/// <summary>
/// This function calculates all the possible combinations of MCS
/// </summary>
/// <param name="molecule1"></param>
/// <param name="molecule2"></param>
/// <param name="shouldMatchBonds"></param>
/// <exception cref="CDKException"></exception>
public void CalculateOverlapsAndReduce(IAtomContainer molecule1, IAtomContainer molecule2, bool shouldMatchBonds)
{
Source = molecule1;
Target = molecule2;
Mappings = new List <IReadOnlyDictionary <int, int> >();
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)
{
/* UnComment this to get one Unique Mapping */
//List reducedList = RemoveRedundantMappingsForSingleAtomCase(overlaps);
//int counter = 0;
IdentifySingleAtomsMatchedParts(overlaps, Source, Target);
}
}
else
{
var overlaps = CDKMCS.Search(Source, Target, new BitArray(Source.Bonds.Count), new BitArray(Target.Bonds.Count), true, true, 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);
}
/// <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 CalculateOverlapsAndReduceExactMatch(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.Search(Source, Target, new BitArray(Source.Bonds.Count), new BitArray(Target.Bonds.Count), true,
true, 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);
}
