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
}
}
internal static bool IsFurtherMappingPossible(IAtomContainer source, IAtomContainer target,
McgregorHelper mcGregorHelper, bool shouldMatchBonds)
{
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++)
{
// Console.Out.WriteLine("i " + row);
string g1A = cBondNeighborsA[row * 4 + 0];
string g2A = cBondNeighborsA[row * 4 + 1];
for (int column = 0; column < neighborBondNumB; column++)
{
string g1B = cBondNeighborsB[column * 4 + 0];
string g2B = cBondNeighborsB[column * 4 + 1];
if (IsAtomMatch(g1A, g2A, g1B, g2B))
{
try
{
int indexI = iBondNeighborAtomsA[row * 3 + 0];
int indexIPlus1 = iBondNeighborAtomsA[row * 3 + 1];
int indexJ = iBondNeighborAtomsB[column * 3 + 0];
int indexJPlus1 = iBondNeighborAtomsB[column * 3 + 1];
IAtom r1A = source.Atoms[indexI];
IAtom r2A = source.Atoms[indexIPlus1];
IBond reactantBond = source.GetBond(r1A, r2A);
IAtom p1B = target.Atoms[indexJ];
IAtom p2B = target.Atoms[indexJPlus1];
IBond productBond = target.GetBond(p1B, p2B);
if (IsMatchFeasible(source, reactantBond, target, productBond, shouldMatchBonds))
{
return(true);
}
}
catch (Exception e)
{
Console.Out.WriteLine(e.StackTrace);
}
}
}
}
return(false);
}
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;
}
}
}
}
}
/// <summary>
/// The function is called in function partsearch. The function is given a temporary matrix and a position (row/column)
/// within this matrix. First the function sets all entries to zero, which can be exlcuded in respect to the current
/// atom by atom matching. After this the function replaces all entries in the same row and column of the current
/// position by zeros. Only the entry of the current position is set to one.
/// Return value "count_arcsleft" counts the number of arcs, which are still in the matrix.
/// </summary>
internal static void RemoveRedundantArcs(int row, int column, IList <int> marcs, McgregorHelper mcGregorHelper)
{
int neighborBondNumA = mcGregorHelper.NeighborBondNumA;
int neighborBondNumB = mcGregorHelper.NeighborBondNumB;
var iBondNeighborAtomsA = mcGregorHelper.GetIBondNeighborAtomsA();
var iBondNeighborAtomsB = mcGregorHelper.GetIBondNeighborAtomsB();
int g1Atom = iBondNeighborAtomsA[row * 3 + 0];
int g2Atom = iBondNeighborAtomsA[row * 3 + 1];
int g3Atom = iBondNeighborAtomsB[column * 3 + 0];
int g4Atom = iBondNeighborAtomsB[column * 3 + 1];
for (int x = 0; x < neighborBondNumA; x++)
{
int rowAtom1 = iBondNeighborAtomsA[x * 3 + 0];
int rowAtom2 = iBondNeighborAtomsA[x * 3 + 1];
for (int y = 0; y < neighborBondNumB; y++)
{
int columnAtom3 = iBondNeighborAtomsB[y * 3 + 0];
int columnAtom4 = iBondNeighborAtomsB[y * 3 + 1];
if (McGregorChecks.Cases(g1Atom, g2Atom, g3Atom, g4Atom, rowAtom1, rowAtom2, columnAtom3,
columnAtom4))
{
marcs[x * neighborBondNumB + y] = 0;
}
}
}
for (int v = 0; v < neighborBondNumA; v++)
{
marcs[v * neighborBondNumB + column] = 0;
}
for (int w = 0; w < neighborBondNumB; w++)
{
marcs[row * neighborBondNumB + w] = 0;
}
marcs[row * neighborBondNumB + column] = 1;
}