/// <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 CalculateSubGraphs(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.GetSubgraphMaps(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);
}
public void TestSFBug1708336()
{
var atomContainer = builder.NewAtomContainer();
atomContainer.Atoms.Add(builder.NewAtom("C"));
atomContainer.Atoms.Add(builder.NewAtom("C"));
atomContainer.Atoms.Add(builder.NewAtom("N"));
atomContainer.AddBond(atomContainer.Atoms[0], atomContainer.Atoms[1], BondOrder.Single);
atomContainer.AddBond(atomContainer.Atoms[1], atomContainer.Atoms[2], BondOrder.Single);
var query = new QueryAtomContainer();
var a1 = new SymbolQueryAtom()
{
Symbol = "C"
};
var a2 = new Isomorphisms.Matchers.SMARTS.AnyAtom();
var b1 = new OrderQueryBond(a1, a2, BondOrder.Single);
var a3 = new SymbolQueryAtom()
{
Symbol = "C"
};
var b2 = new OrderQueryBond(a2, a3, BondOrder.Single);
query.Atoms.Add(a1);
query.Atoms.Add(a2);
query.Atoms.Add(a3);
query.Bonds.Add(b1);
query.Bonds.Add(b2);
var list = CDKMCS.GetSubgraphMaps(atomContainer, query, true);
Assert.IsTrue(list.Count == 0);
}