/// <summary> Constructor for the RNode object
///
/// </summary>
/// <param name="id1"> number of the bond in the graphe 1
/// </param>
/// <param name="id2"> number of the bond in the graphe 2
/// </param>
public RNode(int id1, int id2)
{
rMap = new RMap(id1, id2);
extension = new System.Collections.BitArray(64);
forbidden = new System.Collections.BitArray(64);
}
/// <summary> Constructor for the RNode object
///
/// </summary>
/// <param name="id1"> number of the bond in the graphe 1
/// </param>
/// <param name="id2"> number of the bond in the graphe 2
/// </param>
public RNode(int id1, int id2)
{
rMap = new RMap(id1, id2);
extension = new System.Collections.BitArray(64);
forbidden = new System.Collections.BitArray(64);
}
/// <summary> This makes a map of matching atoms out of a map of matching bonds as produced by the get(Subgraph|Ismorphism)Map methods.
///
/// </summary>
/// <param name="l"> The list produced by the getMap method.
/// </param>
/// <param name="g1"> The first atom container.
/// </param>
/// <param name="g2"> The second one (first and second as in getMap)
/// </param>
/// <returns> The mapping found projected on g1. This is a List of RMap objects containing Ids of matching atoms.
/// </returns>
public static System.Collections.IList makeAtomsMapOfBondsMap(System.Collections.IList l, IAtomContainer g1, IAtomContainer g2)
{
if (l == null)
return (l);
IBond[] bonds1 = g1.Bonds;
IBond[] bonds2 = g2.Bonds;
System.Collections.IList result = System.Collections.ArrayList.Synchronized(new System.Collections.ArrayList(10));
for (int i = 0; i < l.Count; i++)
{
IBond bond1 = bonds1[((RMap)l[i]).Id1];
IBond bond2 = bonds2[((RMap)l[i]).Id2];
IAtom[] atom1 = bond1.getAtoms();
IAtom[] atom2 = bond2.getAtoms();
for (int j = 0; j < 2; j++)
{
IBond[] bondsConnectedToAtom1j = g1.getConnectedBonds(atom1[j]);
for (int k = 0; k < bondsConnectedToAtom1j.Length; k++)
{
if (bondsConnectedToAtom1j[k] != bond1)
{
IBond testBond = bondsConnectedToAtom1j[k];
for (int m = 0; m < l.Count; m++)
{
IBond testBond2;
if (((RMap)l[m]).Id1 == g1.getBondNumber(testBond))
{
testBond2 = bonds2[((RMap)l[m]).Id2];
for (int n = 0; n < 2; n++)
{
System.Collections.IList bondsToTest = g2.getConnectedBondsVector(atom2[n]);
if (bondsToTest.Contains(testBond2))
{
RMap map;
if (j == n)
{
map = new RMap(g1.getAtomNumber(atom1[0]), g2.getAtomNumber(atom2[0]));
}
else
{
map = new RMap(g1.getAtomNumber(atom1[1]), g2.getAtomNumber(atom2[0]));
}
if (!result.Contains(map))
{
result.Add(map);
}
RMap map2;
if (j == n)
{
map2 = new RMap(g1.getAtomNumber(atom1[1]), g2.getAtomNumber(atom2[1]));
}
else
{
map2 = new RMap(g1.getAtomNumber(atom1[0]), g2.getAtomNumber(atom2[1]));
}
if (!result.Contains(map2))
{
result.Add(map2);
}
}
}
}
}
}
}
}
}
return (result);
}