/// <summary> Builds the nodes of the RGraph ( resolution graph ), from
/// two atom containers (description of the two molecules to compare)
///
/// </summary>
/// <param name="gr"> the target RGraph
/// </param>
/// <param name="ac1"> description of the first molecule
/// </param>
/// <param name="ac2"> description of the second molecule
/// </param>
private static void nodeConstructor(RGraph gr, IAtomContainer ac1, IAtomContainer ac2)
{
// resets the target graph.
gr.clear();
IBond[] bondsA1 = ac1.Bonds;
IBond[] bondsA2 = ac2.Bonds;
// compares each bond of G1 to each bond of G2
for (int i = 0; i < bondsA1.Length; i++)
{
for (int j = 0; j < bondsA2.Length; j++)
{
if (timeout > -1 && ((System.DateTime.Now.Ticks - 621355968000000000) / 10000 - start) > timeout)
throw new CDKException("Timeout exceeded in getOverlaps");
IBond bondA2 = bondsA2[j];
if (bondA2 is IQueryBond)
{
IQueryBond queryBond = (IQueryBond)bondA2;
IQueryAtom atom1 = (IQueryAtom)(bondA2.getAtomAt(0));
IQueryAtom atom2 = (IQueryAtom)(bondA2.getAtomAt(1));
IBond bond = bondsA1[i];
if (queryBond.matches(bond))
{
// ok, bonds match
if (atom1.matches(bond.getAtomAt(0)) && atom2.matches(bond.getAtomAt(1)) || atom1.matches(bond.getAtomAt(1)) && atom2.matches(bond.getAtomAt(0)))
{
// ok, atoms match in either order
gr.addNode(new RNode(i, j));
}
}
}
else
{
// if both bonds are compatible then create an association node
// in the resolution graph
if (((bondsA1[i].Order == bondsA2[j].Order && bondsA1[i].getFlag(CDKConstants.ISAROMATIC) == bondsA2[j].getFlag(CDKConstants.ISAROMATIC)) || (bondsA1[i].getFlag(CDKConstants.ISAROMATIC) && bondsA2[j].getFlag(CDKConstants.ISAROMATIC))) && ((bondsA1[i].getAtomAt(0).Symbol.Equals(bondsA2[j].getAtomAt(0).Symbol) && bondsA1[i].getAtomAt(1).Symbol.Equals(bondsA2[j].getAtomAt(1).Symbol)) || (bondsA1[i].getAtomAt(0).Symbol.Equals(bondsA2[j].getAtomAt(1).Symbol) && bondsA1[i].getAtomAt(1).Symbol.Equals(bondsA2[j].getAtomAt(0).Symbol))))
{
gr.addNode(new RNode(i, j));
}
}
}
}
}
/// <summary> Build edges of the RGraphs
/// This method create the edge of the RGraph and
/// calculates the incompatibility and neighbourhood
/// relationships between RGraph nodes.
///
/// </summary>
/// <param name="gr"> the rGraph
/// </param>
/// <param name="ac1"> Description of the first molecule
/// </param>
/// <param name="ac2"> Description of the second molecule
/// </param>
private static void arcConstructor(RGraph gr, IAtomContainer ac1, IAtomContainer ac2)
{
// each node is incompatible with himself
for (int i = 0; i < gr.Graph.Count; i++)
{
RNode x = (RNode)gr.Graph[i];
SupportClass.BitArraySupport.Set(x.Forbidden, i);
}
IBond a1;
IBond a2;
IBond b1;
IBond b2;
IBond[] bondsA1 = ac1.Bonds;
IBond[] bondsA2 = ac2.Bonds;
gr.FirstGraphSize = ac1.getBondCount();
gr.SecondGraphSize = ac2.getBondCount();
for (int i = 0; i < gr.Graph.Count; i++)
{
RNode x = (RNode)gr.Graph[i];
// two nodes are neighbours if their adjacency
// relationship in are equivalent in G1 and G2
// else they are incompatible.
for (int j = i + 1; j < gr.Graph.Count; j++)
{
if (timeout > -1 && ((System.DateTime.Now.Ticks - 621355968000000000) / 10000 - start) > timeout)
throw new CDKException("Timeout exceeded in getOverlaps");
RNode y = (RNode)gr.Graph[j];
a1 = bondsA1[((RNode)gr.Graph[i]).RMap.Id1];
a2 = bondsA2[((RNode)gr.Graph[i]).RMap.Id2];
b1 = bondsA1[((RNode)gr.Graph[j]).RMap.Id1];
b2 = bondsA2[((RNode)gr.Graph[j]).RMap.Id2];
if (a2 is IQueryBond)
{
if (a1.Equals(b1) || a2.Equals(b2) || !queryAdjacency(a1, b1, a2, b2))
{
SupportClass.BitArraySupport.Set(x.Forbidden, j);
SupportClass.BitArraySupport.Set(y.Forbidden, i);
}
else if (hasCommonAtom(a1, b1))
{
SupportClass.BitArraySupport.Set(x.Extension, j);
SupportClass.BitArraySupport.Set(y.Extension, i);
}
}
else
{
if (a1.Equals(b1) || a2.Equals(b2) || (!getCommonSymbol(a1, b1).Equals(getCommonSymbol(a2, b2))))
{
SupportClass.BitArraySupport.Set(x.Forbidden, j);
SupportClass.BitArraySupport.Set(y.Forbidden, i);
}
else if (hasCommonAtom(a1, b1))
{
SupportClass.BitArraySupport.Set(x.Extension, j);
SupportClass.BitArraySupport.Set(y.Extension, i);
}
}
}
}
}
//////////////////////////////////////////////////
// Internal methods
/// <summary> Builds the RGraph ( resolution graph ), from two atomContainer
/// (description of the two molecules to compare)
/// This is the interface point between the CDK model and
/// the generic MCSS algorithm based on the RGRaph.
///
/// </summary>
/// <param name="g1"> Description of the first molecule
/// </param>
/// <param name="g2"> Description of the second molecule
/// </param>
/// <returns> the rGraph
/// </returns>
public static RGraph buildRGraph(IAtomContainer g1, IAtomContainer g2)
{
RGraph rGraph = new RGraph();
nodeConstructor(rGraph, g1, g2);
arcConstructor(rGraph, g1, g2);
return rGraph;
}
