartsString)
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self.assertTrue(qm is not None)
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for m in ms:
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self.assertTrue(m.HasSubstructMatch(qm))
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def test2(self):
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smis = (
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"CHEMBL122452 CN(CCCN(C)CCc1ccccc1)CCOC(c1ccccc1)c1ccccc1",
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"CHEMBL123252 CN(CCCc1ccccc1)CCCN(C)CCOC(c1ccccc1)c1ccccc1",
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"CHEMBL121611 Fc1ccc(C(OCCNCCCNCCc2ccccc2)c2ccc(F)cc2)cc1",
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"CHEMBL121050 O=C(Cc1ccccc1)NCCCCNCCOC(c1ccc(F)cc1)c1ccc(F)cc1",
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"CHEMBL333667 O=C(Cc1ccccc1)NCCNCCOC(c1ccc(F)cc1)c1ccc(F)cc1",
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"CHEMBL121486 O=C(Cc1ccc(Br)cc1)NC=CNCCOC(c1ccc(F)cc1)c1ccc(F)cc1",
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"CHEMBL123830 O=C(Cc1ccc(F)cc1)NCCNCCOC(c1ccc(F)cc1)c1ccc(F)cc1",
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"CHEMBL420900 O=C(Cc1ccccc1)NCCCNCCOC(c1ccc(F)cc1)c1ccc(F)cc1",
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"CHEMBL121460 CN(CCOC(c1ccc(F)cc1)c1ccc(F)cc1)CCN(C)CCOC(c1ccc(F)cc1)c1ccc(F)cc1",
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"CHEMBL120901 COC(=O)C1C2CCC(CC1C(=O)Oc1ccccc1)N2C",
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"CHEMBL122859 O=C1CN(CCc2ccccc2)CCN1CCOC(c1ccc(F)cc1)c1ccc(F)cc1",
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"CHEMBL121027 CN(CCOC(c1ccccc1)c1ccccc1)CCN(C)CCc1ccc(F)cc1",
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)
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ms = [Chem.MolFromSmiles(x.split()[1]) for x in smis]
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qm = ms[0]
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ms = ms[1:]
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mcs = rdFMCS.FindMCS(ms)
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self.assertEqual(mcs.numBonds, 9)
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self.assertEqual(mcs.numAtoms, 10)
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qm = Chem.MolFromSmarts(mcs.smartsString)
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self.assertTrue(qm is not None)
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for m in ms:
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self.assertTrue(m.HasSubstructMatch(qm))
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# smarts too hard to canonicalize this
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# self.assertEqual(mcs.smartsString,'[#6]-,:[#6]-,:[#6]-,:[#6]-,:[#6](-[#6]-[#8]-[#6]:,-[#6])-,:[#6]')
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mcs = rdFMCS.FindMCS(ms, threshold=0.8)
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self.assertEqual(mcs.numBonds, 20)
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self.assertEqual(mcs.numAtoms, 19)
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qm = Chem.MolFromSmarts(mcs.smartsString)
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self.assertTrue(qm is not None)
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nHits = 0
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for m in ms:
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if m.HasSubstructMatch(qm):
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nHits += 1
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self.assertTrue(nHits >= int(0.8 * len(smis)))
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# smarts too hard to canonicalize this
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# 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')
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def test3IsotopeMatch(self):
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smis = (
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"CC[14NH2]",
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"CC[14CH3]",
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)
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ms = [Chem.MolFromSmiles(x) for x in smis]
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mcs = rdFMCS.FindMCS(ms)
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self.assertEqual(mcs.numBonds, 1)
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self.assertEqual(mcs.numAtoms, 2)
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qm = Chem.MolFromSmarts(mcs.smartsString)
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mcs = rdFMCS.FindMCS(ms, atomCompare=rdFMCS.AtomCompare.CompareIsotopes)
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self.assertEqual(mcs.numBonds, 2)
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self.assertEqual(mcs.numAtoms, 3)
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qm = Chem.MolFromSmarts(mcs.smartsString)
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self.assertTrue(Chem.MolFromSmiles('CC[14CH3]').HasSubstructMatch(qm))
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self.assertFalse(Chem.MolFromSmiles('CC[13CH3]').HasSubstructMatch(qm))
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self.assertTrue(Chem.MolFromSmiles('OO[14CH3]').HasSubstructMatch(qm))
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self.assertFalse(Chem.MolFromSmiles('O[13CH2][14CH3]').HasSubstructMatch(qm))
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def test4RingMatches(self):
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smis = ['CCCCC', 'CCC1CCCCC1']
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ms = [Chem.MolFromSmiles(x) for x in smis]
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mcs = rdFMCS.FindMCS(ms)
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self.assertEqual(mcs.numBonds, 4)
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self.assertEqual(mcs.numAtoms, 5)
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self.assertEqual(mcs.smartsString, '[#6]-[#6]-[#6]-[#6]-[#6]')
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mcs = rdFMCS.FindMCS(ms, completeRingsOnly=True)
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self.assertEqual(mcs.numBonds, 2)
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self.assertEqual(mcs.numAtoms, 3)
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self.assertEqual(mcs.smartsString, '[#6]-[#6]-[#6]')
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mcs = rdFMCS.FindMCS(ms, ringMatchesRingOnly=True)
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self.assertEqual(mcs.numBonds, 1)
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self.assertEqual(mcs.numAtoms, 2)
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self.assertEqual(mcs.smartsString, '[#6]-[#6]')
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smis = ['CC1CCC1', 'CCC1CCCCC1']
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ms = [Chem.MolFromSmiles(x) for x in smis]
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mcs = rdFMCS.FindMCS(ms)
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self.assertEqual(mcs.numBonds, 4)
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self.assertEqual(mcs.numAtoms, 5)
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self.assertEqual(mcs.smartsString, '[#6]-[#6](-[#6]-[#6])-[#6]')
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mcs = rdFMCS.FindMCS(ms, completeRingsOnly=True)
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self.assertEqual(mcs.numBonds, 0)
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self.assertEqual(mcs.numAtoms, 0)
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self.assertEqual(mcs.smartsString, '')
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mcs = rdFMCS.FindMCS(ms, ringMatchesRingOnly=True)
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self.assertEqual(mcs.numBonds, 4)
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self.assertEqual(mcs.numAtoms, 5)
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self.assertEqual(mcs.smartsString, '[#6]-[#6](-[#6]-[#6])-[#6]')
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def test5AnyMatch(self):
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smis = ('c1ccccc1C', 'c1ccccc1O', 'c1ccccc1Cl')
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ms = [Chem.MolFromSmiles(x) for x in smis]
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mcs = rdFMCS.FindMCS(ms, atomCompare=rdFMCS.AtomCompare.CompareAny)
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self.assertEqual(mcs.numBonds, 7)
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self.assertEqual(mcs.numAtoms, 7)
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qm = Chem.MolFromSmarts(mcs.smartsString)
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for m in ms:
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self.assertTrue(m.HasSubstructMatch(qm))
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smis = ('c1cccnc1C', 'c1cnncc1O', 'c1cccnc1Cl')
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ms = [Chem.MolFromSmiles(x) for x in smis]
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mcs = rdFMCS.FindMCS(ms, atomCompare=rdFMCS.AtomCompare.CompareAny)
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self.assertEqual(mcs.numBonds, 7)
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self.assertEqual(mcs.numAtoms, 7)
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qm = Chem.MolFromSmarts(mcs.smartsString)
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for m in ms:
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self.assertTrue(m.HasSubstructMatch(qm))
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def test6MatchValences(self):
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ms = (Chem.MolFromSmiles('NC1OC1'), Chem.MolFromSmiles('C1OC1[N+](=O)[O-]'))
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mcs = rdFMCS.FindMCS(ms)
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self.assertEqual(mcs.numBonds, 4)
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self.assertEqual(mcs.numAtoms, 4)
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mcs = rdFMCS.FindMCS(ms, matchValences=True)
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self.assertEqual(mcs.numBonds, 3)
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self.assertEqual(mcs.numAtoms, 3)
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def test7Seed(self):
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smis = ['C1CCC1CC1CC1', 'C1CCC1OC1CC1', 'C1CCC1NC1CC1', 'C1CCC1SC1CC1']
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ms = [Chem.MolFromSmiles(x) for x in smis]
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r = rdFMCS.FindMCS(ms)
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self.assertEqual(r.smartsString, "[#6]1-[#6]-[#6]-[#6]-1")
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r = rdFMCS.FindMCS(ms, seedSmarts='C1CC1')
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self.assertEqual(r.smartsString, "[#6]1-[#6]-[#6]-1")
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r = rdFMCS.FindMCS(ms, seedSmarts='C1OC1')
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self.assertEqual(r.smartsString, "")
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def test8MatchParams(self):
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smis = ("CCC1NC1", "CCC1N(C)C1", "CCC1OC1")
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ms = [Chem.MolFromSmiles(x) for x in smis]
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mcs = rdFMCS.FindMCS(ms)
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self.assertEqual(mcs.numAtoms, 4)
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ps = rdFMCS.MCSParameters()
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ps.BondCompareParameters.CompleteRingsOnly = True
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mcs = rdFMCS.FindMCS(ms, ps)
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self.assertEqual(mcs.numAtoms, 3)
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ps = rdFMCS.MCSParameters()
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ps.SetAtomTyper(rdFMCS.AtomCompare.CompareAny)
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mcs = rdFMCS.FindMCS(ms, ps)
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self.assertEqual(mcs.numAtoms, 5)
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def test9MatchCharge(self):
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smis = ("CCNC", "CCN(C)C", "CC[N+](C)C")
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ms = [Chem.MolFromSmiles(x) for x in smis]
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mcs = rdFMCS.FindMCS(ms)
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self.assertEqual(mcs.numAtoms, 4)
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ps = rdFMCS.MCSParameters()
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ps.AtomCompareParameters.MatchFormalCharge = True
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mcs = rdFMCS.FindMCS(ms, ps)
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self.assertEqual(mcs.numAtoms, 2)
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def test10MatchChargeAndParams(self):
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smis = ("CCNC", "CCN(C)C", "CC[N+](C)C", "CC[C+](C)C")
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ms = [Chem.MolFromSmiles(x) for x in smis]
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mcs = rdFMCS.FindMCS(ms)
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self.assertEqual(mcs.numAtoms, 2)
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ps = rdFMCS.MCSParameters()
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ps.SetAtomTyper(rdFMCS.AtomCompare.CompareAny)
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mcs = rdFMCS.FindMCS(ms, ps)
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self.assertEqual(mcs.numAtoms, 4)
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ps.AtomCompareParameters.MatchFormalCharge = True
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mcs = rdFMCS.FindMCS(ms, ps)
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self.assertEqual(mcs.numAtoms, 2)
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def test11Github2034(self):
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smis = ("C1CC1N2CC2", "C1CC1N")
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ms = [Chem.MolFromSmiles(x) for x in smis]
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mcs = rdFMCS.FindMCS(ms)
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self.assertEqual(mcs.numAtoms, 4)
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self.assertEqual(mcs.numBonds, 4)
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mcs = rdFMCS.FindMCS(ms, ringMatchesRingOnly=True)
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self.assertEqual(mcs.numAtoms, 3)
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self.assertEqual(mcs.numBonds, 3)
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ps = rdFMCS.MCSParameters()
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ps.AtomCompareParameters.RingMatchesRingOnly = True
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mcs = rdFMCS.FindMCS(ms, ps)
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self.assertEqual(mcs.numAtoms, 3)
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self.assertEqual(mcs.numBonds, 3)
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if __name__ == "__main__":
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unittest.main()
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