private int CountBoundMultiplicity(List <AtomBehavior> atoms, AtomBehavior atom)
{
int count = 0;
foreach (AtomBehavior currentAtom in atoms)
{
if (currentAtom == atom)
{
count++;
}
}
Debug.Log("CountBoundMultiplicity : " + atom);
Debug.Log("CountBoundMultiplicity : " + count);
return(count);
}
private List <AtomBehavior> GetStartingPointsByType(GameObject[] molecule, AtomType symbol)
{
List <AtomBehavior> atomsFound = new List <AtomBehavior>();
foreach (GameObject atom in molecule)
{
AtomBehavior atomScript = atom.GetComponent <AtomBehavior>();
if (atomScript.Symbol == symbol)
{
atomsFound.Add(atomScript);
}
}
Debug.Log("GetStartingPointsByType size : " + atomsFound.Count);
return(atomsFound);
}
private bool CompareBranchFrom(ref string smiles, AtomBehavior startingPoint)
{
Debug.Log("CompareBranchFrom current smiles : " + smiles);
// First, we record the SMILES' last state to restore it if this branch does not match
string smilesLastState = string.Copy(smiles);
// We also keep track of the processed atoms in this branch to clear them at the end if it does not match
List <AtomBehavior> atomsTrack = new List <AtomBehavior>();
startingPoint.Mark();
atomsTrack.Add(startingPoint);
List <AtomBehavior> nonMarkedNeighboursOfInterest;
AtomType nextSymbol = AtomType.Void;
while (!smiles.Equals("") && smiles[0] != ')')
{
Debug.Log("In while loop : smiles is ." + smiles + ".");
Debug.Log("CompareBranchFrom : the smiles is not empty, entering the while loop");
// an opening parenthesis means a new branch
if (smiles[0] == '(')
{
smiles = smiles.Substring(1);
// the method is called recursively for each new branch
if (!CompareBranchFrom(ref smiles, startingPoint))
{
smiles = string.Copy(smilesLastState);
ResetAllMarks(atomsTrack);
return(false);
}
}
else
{
if (smiles[0] == '=')
{
smiles = smiles.Substring(1);
nextSymbol = GetSmilesStartingSymbol(ref smiles);
nonMarkedNeighboursOfInterest = startingPoint.GetNonMarkedNeighboursByBondType(2);
}
else if (smiles[0] == '#')
{
smiles = smiles.Substring(1);
nextSymbol = GetSmilesStartingSymbol(ref smiles);
nonMarkedNeighboursOfInterest = startingPoint.GetNonMarkedNeighboursByBondType(3);
}
else
{
nextSymbol = GetSmilesStartingSymbol(ref smiles);
nonMarkedNeighboursOfInterest = startingPoint.GetNonMarkedNeighboursOfInterest();
}
Debug.Log("In while loop : nb of NoI is " + nonMarkedNeighboursOfInterest.Count);
if (nonMarkedNeighboursOfInterest.Count == 1 && nonMarkedNeighboursOfInterest[0].Symbol == nextSymbol)
{
startingPoint = nonMarkedNeighboursOfInterest[0];
startingPoint.Mark();
atomsTrack.Add(startingPoint);
}
else
{
smiles = string.Copy(smilesLastState);
ResetAllMarks(atomsTrack);
return(false);
}
}
}
// if we are at the end of the branch and there are more neighbours of interest to be processed (i.e. unmarked)...
nonMarkedNeighboursOfInterest = startingPoint.GetNonMarkedNeighboursOfInterest();
Debug.Log("CompareBranchFrom non marked NoI size : " + nonMarkedNeighboursOfInterest.Count);
if (nonMarkedNeighboursOfInterest.Count > 0)
{
Debug.Log("CompareBranchFrom : there are non marked NoI");
// ...the SMILES does not match the current branch
smiles = string.Copy(smilesLastState);
ResetAllMarks(atomsTrack);
foreach (AtomBehavior atom in atomsTrack)
{
Debug.Log("Atom marked : " + atom.isMarked());
}
return(false);
}
if (!smiles.Equals(""))
{
smiles = smiles.Substring(1);
}
// else, the SMILES does match the current branch
return(true);
}