# $Id$ # # Copyright (C) 2003-2005 Rational Discovery LLC # All Rights Reserved # """ This is a rough coverage test of the python wrapper it's intended to be shallow, but broad """ import unittest,os from rdkit.six.moves import cPickle from rdkit import RDConfig from rdkit.RDLogger import logger logger=logger() from rdkit import Chem from rdkit.Chem import FragmentCatalog from rdkit import DataStructs class TestCase(unittest.TestCase): def setUp(self) : self.fName=os.path.join(RDConfig.RDBaseDir,'Code','GraphMol', 'FragCatalog','test_data','funcGroups.txt') self.smiName=os.path.join(RDConfig.RDBaseDir,'Code','GraphMol', 'FragCatalog','test_data','mols.smi') def test0Params(self) : fparams = FragmentCatalog.FragCatParams(1, 6, self.fName, 1.0e-8) ctype = fparams.GetTypeString() self.assertEqual(ctype,"Fragment Catalog Parameters") self.assertEqual(fparams.GetLowerFragLength(),1) self.assertEqual(fparams.GetUpperFragLength(),6) ngps = fparams.GetNumFuncGroups() self.assertEqual(ngps,15) for i in range(ngps) : mol = fparams.GetFuncGroup(i) def test1Catalog(self) : fparams = FragmentCatalog.FragCatParams(1, 6, self.fName, 1.0e-8) fcat = FragmentCatalog.FragCatalog(fparams) self.assertEqual(fcat.GetNumEntries(),0) self.assertEqual( fcat.GetFPLength(),0) nparams = fcat.GetCatalogParams() self.assertEqual(nparams.GetLowerFragLength(),1) self.assertEqual(nparams.GetUpperFragLength(),6) def test2Generator(self) : fparams = FragmentCatalog.FragCatParams(1, 6, self.fName, 1.0e-8) fcat = FragmentCatalog.FragCatalog(fparams) fgen = FragmentCatalog.FragCatGenerator() suppl = Chem.SmilesMolSupplier(self.smiName," ",0,1,0) for mol in suppl: nent = fgen.AddFragsFromMol(mol, fcat) self.assertEqual(fcat.GetNumEntries(),21) self.assertEqual(fcat.GetFPLength(),21) for id in range(fcat.GetNumEntries()): self.assertEqual( fcat.GetEntryBitId(id),id) self.assertEqual( fcat.GetEntryOrder(id),fcat.GetBitOrder(id)) self.assertEqual( fcat.GetEntryDescription(id),fcat.GetBitDescription(id)) self.assertEqual( tuple(fcat.GetEntryFuncGroupIds(id)),tuple(fcat.GetBitFuncGroupIds(id))) def test3FPgenerator(self) : with open(self.smiName,'r') as smiF: smiLines = smiF.readlines() fparams = FragmentCatalog.FragCatParams(1, 6, self.fName) fcat = FragmentCatalog.FragCatalog(fparams) fgen = FragmentCatalog.FragCatGenerator() suppl = Chem.SmilesMolSupplier(self.smiName," ",0,1,0) smiles = [] for mol in suppl: nent = fgen.AddFragsFromMol(mol, fcat) smiles.append(Chem.MolToSmiles(mol)) self.assertEqual( fcat.GetNumEntries(),21) self.assertEqual( fcat.GetFPLength(),21) fpgen = FragmentCatalog.FragFPGenerator() obits = [3,2,3,3,2,3,5,5,5,4,5,6] obls = [(0,1,2),(1,3),(1,4,5),(1,6,7),(0,8),(0,6,9),(0,1,2,3,10), (0,1,2,8,11),(1,3,4,5,12),(1,4,5,13),(1,3,6,7,14),(0,1,6,7,9,15)] for i in range(len(smiles)): smi = smiles[i] mol = Chem.MolFromSmiles(smi) fp = fpgen.GetFPForMol(mol, fcat) if i < len(obits): self.assertEqual(fp.GetNumOnBits(),obits[i]) obl = fp.GetOnBits() if i < len(obls): self.assertEqual( tuple(obl),obls[i]) def test4Serialize(self) : with open(self.smiName,'r') as smiF: smiLines = smiF.readlines() fparams = FragmentCatalog.FragCatParams(1, 6, self.fName) fcat = FragmentCatalog.FragCatalog(fparams) fgen = FragmentCatalog.FragCatGenerator() suppl = Chem.SmilesMolSupplier(self.smiName," ",0,1,0) smiles = [] for mol in suppl: nent = fgen.AddFragsFromMol(mol, fcat) smiles.append(Chem.MolToSmiles(mol)) self.assertEqual( fcat.GetNumEntries(), 21) self.assertEqual( fcat.GetFPLength(), 21) pkl = cPickle.dumps(fcat) fcat2 = cPickle.loads(pkl) self.assertEqual( fcat2.GetNumEntries(), 21) self.assertEqual( fcat2.GetFPLength(), 21 ) fpgen = FragmentCatalog.FragFPGenerator() for i in range(len(smiles)): smi = smiles[i] mol = Chem.MolFromSmiles(smi) fp1 = fpgen.GetFPForMol(mol, fcat) fp2 = fpgen.GetFPForMol(mol, fcat2) self.assertEqual( fp1.GetNumOnBits(), fp2.GetNumOnBits()) obl1 = fp1.GetOnBits() obl2 = fp2.GetOnBits() self.assertEqual( tuple(obl1), tuple(obl2)) def test5FPsize(self) : with open(self.smiName,'r') as smiF: smiLines = smiF.readlines() fparams = FragmentCatalog.FragCatParams(6, 6, self.fName) fcat = FragmentCatalog.FragCatalog(fparams) fgen = FragmentCatalog.FragCatGenerator() suppl = [Chem.MolFromSmiles('C1CCCOC1O')] for mol in suppl: nent = fgen.AddFragsFromMol(mol, fcat) self.assertEqual( fcat.GetFPLength(), 1) for i in range(fcat.GetFPLength()): self.assertEqual(fcat.GetBitOrder(i),6) self.assertEqual(fcat.GetBitDescription(i),"C1CC<-O>OCC1") self.assertEqual(tuple(fcat.GetBitFuncGroupIds(i)),(1,)) def test6DownEntries(self) : fparams = FragmentCatalog.FragCatParams(1, 6, self.fName, 1.0e-8) fcat = FragmentCatalog.FragCatalog(fparams) fgen = FragmentCatalog.FragCatGenerator() suppl = Chem.SmilesMolSupplier(self.smiName," ",0,1,0) for mol in suppl: nent = fgen.AddFragsFromMol(mol, fcat) self.assertEqual( fcat.GetNumEntries(), 21) self.assertEqual( fcat.GetFPLength(), 21) self.assertEqual( tuple(fcat.GetEntryDownIds(0)), (2,8,9,16)) self.assertEqual( tuple(fcat.GetEntryDownIds(1)), (2,3,5,7)) def test7Issue116(self): smiList = ['Cc1ccccc1'] suppl = Chem.SmilesMolSupplierFromText('\n'.join(smiList), ',',0,-1,0) fparams = FragmentCatalog.FragCatParams(2, 2, self.fName, 1.0e-8) cat = FragmentCatalog.FragCatalog(fparams) fgen = FragmentCatalog.FragCatGenerator() for mol in suppl: nent = fgen.AddFragsFromMol(mol, cat) self.assertEqual( cat.GetFPLength(), 2) self.assertEqual( cat.GetBitDescription(0), 'ccC') fpgen = FragmentCatalog.FragFPGenerator() mol = Chem.MolFromSmiles('Cc1ccccc1') fp = fpgen.GetFPForMol(mol,cat) self.assertEqual( fp[0], 1 ) self.assertEqual( fp[1], 1 ) mol = Chem.MolFromSmiles('c1ccccc1-c1ccccc1') fp = fpgen.GetFPForMol(mol,cat) self.assertEqual( fp[0], 0) self.assertEqual( fp[1], 1) def test8Issue118(self): smiList = ['CCN(C(N)=O)N=O'] fName=os.path.join(RDConfig.RDDataDir,'FunctionalGroups.txt') suppl = Chem.SmilesMolSupplierFromText('\n'.join(smiList), ',',0,-1,0) fparams = FragmentCatalog.FragCatParams(2, 4, fName, 1.0e-8) cat = FragmentCatalog.FragCatalog(fparams) fgen = FragmentCatalog.FragCatGenerator() for mol in suppl: nent = fgen.AddFragsFromMol(mol, cat) self.assertEqual( cat.GetFPLength(), 1 ) self.assertEqual( cat.GetBitDescription(0), 'CCN(<-C(=O)N>)<-N=O>') if __name__ == '__main__': unittest.main()