# $Id: rough_test.py 997 2009-02-25 06:12:43Z glandrum $ # # 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 import RDConfig from rdkit.RDLogger import logger logger=logger() from rdkit import Chem from rdkit.Chem import FragmentCatalog from rdkit import DataStructs import cPickle 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() assert(ctype == "Fragment Catalog Parameters") assert(fparams.GetLowerFragLength() == 1) assert(fparams.GetUpperFragLength() == 6) ngps = fparams.GetNumFuncGroups() assert 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) assert(fcat.GetNumEntries() == 0) assert( fcat.GetFPLength() == 0) nparams = fcat.GetCatalogParams() assert(nparams.GetLowerFragLength() == 1) assert(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) assert fcat.GetNumEntries()==21 assert fcat.GetFPLength()==21 for id in range(fcat.GetNumEntries()): assert fcat.GetEntryBitId(id)==id assert fcat.GetEntryOrder(id)==fcat.GetBitOrder(id) assert fcat.GetEntryDescription(id)==fcat.GetBitDescription(id) assert tuple(fcat.GetEntryFuncGroupIds(id))==tuple(fcat.GetBitFuncGroupIds(id)) def test3FPgenerator(self) : smiLines = open(self.smiName,'r').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)) assert fcat.GetNumEntries()==21 assert fcat.GetFPLength()==21,fcat.GetFPLength() 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): assert fp.GetNumOnBits()==obits[i],'%s: %s'%(smi,str(fp.GetOnBits())) obl = fp.GetOnBits() if i < len(obls): assert tuple(obl)==obls[i],'%s: %s'%(smi,obl) def test4Serialize(self) : smiLines = open(self.smiName,'r').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)) assert fcat.GetNumEntries()==21 assert fcat.GetFPLength()==21,fcat.GetFPLength() pkl = cPickle.dumps(fcat) fcat2 = cPickle.loads(pkl) assert fcat2.GetNumEntries()==21 assert fcat2.GetFPLength()==21,fcat2.GetFPLength() 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) assert fp1.GetNumOnBits()==fp2.GetNumOnBits() obl1 = fp1.GetOnBits() obl2 = fp2.GetOnBits() assert tuple(obl1)==tuple(obl2) def test5FPsize(self) : smiLines = open(self.smiName,'r').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) assert fcat.GetFPLength()==1 for i in range(fcat.GetFPLength()): assert fcat.GetBitOrder(i)==6 assert fcat.GetBitDescription(i)=="C1CCOC<-O>C1",fcat.GetBitDescription(i) assert 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) assert fcat.GetNumEntries()==21 assert fcat.GetFPLength()==21 assert tuple(fcat.GetEntryDownIds(0))==(2,8,9,16) assert 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) assert cat.GetFPLength()==2 assert cat.GetBitDescription(0)=='ccC' fpgen = FragmentCatalog.FragFPGenerator() mol = Chem.MolFromSmiles('Cc1ccccc1') fp = fpgen.GetFPForMol(mol,cat) assert fp[0] assert fp[1] mol = Chem.MolFromSmiles('c1ccccc1-c1ccccc1') fp = fpgen.GetFPForMol(mol,cat) assert not fp[0] assert fp[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) assert cat.GetFPLength()==1 assert cat.GetBitDescription(0)=='CCN(<-C(=O)N>)<-N=O>' if __name__ == '__main__': unittest.main()