public void TestSingleAtomMatching2() { var sp = CDK.SmilesParser; var target = sp.ParseSmiles("CNC"); var queryac = sp.ParseSmiles("C"); var query = QueryAtomContainerCreator.CreateSymbolAndBondOrderQueryContainer(queryac); var matches = CDKMCS.GetIsomorphMaps(target, query, true); Assert.AreEqual(2, matches.Count); Assert.AreEqual(1, matches[0].Count); Assert.AreEqual(1, matches[1].Count); var map1 = matches[0][0]; var map2 = matches[1][0]; Assert.AreEqual(0, map1.Id1); Assert.AreEqual(0, map1.Id2); Assert.AreEqual(2, map2.Id1); Assert.AreEqual(0, map2.Id2); var atomMappings = CDKMCS.MakeAtomsMapsOfBondsMaps(matches, target, query); Assert.AreEqual(matches, atomMappings); }
/// <summary> /// This function calculates only one solution (exact) because we are looking at the /// molecules which are exactly same in terms of the bonds and atoms determined by the /// Fingerprint /// </summary> /// <param name="molecule1"></param> /// <param name="molecule2"></param> /// <param name="shouldMatchBonds"></param> /// <exception cref="CDKException"></exception> public void CalculateIsomorphs(IAtomContainer molecule1, IAtomContainer molecule2, bool shouldMatchBonds) { Source = molecule1; Target = molecule2; Mappings = new List <IReadOnlyDictionary <int, int> >(); //Console.Out.WriteLine("Searching: "); //List overlaps = UniversalIsomorphismTesterBondTypeInSensitive.GetSubgraphAtomsMap(source, target); if ((Source.Atoms.Count == 1) || (Target.Atoms.Count == 1)) { List <CDKRMap> overlaps = CDKMCS.CheckSingleAtomCases(Source, Target); int nAtomsMatched = overlaps.Count; nAtomsMatched = (nAtomsMatched > 0) ? 1 : 0; if (nAtomsMatched > 0) { IdentifySingleAtomsMatchedParts(overlaps, Source, Target); } } else { var overlaps = CDKMCS.GetIsomorphMaps(Source, Target, shouldMatchBonds); var reducedList = RemoveSubGraph(overlaps); var allMaxOverlaps = GetAllMaximum(reducedList); while (allMaxOverlaps.Count != 0) { var maxOverlapsAtoms = MakeAtomsMapOfBondsMap(allMaxOverlaps.Peek(), Source, Target); IdentifyMatchedParts(maxOverlapsAtoms, Source, Target); allMaxOverlaps.Pop(); } } FinalMappings.Instance.Set(Mappings); }