/// <summary>
/// Start McGregor search and extend the mappings if possible.
/// </summary>
/// <param name="largestMappingSize"></param>
/// <param name="cliqueVector"></param>
/// <param name="compGraphNodes"></param>
/// <exception cref="IOException"></exception>
public void StartMcGregorIteration(int largestMappingSize,
IReadOnlyList <int> cliqueVector,
IReadOnlyList <int> compGraphNodes)
{
this.globalMCSSize = (largestMappingSize / 2);
List <string> cTab1Copy = McGregorChecks.GenerateCTabCopy(source);
List <string> cTab2Copy = McGregorChecks.GenerateCTabCopy(target);
//find mapped atoms of both molecules and store these in mappedAtoms
List <int> mappedAtoms = new List <int>();
int mappedAtomCount = 0;
List <int> iBondNeighborAtomsA = new List <int>();
var cBondNeighborsA = new List <string>();
List <int> iBondSetA = new List <int>();
var cBondSetA = new List <string>();
List <int> iBondNeighborAtomsB = new List <int>();
List <int> iBondSetB = new List <int>();
var cBondNeighborsB = new List <string>();
var cBondSetB = new List <string>();
int cliqueSize = cliqueVector.Count;
int vecSize = compGraphNodes.Count;
int cliqueNumber = 0;
for (int a = 0; a < cliqueSize; a++)
{
//go through all clique nodes
cliqueNumber = cliqueVector[a];
for (int b = 0; b < vecSize; b += 3)
{
//go through all nodes in the compatibility graph
if (cliqueNumber == compGraphNodes[b + 2])
{
mappedAtoms.Add(compGraphNodes[b]);
mappedAtoms.Add(compGraphNodes[b + 1]);
mappedAtomCount++;
}
}
}
//find unmapped atoms of molecule A
List <int> unmappedAtomsMolA = McGregorChecks.MarkUnMappedAtoms(true, source, mappedAtoms, cliqueSize);
int counter = 0;
int setNumA = 0;
int setNumB = 0;
int localNeighborBondnumA = 0; //number of remaining molecule A bonds after the clique search, which are neighbors of the MCS_1
int localNeighborBondNumB = 0; //number of remaining molecule B bonds after the clique search, which are neighbors of the MCS_1
//Extract bonds which are related with unmapped atoms of molecule A.
//In case that unmapped atoms are connected with already mapped atoms, the mapped atoms are labelled with
//new special signs -> the result are two vectors: cBondNeighborsA and int_bonds_molA, which contain those
//bonds of molecule A, which are relevant for the McGregorBondTypeInSensitive algorithm.
//The special signs must be transfered to the corresponding atoms of molecule B
QueryProcessor queryProcess = new QueryProcessor(cTab1Copy, cTab2Copy, SIGNS, localNeighborBondnumA,
setNumA, iBondNeighborAtomsA, cBondNeighborsA, cliqueSize, iBondSetA, cBondSetA);
queryProcess.Process(source, target, unmappedAtomsMolA, mappedAtoms, counter);
cTab1Copy = queryProcess.CTab1;
cTab2Copy = queryProcess.CTab2;
setNumA = queryProcess.BondNumA;
localNeighborBondnumA = queryProcess.NeighborBondNumA;
iBondNeighborAtomsA = queryProcess.IBondNeighboursA;
cBondNeighborsA = queryProcess.CBondNeighborsA;
//find unmapped atoms of molecule B
List <int> unmappedAtomsMolB = McGregorChecks.MarkUnMappedAtoms(false, target, mappedAtoms, cliqueSize);
//Extract bonds which are related with unmapped atoms of molecule B.
//In case that unmapped atoms are connected with already mapped atoms, the mapped atoms are labelled with
//new special signs -> the result are two vectors: cBondNeighborsA and int_bonds_molB, which contain those
//bonds of molecule B, which are relevant for the McGregorBondTypeInSensitive algorithm.
//The special signs must be transfered to the corresponding atoms of molecule A
TargetProcessor targetProcess = new TargetProcessor(cTab1Copy, cTab2Copy, SIGNS, localNeighborBondNumB,
setNumB, iBondNeighborAtomsB, cBondNeighborsB, localNeighborBondnumA, iBondNeighborAtomsA,
cBondNeighborsA);
targetProcess.Process(target, unmappedAtomsMolB, cliqueSize, iBondSetB, cBondSetB, mappedAtoms, counter);
cTab1Copy = targetProcess.CTab1;
cTab2Copy = targetProcess.CTab2;
setNumB = targetProcess.BondNumB;
localNeighborBondNumB = targetProcess.NeighborBondNumB;
iBondNeighborAtomsB = targetProcess.IBondNeighboursB;
cBondNeighborsB = targetProcess.CBondNeighborsB;
bool dummy = false;
McgregorHelper mcGregorHelper = new McgregorHelper(dummy, mappedAtomCount, mappedAtoms, localNeighborBondnumA,
localNeighborBondNumB, iBondNeighborAtomsA, iBondNeighborAtomsB, cBondNeighborsA, cBondNeighborsB,
setNumA, setNumB, iBondSetA, iBondSetB, cBondSetA, cBondSetB);
Iterator(mcGregorHelper);
}
private void SearchAndExtendMappings(Stack <IReadOnlyList <int> > bestarcsCopy, McgregorHelper mcGregorHelper)
{
int mappedAtomCount = mcGregorHelper.MappedAtomCount;
int setNumA = mcGregorHelper.SetNumA;
int setNumB = mcGregorHelper.SetNumB;
var iBondSetA = mcGregorHelper.GetIBondSetA();
var iBondSetB = mcGregorHelper.GetIBondSetB();
var cBondSetA = mcGregorHelper.GetCBondSetA();
var cBondSetB = mcGregorHelper.GetCBondSetB();
while (bestarcsCopy.Count != 0)
{
var mArcsVector = new List <int>(bestarcsCopy.Peek());
var newMapping = FindMcGregorMapping(mArcsVector, mcGregorHelper);
int newMapingSize = newMapping.Count / 2;
bool noFurtherMappings = false;
if (mappedAtomCount == newMapingSize)
{
noFurtherMappings = true;
}
List <int> newINeighborsA = new List <int>(); //instead of iBondNeighborAtomsA
List <int> newINeighborsB = new List <int>(); //instead of iBondNeighborAtomsB
var newCNeighborsA = new List <string>(); //instead of cBondNeighborsA
var newCNeighborsB = new List <string>(); //instead of cBondNeighborsB
List <int> newIBondSetA = new List <int>(); //instead of iBondSetA
List <int> newIBondSetB = new List <int>(); //instead of iBondSetB
var newCBondSetA = new List <string>(); //instead of cBondSetA
var newCBondSetB = new List <string>(); //instead of cBondSetB
//new values for setNumA + setNumB
//new arrays for iBondSetA + iBondSetB + cBondSetB + cBondSetB
List <string> cSetACopy = McGregorChecks.GenerateCSetCopy(setNumA, cBondSetA);
List <string> cSetBCopy = McGregorChecks.GenerateCSetCopy(setNumB, cBondSetB);
//find unmapped atoms of molecule A
List <int> unmappedAtomsMolA = new List <int>();
int unmappedNumA = 0;
bool atomAIsUnmapped = true;
for (int a = 0; a < source.Atoms.Count; a++)
{
for (int b = 0; b < newMapingSize; b++)
{
if (a == newMapping[b * 2 + 0])
{
atomAIsUnmapped = false;
}
}
if (atomAIsUnmapped)
{
unmappedAtomsMolA.Insert(unmappedNumA++, a);
}
atomAIsUnmapped = true;
}
//The special signs must be transfered to the corresponding atoms of molecule B
int counter = 0;
//number of remaining molecule A bonds after the clique search, which aren't neighbors
int newSetBondNumA = 0; //instead of setNumA
int newNeighborNumA = 0; //instead of localNeighborBondnumA
QueryProcessor queryProcess = new QueryProcessor(cSetACopy, cSetBCopy, SIGNS, newNeighborNumA,
newSetBondNumA, newINeighborsA, newCNeighborsA, newMapingSize, newIBondSetA, newCBondSetA);
queryProcess.Process(setNumA, setNumB, iBondSetA, iBondSetB, unmappedAtomsMolA, newMapping, counter);
cSetACopy = queryProcess.CTab1;
cSetBCopy = queryProcess.CTab2;
newSetBondNumA = queryProcess.BondNumA;
newNeighborNumA = queryProcess.NeighborBondNumA;
newINeighborsA = queryProcess.IBondNeighboursA;
newCNeighborsA = queryProcess.CBondNeighborsA;
//find unmapped atoms of molecule B
List <int> unmappedAtomsMolB = new List <int>();
int unmappedNumB = 0;
bool atomBIsUnmapped = true;
for (int a = 0; a < target.Atoms.Count; a++)
{
for (int b = 0; b < newMapingSize; b++)
{
if (a == newMapping[b * 2 + 1])
{
atomBIsUnmapped = false;
}
}
if (atomBIsUnmapped)
{
unmappedAtomsMolB.Insert(unmappedNumB++, a);
}
atomBIsUnmapped = true;
}
//number of remaining molecule B bonds after the clique search, which aren't neighbors
int newSetBondNumB = 0; //instead of setNumB
int newNeighborNumB = 0; //instead of localNeighborBondNumB
TargetProcessor targetProcess = new TargetProcessor(cSetACopy, cSetBCopy, SIGNS, newNeighborNumB,
newSetBondNumB, newINeighborsB, newCNeighborsB, newNeighborNumA, newINeighborsA,
newCNeighborsA);
targetProcess.Process(setNumB, unmappedAtomsMolB, newMapingSize, iBondSetB, cBondSetB, newMapping,
counter, newIBondSetB, newCBondSetB);
cSetACopy = targetProcess.CTab1;
cSetBCopy = targetProcess.CTab2;
newSetBondNumB = targetProcess.BondNumB;
newNeighborNumB = targetProcess.NeighborBondNumB;
newINeighborsB = targetProcess.IBondNeighboursB;
newCNeighborsB = targetProcess.CBondNeighborsB;
// Console.Out.WriteLine("Mapped Atoms before Iterator2: " + mappedAtoms);
McgregorHelper newMH = new McgregorHelper(noFurtherMappings, newMapingSize, newMapping, newNeighborNumA,
newNeighborNumB, newINeighborsA, newINeighborsB, newCNeighborsA, newCNeighborsB,
newSetBondNumA, newSetBondNumB, newIBondSetA, newIBondSetB, newCBondSetA, newCBondSetB);
Iterator(newMH);
bestarcsCopy.Pop();
// Console.Out.WriteLine("End of the iterator!!!!");
}
}
/// <summary>
/// Start McGregor search and extend the mappings if possible.
/// </summary>
/// <param name="largestMappingSize"></param>
/// <param name="presentMapping"></param>
/// <exception cref="IOException"></exception>
public void StartMcGregorIteration(int largestMappingSize, IReadOnlyDictionary <int, int> presentMapping)
{
this.globalMCSSize = (largestMappingSize / 2);
var cTab1Copy = McGregorChecks.GenerateCTabCopy(source);
var cTab2Copy = McGregorChecks.GenerateCTabCopy(target);
//find mapped atoms of both molecules and store these in mappedAtoms
List <int> mappedAtoms = new List <int>();
// Console.Out.WriteLine("\nMapped Atoms");
foreach (var map in presentMapping)
{
// Console.Out.WriteLine("i:" + map.Key + " j:" + map.Value);
mappedAtoms.Add(map.Key);
mappedAtoms.Add(map.Value);
}
int mappingSize = presentMapping.Count;
List <int> iBondNeighborsA = new List <int>();
var cBondNeighborsA = new List <string>();
List <int> iBondSetA = new List <int>();
var cBondSetA = new List <string>();
List <int> iBondNeighborsB = new List <int>();
List <int> iBondSetB = new List <int>();
var cBondNeighborsB = new List <string>();
var cBondSetB = new List <string>();
//find unmapped atoms of molecule A
List <int> unmappedAtomsMolA = McGregorChecks.MarkUnMappedAtoms(true, source, presentMapping);
int counter = 0;
int gSetBondNumA = 0;
int gSetBondNumB = 0;
int gNeighborBondnumA = 0; //number of remaining molecule A bonds after the clique search, which are neighbors of the MCS_1
int gNeighborBondNumB = 0; //number of remaining molecule B bonds after the clique search, which are neighbors of the MCS_1
QueryProcessor queryProcess = new QueryProcessor(cTab1Copy, cTab2Copy, SIGNS, gNeighborBondnumA,
gSetBondNumA, iBondNeighborsA, cBondNeighborsA, mappingSize, iBondSetA, cBondSetA);
if (!(source is IQueryAtomContainer))
{
queryProcess.Process(source, target, unmappedAtomsMolA, mappedAtoms, counter);
}
else
{
queryProcess.Process((IQueryAtomContainer)source, target, unmappedAtomsMolA, mappedAtoms, counter);
}
cTab1Copy = queryProcess.CTab1;
cTab2Copy = queryProcess.CTab2;
gSetBondNumA = queryProcess.BondNumA;
gNeighborBondnumA = queryProcess.NeighborBondNumA;
iBondNeighborsA = queryProcess.IBondNeighboursA;
cBondNeighborsA = queryProcess.CBondNeighborsA;
//find unmapped atoms of molecule B
List <int> unmappedAtomsMolB = McGregorChecks.MarkUnMappedAtoms(false, target, presentMapping);
// Console.Out.WriteLine("unmappedAtomsMolB: " + unmappedAtomsMolB.Count);
//Extract bonds which are related with unmapped atoms of molecule B.
//In case that unmapped atoms are connected with already mapped atoms, the mapped atoms are labelled with
//new special signs -> the result are two vectors: cBondNeighborsA and int_bonds_molB, which contain those
//bonds of molecule B, which are relevant for the McGregorBondTypeInSensitive algorithm.
//The special signs must be transfered to the corresponding atoms of molecule A
TargetProcessor targetProcess = new TargetProcessor(cTab1Copy, cTab2Copy, SIGNS, gNeighborBondNumB,
gSetBondNumB, iBondNeighborsB, cBondNeighborsB, gNeighborBondnumA, iBondNeighborsA,
cBondNeighborsA);
targetProcess.Process(target, unmappedAtomsMolB, mappingSize, iBondSetB, cBondSetB, mappedAtoms,
counter);
cTab1Copy = targetProcess.CTab1;
cTab2Copy = targetProcess.CTab2;
gSetBondNumB = targetProcess.BondNumB;
gNeighborBondNumB = targetProcess.NeighborBondNumB;
iBondNeighborsB = targetProcess.IBondNeighboursB;
cBondNeighborsB = targetProcess.CBondNeighborsB;
bool dummy = false;
McgregorHelper mcGregorHelper = new McgregorHelper(dummy, presentMapping.Count, mappedAtoms,
gNeighborBondnumA, gNeighborBondNumB, iBondNeighborsA, iBondNeighborsB, cBondNeighborsA,
cBondNeighborsB, gSetBondNumA, gSetBondNumB, iBondSetA, iBondSetB, cBondSetA, cBondSetB);
Iterator(mcGregorHelper);
}
