/** * Main method to be called to resolve overlap situations. * * @param ac The atomcontainer in which the atom or bond overlap exists * @param sssr A ring set for this atom container if one exists, otherwhise null */ public double resolveOverlap(IAtomContainer ac, IRingSet sssr) { Vector overlappingAtoms = new Vector(); Vector overlappingBonds = new Vector(); logger.debug("Start of resolveOverlap"); double overlapScore = getOverlapScore(ac, overlappingAtoms, overlappingBonds); if (overlapScore > 0) { overlapScore = displace(ac, overlappingAtoms, overlappingBonds); } logger.debug("overlapScore = " + overlapScore); logger.debug("End of resolveOverlap"); return overlapScore; }
/** * Main method to be called to resolve overlap situations. * * @param ac The atomcontainer in which the atom or bond overlap exists * @param sssr A ring set for this atom container if one exists, otherwhise null */ public double resolveOverlap(IAtomContainer ac, IRingSet sssr) { Vector overlappingAtoms = new Vector(); Vector overlappingBonds = new Vector(); logger.debug("Start of resolveOverlap"); double overlapScore = getOverlapScore(ac, overlappingAtoms, overlappingBonds); if (overlapScore > 0) { overlapScore = displace(ac, overlappingAtoms, overlappingBonds); } logger.debug("overlapScore = " + overlapScore); logger.debug("End of resolveOverlap"); return overlapScore; }