# $Id$ # # 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 os import pickle import unittest from rdkit import RDConfig from rdkit.RDLogger import logger logger = logger() from rdkit import Chem, DataStructs from rdkit.Chem import FragmentCatalog 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 = pickle.dumps(fcat) fcat2 = pickle.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()