StereoDetector.java

package stereo;

import java.util.ArrayList;
import java.util.List;

import org.openscience.cdk.graph.invariant.MorganNumbersTools;
import org.openscience.cdk.interfaces.IAtom;
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomParity;

public class StereoDetector {

    /**
     * Find stereo centers based on the connectivity alone, using Morgan numbers
     * 
     * @param container
     *            the atom container to search
     * 
     * @return a list of IAtomParity objects representing possible stereocenters
     */
    public static List<IAtomParity> findStereoCenters(IAtomContainer container) {
        List<IAtomParity> centers = new ArrayList<IAtomParity>();
        long[] morganNumbers = MorganNumbersTools.getMorganNumbers(container);
        
        for (IAtom atom : container.atoms()) {
            List<IAtom> neighbours = container.getConnectedAtomsList(atom);
            if (neighbours.size() != 4) continue;
            
            IAtom first = neighbours.get(0);
            IAtom second = neighbours.get(1);
            IAtom third = neighbours.get(2);
            IAtom fourth = neighbours.get(3);
            
            // a 'half-matrix' all-v-all comparison
            if (isSame(first, second, container, morganNumbers) 
                    ||  isSame(first, third, container, morganNumbers)
                    ||  isSame(first, fourth, container, morganNumbers)
                    ||  isSame(second, third, container, morganNumbers)
                    ||  isSame(second, fourth, container, morganNumbers)
                    ||  isSame(third, fourth, container, morganNumbers)) {
                continue;
            } else {
                int parity = -1;    // hmmm.
                IAtomParity center = 
                    container.getBuilder().newAtomParity(
                            atom, first, second, third, fourth, parity);
                centers.add(center);
            }

        }
        return centers;
    }
    
    public static boolean isSame(IAtom a, IAtom b, IAtomContainer container, long[] morganNumbers) {
        int indexA = container.getAtomNumber(a);
        int indexB = container.getAtomNumber(b);
        long morganNumberA = morganNumbers[indexA];
        long morganNumberB = morganNumbers[indexB];
        return morganNumberA == morganNumberB 
            && a.getSymbol().equals(b.getSymbol());
    }

}