private bool UnMappedAtomsEqualsIndexI(int setNumA, int setNumB, IList <int> iBondSetA,
IList <int> iBondSetB, int atomIndex, int counter, IList <int> newMapping, int indexI,
int indexJ, int order)
{
bool normalBond = true;
for (int c = 0; c < newNeighborNumA; c++)
{
if (newMapping[c * 2 + 0].Equals(indexI))
{
SetBondNeighbors(indexI, indexJ, order);
if (string.Equals(cTab1Copy[atomIndex * 4 + 2], "X", StringComparison.OrdinalIgnoreCase))
{
Step3(atomIndex, counter);
McGregorChecks.ChangeCharBonds(indexJ, signs[counter], setNumA, iBondSetA, cTab1Copy);
int corAtom = McGregorChecks.SearchCorrespondingAtom(newNeighborNumA, indexJ, 1, newMapping);
McGregorChecks.ChangeCharBonds(corAtom, signs[counter], setNumB, iBondSetB, cTab2Copy);
counter++;
}
else
{
Step4(atomIndex);
}
normalBond = false;
neighborBondNumA++;
}
}
return(normalBond);
}
private bool UnMappedAtomsEqualsIndexJ(IAtomContainer target, int mappingSize, int atomIndex, int counter,
IList <int> mappedAtoms, int indexI, int indexJ, int order)
{
bool normalBond = true;
for (int c = 0; c < mappingSize; c++)
{
if (mappedAtoms[c * 2 + 1].Equals(indexI))
{
SetBondNeighbors(indexI, indexJ, order);
if (string.Equals(cTab2Copy[atomIndex * 4 + 2], "X", StringComparison.OrdinalIgnoreCase))
{
Step3(atomIndex, counter);
McGregorChecks
.ChangeCharBonds(indexI, signArray[counter], target.Bonds.Count, target, cTab2Copy);
int corAtom = McGregorChecks.SearchCorrespondingAtom(mappingSize, indexI, 2, mappedAtoms);
McGregorChecks.ChangeCharBonds(corAtom, signArray[counter], newNeighborNumA, newINeighborsA,
newCNeighborsA);
// ChangeCharBonds(corAtom, signArray[counter], query.Bonds.Count, query, cTab1Copy);
counter++;
}
else
{
Step4(atomIndex);
}
normalBond = false;
neighborBondNumB++;
}
}
return(normalBond);
}
