FragmentAlignement.java

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package denoptim.fragmenter;
 
import java.util.Iterator;
 
import javax.vecmath.Point3d;
 
import org.biojava.nbio.structure.geometry.SuperPositionSVD;
import org.jgrapht.GraphMapping;
 
import denoptim.exception.DENOPTIMException;
import denoptim.graph.FragIsomorphEdge;
import denoptim.graph.FragIsomorphNode;
import denoptim.graph.Fragment;
import denoptim.graph.FragmentIsomorphismInspector;
 
public class FragmentAlignement
{
    private double minRMSD = Double.MAX_VALUE;
    
    private GraphMapping<FragIsomorphNode, FragIsomorphEdge> bestMapping = null;
    
//------------------------------------------------------------------------------
    
    public FragmentAlignement(Fragment fragA, Fragment fragB) throws DENOPTIMException 
    {
        // Map graph nodes (atom and APs)
        FragmentIsomorphismInspector fii = 
                new FragmentIsomorphismInspector(fragA, fragB);
        if(!fii.isomorphismExists())
        {
            throw new DENOPTIMException("Failed to find isomorphism.");
        }
 
        int nPoints = fragA.getJGraphFragIsomorphism().vertexSet().size();
        
        // Get lowest RMSD among all mappings
        Iterator<GraphMapping<FragIsomorphNode, FragIsomorphEdge>> 
            mapingIterator = fii.getMappings();
        if (mapingIterator == null)
        {
            throw new DENOPTIMException("Mapping of isomorphism timed-out!");
        }
        
        while (mapingIterator.hasNext())
        {
            GraphMapping<FragIsomorphNode, FragIsomorphEdge> mapping = 
                    mapingIterator.next();
            
            // Translate graph nodes/vertexes into points to align
            Point3d[] ptsA = new Point3d[nPoints];
            Point3d[] ptsB = new Point3d[nPoints];
            int index = -1;
            for (FragIsomorphNode nA : fragA.getJGraphFragIsomorphism().vertexSet())
            {
                index++;
                FragIsomorphNode nB = mapping.getVertexCorrespondence(nA,
                        true);
                ptsA[index] = nA.getPoint3d();
                ptsB[index] = nB.getPoint3d();
            }
            
            // Align atoms
            SuperPositionSVD svd = new SuperPositionSVD(false);
            double rmsd = svd.getRmsd(ptsA,ptsB);
            if (rmsd < minRMSD)
            {
                minRMSD = rmsd;
                bestMapping = mapping;
            }
        }
    }
    
//------------------------------------------------------------------------------
 
    public GraphMapping<FragIsomorphNode, FragIsomorphEdge> getLowestRMSDMapping()
    {
        return bestMapping;
    }
    
//------------------------------------------------------------------------------
 
    public double getMinimumRMSD()
    {
        return minRMSD;
    }
    
//------------------------------------------------------------------------------
 
}