# $Id$ # # Copyright (c) 2007, Novartis Institutes for BioMedical Research Inc. # All rights reserved. # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are # met: # # * Redistributions of source code must retain the above copyright # notice, this list of conditions and the following disclaimer. # * Redistributions in binary form must reproduce the above # copyright notice, this list of conditions and the following # disclaimer in the documentation and/or other materials provided # with the distribution. # * Neither the name of Novartis Institutes for BioMedical Research Inc. # nor the names of its contributors may be used to endorse or promote # products derived from this software without specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS # "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT # LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR # A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT # OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, # SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT # LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, # DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY # THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT # (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE # OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. # from rdkit import rdBase from rdkit import Chem from rdkit.Chem import rdChemReactions from rdkit import Geometry from rdkit import RDConfig import unittest import os,sys import cPickle def feq(v1,v2,tol2=1e-4): return abs(v1-v2)<=tol2 def ptEq(pt1, pt2, tol=1e-4): return feq(pt1.x,pt2.x,tol) and feq(pt1.y,pt2.y,tol) and feq(pt1.z,pt2.z,tol) class TestCase(unittest.TestCase) : def setUp(self): self.dataDir = os.path.join(RDConfig.RDBaseDir,'Code','GraphMol','ChemReactions','testData') def test1Basics(self): rxn = rdChemReactions.ChemicalReaction() self.failUnless(rxn.GetNumReactantTemplates()==0) self.failUnless(rxn.GetNumProductTemplates()==0) r1= Chem.MolFromSmarts('[C:1](=[O:2])O') rxn.AddReactantTemplate(r1) self.failUnless(rxn.GetNumReactantTemplates()==1) r1= Chem.MolFromSmarts('[N:3]') rxn.AddReactantTemplate(r1) self.failUnless(rxn.GetNumReactantTemplates()==2) r1= Chem.MolFromSmarts('[C:1](=[O:2])[N:3]') rxn.AddProductTemplate(r1) self.failUnless(rxn.GetNumProductTemplates()==1) reacts = (Chem.MolFromSmiles('C(=O)O'),Chem.MolFromSmiles('N')) ps = rxn.RunReactants(reacts) self.failUnless(len(ps)==1) self.failUnless(len(ps[0])==1) self.failUnless(ps[0][0].GetNumAtoms()==3) ps = rxn.RunReactants(list(reacts)) self.failUnless(len(ps)==1) self.failUnless(len(ps[0])==1) self.failUnless(ps[0][0].GetNumAtoms()==3) def test2DaylightParser(self): rxn = rdChemReactions.ReactionFromSmarts('[C:1](=[O:2])O.[N:3]>>[C:1](=[O:2])[N:3]') self.failUnless(rxn) self.failUnless(rxn.GetNumReactantTemplates()==2) self.failUnless(rxn.GetNumProductTemplates()==1) self.failUnless(rxn._getImplicitPropertiesFlag()) reacts = (Chem.MolFromSmiles('C(=O)O'),Chem.MolFromSmiles('N')) ps = rxn.RunReactants(reacts) self.failUnless(len(ps)==1) self.failUnless(len(ps[0])==1) self.failUnless(ps[0][0].GetNumAtoms()==3) reacts = (Chem.MolFromSmiles('CC(=O)OC'),Chem.MolFromSmiles('CN')) ps = rxn.RunReactants(reacts) self.failUnless(len(ps)==1) self.failUnless(len(ps[0])==1) self.failUnless(ps[0][0].GetNumAtoms()==5) def test3MDLParsers(self): fileN = os.path.join(self.dataDir,'AmideBond.rxn') rxn = rdChemReactions.ReactionFromRxnFile(fileN) self.failUnless(rxn) self.failIf(rxn._getImplicitPropertiesFlag()) self.failUnless(rxn.GetNumReactantTemplates()==2) self.failUnless(rxn.GetNumProductTemplates()==1) reacts = (Chem.MolFromSmiles('C(=O)O'),Chem.MolFromSmiles('N')) ps = rxn.RunReactants(reacts) self.failUnless(len(ps)==1) self.failUnless(len(ps[0])==1) self.failUnless(ps[0][0].GetNumAtoms()==3) rxnBlock = file(fileN,'r').read() rxn = rdChemReactions.ReactionFromRxnBlock(rxnBlock) self.failUnless(rxn) self.failUnless(rxn.GetNumReactantTemplates()==2) self.failUnless(rxn.GetNumProductTemplates()==1) reacts = (Chem.MolFromSmiles('C(=O)O'),Chem.MolFromSmiles('N')) ps = rxn.RunReactants(reacts) self.failUnless(len(ps)==1) self.failUnless(len(ps[0])==1) self.failUnless(ps[0][0].GetNumAtoms()==3) def test4ErrorHandling(self): self.failUnlessRaises(ValueError,lambda x='[C:1](=[O:2])Q.[N:3]>>[C:1](=[O:2])[N:3]':rdChemReactions.ReactionFromSmarts(x)) self.failUnlessRaises(ValueError,lambda x='[C:1](=[O:2])O.[N:3]>>[C:1](=[O:2])[N:3]Q':rdChemReactions.ReactionFromSmarts(x)) self.failUnlessRaises(ValueError,lambda x='[C:1](=[O:2])O.[N:3]>>[C:1](=[O:2])[N:3]>>CC':rdChemReactions.ReactionFromSmarts(x)) block="""$RXN ISIS 082120061354 3 1 $MOL -ISIS- 08210613542D 3 2 0 0 0 0 0 0 0 0999 V2000 -1.4340 -0.6042 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0 -0.8639 -0.9333 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4340 0.0542 0.0000 O 0 0 0 0 0 0 0 0 0 1 0 0 1 2 1 0 0 0 0 1 3 2 0 0 0 0 M END $MOL -ISIS- 08210613542D 1 0 0 0 0 0 0 0 0 0999 V2000 2.2125 -0.7833 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0 M END $MOL -ISIS- 08210613542D 3 2 0 0 0 0 0 0 0 0999 V2000 9.5282 -0.8083 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0 8.9579 -0.4792 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0 8.9579 0.1792 0.0000 O 0 0 0 0 0 0 0 0 0 1 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 M END """ self.failUnlessRaises(ValueError,lambda x=block:rdChemReactions.ReactionFromRxnBlock(x)) block="""$RXN ISIS 082120061354 2 1 $MOL -ISIS- 08210613542D 4 2 0 0 0 0 0 0 0 0999 V2000 -1.4340 -0.6042 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0 -0.8639 -0.9333 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4340 0.0542 0.0000 O 0 0 0 0 0 0 0 0 0 1 0 0 1 2 1 0 0 0 0 1 3 2 0 0 0 0 M END $MOL -ISIS- 08210613542D 1 0 0 0 0 0 0 0 0 0999 V2000 2.2125 -0.7833 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0 M END $MOL -ISIS- 08210613542D 3 2 0 0 0 0 0 0 0 0999 V2000 9.5282 -0.8083 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0 8.9579 -0.4792 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0 8.9579 0.1792 0.0000 O 0 0 0 0 0 0 0 0 0 1 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 M END """ #self.failUnlessRaises(ValueError,lambda x=block:rdChemReactions.ReactionFromRxnBlock(x)) block="""$RXN ISIS 082120061354 2 1 $MOL -ISIS- 08210613542D 3 2 0 0 0 0 0 0 0 0999 V2000 -1.4340 -0.6042 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0 -0.8639 -0.9333 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.4340 0.0542 0.0000 O 0 0 0 0 0 0 0 0 0 1 0 0 1 2 1 0 0 0 0 1 3 2 0 0 0 0 M END $MOL -ISIS- 08210613542D 1 0 0 0 0 0 0 0 0 0999 V2000 2.2125 -0.7833 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0 M END $MOL -ISIS- 08210613542D 3 1 0 0 0 0 0 0 0 0999 V2000 9.5282 -0.8083 0.0000 N 0 0 0 0 0 0 0 0 0 3 0 0 8.9579 -0.4792 0.0000 C 0 0 0 0 0 0 0 0 0 2 0 0 8.9579 0.1792 0.0000 O 0 0 0 0 0 0 0 0 0 1 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 M END """ #self.failUnlessRaises(ValueError,lambda x=block:rdChemReactions.ReactionFromRxnBlock(x)) def test5Validation(self): rxn = rdChemReactions.ReactionFromSmarts('[C:1](=[O:2])O.[N:3]>>[C:1](=[O:2])[N:3]') self.failUnless(rxn) self.failUnless(rxn.Validate()==(0,0)) rxn = rdChemReactions.ReactionFromSmarts('[C:1](=[O:1])O.[N:3]>>[C:1](=[O:2])[N:3]') self.failUnless(rxn) self.failUnless(rxn.Validate()==(1,1)) rxn = rdChemReactions.ReactionFromSmarts('[C:1](=[O:2])[O:4].[N:3]>>[C:1](=[O:2])[N:3]') self.failUnless(rxn) self.failUnless(rxn.Validate()==(1,0)) rxn = rdChemReactions.ReactionFromSmarts('[C:1](=[O:2])O.[N:3]>>[C:1](=[O:2])[N:3][C:5]') self.failUnless(rxn) self.failUnless(rxn.Validate()==(1,0)) def test6Exceptions(self): rxn = rdChemReactions.ReactionFromSmarts('[C:1]Cl>>[C:1]') self.failUnless(rxn) self.failUnlessRaises(ValueError,lambda x=rxn:x.RunReactants(())) self.failUnlessRaises(ValueError,lambda x=rxn:x.RunReactants((Chem.MolFromSmiles('CC'),Chem.MolFromSmiles('C')))) ps=rxn.RunReactants((Chem.MolFromSmiles('CCCl'),)) self.failUnless(len(ps)==1) self.failUnless(len(ps[0])==1) def _test7Leak(self): rxn = rdChemReactions.ReactionFromSmarts('[C:1]Cl>>[C:1]') self.failUnless(rxn) print 'running: ' for i in range(1e5): ps=rxn.RunReactants((Chem.MolFromSmiles('CCCl'),)) self.failUnless(len(ps)==1) self.failUnless(len(ps[0])==1) if not i%1000: print i def test8Properties(self): rxn = rdChemReactions.ReactionFromSmarts('[O:1]>>[O:1][3#0]') self.failUnless(rxn) ps=rxn.RunReactants((Chem.MolFromSmiles('CO'),)) self.failUnless(len(ps)==1) self.failUnless(len(ps[0])==1) Chem.SanitizeMol(ps[0][0]) self.failUnlessEqual(ps[0][0].GetAtomWithIdx(1).GetIsotope(),3); def test9AromaticityTransfer(self): # this was issue 2664121 mol = Chem.MolFromSmiles('c1ccc(C2C3(Cc4c(cccc4)C2)CCCC3)cc1') rxn = rdChemReactions.ReactionFromSmarts('[A:1]1~[*:2]~[*:3]~[*:4]~[*:5]~[A:6]-;@1>>[*:1]~[*:2]~[*:3]~[*:4]~[*:5]~[*:6]') products = rxn.RunReactants([mol]) self.failUnlessEqual(len(products),6) for p in products: self.failUnlessEqual(len(p),1) Chem.SanitizeMol(p[0]) def test10DotSeparation(self): rxn = rdChemReactions.ReactionFromSmarts('[C:1]1[O:2][N:3]1>>[C:1]1[O:2].[N:3]1') mol = Chem.MolFromSmiles('C1ON1') products = rxn.RunReactants([mol]) self.failUnlessEqual(len(products),1) for p in products: self.failUnlessEqual(len(p),1) self.failUnlessEqual(p[0].GetNumAtoms(),3) self.failUnlessEqual(p[0].GetNumBonds(),2) def test11ImplicitProperties(self): rxn = rdChemReactions.ReactionFromSmarts('[C:1]O>>[C:1]') mol = Chem.MolFromSmiles('CCO') products = rxn.RunReactants([mol]) self.failUnlessEqual(len(products),1) for p in products: self.failUnlessEqual(len(p),1) self.failUnlessEqual(Chem.MolToSmiles(p[0]),'CC') mol2 = Chem.MolFromSmiles('C[CH-]O') products = rxn.RunReactants([mol2]) self.failUnlessEqual(len(products),1) for p in products: self.failUnlessEqual(len(p),1) self.failUnlessEqual(Chem.MolToSmiles(p[0]),'[CH2-]C') rxn._setImplicitPropertiesFlag(False) products = rxn.RunReactants([mol]) self.failUnlessEqual(len(products),1) for p in products: self.failUnlessEqual(len(p),1) self.failUnlessEqual(Chem.MolToSmiles(p[0]),'CC') products = rxn.RunReactants([mol2]) self.failUnlessEqual(len(products),1) for p in products: self.failUnlessEqual(len(p),1) self.failUnlessEqual(Chem.MolToSmiles(p[0]),'CC') def test12Pickles(self): rxn = rdChemReactions.ReactionFromSmarts('[C:1]1[O:2][N:3]1>>[C:1]1[O:2].[N:3]1') pkl = cPickle.dumps(rxn) rxn = cPickle.loads(pkl) mol = Chem.MolFromSmiles('C1ON1') products = rxn.RunReactants([mol]) self.failUnlessEqual(len(products),1) for p in products: self.failUnlessEqual(len(p),1) self.failUnlessEqual(p[0].GetNumAtoms(),3) self.failUnlessEqual(p[0].GetNumBonds(),2) rxn = rdChemReactions.ChemicalReaction(rxn.ToBinary()) products = rxn.RunReactants([mol]) self.failUnlessEqual(len(products),1) for p in products: self.failUnlessEqual(len(p),1) self.failUnlessEqual(p[0].GetNumAtoms(),3) self.failUnlessEqual(p[0].GetNumBonds(),2) def test13GetTemplates(self): rxn = rdChemReactions.ReactionFromSmarts('[C:1]1[O:2][N:3]1>>[C:1][O:2].[N:3]') r1 = rxn.GetReactantTemplate(0) sma=Chem.MolToSmarts(r1) self.failUnlessEqual(sma,'[C:1]1-,:[O:2]-,:[N:3]-,:1') p1 = rxn.GetProductTemplate(0) sma=Chem.MolToSmarts(p1) self.failUnlessEqual(sma,'[C:1]-,:[O:2]') p2 = rxn.GetProductTemplate(1) sma=Chem.MolToSmarts(p2) self.failUnlessEqual(sma,'[N:3]') self.failUnlessRaises(ValueError,lambda :rxn.GetProductTemplate(2)) self.failUnlessRaises(ValueError,lambda :rxn.GetReactantTemplate(1)) def test14Matchers(self): rxn = rdChemReactions.ReactionFromSmarts('[C;!$(C(-O)-O):1](=[O:2])[O;H,-1].[N;!H0:3]>>[C:1](=[O:2])[N:3]') self.failUnless(rxn) rxn.Initialize() self.failUnless(rxn.IsMoleculeReactant(Chem.MolFromSmiles('OC(=O)C'))) self.failIf(rxn.IsMoleculeReactant(Chem.MolFromSmiles('OC(=O)O'))) self.failUnless(rxn.IsMoleculeReactant(Chem.MolFromSmiles('CNC'))) self.failIf(rxn.IsMoleculeReactant(Chem.MolFromSmiles('CN(C)C'))) self.failUnless(rxn.IsMoleculeProduct(Chem.MolFromSmiles('NC(=O)C'))) self.failUnless(rxn.IsMoleculeProduct(Chem.MolFromSmiles('CNC(=O)C'))) self.failIf(rxn.IsMoleculeProduct(Chem.MolFromSmiles('COC(=O)C'))) def test15Replacements(self): rxn = rdChemReactions.ReactionFromSmarts('[{amine}:1]>>[*:1]-C', replacements={'{amine}':'$([N;!H0;$(N-[#6]);!$(N-[!#6;!#1]);!$(N-C=[O,N,S])])'}) self.failUnless(rxn) rxn.Initialize() reactants = (Chem.MolFromSmiles('CCN'),) ps = rxn.RunReactants(reactants) self.failUnlessEqual(len(ps),1) self.failUnlessEqual(len(ps[0]),1) self.failUnlessEqual(ps[0][0].GetNumAtoms(),4) def test16GetReactingAtoms(self): rxn = rdChemReactions.ReactionFromSmarts("[O:1][C:2].[N:3]>>[N:1][C:2].[N:3]") self.failUnless(rxn) rxn.Initialize() rAs = rxn.GetReactingAtoms() self.failUnlessEqual(len(rAs),2) self.failUnlessEqual(len(rAs[0]),1) self.failUnlessEqual(len(rAs[1]),0) rxn = rdChemReactions.ReactionFromSmarts("[O:1]C>>[O:1]C") self.failUnless(rxn) rxn.Initialize() rAs = rxn.GetReactingAtoms() self.failUnlessEqual(len(rAs),1) self.failUnlessEqual(len(rAs[0]),2) rAs = rxn.GetReactingAtoms(True) self.failUnlessEqual(len(rAs),1) self.failUnlessEqual(len(rAs[0]),1) def test17AddRecursiveQueriesToReaction(self): rxn = rdChemReactions.ReactionFromSmarts("[C:1][O:2].[N:3]>>[C:1][N:2]") self.failUnless(rxn) rxn.Initialize() qs = {'aliphatic':Chem.MolFromSmiles('CC')} rxn.GetReactantTemplate(0).GetAtomWithIdx(0).SetProp('query', 'aliphatic') rxn.AddRecursiveQueriesToReaction(qs,'query') q = rxn.GetReactantTemplate(0) m = Chem.MolFromSmiles('CCOC') self.failUnless(m.HasSubstructMatch(q)) m = Chem.MolFromSmiles('CO') self.failIf(m.HasSubstructMatch(q)) rxn = rdChemReactions.ReactionFromSmarts("[C:1][O:2].[N:3]>>[C:1][N:2]") rxn.Initialize() rxn.GetReactantTemplate(0).GetAtomWithIdx(0).SetProp('query', 'aliphatic') labels = rxn.AddRecursiveQueriesToReaction(qs,'query', getLabels=True) self.failUnless(len(labels), 1) def test18GithubIssue16(self): rxn = rdChemReactions.ReactionFromSmarts("[F:1]>>[Cl:1]") self.failUnless(rxn) rxn.Initialize() self.failUnlessRaises(ValueError,lambda : rxn.RunReactants((None,))) if __name__ == '__main__': unittest.main()