# $Id: rough_test.py 2007 2012-03-28 07:06:44Z glandrum $ # # Copyright (C) 2003-2011 Greg Landrum and Rational Discovery LLC # All Rights Reserved # """ This is a rough coverage test of the python wrapper it's intended to be shallow, but broad """ from rdkit import RDConfig,rdBase import os,sys,tempfile import unittest from rdkit import DataStructs from rdkit import Chem def feq(v1,v2,tol2=1e-4): return abs(v1-v2)<=tol2 class TestCase(unittest.TestCase): def setUp(self): pass def test0Except(self): try: Chem.tossit() except IndexError: ok=1 else: ok=0 assert ok def test1Table(self): tbl = Chem.GetPeriodicTable() self.failUnless(tbl) self.failUnless(feq(tbl.GetAtomicWeight(6),12.011)) self.failUnless(feq(tbl.GetAtomicWeight("C"),12.011)) self.failUnless(tbl.GetAtomicNumber('C')==6) self.failUnless(feq(tbl.GetRvdw(6),1.950)) self.failUnless(feq(tbl.GetRvdw("C"),1.950)) self.failUnless(feq(tbl.GetRcovalent(6),0.680)) self.failUnless(feq(tbl.GetRcovalent("C"),0.680)) self.failUnless(tbl.GetDefaultValence(6)==4) self.failUnless(tbl.GetDefaultValence("C")==4) self.failUnless(tuple(tbl.GetValenceList(6))==(4,)) self.failUnless(tuple(tbl.GetValenceList("C"))==(4,)) self.failUnless(tuple(tbl.GetValenceList(16))==(2,4,6)) self.failUnless(tuple(tbl.GetValenceList("S"))==(2,4,6)) self.failUnless(tbl.GetNOuterElecs(6)==4) self.failUnless(tbl.GetNOuterElecs("C")==4) def test2Atom(self): atom = Chem.Atom(6) self.failUnless(atom) self.failUnless(atom.GetAtomicNum()==6) atom.SetAtomicNum(8) self.failUnless(atom.GetAtomicNum()==8) atom = Chem.Atom("C") self.failUnless(atom) self.failUnless(atom.GetAtomicNum()==6) def test3Bond(self): # No longer relevant, bonds are not constructible from Python pass def test4Mol(self): mol = Chem.Mol() self.failUnless(mol) def test5Smiles(self): mol = Chem.MolFromSmiles('n1ccccc1') self.failUnless(mol) self.failUnless(mol.GetNumAtoms()==6) self.failUnless(mol.GetNumAtoms(1)==6) self.failUnless(mol.GetNumAtoms(0)==11) at = mol.GetAtomWithIdx(2) self.failUnless(at.GetAtomicNum()==6) at = mol.GetAtomWithIdx(0) self.failUnless(at.GetAtomicNum()==7) def _test6Bookmarks(self): mol = Chem.MolFromSmiles('n1ccccc1') self.failUnless(mol) self.failUnless(not mol.HasAtomBookmark(0)) mol.SetAtomBookmark(mol.GetAtomWithIdx(0),0) mol.SetAtomBookmark(mol.GetAtomWithIdx(1),1) self.failUnless(mol.HasAtomBookmark(0)) self.failUnless(mol.HasAtomBookmark(1)) if 1: self.failUnless(not mol.HasBondBookmark(0)) self.failUnless(not mol.HasBondBookmark(1)) mol.SetBondBookmark(mol.GetBondWithIdx(0),0) mol.SetBondBookmark(mol.GetBondWithIdx(1),1) self.failUnless(mol.HasBondBookmark(0)) self.failUnless(mol.HasBondBookmark(1)) at = mol.GetAtomWithBookmark(0) self.failUnless(at) self.failUnless(at.GetAtomicNum()==7) mol.ClearAtomBookmark(0) self.failUnless(not mol.HasAtomBookmark(0)) self.failUnless(mol.HasAtomBookmark(1)) mol.ClearAllAtomBookmarks() self.failUnless(not mol.HasAtomBookmark(0)) self.failUnless(not mol.HasAtomBookmark(1)) mol.SetAtomBookmark(mol.GetAtomWithIdx(1),1) if 1: self.failUnless(mol.HasBondBookmark(0)) self.failUnless(mol.HasBondBookmark(1)) bond = mol.GetBondWithBookmark(0) self.failUnless(bond) mol.ClearBondBookmark(0) self.failUnless(not mol.HasBondBookmark(0)) self.failUnless(mol.HasBondBookmark(1)) mol.ClearAllBondBookmarks() self.failUnless(not mol.HasBondBookmark(0)) self.failUnless(not mol.HasBondBookmark(1)) self.failUnless(mol.HasAtomBookmark(1)) def test7Atom(self): mol = Chem.MolFromSmiles('n1ccccc1C[CH2-]') self.failUnless(mol) Chem.SanitizeMol(mol) a0 = mol.GetAtomWithIdx(0) a1 = mol.GetAtomWithIdx(1) a6 = mol.GetAtomWithIdx(6) a7 = mol.GetAtomWithIdx(7) self.failUnless(a0.GetAtomicNum()==7) self.failUnless(a0.GetSymbol()=='N') self.failUnless(a0.GetIdx()==0) aList = [a0,a1,a6,a7] self.failUnless(a0.GetDegree()==2) self.failUnless(a1.GetDegree()==2) self.failUnless(a6.GetDegree()==2) self.failUnless(a7.GetDegree()==1) self.failUnless([x.GetDegree() for x in aList]==[2,2,2,1]) self.failUnless([x.GetTotalNumHs() for x in aList]==[0,1,2,2]) self.failUnless([x.GetNumImplicitHs() for x in aList]==[0,1,2,0]) self.failUnless([x.GetExplicitValence() for x in aList]==[3,3,2,3]) self.failUnless([x.GetImplicitValence() for x in aList]==[0,1,2,0]) self.failUnless([x.GetFormalCharge() for x in aList]==[0,0,0,-1]) self.failUnless([x.GetNoImplicit() for x in aList]==[0,0,0,1]) self.failUnless([x.GetNumExplicitHs() for x in aList]==[0,0,0,2]) self.failUnless([x.GetIsAromatic() for x in aList]==[1,1,0,0]) self.failUnless([x.GetHybridization() for x in aList]==[Chem.HybridizationType.SP2,Chem.HybridizationType.SP2, Chem.HybridizationType.SP3,Chem.HybridizationType.SP3],\ [x.GetHybridization() for x in aList]) def test8Bond(self): mol = Chem.MolFromSmiles('n1ccccc1CC(=O)O') self.failUnless(mol) Chem.SanitizeMol(mol) # note bond numbering is funny because of ring closure b0 = mol.GetBondWithIdx(0) b6 = mol.GetBondWithIdx(6) b7 = mol.GetBondWithIdx(7) b8 = mol.GetBondWithIdx(8) bList = [b0,b6,b7,b8] self.failUnless([x.GetBondType() for x in bList] == [Chem.BondType.AROMATIC,Chem.BondType.SINGLE, Chem.BondType.DOUBLE,Chem.BondType.SINGLE]) self.failUnless([x.GetIsAromatic() for x in bList] == [1,0,0,0]) self.failUnless([x.GetIsConjugated()!=0 for x in bList] == [1,0,1,1],[x.GetIsConjugated()!=0 for x in bList]) self.failUnless([x.GetBeginAtomIdx() for x in bList] == [0,6,7,7],[x.GetBeginAtomIdx() for x in bList]) self.failUnless([x.GetBeginAtom().GetIdx() for x in bList] == [0,6,7,7]) self.failUnless([x.GetEndAtomIdx() for x in bList] == [1,7,8,9]) self.failUnless([x.GetEndAtom().GetIdx() for x in bList] == [1,7,8,9]) def test9Smarts(self): query1 = Chem.MolFromSmarts('C(=O)O') self.failUnless(query1) query2 = Chem.MolFromSmarts('C(=O)[O,N]') self.failUnless(query2) query3 = Chem.MolFromSmarts('[$(C(=O)O)]') self.failUnless(query3) mol = Chem.MolFromSmiles('CCC(=O)O') self.failUnless(mol) self.failUnless(mol.HasSubstructMatch(query1)) self.failUnless(mol.HasSubstructMatch(query2)) self.failUnless(mol.HasSubstructMatch(query3)) mol = Chem.MolFromSmiles('CCC(=O)N') self.failUnless(mol) self.failUnless(not mol.HasSubstructMatch(query1)) self.failUnless(mol.HasSubstructMatch(query2)) self.failUnless(not mol.HasSubstructMatch(query3)) def test10Iterators(self): mol = Chem.MolFromSmiles('CCOC') self.failUnless(mol) for atom in mol.GetAtoms(): self.failUnless(atom) ats = mol.GetAtoms() try: ats[1] except: ok = 0 else: ok = 1 self.failUnless(ok) try: ats[12] except IndexError: ok = 1 else: ok = 0 self.failUnless(ok) if 0: for atom in mol.GetHeteros(): self.failUnless(atom) ats = mol.GetHeteros() try: ats[0] except: ok = 0 else: ok = 1 self.failUnless(ok) self.failUnless(ats[0].GetIdx()==2) try: ats[12] except IndexError: ok = 1 else: ok = 0 self.failUnless(ok) for bond in mol.GetBonds(): self.failUnless(bond) bonds = mol.GetBonds() try: bonds[1] except: ok = 0 else: ok = 1 self.failUnless(ok) try: bonds[12] except IndexError: ok = 1 else: ok = 0 self.failUnless(ok) if 0: mol = Chem.MolFromSmiles('c1ccccc1C') for atom in mol.GetAromaticAtoms(): self.failUnless(atom) ats = mol.GetAromaticAtoms() try: ats[0] except: ok = 0 else: ok = 1 self.failUnless(ok) self.failUnless(ats[0].GetIdx()==0) self.failUnless(ats[1].GetIdx()==1) self.failUnless(ats[2].GetIdx()==2) try: ats[12] except IndexError: ok = 1 else: ok = 0 self.failUnless(ok) def test11MolOps(self) : mol = Chem.MolFromSmiles('C1=CC=C(C=C1)P(C2=CC=CC=C2)C3=CC=CC=C3') self.failUnless(mol) smi = Chem.MolToSmiles(mol) Chem.SanitizeMol(mol) nr = Chem.GetSymmSSSR(mol) self.failUnless((len(nr) == 3)) def test12Smarts(self): query1 = Chem.MolFromSmarts('C(=O)O') self.failUnless(query1) query2 = Chem.MolFromSmarts('C(=O)[O,N]') self.failUnless(query2) query3 = Chem.MolFromSmarts('[$(C(=O)O)]') self.failUnless(query3) mol = Chem.MolFromSmiles('CCC(=O)O') self.failUnless(mol) self.failUnless(mol.HasSubstructMatch(query1)) self.failUnless(mol.GetSubstructMatch(query1)==(2,3,4)) self.failUnless(mol.HasSubstructMatch(query2)) self.failUnless(mol.GetSubstructMatch(query2)==(2,3,4)) self.failUnless(mol.HasSubstructMatch(query3)) self.failUnless(mol.GetSubstructMatch(query3)==(2,)) mol = Chem.MolFromSmiles('CCC(=O)N') self.failUnless(mol) self.failUnless(not mol.HasSubstructMatch(query1)) self.failUnless(not mol.GetSubstructMatch(query1)) self.failUnless(mol.HasSubstructMatch(query2)) self.failUnless(mol.GetSubstructMatch(query2)==(2,3,4)) self.failUnless(not mol.HasSubstructMatch(query3)) mol = Chem.MolFromSmiles('OC(=O)CC(=O)O') self.failUnless(mol) self.failUnless(mol.HasSubstructMatch(query1)) self.failUnless(mol.GetSubstructMatch(query1)==(1,2,0)) self.failUnless(mol.GetSubstructMatches(query1)==((1,2,0),(4,5,6))) self.failUnless(mol.HasSubstructMatch(query2)) self.failUnless(mol.GetSubstructMatch(query2)==(1,2,0)) self.failUnless(mol.GetSubstructMatches(query2)==((1,2,0),(4,5,6))) self.failUnless(mol.HasSubstructMatch(query3)) self.failUnless(mol.GetSubstructMatches(query3)==((1,),(4,))) def test13Smarts(self): # previous smarts problems: query = Chem.MolFromSmarts('N(=,-C)') self.failUnless(query) mol = Chem.MolFromSmiles('N#C') self.failUnless(not mol.HasSubstructMatch(query)) mol = Chem.MolFromSmiles('N=C') self.failUnless(mol.HasSubstructMatch(query)) mol = Chem.MolFromSmiles('NC') self.failUnless(mol.HasSubstructMatch(query)) query = Chem.MolFromSmarts('[Cl,$(O)]') mol = Chem.MolFromSmiles('C(=O)O') self.failUnless(len(mol.GetSubstructMatches(query))==2) mol = Chem.MolFromSmiles('C(=N)N') self.failUnless(len(mol.GetSubstructMatches(query))==0) query = Chem.MolFromSmarts('[$([O,S]-[!$(*=O)])]') mol = Chem.MolFromSmiles('CC(S)C(=O)O') self.failUnless(len(mol.GetSubstructMatches(query))==1) mol = Chem.MolFromSmiles('C(=O)O') self.failUnless(len(mol.GetSubstructMatches(query))==0) def test14Hs(self): m = Chem.MolFromSmiles('CC(=O)[OH]') self.failUnless(m.GetNumAtoms()==4) m2 = Chem.AddHs(m,1) self.failUnless(m2.GetNumAtoms()==5) m2 = Chem.RemoveHs(m2,1) self.failUnless(m2.GetNumAtoms()==5) m2 = Chem.RemoveHs(m2,0) self.failUnless(m2.GetNumAtoms()==4) m2 = Chem.AddHs(m,0) self.failUnless(m2.GetNumAtoms()==8) m2 = Chem.RemoveHs(m2,1) self.failUnless(m2.GetNumAtoms()==5) m2 = Chem.RemoveHs(m2) self.failUnless(m2.GetNumAtoms()==4) m = Chem.MolFromSmiles('CC[H]',False) self.failUnless(m.GetNumAtoms()==3) m2 = Chem.MergeQueryHs(m) self.failUnless(m2.GetNumAtoms()==2) self.failUnless(m2.GetAtomWithIdx(1).HasQuery()) def test15Neighbors(self): m = Chem.MolFromSmiles('CC(=O)[OH]') self.failUnless(m.GetNumAtoms()==4) a = m.GetAtomWithIdx(1) ns = a.GetNeighbors() self.failUnless(len(ns)==3) bs = a.GetBonds() self.failUnless(len(bs)==3) for b in bs: try: a2 = b.GetOtherAtom(a) except: a2=None self.failUnless(a2) self.failUnless(len(bs)==3) def test16Pickle(self): import cPickle m = Chem.MolFromSmiles('C1=CN=CC=C1') pkl = cPickle.dumps(m) m2 = cPickle.loads(pkl) smi1 = Chem.MolToSmiles(m) smi2 = Chem.MolToSmiles(m2) self.failUnless(smi1==smi2) def test16Props(self): m = Chem.MolFromSmiles('C1=CN=CC=C1') self.failUnless(not m.HasProp('prop1')) self.failUnless(not m.HasProp('prop2')) self.failUnless(not m.HasProp('prop2')) m.SetProp('prop1','foob') self.failUnless(not m.HasProp('prop2')) self.failUnless(m.HasProp('prop1')) self.failUnless(m.GetProp('prop1')=='foob') self.failUnless(not m.HasProp('propo')) try: m.GetProp('prop2') except KeyError: ok=1 else: ok=0 self.failUnless(ok) # test computed properties m.SetProp('cprop1', 'foo', 1) m.SetProp('cprop2', 'foo2', 1) m.ClearComputedProps() self.failUnless(not m.HasProp('cprop1')) self.failUnless(not m.HasProp('cprop2')) def test17Kekulize(self): m = Chem.MolFromSmiles('c1ccccc1') smi = Chem.MolToSmiles(m) self.failUnless(smi=='c1ccccc1') Chem.Kekulize(m) smi = Chem.MolToSmiles(m) self.failUnless(smi=='c1ccccc1') m = Chem.MolFromSmiles('c1ccccc1') smi = Chem.MolToSmiles(m) self.failUnless(smi=='c1ccccc1') Chem.Kekulize(m,1) smi = Chem.MolToSmiles(m) self.failUnless(smi=='C1=CC=CC=C1', smi) def test18Paths(self): m = Chem.MolFromSmiles("C1CC2C1CC2") #self.failUnless(len(Chem.FindAllPathsOfLengthN(m,1,useBonds=1))==7) #print Chem.FindAllPathsOfLengthN(m,3,useBonds=0) self.failUnless(len(Chem.FindAllPathsOfLengthN(m,2,useBonds=1))==10, Chem.FindAllPathsOfLengthN(m,2,useBonds=1)) self.failUnless(len(Chem.FindAllPathsOfLengthN(m,3,useBonds=1))==14) m = Chem.MolFromSmiles('C1CC1C') self.failUnless(m) self.failUnless(len(Chem.FindAllPathsOfLengthN(m,1,useBonds=1))==4) self.failUnless(len(Chem.FindAllPathsOfLengthN(m,2,useBonds=1))==5) self.failUnless(len(Chem.FindAllPathsOfLengthN(m,3,useBonds=1))==3,Chem.FindAllPathsOfLengthN(m,3,useBonds=1)) self.failUnless(len(Chem.FindAllPathsOfLengthN(m,4,useBonds=1))==1,Chem.FindAllPathsOfLengthN(m,4,useBonds=1)) self.failUnless(len(Chem.FindAllPathsOfLengthN(m,5,useBonds=1))==0,Chem.FindAllPathsOfLengthN(m,5,useBonds=1)) # # Hexane example from Hall-Kier Rev.Comp.Chem. paper # Rev. Comp. Chem. vol 2, 367-422, (1991) # m = Chem.MolFromSmiles("CCCCCC") self.failUnless(len(Chem.FindAllPathsOfLengthN(m,1,useBonds=1))==5) self.failUnless(len(Chem.FindAllPathsOfLengthN(m,2,useBonds=1))==4) self.failUnless(len(Chem.FindAllPathsOfLengthN(m,3,useBonds=1))==3) m = Chem.MolFromSmiles("CCC(C)CC") self.failUnless(len(Chem.FindAllPathsOfLengthN(m,1,useBonds=1))==5) self.failUnless(len(Chem.FindAllPathsOfLengthN(m,2,useBonds=1))==5) self.failUnless(len(Chem.FindAllPathsOfLengthN(m,3,useBonds=1))==4,Chem.FindAllPathsOfLengthN(m,3,useBonds=1)) m = Chem.MolFromSmiles("CCCC(C)C") self.failUnless(len(Chem.FindAllPathsOfLengthN(m,1,useBonds=1))==5) self.failUnless(len(Chem.FindAllPathsOfLengthN(m,2,useBonds=1))==5) self.failUnless(len(Chem.FindAllPathsOfLengthN(m,3,useBonds=1))==3) m = Chem.MolFromSmiles("CC(C)C(C)C") self.failUnless(len(Chem.FindAllPathsOfLengthN(m,1,useBonds=1))==5) self.failUnless(len(Chem.FindAllPathsOfLengthN(m,2,useBonds=1))==6) self.failUnless(len(Chem.FindAllPathsOfLengthN(m,3,useBonds=1))==4) m = Chem.MolFromSmiles("CC(C)(C)CC") self.failUnless(len(Chem.FindAllPathsOfLengthN(m,1,useBonds=1))==5) self.failUnless(len(Chem.FindAllPathsOfLengthN(m,2,useBonds=1))==7) self.failUnless(len(Chem.FindAllPathsOfLengthN(m,3,useBonds=1))==3,Chem.FindAllPathsOfLengthN(m,3,useBonds=1)) m = Chem.MolFromSmiles("C1CCCCC1") self.failUnless(len(Chem.FindAllPathsOfLengthN(m,1,useBonds=1))==6) self.failUnless(len(Chem.FindAllPathsOfLengthN(m,2,useBonds=1))==6) self.failUnless(len(Chem.FindAllPathsOfLengthN(m,3,useBonds=1))==6) m = Chem.MolFromSmiles("C1CC2C1CC2") self.failUnless(len(Chem.FindAllPathsOfLengthN(m,1,useBonds=1))==7) self.failUnless(len(Chem.FindAllPathsOfLengthN(m,2,useBonds=1))==10, Chem.FindAllPathsOfLengthN(m,2,useBonds=1)) self.failUnless(len(Chem.FindAllPathsOfLengthN(m,3,useBonds=1))==14) m = Chem.MolFromSmiles("CC2C1CCC12") self.failUnless(len(Chem.FindAllPathsOfLengthN(m,1,useBonds=1))==7) self.failUnless(len(Chem.FindAllPathsOfLengthN(m,2,useBonds=1))==11) # FIX: this result disagrees with the paper (which says 13), # but it seems right self.failUnless(len(Chem.FindAllPathsOfLengthN(m,3,useBonds=1))==15, Chem.FindAllPathsOfLengthN(m,3,useBonds=1)) def test19Subgraphs(self): m = Chem.MolFromSmiles('C1CC1C') self.failUnless(m) self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,1,0))==4) self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,2))==5) self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,3))==4) self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,4))==1) self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,5))==0) # # Hexane example from Hall-Kier Rev.Comp.Chem. paper # Rev. Comp. Chem. vol 2, 367-422, (1991) # m = Chem.MolFromSmiles("CCCCCC") self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,1))==5) self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,2))==4) self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,3))==3) l = Chem.FindAllSubgraphsOfLengthMToN(m,1,3) self.failUnlessEqual(len(l),3) self.failUnlessEqual(len(l[0]),5) self.failUnlessEqual(len(l[1]),4) self.failUnlessEqual(len(l[2]),3) self.failUnlessRaises(ValueError,lambda :Chem.FindAllSubgraphsOfLengthMToN(m,4,3)) m = Chem.MolFromSmiles("CCC(C)CC") self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,1))==5) self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,2))==5) self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,3))==5) m = Chem.MolFromSmiles("CCCC(C)C") self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,1))==5) self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,2))==5) self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,3))==4) m = Chem.MolFromSmiles("CC(C)C(C)C") self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,1))==5) self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,2))==6) self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,3))==6) m = Chem.MolFromSmiles("CC(C)(C)CC") self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,1))==5) self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,2))==7) self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,3))==7,Chem.FindAllSubgraphsOfLengthN(m,3)) m = Chem.MolFromSmiles("C1CCCCC1") self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,1))==6) self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,2))==6) self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,3))==6) #self.failUnless(len(Chem.FindUniqueSubgraphsOfLengthN(m,1))==1) self.failUnless(len(Chem.FindUniqueSubgraphsOfLengthN(m,2))==1) self.failUnless(len(Chem.FindUniqueSubgraphsOfLengthN(m,3))==1) m = Chem.MolFromSmiles("C1CC2C1CC2") self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,1))==7) self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,2))==10) self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,3))==16) m = Chem.MolFromSmiles("CC2C1CCC12") self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,1))==7) self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,2))==11) self.failUnless(len(Chem.FindAllSubgraphsOfLengthN(m,3))==18, len(Chem.FindAllSubgraphsOfLengthN(m,3))) def test20IsInRing(self): m = Chem.MolFromSmiles('C1CCC1C') self.failUnless(m) self.failUnless(m.GetAtomWithIdx(0).IsInRingSize(4)) self.failUnless(m.GetAtomWithIdx(1).IsInRingSize(4)) self.failUnless(m.GetAtomWithIdx(2).IsInRingSize(4)) self.failUnless(m.GetAtomWithIdx(3).IsInRingSize(4)) self.failUnless(not m.GetAtomWithIdx(4).IsInRingSize(4)) self.failUnless(not m.GetAtomWithIdx(0).IsInRingSize(3)) self.failUnless(not m.GetAtomWithIdx(1).IsInRingSize(3)) self.failUnless(not m.GetAtomWithIdx(2).IsInRingSize(3)) self.failUnless(not m.GetAtomWithIdx(3).IsInRingSize(3)) self.failUnless(not m.GetAtomWithIdx(4).IsInRingSize(3)) self.failUnless(m.GetBondWithIdx(0).IsInRingSize(4)) self.failUnless(not m.GetBondWithIdx(3).IsInRingSize(4)) self.failUnless(not m.GetBondWithIdx(0).IsInRingSize(3)) self.failUnless(not m.GetBondWithIdx(3).IsInRingSize(3)) def test21Robustification(self): ok = False # FIX: at the moment I can't figure out how to catch the # actual exception that BPL is throwinng when it gets # invalid arguments (Boost.Python.ArgumentError) try: Chem.MolFromSmiles('C=O').HasSubstructMatch(Chem.MolFromSmarts('fiib')) #except ValueError: # ok=True except: ok=True self.failUnless(ok ) def test22DeleteSubstruct(self) : query = Chem.MolFromSmarts('C(=O)O') mol = Chem.MolFromSmiles('CCC(=O)O') nmol = Chem.DeleteSubstructs(mol, query) self.failUnless(Chem.MolToSmiles(nmol) == 'CC') mol = Chem.MolFromSmiles('CCC(=O)O.O=CO') # now delete only fragments nmol = Chem.DeleteSubstructs(mol, query, 1) self.failUnless(Chem.MolToSmiles(nmol) == 'CCC(=O)O',Chem.MolToSmiles(nmol)) mol = Chem.MolFromSmiles('CCC(=O)O.O=CO') nmol = Chem.DeleteSubstructs(mol, query, 0) self.failUnless(Chem.MolToSmiles(nmol) == 'CC') mol = Chem.MolFromSmiles('CCCO') nmol = Chem.DeleteSubstructs(mol, query, 0) self.failUnless(Chem.MolToSmiles(nmol) == 'CCCO') # Issue 96 prevented this from working: mol = Chem.MolFromSmiles('CCC(=O)O.O=CO') nmol = Chem.DeleteSubstructs(mol, query, 1) self.failUnless(Chem.MolToSmiles(nmol) == 'CCC(=O)O') nmol = Chem.DeleteSubstructs(nmol, query, 1) self.failUnless(Chem.MolToSmiles(nmol) == 'CCC(=O)O') nmol = Chem.DeleteSubstructs(nmol, query, 0) self.failUnless(Chem.MolToSmiles(nmol) == 'CC') def test23MolFileParsing(self) : fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','triazine.mol') #fileN = "../FileParsers/test_data/triazine.mol" inD = open(fileN,'r').read() m1 = Chem.MolFromMolBlock(inD) self.failUnless(m1 is not None) self.failUnless(m1.GetNumAtoms()==9) m1 = Chem.MolFromMolFile(fileN) self.failUnless(m1 is not None) self.failUnless(m1.GetNumAtoms()==9) fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','triazine.mof') self.failUnlessRaises(IOError,lambda :Chem.MolFromMolFile(fileN)) fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','list-query.mol') query = Chem.MolFromMolFile(fileN) smi = Chem.MolToSmiles(query) self.failUnlessEqual(smi,'c1ccccc1') smi = Chem.MolToSmarts(query) self.failUnlessEqual(smi,'[#6]1:[#6]:[#6]:[#6]:[#6]:[#6,#7,#15]:1',smi) query = Chem.MolFromMolFile(fileN,sanitize=False) smi = Chem.MolToSmiles(query) self.failUnlessEqual(smi,'C1=CC=CC=C1') query.UpdatePropertyCache() smi = Chem.MolToSmarts(query) self.failUnlessEqual(smi,'[#6]1=[#6]-[#6]=[#6]-[#6]=[#6,#7,#15]-1') smi = "C1=CC=CC=C1" mol = Chem.MolFromSmiles(smi,0) self.failUnless(mol.HasSubstructMatch(query)) Chem.SanitizeMol(mol) self.failUnless(not mol.HasSubstructMatch(query)) mol = Chem.MolFromSmiles('N1=CC=CC=C1',0) self.failUnless(mol.HasSubstructMatch(query)) mol = Chem.MolFromSmiles('S1=CC=CC=C1',0) self.failUnless(not mol.HasSubstructMatch(query)) mol = Chem.MolFromSmiles('P1=CC=CC=C1',0) self.failUnless(mol.HasSubstructMatch(query)) fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','issue123.mol') mol = Chem.MolFromMolFile(fileN) self.failUnless(mol) self.failUnlessEqual(mol.GetNumAtoms(),23) mol = Chem.MolFromMolFile(fileN,removeHs=False) self.failUnless(mol) self.failUnlessEqual(mol.GetNumAtoms(),39) # test23 was for Chem.DaylightFingerprint, which is deprecated def test24RDKFingerprint(self): from rdkit import DataStructs m1 = Chem.MolFromSmiles('C1=CC=CC=C1') fp1 = Chem.RDKFingerprint(m1) self.failUnless(len(fp1)==2048) m2 = Chem.MolFromSmiles('C1=CC=CC=C1') fp2 = Chem.RDKFingerprint(m2) tmp = DataStructs.TanimotoSimilarity(fp1,fp2) self.failUnless(tmp==1.0,tmp) m2 = Chem.MolFromSmiles('C1=CC=CC=N1') fp2 = Chem.RDKFingerprint(m2) self.failUnless(len(fp2)==2048) tmp = DataStructs.TanimotoSimilarity(fp1,fp2) self.failUnless(tmp<1.0,tmp) self.failUnless(tmp>0.0,tmp) fp3 = Chem.RDKFingerprint(m1,tgtDensity=0.3) self.failUnless(len(fp3)<2048) m1 = Chem.MolFromSmiles('C1=CC=CC=C1') fp1 = Chem.RDKFingerprint(m1) m2 = Chem.MolFromSmiles('C1=CC=CC=N1') fp2 = Chem.RDKFingerprint(m2) self.failIfEqual(fp1,fp2) atomInvariants=[1]*6 fp1 = Chem.RDKFingerprint(m1,atomInvariants=atomInvariants) fp2 = Chem.RDKFingerprint(m2,atomInvariants=atomInvariants) self.failUnlessEqual(fp1,fp2) m2 = Chem.MolFromSmiles('C1CCCCN1') fp1 = Chem.RDKFingerprint(m1,atomInvariants=atomInvariants,useBondOrder=False) fp2 = Chem.RDKFingerprint(m2,atomInvariants=atomInvariants,useBondOrder=False) self.failUnlessEqual(fp1,fp2) def test25SDMolSupplier(self) : fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','NCI_aids_few.sdf') #fileN = "../FileParsers/test_data/NCI_aids_few.sdf" sdSup = Chem.SDMolSupplier(fileN) molNames = ["48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213", "220", "229", "256"] chgs192 = {8:1, 11:1, 15:-1, 18:-1, 20:1, 21:1, 23:-1, 25:-1} i = 0 for mol in sdSup : self.failUnless(mol) self.failUnless(mol.GetProp("_Name") == molNames[i]) i += 1 if (mol.GetProp("_Name") == "192") : # test parsed charges on one of the molecules for id in chgs192.keys() : self.failUnless(mol.GetAtomWithIdx(id).GetFormalCharge() == chgs192[id]) sdSup.reset() ns = [mol.GetProp("_Name") for mol in sdSup] self.failUnless(ns == molNames) sdSup = Chem.SDMolSupplier(fileN, 0) for mol in sdSup : self.failUnless(not mol.HasProp("numArom")) sdSup = Chem.SDMolSupplier(fileN) self.failUnless(len(sdSup) == 16) mol = sdSup[5] self.failUnless(mol.GetProp("_Name") == "170") # test handling of H removal: fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','withHs.sdf') sdSup = Chem.SDMolSupplier(fileN) m = sdSup.next() self.failUnless(m) self.failUnless(m.GetNumAtoms()==23) m = sdSup.next() self.failUnless(m) print m.GetNumAtoms() self.failUnless(m.GetNumAtoms()==28) sdSup = Chem.SDMolSupplier(fileN,removeHs=False) m = sdSup.next() self.failUnless(m) self.failUnless(m.GetNumAtoms()==39) m = sdSup.next() self.failUnless(m) self.failUnless(m.GetNumAtoms()==30) d = file(fileN,'r').read() sdSup.SetData(d) m = sdSup.next() self.failUnless(m) self.failUnless(m.GetNumAtoms()==23) m = sdSup.next() self.failUnless(m) print m.GetNumAtoms() self.failUnless(m.GetNumAtoms()==28) sdSup.SetData(d,removeHs=False) m = sdSup.next() self.failUnless(m) self.failUnless(m.GetNumAtoms()==39) m = sdSup.next() self.failUnless(m) self.failUnless(m.GetNumAtoms()==30) def test26SmiMolSupplier(self) : fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','first_200.tpsa.csv') #fileN = "../FileParsers/test_data/first_200.tpsa.csv" smiSup = Chem.SmilesMolSupplier(fileN, ",", 0, -1) mol = smiSup[16]; self.failUnless(mol.GetProp("TPSA") == "46.25") mol = smiSup[8]; self.failUnless(mol.GetProp("TPSA") == "65.18") self.failUnless(len(smiSup) == 200) fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','fewSmi.csv') #fileN = "../FileParsers/test_data/fewSmi.csv" smiSup = Chem.SmilesMolSupplier(fileN, delimiter=",", smilesColumn=1, nameColumn=0, titleLine=0) names = ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10"] i = 0 for mol in smiSup: self.failUnless(mol.GetProp("_Name") == names[i]) i += 1 mol = smiSup[3] self.failUnless(mol.GetProp("_Name") == "4") self.failUnless(mol.GetProp("Column_2") == "82.78") # and test doing a supplier from text: inD = open(fileN,'r').read() smiSup.SetData(inD, delimiter=",", smilesColumn=1, nameColumn=0, titleLine=0) names = ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10"] i = 0 # iteration interface: for mol in smiSup: self.failUnless(mol.GetProp("_Name") == names[i]) i += 1 self.failUnless(i==10) # random access: mol = smiSup[3] self.failUnless(len(smiSup)==10) self.failUnless(mol.GetProp("_Name") == "4") self.failUnless(mol.GetProp("Column_2") == "82.78") # issue 113: smiSup.SetData(inD, delimiter=",", smilesColumn=1, nameColumn=0, titleLine=0) self.failUnless(len(smiSup)==10) # and test failure handling: inD = """mol-1,CCC mol-2,CCCC mol-3,fail mol-4,CCOC """ smiSup.SetData(inD, delimiter=",", smilesColumn=1, nameColumn=0, titleLine=0) # there are 4 entries in the supplier: self.failUnless(len(smiSup)==4) # but the 3rd is a None: self.failUnless(smiSup[2] is None) text="Id SMILES Column_2\n"+\ "mol-1 C 1.0\n"+\ "mol-2 CC 4.0\n"+\ "mol-4 CCCC 16.0" smiSup.SetData(text, delimiter=" ", smilesColumn=1, nameColumn=0, titleLine=1) self.failUnless(len(smiSup)==3) self.failUnless(smiSup[0]) self.failUnless(smiSup[1]) self.failUnless(smiSup[2]) m = [x for x in smiSup] self.failUnless(smiSup[2]) self.failUnless(len(m)==3) self.failUnless(m[0].GetProp("Column_2")=="1.0") # test simple parsing and Issue 114: smis = ['CC','CCC','CCOC','CCCOCC','CCCOCCC'] inD = '\n'.join(smis) smiSup.SetData(inD, delimiter=",", smilesColumn=0, nameColumn=-1, titleLine=0) self.failUnless(len(smiSup)==5) m = [x for x in smiSup] self.failUnless(smiSup[4]) self.failUnless(len(m)==5) # order dependance: smiSup.SetData(inD, delimiter=",", smilesColumn=0, nameColumn=-1, titleLine=0) self.failUnless(smiSup[4]) self.failUnless(len(smiSup)==5) # this was a nasty BC: # asking for a particular entry with a higher index than what we've # already seen resulted in a duplicate: smis = ['CC','CCC','CCOC','CCCCOC'] inD = '\n'.join(smis) smiSup.SetData(inD, delimiter=",", smilesColumn=0, nameColumn=-1, titleLine=0) m = smiSup.next() m = smiSup[3] self.failUnless(len(smiSup)==4) try: smiSup[4] except: ok=1 else: ok=0 self.failUnless(ok) smiSup.SetData(inD, delimiter=",", smilesColumn=0, nameColumn=-1, titleLine=0) try: smiSup[4] except: ok=1 else: ok=0 self.failUnless(ok) sys.stderr.write('>>> This may result in an infinite loop. It should finish almost instantly\n') self.failUnless(len(smiSup)==4) sys.stderr.write('<<< OK, it finished.\n') def test27SmilesWriter(self) : fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','fewSmi.csv') #fileN = "../FileParsers/test_data/fewSmi.csv" smiSup = Chem.SmilesMolSupplier(fileN, delimiter=",", smilesColumn=1, nameColumn=0, titleLine=0) propNames = [] propNames.append("Column_2") ofile = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','Wrap','test_data','outSmiles.txt') writer = Chem.SmilesWriter(ofile) writer.SetProps(propNames) for mol in smiSup : writer.write(mol) writer.flush() def test28SmilesReverse(self): names = ["1", "2", "3", "4", "5", "6", "7", "8", "9", "10"] props = ["34.14","25.78","106.51","82.78","60.16","87.74","37.38","77.28","65.18","0.00"] ofile = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','Wrap','test_data','outSmiles.txt') #ofile = "test_data/outSmiles.csv" smiSup = Chem.SmilesMolSupplier(ofile) i = 0 for mol in smiSup: #print [repr(x) for x in mol.GetPropNames()] self.failUnless(mol.GetProp("_Name") == names[i]) self.failUnless(mol.GetProp("Column_2") == props[i]) i += 1 def writerSDFile(self) : fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','NCI_aids_few.sdf') #fileN = "../FileParsers/test_data/NCI_aids_few.sdf" ofile = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','Wrap','test_data','outNCI_few.sdf'); writer = Chem.SDWriter(ofile); sdSup = Chem.SDMolSupplier(fileN) for mol in sdSup : writer.write(mol) writer.flush() def test29SDWriterLoop(self) : self.writerSDFile() fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','Wrap', 'test_data','outNCI_few.sdf') sdSup = Chem.SDMolSupplier(fileN) molNames = ["48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213", "220", "229", "256"] chgs192 = {8:1, 11:1, 15:-1, 18:-1, 20:1, 21:1, 23:-1, 25:-1} i = 0 for mol in sdSup : #print 'mol:',mol #print '\t',molNames[i] self.failUnless(mol.GetProp("_Name") == molNames[i]) i += 1 if (mol.GetProp("_Name") == "192") : # test parsed charges on one of the molecules for id in chgs192.keys() : self.failUnless(mol.GetAtomWithIdx(id).GetFormalCharge() == chgs192[id]) def test30Issues109and110(self) : """ issues 110 and 109 were both related to handling of explicit Hs in SMILES input. """ m1 = Chem.MolFromSmiles('N12[CH](SC(C)(C)[CH]1C(O)=O)[CH](C2=O)NC(=O)[CH](N)c3ccccc3') self.failUnless(m1.GetNumAtoms()==24) m2 = Chem.MolFromSmiles('C1C=C([CH](N)C(=O)N[C]2([H])[C]3([H])SC(C)(C)[CH](C(=O)O)N3C(=O)2)C=CC=1') self.failUnless(m2.GetNumAtoms()==24) smi1 = Chem.MolToSmiles(m1) smi2 = Chem.MolToSmiles(m2) self.failUnless(smi1==smi2) m1 = Chem.MolFromSmiles('[H]CCl') self.failUnless(m1.GetNumAtoms()==2) self.failUnless(m1.GetAtomWithIdx(0).GetNumExplicitHs()==0) m1 = Chem.MolFromSmiles('[H][CH2]Cl') self.failUnless(m1.GetNumAtoms()==2) self.failUnless(m1.GetAtomWithIdx(0).GetNumExplicitHs()==3) m2 = Chem.AddHs(m1) self.failUnless(m2.GetNumAtoms()==5) m2 = Chem.RemoveHs(m2) self.failUnless(m2.GetNumAtoms()==2) def test31ChiralitySmiles(self) : m1 = Chem.MolFromSmiles('F[C@](Br)(I)Cl') self.failUnless(m1 is not None) self.failUnless(m1.GetNumAtoms()==5) self.failUnless(Chem.MolToSmiles(m1,1)=='F[C@](Cl)(Br)I',Chem.MolToSmiles(m1,1)) m1 = Chem.MolFromSmiles('CC1C[C@@]1(Cl)F') self.failUnless(m1 is not None) self.failUnless(m1.GetNumAtoms()==6) self.failUnless(Chem.MolToSmiles(m1,1)=='CC1C[C@]1(F)Cl',Chem.MolToSmiles(m1,1)) m1 = Chem.MolFromSmiles('CC1C[C@]1(Cl)F') self.failUnless(m1 is not None) self.failUnless(m1.GetNumAtoms()==6) self.failUnless(Chem.MolToSmiles(m1,1)=='CC1C[C@@]1(F)Cl',Chem.MolToSmiles(m1,1)) def test31aChiralitySubstructs(self) : m1 = Chem.MolFromSmiles('CC1C[C@@]1(Cl)F') self.failUnless(m1 is not None) self.failUnless(m1.GetNumAtoms()==6) self.failUnless(Chem.MolToSmiles(m1,1)=='CC1C[C@]1(F)Cl',Chem.MolToSmiles(m1,1)) m2 = Chem.MolFromSmiles('CC1C[C@]1(Cl)F') self.failUnless(m2 is not None) self.failUnless(m2.GetNumAtoms()==6) self.failUnless(Chem.MolToSmiles(m2,1)=='CC1C[C@@]1(F)Cl',Chem.MolToSmiles(m2,1)) self.failUnless(m1.HasSubstructMatch(m1)) self.failUnless(m1.HasSubstructMatch(m2)) self.failUnless(m1.HasSubstructMatch(m1,useChirality=True)) self.failUnless(not m1.HasSubstructMatch(m2,useChirality=True)) def _test32MolFilesWithChirality(self) : inD = """chiral1.mol ChemDraw10160313232D 5 4 0 0 0 0 0 0 0 0999 V2000 0.0553 0.6188 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 0.0553 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7697 -0.6188 0.0000 I 0 0 0 0 0 0 0 0 0 0 0 0 -0.6592 -0.6188 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -0.7697 -0.2062 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 1 1 2 5 1 0 M END """ m1 = Chem.MolFromMolBlock(inD) self.failUnless(m1 is not None) self.failUnless(m1.GetNumAtoms()==5) self.failUnless(smi=='F[C@](Cl)(Br)I',smi) inD = """chiral2.cdxml ChemDraw10160314052D 5 4 0 0 0 0 0 0 0 0999 V2000 0.0553 0.6188 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 0.0553 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.7697 -0.6188 0.0000 I 0 0 0 0 0 0 0 0 0 0 0 0 -0.6592 -0.6188 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -0.7697 -0.2062 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 1 6 2 5 1 0 M END """ m1 = Chem.MolFromMolBlock(inD) self.failUnless(m1 is not None) self.failUnless(m1.GetNumAtoms()==5) self.failUnless(Chem.MolToSmiles(m1,1)=='F[C@@](Cl)(Br)I') inD = """chiral1.mol ChemDraw10160313232D 5 4 0 0 0 0 0 0 0 0999 V2000 0.0553 0.6188 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 0.0553 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7697 -0.2062 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 -0.6592 -0.6188 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 0.7697 -0.6188 0.0000 I 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 1 1 2 5 1 0 M END """ m1 = Chem.MolFromMolBlock(inD) self.failUnless(m1 is not None) self.failUnless(m1.GetNumAtoms()==5) self.failUnless(Chem.MolToSmiles(m1,1)=='F[C@](Cl)(Br)I') inD = """chiral1.mol ChemDraw10160313232D 5 4 0 0 0 0 0 0 0 0999 V2000 0.0553 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.7697 -0.2062 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 -0.6592 -0.6188 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 0.7697 -0.6188 0.0000 I 0 0 0 0 0 0 0 0 0 0 0 0 0.0553 0.6188 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 1 3 1 1 1 4 1 0 1 5 1 0 M END """ m1 = Chem.MolFromMolBlock(inD) self.failUnless(m1 is not None) self.failUnless(m1.GetNumAtoms()==5) self.failUnless(Chem.MolToSmiles(m1,1)=='F[C@](Cl)(Br)I') inD = """chiral3.mol ChemDraw10160314362D 4 3 0 0 0 0 0 0 0 0999 V2000 0.4125 0.6188 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 0.4125 -0.2062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.3020 -0.6188 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -0.4125 -0.2062 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 1 2 4 1 0 M END """ m1 = Chem.MolFromMolBlock(inD) self.failUnless(m1 is not None) self.failUnless(m1.GetNumAtoms()==4) self.failUnless(Chem.MolToSmiles(m1,1)=='F[C@H](Cl)Br') inD = """chiral4.mol ChemDraw10160314362D 4 3 0 0 0 0 0 0 0 0999 V2000 0.4125 0.6188 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 0.4125 -0.2062 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.3020 -0.6188 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -0.4125 -0.2062 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 1 2 4 1 0 M END """ m1 = Chem.MolFromMolBlock(inD) self.failUnless(m1 is not None) self.failUnless(m1.GetNumAtoms()==4) self.failUnless(Chem.MolToSmiles(m1,1)=='FN(Cl)Br') inD = """chiral5.mol ChemDraw10160314362D 4 3 0 0 0 0 0 0 0 0999 V2000 0.4125 0.6188 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 0.4125 -0.2062 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 -0.3020 -0.6188 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 -0.4125 -0.2062 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 1 2 4 1 0 M CHG 1 2 1 M END """ m1 = Chem.MolFromMolBlock(inD) self.failUnless(m1 is not None) self.failUnless(m1.GetNumAtoms()==4) self.failUnless(Chem.MolToSmiles(m1,1)=='F[N@H+](Cl)Br') inD="""Case 10-14-3 ChemDraw10140308512D 4 3 0 0 0 0 0 0 0 0999 V2000 -0.8250 -0.4125 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8250 -0.4125 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.4125 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 2 4 1 1 M END """ m1 = Chem.MolFromMolBlock(inD) self.failUnless(m1 is not None) self.failUnless(m1.GetNumAtoms()==4) self.failUnless(Chem.MolToSmiles(m1,1)=='F[C@H](Cl)Br') inD="""Case 10-14-4 ChemDraw10140308512D 4 3 0 0 0 0 0 0 0 0999 V2000 -0.8250 -0.4125 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 -0.4125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.8250 -0.4125 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 0.0000 0.4125 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 1 2 4 1 0 M END """ m1 = Chem.MolFromMolBlock(inD) self.failUnless(m1 is not None) self.failUnless(m1.GetNumAtoms()==4) self.failUnless(Chem.MolToSmiles(m1,1)=='F[C@H](Cl)Br') inD="""chiral4.mol ChemDraw10160315172D 6 6 0 0 0 0 0 0 0 0999 V2000 -0.4422 0.1402 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4422 -0.6848 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2723 -0.2723 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8547 0.8547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6848 0.4422 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 0.8547 -0.8547 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 1 1 0 1 4 1 0 3 5 1 1 3 6 1 0 M END """ m1 = Chem.MolFromMolBlock(inD) self.failUnless(m1 is not None) self.failUnless(m1.GetNumAtoms()==6) self.failUnless(Chem.MolToSmiles(m1,1)=='CC1C[C@@]1(F)Cl',Chem.MolToSmiles(m1,1)) inD="""chiral4.mol ChemDraw10160315172D 6 6 0 0 0 0 0 0 0 0999 V2000 -0.4422 0.1402 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.4422 -0.6848 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.2723 -0.2723 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.8547 0.8547 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 0.6848 0.4422 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0 0.8547 -0.8547 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 1 0 3 1 1 0 1 4 1 0 3 5 1 6 3 6 1 0 M END """ m1 = Chem.MolFromMolBlock(inD) self.failUnless(m1 is not None) self.failUnless(m1.GetNumAtoms()==6) self.failUnless(Chem.MolToSmiles(m1,1)=='CC1C[C@]1(F)Cl',Chem.MolToSmiles(m1,1)) def test33Issue65(self) : """ issue 65 relates to handling of [H] in SMARTS """ m1 = Chem.MolFromSmiles('OC(O)(O)O') m2 = Chem.MolFromSmiles('OC(O)O') m3 = Chem.MolFromSmiles('OCO') q1 = Chem.MolFromSmarts('OC[H]',1) q2 = Chem.MolFromSmarts('O[C;H1]',1) q3 = Chem.MolFromSmarts('O[C;H1][H]',1) self.failUnless(not m1.HasSubstructMatch(q1)) self.failUnless(not m1.HasSubstructMatch(q2)) self.failUnless(not m1.HasSubstructMatch(q3)) self.failUnless(m2.HasSubstructMatch(q1)) self.failUnless(m2.HasSubstructMatch(q2)) self.failUnless(m2.HasSubstructMatch(q3)) self.failUnless(m3.HasSubstructMatch(q1)) self.failUnless(not m3.HasSubstructMatch(q2)) self.failUnless(not m3.HasSubstructMatch(q3)) m1H = Chem.AddHs(m1) m2H = Chem.AddHs(m2) m3H = Chem.AddHs(m3) q1 = Chem.MolFromSmarts('OC[H]') q2 = Chem.MolFromSmarts('O[C;H1]') q3 = Chem.MolFromSmarts('O[C;H1][H]') self.failUnless(not m1H.HasSubstructMatch(q1)) self.failUnless(not m1H.HasSubstructMatch(q2)) self.failUnless(not m1H.HasSubstructMatch(q3)) #m2H.Debug() self.failUnless(m2H.HasSubstructMatch(q1)) self.failUnless(m2H.HasSubstructMatch(q2)) self.failUnless(m2H.HasSubstructMatch(q3)) self.failUnless(m3H.HasSubstructMatch(q1)) self.failUnless(not m3H.HasSubstructMatch(q2)) self.failUnless(not m3H.HasSubstructMatch(q3)) def test34Issue124(self) : """ issue 124 relates to calculation of the distance matrix """ m = Chem.MolFromSmiles('CC=C') d = Chem.GetDistanceMatrix(m,0) self.failUnless(feq(d[0,1],1.0)) self.failUnless(feq(d[0,2],2.0)) # force an update: d = Chem.GetDistanceMatrix(m,1,0,1) self.failUnless(feq(d[0,1],1.0)) self.failUnless(feq(d[0,2],1.5)) def test35ChiralityPerception(self) : """ Test perception of chirality and CIP encoding """ m = Chem.MolFromSmiles('F[C@]([C@])(Cl)Br') Chem.AssignStereochemistry(m,1) self.failUnless(m.GetAtomWithIdx(1).HasProp('_CIPCode')) self.failIf(m.GetAtomWithIdx(2).HasProp('_CIPCode')) Chem.RemoveStereochemistry(m) self.failIf(m.GetAtomWithIdx(1).HasProp('_CIPCode')) m = Chem.MolFromSmiles('F[C@H](C)C') Chem.AssignStereochemistry(m,1) self.failUnless(m.GetAtomWithIdx(1).GetChiralTag() == Chem.ChiralType.CHI_UNSPECIFIED) self.failIf(m.GetAtomWithIdx(1).HasProp('_CIPCode')) m = Chem.MolFromSmiles('F\\C=C/Cl') self.failUnless(m.GetBondWithIdx(0).GetStereo()==Chem.BondStereo.STEREONONE) self.failUnless(m.GetBondWithIdx(1).GetStereo()==Chem.BondStereo.STEREOZ) atoms = m.GetBondWithIdx(1).GetStereoAtoms() self.failUnless(0 in atoms) self.failUnless(3 in atoms) self.failUnless(m.GetBondWithIdx(2).GetStereo()==Chem.BondStereo.STEREONONE) Chem.RemoveStereochemistry(m) self.failUnless(m.GetBondWithIdx(1).GetStereo()==Chem.BondStereo.STEREONONE) m = Chem.MolFromSmiles('F\\C=CCl') self.failUnless(m.GetBondWithIdx(1).GetStereo()==Chem.BondStereo.STEREONONE) def test36SubstructMatchStr(self): """ test the _SubstructMatchStr function """ query = Chem.MolFromSmarts('[n,p]1ccccc1') self.failUnless(query) mol = Chem.MolFromSmiles('N1=CC=CC=C1') self.failUnless(mol.HasSubstructMatch(query)) self.failUnless(Chem._HasSubstructMatchStr(mol.ToBinary(),query)) mol = Chem.MolFromSmiles('S1=CC=CC=C1') self.failUnless(not Chem._HasSubstructMatchStr(mol.ToBinary(),query)) self.failUnless(not mol.HasSubstructMatch(query)) mol = Chem.MolFromSmiles('P1=CC=CC=C1') self.failUnless(mol.HasSubstructMatch(query)) self.failUnless(Chem._HasSubstructMatchStr(mol.ToBinary(),query)) def test37SanitException(self): mol = Chem.MolFromSmiles('CC(C)(C)(C)C',0) self.failUnless(mol) self.failUnlessRaises(ValueError,lambda:Chem.SanitizeMol(mol)) def test38TDTSuppliers(self): data="""$SMI CAS<17584-12-2> | $SMI CAS<~> | $SMI CAS<932-53-6> | $SMI CAS<~> |""" suppl = Chem.TDTMolSupplier() suppl.SetData(data,"CAS") i=0; for mol in suppl: self.failUnless(mol) self.failUnless(mol.GetNumAtoms()) self.failUnless(mol.HasProp("CAS")) self.failUnless(mol.HasProp("_Name")) self.failUnless(mol.GetProp("CAS")==mol.GetProp("_Name")) self.failUnless(mol.GetNumConformers()==0) i+=1 self.failUnless(i==4) self.failUnless(len(suppl)==4) def test38Issue266(self): """ test issue 266: generation of kekulized smiles""" mol = Chem.MolFromSmiles('c1ccccc1') Chem.Kekulize(mol) smi = Chem.MolToSmiles(mol) self.failUnless(smi=='c1ccccc1') smi = Chem.MolToSmiles(mol,kekuleSmiles=True) self.failUnless(smi=='C1=CC=CC=C1') def test39Issue273(self): """ test issue 273: MolFileComments and MolFileInfo props ending up in SD files """ fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','Wrap', 'test_data','outNCI_few.sdf') suppl = Chem.SDMolSupplier(fileN) ms = [x for x in suppl] for m in ms: self.failUnless(m.HasProp('_MolFileInfo')) self.failUnless(m.HasProp('_MolFileComments')) fName = tempfile.mktemp('.sdf') w = Chem.SDWriter(fName) w.SetProps(ms[0].GetPropNames()) for m in ms: w.write(m) w = None txt= file(fName,'r').read() os.unlink(fName) self.failUnless(txt.find('MolFileInfo')==-1) self.failUnless(txt.find('MolFileComments')==-1) def test40SmilesRootedAtAtom(self): """ test the rootAtAtom functionality """ smi = 'CN(C)C' m = Chem.MolFromSmiles(smi) self.failUnless(Chem.MolToSmiles(m)=='CN(C)C') self.failUnless(Chem.MolToSmiles(m,rootedAtAtom=1)=='N(C)(C)C') def test41SetStreamIndices(self) : fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','NCI_aids_few.sdf') sdSup = Chem.SDMolSupplier(fileN) molNames = ["48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213", "220", "229", "256"] indices=[0, 2136, 6198, 8520, 11070, 12292, 14025, 15313, 17313, 20125, 22231, 23729, 26147, 28331, 32541, 33991] sdSup._SetStreamIndices(indices) self.failUnless(len(sdSup) == 16) mol = sdSup[5] self.failUnless(mol.GetProp("_Name") == "170") i = 0 for mol in sdSup : self.failUnless(mol) self.failUnless(mol.GetProp("_Name") == molNames[i]) i += 1 ns = [mol.GetProp("_Name") for mol in sdSup] self.failUnless(ns == molNames) # this can also be used to skip molecules in the file: indices=[0, 6198, 12292] sdSup._SetStreamIndices(indices) self.failUnless(len(sdSup) == 3) mol = sdSup[2] self.failUnless(mol.GetProp("_Name") == "170") # or to reorder them: indices=[0, 12292, 6198] sdSup._SetStreamIndices(indices) self.failUnless(len(sdSup) == 3) mol = sdSup[1] self.failUnless(mol.GetProp("_Name") == "170") def test42LifeTheUniverseAndEverything(self) : self.failUnless(True) def test43TplFileParsing(self) : fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','cmpd2.tpl') m1 = Chem.MolFromTPLFile(fileN) self.failUnless(m1 is not None) self.failUnless(m1.GetNumAtoms()==12) self.failUnless(m1.GetNumConformers()==2) m1 = Chem.MolFromTPLFile(fileN,skipFirstConf=True) self.failUnless(m1 is not None) self.failUnless(m1.GetNumAtoms()==12) self.failUnless(m1.GetNumConformers()==1) block = file(fileN,'r').read() m1 = Chem.MolFromTPLBlock(block) self.failUnless(m1 is not None) self.failUnless(m1.GetNumAtoms()==12) self.failUnless(m1.GetNumConformers()==2) def test44TplFileWriting(self) : fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','cmpd2.tpl') m1 = Chem.MolFromTPLFile(fileN) self.failUnless(m1 is not None) self.failUnless(m1.GetNumAtoms()==12) self.failUnless(m1.GetNumConformers()==2) block = Chem.MolToTPLBlock(m1) m1 = Chem.MolFromTPLBlock(block) self.failUnless(m1 is not None) self.failUnless(m1.GetNumAtoms()==12) self.failUnless(m1.GetNumConformers()==2) def test45RingInfo(self): """ test the RingInfo class """ smi = 'CNC' m = Chem.MolFromSmiles(smi) ri = m.GetRingInfo() self.failUnless(ri) self.failUnless(ri.NumRings()==0) self.failIf(ri.IsAtomInRingOfSize(0,3)) self.failIf(ri.IsAtomInRingOfSize(1,3)) self.failIf(ri.IsAtomInRingOfSize(2,3)) self.failIf(ri.IsBondInRingOfSize(1,3)) self.failIf(ri.IsBondInRingOfSize(2,3)) smi = 'C1CC2C1C2' m = Chem.MolFromSmiles(smi) ri = m.GetRingInfo() self.failUnless(ri) self.failUnless(ri.NumRings()==2) self.failIf(ri.IsAtomInRingOfSize(0,3)) self.failUnless(ri.IsAtomInRingOfSize(0,4)) self.failIf(ri.IsBondInRingOfSize(0,3)) self.failUnless(ri.IsBondInRingOfSize(0,4)) self.failUnless(ri.IsAtomInRingOfSize(2,4)) self.failUnless(ri.IsAtomInRingOfSize(2,3)) self.failUnless(ri.IsBondInRingOfSize(2,3)) self.failUnless(ri.IsBondInRingOfSize(2,4)) def test46ReplaceCore(self): """ test the ReplaceCore functionality """ core = Chem.MolFromSmiles('C=O') smi = 'CCC=O' m = Chem.MolFromSmiles(smi) r = Chem.ReplaceCore(m,core) self.failUnless(r) self.failUnless(Chem.MolToSmiles(r,True)=='[1*]CC') smi = 'C1CC(=O)CC1' m = Chem.MolFromSmiles(smi) r = Chem.ReplaceCore(m,core) self.failUnless(r) self.failUnless(Chem.MolToSmiles(r,True) =='[1*]CCCC[2*]') smi = 'C1CC(=N)CC1' m = Chem.MolFromSmiles(smi) r = Chem.ReplaceCore(m,core) self.failIf(r) def test47RWMols(self): """ test the RWMol class """ mol = Chem.MolFromSmiles('C1CCC1') self.failUnless(type(mol)==Chem.Mol) rwmol = Chem.EditableMol(mol) self.failUnless(type(rwmol)==Chem.EditableMol) newAt = Chem.Atom(8) rwmol.ReplaceAtom(0,newAt) self.failUnless(Chem.MolToSmiles(rwmol.GetMol())=='C1COC1') rwmol.RemoveBond(0,1) self.failUnless(Chem.MolToSmiles(rwmol.GetMol())=='CCCO') a = Chem.Atom(7) idx=rwmol.AddAtom(a) self.failUnlessEqual(rwmol.GetMol().GetNumAtoms(),5) self.failUnlessEqual(idx,4) idx=rwmol.AddBond(0,4,order=Chem.BondType.SINGLE) self.failUnlessEqual(idx,4) self.failUnless(Chem.MolToSmiles(rwmol.GetMol())=='CCCON') rwmol.AddBond(4,1,order=Chem.BondType.SINGLE) self.failUnless(Chem.MolToSmiles(rwmol.GetMol())=='C1CNOC1') rwmol.RemoveAtom(3) self.failUnless(Chem.MolToSmiles(rwmol.GetMol())=='CCNO') # practice shooting ourselves in the foot: m = Chem.MolFromSmiles('c1ccccc1') em=Chem.EditableMol(m) em.RemoveAtom(0) m2 = em.GetMol() self.failUnlessRaises(ValueError,lambda : Chem.SanitizeMol(m2)) m = Chem.MolFromSmiles('c1ccccc1') em=Chem.EditableMol(m) em.RemoveBond(0,1) m2 = em.GetMol() self.failUnlessRaises(ValueError,lambda : Chem.SanitizeMol(m2)) # boundary cases: # removing non-existent bonds: m = Chem.MolFromSmiles('c1ccccc1') em=Chem.EditableMol(m) em.RemoveBond(0,2) m2 = em.GetMol() Chem.SanitizeMol(m2) self.failUnless(Chem.MolToSmiles(m2)=='c1ccccc1') # removing non-existent atoms: m = Chem.MolFromSmiles('c1ccccc1') em=Chem.EditableMol(m) self.failUnlessRaises(RuntimeError,lambda:em.RemoveAtom(12)) def test47SmartsPieces(self): """ test the GetAtomSmarts and GetBondSmarts functions """ m =Chem.MolFromSmarts("[C,N]C") self.failUnless(m.GetAtomWithIdx(0).GetSmarts()=='[C,N]') self.failUnless(m.GetAtomWithIdx(1).GetSmarts()=='C') self.failUnless(m.GetBondBetweenAtoms(0,1).GetSmarts()=='-,:') m =Chem.MolFromSmarts("[$(C=O)]-O") self.failUnless(m.GetAtomWithIdx(0).GetSmarts()=='[$(C=O)]') self.failUnless(m.GetAtomWithIdx(1).GetSmarts()=='O') self.failUnless(m.GetBondBetweenAtoms(0,1).GetSmarts()=='-') m =Chem.MolFromSmiles("CO") self.failUnless(m.GetAtomWithIdx(0).GetSmarts()=='C') self.failUnless(m.GetAtomWithIdx(1).GetSmarts()=='O') self.failUnless(m.GetBondBetweenAtoms(0,1).GetSmarts()=='') self.failUnless(m.GetBondBetweenAtoms(0,1).GetSmarts(allBondsExplicit=True)=='-') m =Chem.MolFromSmiles("C=O") self.failUnless(m.GetAtomWithIdx(0).GetSmarts()=='C') self.failUnless(m.GetAtomWithIdx(1).GetSmarts()=='O') self.failUnless(m.GetBondBetweenAtoms(0,1).GetSmarts()=='=') def test48Issue1928819(self): """ test a crash involving looping directly over mol suppliers """ fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','NCI_aids_few.sdf') ms = [x for x in Chem.SDMolSupplier(fileN)] self.failUnlessEqual(len(ms),16) count=0 for m in Chem.SDMolSupplier(fileN): count+=1 self.failUnlessEqual(count,16) fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','fewSmi.csv') count=0 for m in Chem.SmilesMolSupplier(fileN,titleLine=False,smilesColumn=1,delimiter=','): count+=1 self.failUnlessEqual(count,10) fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','acd_few.tdt') count=0 for m in Chem.TDTMolSupplier(fileN): count+=1 self.failUnlessEqual(count,10) def test49Issue1932365(self): """ test aromatic Se and Te from smiles/smarts """ m = Chem.MolFromSmiles('c1ccc[se]1') self.failUnless(m) self.failUnless(m.GetAtomWithIdx(0).GetIsAromatic()) self.failUnless(m.GetAtomWithIdx(4).GetIsAromatic()) m = Chem.MolFromSmiles('c1ccc[te]1') self.failUnless(m) self.failUnless(m.GetAtomWithIdx(0).GetIsAromatic()) self.failUnless(m.GetAtomWithIdx(4).GetIsAromatic()) m = Chem.MolFromSmiles('C1=C[Se]C=C1') self.failUnless(m) self.failUnless(m.GetAtomWithIdx(0).GetIsAromatic()) self.failUnless(m.GetAtomWithIdx(2).GetIsAromatic()) m = Chem.MolFromSmiles('C1=C[Te]C=C1') self.failUnless(m) self.failUnless(m.GetAtomWithIdx(0).GetIsAromatic()) self.failUnless(m.GetAtomWithIdx(2).GetIsAromatic()) p = Chem.MolFromSmarts('[se]') self.failUnless(Chem.MolFromSmiles('c1ccc[se]1').HasSubstructMatch(p)) self.failIf(Chem.MolFromSmiles('C1=CCC[Se]1').HasSubstructMatch(p)) p = Chem.MolFromSmarts('[te]') self.failUnless(Chem.MolFromSmiles('c1ccc[te]1').HasSubstructMatch(p)) self.failIf(Chem.MolFromSmiles('C1=CCC[Te]1').HasSubstructMatch(p)) def test50Issue1968608(self): """ test sf.net issue 1968608 """ smarts = Chem.MolFromSmarts("[r5]") mol = Chem.MolFromSmiles("N12CCC36C1CC(C(C2)=CCOC4CC5=O)C4C3N5c7ccccc76") count = len(mol.GetSubstructMatches(smarts, uniquify=0)) self.failUnless(count==9) def test51RadicalHandling(self): """ test handling of atoms with radicals """ mol = Chem.MolFromSmiles("[C]C") self.failUnless(mol) atom=mol.GetAtomWithIdx(0) self.failUnless(atom.GetNumRadicalElectrons()==3) self.failUnless(atom.GetNoImplicit()) atom.SetNoImplicit(False) atom.SetNumRadicalElectrons(1) mol.UpdatePropertyCache() self.failUnless(atom.GetNumRadicalElectrons()==1) self.failUnless(atom.GetNumImplicitHs()==2) mol = Chem.MolFromSmiles("[c]1ccccc1") self.failUnless(mol) atom=mol.GetAtomWithIdx(0) self.failUnless(atom.GetNumRadicalElectrons()==1) self.failUnless(atom.GetNoImplicit()) mol = Chem.MolFromSmiles("[n]1ccccc1") self.failUnless(mol) atom=mol.GetAtomWithIdx(0) self.failUnless(atom.GetNumRadicalElectrons()==0) self.failUnless(atom.GetNoImplicit()) def test52MolFrags(self): """ test GetMolFrags functionality """ mol = Chem.MolFromSmiles("C.CC") self.failUnless(mol) fs = Chem.GetMolFrags(mol) self.failUnless(len(fs)==2) self.failUnless(len(fs[0])==1) self.failUnless(tuple(fs[0])==(0,)) self.failUnless(len(fs[1])==2) self.failUnless(tuple(fs[1])==(1,2)) fs = Chem.GetMolFrags(mol,True) self.failUnless(len(fs)==2) self.failUnless(fs[0].GetNumAtoms()==1) self.failUnless(fs[1].GetNumAtoms()==2) mol = Chem.MolFromSmiles("CCC") self.failUnless(mol) fs = Chem.GetMolFrags(mol) self.failUnless(len(fs)==1) self.failUnless(len(fs[0])==3) self.failUnless(tuple(fs[0])==(0,1,2)) fs = Chem.GetMolFrags(mol,True) self.failUnless(len(fs)==1) self.failUnless(fs[0].GetNumAtoms()==3) def test53Matrices(self) : """ test adjacency and distance matrices """ m = Chem.MolFromSmiles('CC=C') d = Chem.GetDistanceMatrix(m,0) self.failUnless(feq(d[0,1],1.0)) self.failUnless(feq(d[0,2],2.0)) self.failUnless(feq(d[1,0],1.0)) self.failUnless(feq(d[2,0],2.0)) a = Chem.GetAdjacencyMatrix(m,0) self.failUnless(a[0,1]==1) self.failUnless(a[0,2]==0) self.failUnless(a[1,2]==1) self.failUnless(a[1,0]==1) self.failUnless(a[2,0]==0) m = Chem.MolFromSmiles('C1CC1') d = Chem.GetDistanceMatrix(m,0) self.failUnless(feq(d[0,1],1.0)) self.failUnless(feq(d[0,2],1.0)) a = Chem.GetAdjacencyMatrix(m,0) self.failUnless(a[0,1]==1) self.failUnless(a[0,2]==1) self.failUnless(a[1,2]==1) m = Chem.MolFromSmiles('CC.C') d = Chem.GetDistanceMatrix(m,0) self.failUnless(feq(d[0,1],1.0)) self.failUnless(d[0,2]>1000) self.failUnless(d[1,2]>1000) a = Chem.GetAdjacencyMatrix(m,0) self.failUnless(a[0,1]==1) self.failUnless(a[0,2]==0) self.failUnless(a[1,2]==0) def test54Mol2Parser(self): """ test the mol2 parser """ fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','pyrazole_pyridine.mol2') m = Chem.MolFromMol2File(fileN) self.failUnless(m.GetNumAtoms()==5) self.failUnless(Chem.MolToSmiles(m)=='c1cn[nH]c1',Chem.MolToSmiles(m)) def test55LayeredFingerprint(self): m1 = Chem.MolFromSmiles('CC(C)C') fp1 = Chem.LayeredFingerprint(m1) self.failUnlessEqual(len(fp1),2048) atomCounts=[0]*m1.GetNumAtoms() fp2 = Chem.LayeredFingerprint(m1,atomCounts=atomCounts) self.failUnlessEqual(fp1,fp2) self.failUnlessEqual(atomCounts,[4,7,4,4]) fp2 = Chem.LayeredFingerprint(m1,atomCounts=atomCounts) self.failUnlessEqual(fp1,fp2) self.failUnlessEqual(atomCounts,[8,14,8,8]) pbv=DataStructs.ExplicitBitVect(2048) fp3 = Chem.LayeredFingerprint(m1,setOnlyBits=pbv) self.failUnlessEqual(fp3.GetNumOnBits(),0) fp3 = Chem.LayeredFingerprint(m1,setOnlyBits=fp2) self.failUnlessEqual(fp3,fp2) m2=Chem.MolFromSmiles('CC') fp4 = Chem.LayeredFingerprint(m2) atomCounts=[0]*m1.GetNumAtoms() fp3 = Chem.LayeredFingerprint(m1,setOnlyBits=fp4,atomCounts=atomCounts) self.failUnlessEqual(atomCounts,[1,3,1,1]) m2=Chem.MolFromSmiles('CCC') fp4 = Chem.LayeredFingerprint(m2) atomCounts=[0]*m1.GetNumAtoms() fp3 = Chem.LayeredFingerprint(m1,setOnlyBits=fp4,atomCounts=atomCounts) self.failUnlessEqual(atomCounts,[3,6,3,3]) def test56LazySDMolSupplier(self) : if not hasattr(Chem,'CompressedSDMolSupplier'): return self.failUnlessRaises(ValueError,lambda : Chem.CompressedSDMolSupplier('nosuchfile.sdf.gz')) fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','NCI_aids_few.sdf.gz') sdSup = Chem.CompressedSDMolSupplier(fileN) molNames = ["48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213", "220", "229", "256"] chgs192 = {8:1, 11:1, 15:-1, 18:-1, 20:1, 21:1, 23:-1, 25:-1} i = 0 for mol in sdSup : self.failUnless(mol) self.failUnless(mol.GetProp("_Name") == molNames[i]) i += 1 if (mol.GetProp("_Name") == "192") : # test parsed charges on one of the molecules for id in chgs192.keys() : self.failUnless(mol.GetAtomWithIdx(id).GetFormalCharge() == chgs192[id]) self.failUnlessEqual(i,16) sdSup = Chem.CompressedSDMolSupplier(fileN) ns = [mol.GetProp("_Name") for mol in sdSup] self.failUnless(ns == molNames) sdSup = Chem.CompressedSDMolSupplier(fileN, 0) for mol in sdSup : self.failUnless(not mol.HasProp("numArom")) def test57AddRecursiveQuery(self): q1 = Chem.MolFromSmiles('CC') q2 = Chem.MolFromSmiles('CO') Chem.AddRecursiveQuery(q1,q2,1) m1 = Chem.MolFromSmiles('OCC') self.failUnless(m1.HasSubstructMatch(q2)) self.failUnless(m1.HasSubstructMatch(q1)) self.failUnless(m1.HasSubstructMatch(q1)) self.failUnless(m1.GetSubstructMatch(q1)==(2,1)) q3 = Chem.MolFromSmiles('CS') Chem.AddRecursiveQuery(q1,q3,1) self.failIf(m1.HasSubstructMatch(q3)) self.failIf(m1.HasSubstructMatch(q1)) m2 = Chem.MolFromSmiles('OC(S)C') self.failUnless(m2.HasSubstructMatch(q1)) self.failUnless(m2.GetSubstructMatch(q1)==(3,1)) m3 = Chem.MolFromSmiles('SCC') self.failUnless(m3.HasSubstructMatch(q3)) self.failIf(m3.HasSubstructMatch(q1)) q1 = Chem.MolFromSmiles('CC') Chem.AddRecursiveQuery(q1,q2,1) Chem.AddRecursiveQuery(q1,q3,1,False) self.failUnless(m3.HasSubstructMatch(q1)) self.failUnless(m3.GetSubstructMatch(q1)==(2,1)) def test58Issue2983794(self) : fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','Wrap', 'test_data','issue2983794.sdf') m1 = Chem.MolFromMolFile(fileN) self.failUnless(m1) em = Chem.EditableMol(m1) em.RemoveAtom(0) m2 = em.GetMol() self.failUnlessRaises(ValueError,lambda:Chem.Kekulize(m2)) def test59Issue3007178(self) : m = Chem.MolFromSmiles('CCC') a = m.GetAtomWithIdx(0) m=None self.failUnlessEqual(Chem.MolToSmiles(a.GetOwningMol()),'CCC') a=None m = Chem.MolFromSmiles('CCC') b = m.GetBondWithIdx(0) m=None self.failUnlessEqual(Chem.MolToSmiles(b.GetOwningMol()),'CCC') def test60SmilesWriterClose(self) : fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','fewSmi.csv') smiSup = Chem.SmilesMolSupplier(fileN, delimiter=",", smilesColumn=1, nameColumn=0, titleLine=0) ms = [x for x in smiSup] ofile = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','Wrap','test_data','outSmiles.txt') writer = Chem.SmilesWriter(ofile) for mol in ms: writer.write(mol) writer.close() newsup=Chem.SmilesMolSupplier(ofile) newms = [x for x in newsup] self.failUnlessEqual(len(ms),len(newms)) def test61PathToSubmol(self): m = Chem.MolFromSmiles('CCCCCC1C(O)CC(O)N1C=CCO') env = Chem.FindAtomEnvironmentOfRadiusN(m,2,11) self.failUnlessEqual(len(env),8) amap={} submol = Chem.PathToSubmol(m,env,atomMap=amap) self.failUnlessEqual(submol.GetNumAtoms(),len(amap.keys())) self.failUnlessEqual(submol.GetNumAtoms(),9) smi=Chem.MolToSmiles(submol,rootedAtAtom=amap[11]) self.failUnlessEqual(smi[0],'N') refsmi = Chem.MolToSmiles(Chem.MolFromSmiles('N(C=C)(C(C)C)C(O)C')) csmi = Chem.MolToSmiles(Chem.MolFromSmiles(smi)) self.failUnlessEqual(refsmi,csmi) def test62SmilesAndSmartsReplacements(self): mol = Chem.MolFromSmiles('C{branch}C',replacements={'{branch}':'C1(CC1)'}) self.failUnlessEqual(mol.GetNumAtoms(),5) mol = Chem.MolFromSmarts('C{branch}C',replacements={'{branch}':'C1(CC1)'}) self.failUnlessEqual(mol.GetNumAtoms(),5) mol = Chem.MolFromSmiles('C{branch}C{acid}',replacements={'{branch}':'C1(CC1)', '{acid}':"C(=O)O"}) self.failUnlessEqual(mol.GetNumAtoms(),8) def test63Issue3313539(self): fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','rgroups1.mol') m = Chem.MolFromMolFile(fileN) self.failUnless(m is not None) at = m.GetAtomWithIdx(3) self.failUnless(at is not None) self.failUnless(at.HasProp('_MolFileRLabel')) p = at.GetProp('_MolFileRLabel') self.failUnlessEqual(p,'2') at = m.GetAtomWithIdx(4) self.failUnless(at is not None) self.failUnless(at.HasProp('_MolFileRLabel')) p = at.GetProp('_MolFileRLabel') self.failUnlessEqual(p,'1') def test64MoleculeCleanup(self): m = Chem.MolFromSmiles('CN(=O)=O',False) self.failUnless(m) self.failUnless(m.GetAtomWithIdx(1).GetFormalCharge()==0 and \ m.GetAtomWithIdx(2).GetFormalCharge()==0 and \ m.GetAtomWithIdx(3).GetFormalCharge()==0) self.failUnless(m.GetBondBetweenAtoms(1,3).GetBondType()==Chem.BondType.DOUBLE and \ m.GetBondBetweenAtoms(1,2).GetBondType()==Chem.BondType.DOUBLE ) Chem.Cleanup(m) m.UpdatePropertyCache() self.failUnless(m.GetAtomWithIdx(1).GetFormalCharge()==1 and \ (m.GetAtomWithIdx(2).GetFormalCharge()==-1 or \ m.GetAtomWithIdx(3).GetFormalCharge()==-1)) self.failUnless(m.GetBondBetweenAtoms(1,3).GetBondType()==Chem.BondType.SINGLE or \ m.GetBondBetweenAtoms(1,2).GetBondType()==Chem.BondType.SINGLE ) def test65StreamSupplier(self): import gzip fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','NCI_aids_few.sdf.gz') molNames = ["48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213", "220", "229", "256"] inf = gzip.open(fileN) if 0: sb = Chem.streambuf(inf) suppl = Chem.ForwardSDMolSupplier(sb) else: suppl = Chem.ForwardSDMolSupplier(inf) i = 0 while not suppl.atEnd(): mol = suppl.next() self.failUnless(mol) self.failUnless(mol.GetProp("_Name") == molNames[i]) i += 1 self.failUnlessEqual(i,16) # make sure we have object ownership preserved inf = gzip.open(fileN) suppl = Chem.ForwardSDMolSupplier(inf) inf=None i = 0 while not suppl.atEnd(): mol = suppl.next() self.failUnless(mol) self.failUnless(mol.GetProp("_Name") == molNames[i]) i += 1 self.failUnlessEqual(i,16) def test66StreamSupplierIter(self): import gzip fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','NCI_aids_few.sdf.gz') inf = gzip.open(fileN) if 0: sb = Chem.streambuf(inf) suppl = Chem.ForwardSDMolSupplier(sb) else: suppl = Chem.ForwardSDMolSupplier(inf) molNames = ["48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213", "220", "229", "256"] i = 0 for mol in suppl : self.failUnless(mol) self.failUnless(mol.GetProp("_Name") == molNames[i]) i += 1 self.failUnlessEqual(i,16) def test67StreamSupplierStringIO(self): import gzip,StringIO fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','NCI_aids_few.sdf.gz') sio = StringIO.StringIO(gzip.open(fileN).read()) suppl = Chem.ForwardSDMolSupplier(sio) molNames = ["48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213", "220", "229", "256"] i = 0 for mol in suppl: self.failUnless(mol) self.failUnless(mol.GetProp("_Name") == molNames[i]) i += 1 self.failUnlessEqual(i,16) def test68ForwardSupplierUsingFilename(self): fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','NCI_aids_few.sdf') suppl = Chem.ForwardSDMolSupplier(fileN) molNames = ["48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213", "220", "229", "256"] i = 0 for mol in suppl: self.failUnless(mol) self.failUnless(mol.GetProp("_Name") == molNames[i]) i += 1 self.failUnlessEqual(i,16) self.failUnlessRaises(IOError,lambda : Chem.ForwardSDMolSupplier('nosuchfile.sdf')) def test69StreamSupplierStreambuf(self): import gzip,StringIO fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','NCI_aids_few.sdf.gz') sb = rdBase.streambuf(gzip.open(fileN)) suppl = Chem.ForwardSDMolSupplier(sb) molNames = ["48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213", "220", "229", "256"] i = 0 for mol in suppl: self.failUnless(mol) self.failUnless(mol.GetProp("_Name") == molNames[i]) i += 1 self.failUnlessEqual(i,16) def test70StreamSDWriter(self): import gzip,StringIO fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','NCI_aids_few.sdf.gz') inf = gzip.open(fileN) suppl = Chem.ForwardSDMolSupplier(inf) osio=StringIO.StringIO() w = Chem.SDWriter(osio) molNames = ["48", "78", "128", "163", "164", "170", "180", "186", "192", "203", "210", "211", "213", "220", "229", "256"] i = 0 for mol in suppl : self.failUnless(mol) self.failUnless(mol.GetProp("_Name") == molNames[i]) w.write(mol) i += 1 self.failUnlessEqual(i,16) w.flush() w=None isio=StringIO.StringIO(osio.getvalue()) suppl = Chem.ForwardSDMolSupplier(isio) i = 0 for mol in suppl : self.failUnless(mol) self.failUnless(mol.GetProp("_Name") == molNames[i]) i += 1 self.failUnlessEqual(i,16) def test71StreamSmilesWriter(self): import StringIO fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','esters.sdf') suppl = Chem.ForwardSDMolSupplier(fileN) osio=StringIO.StringIO() w = Chem.SmilesWriter(osio) ms = [x for x in suppl] w.SetProps(ms[0].GetPropNames()) i=0 for mol in ms: self.failUnless(mol) w.write(mol) i+=1 self.failUnlessEqual(i,6) w.flush() w=None txt = osio.getvalue() self.failUnlessEqual(txt.count('ID'),1) self.failUnlessEqual(txt.count('\n'),7) def test72StreamTDTWriter(self): import StringIO fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','esters.sdf') suppl = Chem.ForwardSDMolSupplier(fileN) osio=StringIO.StringIO() w = Chem.TDTWriter(osio) ms = [x for x in suppl] w.SetProps(ms[0].GetPropNames()) i=0 for mol in ms: self.failUnless(mol) w.write(mol) i+=1 self.failUnlessEqual(i,6) w.flush() w=None txt = osio.getvalue() self.failUnlessEqual(txt.count('ID'),6) self.failUnlessEqual(txt.count('NAME'),6) def test73SanitizationOptions(self): m = Chem.MolFromSmiles('c1ccccc1',sanitize=False) res = Chem.SanitizeMol(m,catchErrors=True) self.failUnlessEqual(res,0) m = Chem.MolFromSmiles('c1cccc1',sanitize=False) res = Chem.SanitizeMol(m,catchErrors=True) self.failUnlessEqual(res,Chem.SanitizeFlags.SANITIZE_KEKULIZE) m = Chem.MolFromSmiles('CC(C)(C)(C)C',sanitize=False) res = Chem.SanitizeMol(m,catchErrors=True) self.failUnlessEqual(res,Chem.SanitizeFlags.SANITIZE_PROPERTIES) m = Chem.MolFromSmiles('c1cccc1',sanitize=False) res = Chem.SanitizeMol(m,sanitizeOps=Chem.SanitizeFlags.SANITIZE_ALL^Chem.SanitizeFlags.SANITIZE_KEKULIZE, catchErrors=True) self.failUnlessEqual(res,Chem.SanitizeFlags.SANITIZE_NONE) def test74Issue3510149(self): mol = Chem.MolFromSmiles("CCC1CNCC1CC") atoms = mol.GetAtoms() mol=None for atom in atoms: idx=atom.GetIdx() p= atom.GetOwningMol().GetNumAtoms() mol = Chem.MolFromSmiles("CCC1CNCC1CC") bonds = mol.GetBonds() mol=None for bond in bonds: idx=bond.GetIdx() p= atom.GetOwningMol().GetNumAtoms() mol = Chem.MolFromSmiles("CCC1CNCC1CC") bond = mol.GetBondBetweenAtoms(0,1) mol=None idx=bond.GetBeginAtomIdx() p= bond.GetOwningMol().GetNumAtoms() fileN = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','FileParsers', 'test_data','NCI_aids_few.sdf') sdSup = Chem.SDMolSupplier(fileN) mol = sdSup.next() nats = mol.GetNumAtoms() conf = mol.GetConformer() mol=None self.failUnlessEqual(nats,conf.GetNumAtoms()) conf.GetOwningMol().GetProp("_Name") def test75AllBondsExplicit(self): m = Chem.MolFromSmiles("CCC") smi = Chem.MolToSmiles(m) self.failUnlessEqual(smi,"CCC") smi = Chem.MolToSmiles(m,allBondsExplicit=True) self.failUnlessEqual(smi,"C-C-C") m = Chem.MolFromSmiles("c1ccccc1") smi = Chem.MolToSmiles(m) self.failUnlessEqual(smi,"c1ccccc1") smi = Chem.MolToSmiles(m,allBondsExplicit=True) self.failUnlessEqual(smi,"c1:c:c:c:c:c:1") if __name__ == '__main__': unittest.main()