unplacedNeighbours.addAtom((IAtom)l.get(i)); ap.distributePartners(lastplaced, placedNeighbours, GeometryTools.get2DCenter(placedNeighbours), unplacedNeighbours, 1.4); IRingSet ringset = Cycles.sssr(container).toRingSet(); for(IAtomContainer ring:ringset.atomContainers()){
atomPlacer.distributePartners(atom, placed, centerPlacedAtoms, unplaced, bondLength);
atomPlacer.distributePartners(atom, placed, centerPlacedAtoms, unplaced, bondLength);
unplacedAtoms.addAtom(newAtom); atomPlacer.distributePartners(atom, placedAtoms, center2D, unplacedAtoms, bondLength);
atomPlacer.distributePartners(atom, sharedAtoms, centerOfRingGravity, unplacedPartners, bondLength);
atomPlacer.distributePartners(atom, sharedAtoms, centerOfRingGravity, unplacedPartners, bondLength);
logger.debug("More than one atoms placed already"); logger.debug("trying to place neighbors of atom " + (molecule.indexOf(atom) + 1)); atomPlacer.distributePartners(atom, placedAtoms, GeometryUtil.get2DCenter(placedAtoms), unplacedAtoms, bondLength); direction = new Vector2d(longestUnplacedChain.getAtom(1).getPoint2d());
logger.debug("More than one atoms placed already"); logger.debug("trying to place neighbors of atom " + (molecule.indexOf(atom) + 1)); atomPlacer.distributePartners(atom, placedAtoms, GeometryUtil.get2DCenter(placedAtoms), unplacedAtoms, bondLength); direction = new Vector2d(longestUnplacedChain.getAtom(1).getPoint2d());