Align CDK molecule to substructure

CDKAlign.java

public static void alignMoleculeToSubstructure(IAtomContainer mol,
                                               IAtomContainer sub,
                                               boolean fixBonds) throws CDKException {
    Pattern substructurePattern = Pattern.findSubstructure(sub);
    Mappings mappings = substructurePattern.matchAll(mol);
    Set<IAtom> fixedAtoms = new HashSet<IAtom>();
    Set<IBond> fixedBonds = new HashSet<IBond>();
    for (Map<IChemObject, IChemObject> map : mappings.toAtomBondMap()) {

        GeometryUtil.scaleMolecule(sub,
                                   1.5/GeometryUtil.getBondLengthMedian(sub));

        for (IChemObject substructureObject : map.keySet()) {
            IChemObject targetObject = map.get(substructureObject);
            if (targetObject instanceof IAtom) {
                //set the target atom's position to that of the substructure atom and add it to the fixed atom list
                IAtom targetAtom = (IAtom) targetObject;
                IAtom substructureAtom = (IAtom) substructureObject;
                targetAtom.setPoint2d(new Point2d(substructureAtom.getPoint2d()));
                fixedAtoms.add(targetAtom);
            } else if (fixBonds) {
                //only check bonds if needed
                if (targetObject instanceof IBond) {
                    //add the target bond to the fixed bond list
                    IBond targetBond = (IBond) substructureObject;
                    fixedBonds.add(targetBond);
                }
            }
        }
        //only align to the first matching substructure
        break;
    }
    //generate coordinates for the molecule
    StructureDiagramGenerator sdg = new StructureDiagramGenerator();
    sdg.setMolecule(mol, false, fixedAtoms, fixedBonds);
    sdg.generateCoordinates();
}