# $Id: testMolDescriptors.py 2002 2012-03-25 12:58:42Z glandrum $ # from rdkit import Chem from rdkit.Chem import rdMolDescriptors as rdMD from rdkit import DataStructs from rdkit import RDConfig import unittest def feq(v1, v2, tol=1.e-4) : return abs(v1-v2) < tol class TestCase(unittest.TestCase) : def setUp(self): pass def testAtomPairTypes(self): params = rdMD.AtomPairsParameters mol = Chem.MolFromSmiles("C=C"); self.failUnless(rdMD.GetAtomPairAtomCode(mol.GetAtomWithIdx(0))==\ rdMD.GetAtomPairAtomCode(mol.GetAtomWithIdx(1))) self.failUnless(rdMD.GetAtomPairAtomCode(mol.GetAtomWithIdx(0))==\ 1 | (1 | 1<0.0 and sim<1.0) m = Chem.MolFromSmiles('c1ccccn1') fp2 = rdMD.GetHashedAtomPairFingerprint(m,2048) sim= DataStructs.DiceSimilarity(fp1,fp2) self.failUnless(sim>0.0 and sim<1.0) m = Chem.MolFromSmiles('c1ccccc1') fp1 = rdMD.GetHashedAtomPairFingerprintAsBitVect(m,2048) m = Chem.MolFromSmiles('c1ccccn1') fp2 = rdMD.GetHashedAtomPairFingerprintAsBitVect(m,2048) sim= DataStructs.DiceSimilarity(fp1,fp2) self.failUnless(sim>0.0 and sim<1.0) def testRootedAtomPairs(self): m = Chem.MolFromSmiles('Oc1ccccc1') fp1 = rdMD.GetAtomPairFingerprint(m) fp2 = rdMD.GetAtomPairFingerprint(m,fromAtoms=(0,)) nz1 = fp1.GetNonzeroElements() nz2 = fp2.GetNonzeroElements() for k,v in nz2.iteritems(): self.failUnless(v<=nz1[k]) def testTopologicalTorsions(self): mol = Chem.MolFromSmiles("CC"); fp = rdMD.GetTopologicalTorsionFingerprint(mol) self.failUnless(fp.GetTotalVal()==0) mol = Chem.MolFromSmiles("CCCC"); fp = rdMD.GetTopologicalTorsionFingerprint(mol) self.failUnless(fp.GetTotalVal()==1) fp = rdMD.GetTopologicalTorsionFingerprint(mol,3) self.failUnless(fp.GetTotalVal()==2) mol = Chem.MolFromSmiles("CCCO"); fp = rdMD.GetTopologicalTorsionFingerprint(mol) self.failUnless(fp.GetTotalVal()==1) fp = rdMD.GetTopologicalTorsionFingerprint(mol,3) self.failUnless(fp.GetTotalVal()==2) mol = Chem.MolFromSmiles("CCCCCCCCCCC"); fp = rdMD.GetTopologicalTorsionFingerprint(mol,7) self.failUnlessRaises(ValueError,lambda : rdMD.GetTopologicalTorsionFingerprint(mol,8)) def testHashedTopologicalTorsions(self): mol = Chem.MolFromSmiles("c1ncccc1"); fp1 = rdMD.GetHashedTopologicalTorsionFingerprint(mol) mol = Chem.MolFromSmiles("n1ccccc1"); fp2 = rdMD.GetHashedTopologicalTorsionFingerprint(mol) self.failUnlessEqual(DataStructs.DiceSimilarity(fp1,fp2),1.0) def testRootedTorsions(self): m = Chem.MolFromSmiles('Oc1ccccc1') fp1 = rdMD.GetTopologicalTorsionFingerprint(m) fp2 = rdMD.GetTopologicalTorsionFingerprint(m,fromAtoms=(0,)) nz1 = fp1.GetNonzeroElements() nz2 = fp2.GetNonzeroElements() for k,v in nz2.iteritems(): self.failUnless(v<=nz1[k]) m = Chem.MolFromSmiles('COCC') fp1 = rdMD.GetTopologicalTorsionFingerprint(m) self.failUnlessEqual(len(fp1.GetNonzeroElements()),1) fp1 = rdMD.GetTopologicalTorsionFingerprint(m,fromAtoms=(0,)) self.failUnlessEqual(len(fp1.GetNonzeroElements()),1) fp1 = rdMD.GetTopologicalTorsionFingerprint(m,fromAtoms=(1,)) self.failUnlessEqual(len(fp1.GetNonzeroElements()),0) def testMorganFingerprints(self): mol = Chem.MolFromSmiles('CC(F)(Cl)C(F)(Cl)C') fp = rdMD.GetMorganFingerprint(mol,0) self.failUnless(len(fp.GetNonzeroElements())==4) fp = rdMD.GetMorganFingerprint(mol,1) self.failUnless(len(fp.GetNonzeroElements())==8) fp = rdMD.GetMorganFingerprint(mol,2) self.failUnless(len(fp.GetNonzeroElements())==9) mol = Chem.MolFromSmiles('CC(F)(Cl)[C@](F)(Cl)C') fp = rdMD.GetMorganFingerprint(mol,0) self.failUnless(len(fp.GetNonzeroElements())==4) fp = rdMD.GetMorganFingerprint(mol,1) self.failUnless(len(fp.GetNonzeroElements())==8) fp = rdMD.GetMorganFingerprint(mol,2) self.failUnless(len(fp.GetNonzeroElements())==9) fp = rdMD.GetMorganFingerprint(mol,0,useChirality=True) self.failUnless(len(fp.GetNonzeroElements())==4) fp = rdMD.GetMorganFingerprint(mol,1,useChirality=True) self.failUnless(len(fp.GetNonzeroElements())==9) fp = rdMD.GetMorganFingerprint(mol,2,useChirality=True) self.failUnless(len(fp.GetNonzeroElements())==10) mol = Chem.MolFromSmiles('CCCCC') fp = rdMD.GetMorganFingerprint(mol,0,fromAtoms=(0,)) self.failUnless(len(fp.GetNonzeroElements())==1) mol = Chem.MolFromSmiles('CC1CC1') vs1 = rdMD.GetConnectivityInvariants(mol) self.failUnlessEqual(len(vs1),mol.GetNumAtoms()) fp1 = rdMD.GetMorganFingerprint(mol,2,invariants=vs1) fp2 = rdMD.GetMorganFingerprint(mol,2) self.failUnlessEqual(fp1,fp2) vs2 = rdMD.GetConnectivityInvariants(mol,False) self.failUnlessEqual(len(vs2),mol.GetNumAtoms()) self.failIfEqual(vs1,vs2) fp1 = rdMD.GetMorganFingerprint(mol,2,invariants=vs2) self.failIfEqual(fp1,fp2) mol = Chem.MolFromSmiles('Cc1ccccc1') vs1 = rdMD.GetFeatureInvariants(mol) self.failUnlessEqual(len(vs1),mol.GetNumAtoms()) self.failUnlessEqual(vs1[0],0) self.failIfEqual(vs1[1],0) self.failUnlessEqual(vs1[1],vs1[2]) self.failUnlessEqual(vs1[1],vs1[3]) self.failUnlessEqual(vs1[1],vs1[4]) mol = Chem.MolFromSmiles('FCCCl') vs1 = rdMD.GetFeatureInvariants(mol) self.failUnlessEqual(len(vs1),mol.GetNumAtoms()) self.failUnlessEqual(vs1[1],0) self.failUnlessEqual(vs1[2],0) self.failIfEqual(vs1[0],0) self.failUnlessEqual(vs1[0],vs1[3]) fp1 = rdMD.GetMorganFingerprint(mol,0,invariants=vs1) fp2 = rdMD.GetMorganFingerprint(mol,0,useFeatures=True) self.failUnlessEqual(fp1,fp2) def testCrippen(self): mol = Chem.MolFromSmiles("NCO"); contribs = rdMD._CalcCrippenContribs(mol) def testMolWt(self): mol = Chem.MolFromSmiles("C"); amw = rdMD._CalcMolWt(mol); self.failUnless(feq(amw,16.043,.001)); amw = rdMD._CalcMolWt(mol,True); self.failUnless(feq(amw,12.011,.001)); mol2 = Chem.AddHs(mol); amw = rdMD._CalcMolWt(mol2); self.failUnless(feq(amw,16.043,.001)); amw = rdMD._CalcMolWt(mol2,True); self.failUnless(feq(amw,12.011,.001)); mol = Chem.MolFromSmiles("C"); amw = rdMD.CalcExactMolWt(mol); self.failUnless(feq(amw,16.031,.001)); def testPairValues(self): import base64 testD=(('CCCO','AQAAAAQAAAAAAIAABgAAACGECAABAAAAIoQIAAEAAABBhAgAAQAAACNEGAABAAAAQUQYAAEAAABC\nRBgAAQAAAA==\n'), ('CNc1ccco1','AQAAAAQAAAAAAIAAEAAAACOECgABAAAAJIQKAAIAAABBhQoAAgAAAEKFCgABAAAAIsQKAAEAAABB\nxQoAAQAAAELFCgACAAAAIYQQAAEAAABChRAAAQAAAEOFEAACAAAAYYUQAAEAAAAjhBoAAQAAAEGF\nGgABAAAAQoUaAAIAAABhhRoAAQAAAEKIGgABAAAA\n'), ) for smi,txt in testD: pkl = base64.decodestring(txt) fp = rdMD.GetAtomPairFingerprint(Chem.MolFromSmiles(smi)) fp2 = DataStructs.IntSparseIntVect(pkl) self.failUnlessEqual(DataStructs.DiceSimilarity(fp,fp2),1.0) self.failUnlessEqual(fp,fp2) def testTorsionValues(self): import base64 testD=(('CCCO','AQAAAAgAAAD/////DwAAAAEAAAAAAAAAIECAAAMAAAABAAAA\n'), ('CNc1ccco1','AQAAAAgAAAD/////DwAAAAkAAAAAAAAAIICkSAEAAAABAAAAKVKgSQEAAAABAAAAKVCgUAEAAAAB\nAAAAKVCgUQEAAAABAAAAKVCkCAIAAAABAAAAKdCkCAIAAAABAAAAKVCgSAMAAAABAAAAKVCkSAMA\nAAABAAAAIICkSAMAAAABAAAA\n'), ) for smi,txt in testD: pkl = base64.decodestring(txt) fp = rdMD.GetTopologicalTorsionFingerprint(Chem.MolFromSmiles(smi)) fp2 = DataStructs.LongSparseIntVect(pkl) self.failUnlessEqual(DataStructs.DiceSimilarity(fp,fp2),1.0) self.failUnlessEqual(fp,fp2) def testAtomPairOptions(self): m1 = Chem.MolFromSmiles('c1ccccc1') m2 = Chem.MolFromSmiles('c1ccccn1') fp1 = rdMD.GetAtomPairFingerprint(m1) fp2 = rdMD.GetAtomPairFingerprint(m2) self.failIfEqual(fp1,fp2) fp1 = rdMD.GetAtomPairFingerprint(m1,atomInvariants=[1]*6) fp2 = rdMD.GetAtomPairFingerprint(m2,atomInvariants=[1]*6) self.failUnlessEqual(fp1,fp2) fp1 = rdMD.GetAtomPairFingerprint(m1,atomInvariants=[1]*6) fp2 = rdMD.GetAtomPairFingerprint(m2,atomInvariants=[2]*6) self.failIfEqual(fp1,fp2) fp1 = rdMD.GetHashedAtomPairFingerprintAsBitVect(m1) fp2 = rdMD.GetHashedAtomPairFingerprintAsBitVect(m2) self.failIfEqual(fp1,fp2) fp1 = rdMD.GetHashedAtomPairFingerprintAsBitVect(m1,atomInvariants=[1]*6) fp2 = rdMD.GetHashedAtomPairFingerprintAsBitVect(m2,atomInvariants=[1]*6) self.failUnlessEqual(fp1,fp2) fp1 = rdMD.GetHashedAtomPairFingerprintAsBitVect(m1,atomInvariants=[1]*6) fp2 = rdMD.GetHashedAtomPairFingerprintAsBitVect(m2,atomInvariants=[2]*6) self.failIfEqual(fp1,fp2) fp1 = rdMD.GetTopologicalTorsionFingerprint(m1) fp2 = rdMD.GetTopologicalTorsionFingerprint(m2) self.failIfEqual(fp1,fp2) fp1 = rdMD.GetTopologicalTorsionFingerprint(m1,atomInvariants=[1]*6) fp2 = rdMD.GetTopologicalTorsionFingerprint(m2,atomInvariants=[1]*6) self.failUnlessEqual(fp1,fp2) fp1 = rdMD.GetTopologicalTorsionFingerprint(m1,atomInvariants=[1]*6) fp2 = rdMD.GetTopologicalTorsionFingerprint(m2,atomInvariants=[2]*6) self.failIfEqual(fp1,fp2) fp1 = rdMD.GetHashedTopologicalTorsionFingerprintAsBitVect(m1) fp2 = rdMD.GetHashedTopologicalTorsionFingerprintAsBitVect(m2) self.failIfEqual(fp1,fp2) fp1 = rdMD.GetHashedTopologicalTorsionFingerprintAsBitVect(m1,atomInvariants=[1]*6) fp2 = rdMD.GetHashedTopologicalTorsionFingerprintAsBitVect(m2,atomInvariants=[1]*6) self.failUnlessEqual(fp1,fp2) fp1 = rdMD.GetHashedTopologicalTorsionFingerprintAsBitVect(m1,atomInvariants=[1]*6) fp2 = rdMD.GetHashedTopologicalTorsionFingerprintAsBitVect(m2,atomInvariants=[2]*6) self.failIfEqual(fp1,fp2) if __name__ == '__main__': unittest.main()