private static List <List <int> > LabelAtoms(IAtomContainer atomCont)
{
List <List <int> > labelList = new List <List <int> >();
for (int i = 0; i < atomCont.Atoms.Count; i++)
{
LabelContainer labelContainer = LabelContainer.Instance;
List <int> label = new List <int>(7);
// label.SetSize(7);
for (int a = 0; a < 7; a++)
{
label.Insert(a, 0);
}
IAtom refAtom = atomCont.Atoms[i];
string atom1Type = refAtom.Symbol;
label[0] = labelContainer.GetLabelID(atom1Type);
int countNeighbors = 1;
var connAtoms = atomCont.GetConnectedAtoms(refAtom);
foreach (var negAtom in connAtoms)
{
string atom2Type = negAtom.Symbol;
label[countNeighbors++] = labelContainer.GetLabelID(atom2Type);
}
BubbleSort(label);
labelList.Add(label);
}
return(labelList);
}
/// <summary>
/// compGraphNodesCZero is used to build up of the edges of the compatibility graph
/// </summary>
/// <exception cref="System.IO.IOException"></exception>
internal int CompatibilityGraphNodesIfCEdgeIsZero()
{
int countNodes = 1;
var map = new List <string>();
compGraphNodesCZero = new List <int>(); //Initialize the compGraphNodesCZero List
LabelContainer labelContainer = LabelContainer.Instance;
compGraphNodes.Clear();
for (int i = 0; i < source.Atoms.Count; i++)
{
for (int j = 0; j < target.Atoms.Count; j++)
{
IAtom atom1 = source.Atoms[i];
IAtom atom2 = target.Atoms[j];
//You can also check object equal or charge, hydrogen count etc
if (string.Equals(atom1.Symbol, atom2.Symbol, StringComparison.OrdinalIgnoreCase) && (!map.Contains(i + "_" + j)))
{
compGraphNodesCZero.Add(i);
compGraphNodesCZero.Add(j);
compGraphNodesCZero.Add(labelContainer.GetLabelID(atom1.Symbol)); //i.e C is label 1
compGraphNodesCZero.Add(countNodes);
compGraphNodes.Add(i);
compGraphNodes.Add(j);
compGraphNodes.Add(countNodes++);
map.Add(i + "_" + j);
}
}
}
map.Clear();
return(countNodes);
}