Vector2d v = atomPlacer.getNextBondVector(atom, connectedAtom, distanceMeasure, true); atomPlacer.setMolecule(ac);
logger.debug("Excpetion in detecting E/Z. This could mean that cleanup does not respect E/Z"); bondVector = getNextBondVector(nextAtom, atom, GeometryUtil.get2DCenter(molecule), trans); } else { bondVector = getNextBondVector(nextAtom, atom, GeometryUtil.get2DCenter(molecule), true);
logger.debug("Excpetion in detecting E/Z. This could mean that cleanup does not respect E/Z"); bondVector = getNextBondVector(nextAtom, atom, GeometryUtil.get2DCenter(molecule), trans); } else { bondVector = getNextBondVector(nextAtom, atom, GeometryUtil.get2DCenter(molecule), true);
logger.debug("Less than or equal one atoms placed already"); logger.debug("Trying to get next bond vector."); direction = atomPlacer.getNextBondVector(atom, placedAtoms.getAtom(0), GeometryUtil.get2DCenter(molecule), true);
logger.debug("Less than or equal one atoms placed already"); logger.debug("Trying to get next bond vector."); direction = atomPlacer.getNextBondVector(atom, placedAtoms.getAtom(0), GeometryUtil.get2DCenter(molecule), true);