# $Id$ # # 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()