private void ExtendMapping(int xIndex, int yIndex, McgregorHelper mcGregorHelper, List <int> additionalMapping,
List <int> currentMapping)
{
int atom1MoleculeA = mcGregorHelper.GetIBondNeighborAtomsA()[xIndex * 3 + 0];
int atom2MoleculeA = mcGregorHelper.GetIBondNeighborAtomsA()[xIndex * 3 + 1];
int atom1MoleculeB = mcGregorHelper.GetIBondNeighborAtomsB()[yIndex * 3 + 0];
int atom2MoleculeB = mcGregorHelper.GetIBondNeighborAtomsB()[yIndex * 3 + 1];
IAtom r1A = source.Atoms[atom1MoleculeA];
IAtom r2A = source.Atoms[atom2MoleculeA];
IBond reactantBond = source.GetBond(r1A, r2A);
IAtom p1B = target.Atoms[atom1MoleculeB];
IAtom p2B = target.Atoms[atom2MoleculeB];
IBond productBond = target.GetBond(p1B, p2B);
// Bond Order Check Introduced by Asad
if (McGregorChecks.IsMatchFeasible(source, reactantBond, target, productBond, IsBondMatch))
{
for (int indexZ = 0; indexZ < mcGregorHelper.MappedAtomCount; indexZ++)
{
int mappedAtom1 = currentMapping[indexZ * 2 + 0];
int mappedAtom2 = currentMapping[indexZ * 2 + 1];
if ((mappedAtom1 == atom1MoleculeA) && (mappedAtom2 == atom1MoleculeB))
{
additionalMapping.Add(atom2MoleculeA);
additionalMapping.Add(atom2MoleculeB);
}
else if ((mappedAtom1 == atom1MoleculeA) && (mappedAtom2 == atom2MoleculeB))
{
additionalMapping.Add(atom2MoleculeA);
additionalMapping.Add(atom1MoleculeB);
}
else if ((mappedAtom1 == atom2MoleculeA) && (mappedAtom2 == atom1MoleculeB))
{
additionalMapping.Add(atom1MoleculeA);
additionalMapping.Add(atom2MoleculeB);
}
else if ((mappedAtom1 == atom2MoleculeA) && (mappedAtom2 == atom2MoleculeB))
{
additionalMapping.Add(atom1MoleculeA);
additionalMapping.Add(atom1MoleculeB);
}
}//for loop
}
}
private void SetModifedArcs(McgregorHelper mcGregorHelper)
{
int neighborBondNumA = mcGregorHelper.NeighborBondNumA;
int neighborBondNumB = mcGregorHelper.NeighborBondNumB;
var iBondNeighborAtomsA = mcGregorHelper.GetIBondNeighborAtomsA();
var iBondNeighborAtomsB = mcGregorHelper.GetIBondNeighborAtomsB();
var cBondNeighborsA = mcGregorHelper.GetCBondNeighborsA();
var cBondNeighborsB = mcGregorHelper.GetCBondNeighborsB();
for (int row = 0; row < neighborBondNumA; row++)
{
for (int column = 0; column < neighborBondNumB; column++)
{
string g1A = cBondNeighborsA[row * 4 + 0];
string g2A = cBondNeighborsA[row * 4 + 1];
string g1B = cBondNeighborsB[column * 4 + 0];
string g2B = cBondNeighborsB[column * 4 + 1];
if (MatchGAtoms(g1A, g2A, g1B, g2B))
{
int indexI = iBondNeighborAtomsA[row * 3 + 0];
int indexIPlus1 = iBondNeighborAtomsA[row * 3 + 1];
IAtom r1A = source.Atoms[indexI];
IAtom r2A = source.Atoms[indexIPlus1];
IBond reactantBond = source.GetBond(r1A, r2A);
int indexJ = iBondNeighborAtomsB[column * 3 + 0];
int indexJPlus1 = iBondNeighborAtomsB[column * 3 + 1];
IAtom p1B = target.Atoms[indexJ];
IAtom p2B = target.Atoms[indexJPlus1];
IBond productBond = target.GetBond(p1B, p2B);
if (McGregorChecks.IsMatchFeasible(source, reactantBond, target, productBond, IsBondMatch))
{
modifiedARCS[row * neighborBondNumB + column] = 1;
}
}
}
}
}