MolComparator question

I thought I would write a MolComparator that enforced the direction of coordinate bonds.  I wrote the following code:

    public boolean compareBonds(int queryBondNum, int targetBondNum) {

        boolean match = true;

        final MolBond queryBond = query.getBond(getOrigQueryBond(queryBondNum));

        final MolBond targetBond =

                target.getBond(getOrigTargetBond(targetBondNum));

        if (queryBond.getType() == MolBond.COORDINATE

                && targetBond.getType() == MolBond.COORDINATE) {

            final String SELF = "CoordBondDirnMatcher.compareBonds: ";

            final MolAtom queryAtom1 = queryBond.getAtom1();

            final MolAtom targetAtom1 = targetBond.getAtom1();

            final int qAtom1Num = query.indexOf(queryAtom1);

            final int tAtom1Num = target.indexOf(targetAtom1);

            match = queryAtom1.getAtno() == targetAtom1.getAtno()

                    && queryAtom1.getCharge() == targetAtom1.getCharge()

                    && queryAtom1.getRadical() == targetAtom1.getRadical()

                    && queryAtom1.getMassno() == targetAtom1.getMassno()

                    && queryAtom1.getBondCount() == targetAtom1.getBondCount();

        } // if either bond is not coordinate

        return match;

    } // compareBonds(int, int)

As you can see, I am using atomic number, charge, etc. as a proxy for the atoms matching, but really, I would like to see if queryAtom1 and targetAtom1 match according to the overall match in the structure.  Is there a way to do it?

Hi Bob,

This solution works fine for bonds between different atoms. If you would like to generalize it then you will have to override MolComparator#compareHit(int[], int). Let me know if you need further assistance.

Best Regards,
Gabor

Thanks.  Instead of trying to figure out how to write the MolComparator, I just decided to convert all coordinate bonds A->B into regular single bonds with formal charges, ⁺A-B^–.  That solves the problem.