private static void addExtendedCisTransConfig(ExtendedCisTrans ect, GraphBuilder gb, Map<IAtom, Integer> indices, IAtomContainer container) { IAtom[] ends = ExtendedCisTrans.findTerminalAtoms(container, ect.getFocus()); IBond[] carriers = ect.getCarriers().toArray(new IBond[2]); if (ends != null) { Configuration.DoubleBond config; if (ect.getConfigOrder() == IStereoElement.TOGETHER) config = Configuration.DoubleBond.TOGETHER; else if (ect.getConfigOrder() == IStereoElement.OPPOSITE) config = Configuration.DoubleBond.OPPOSITE; else config = Configuration.DoubleBond.UNSPECIFIED; gb.extendedGeometric(indices.get(ends[0]), indices.get(ends[1])) .configure(indices.get(carriers[0].getOther(ends[0])), indices.get(carriers[1].getOther(ends[1])), config); } } }
endBonds.remove(dbs.get(dbs.size() - 1)); IAtom[] ends = ExtendedCisTrans.findTerminalAtoms(container, focus); assert ends != null; if (ends[0].equals(begAtom)) {
endBonds.remove(dbs.get(dbs.size() - 1)); IAtom[] ends = ExtendedCisTrans.findTerminalAtoms(container, focus); assert ends != null; if (ends[0].equals(begAtom)) {
IAtom[] ends = ExtendedCisTrans.findTerminalAtoms(container, middle); IBond[] bonds = elem.getCarriers().toArray(new IBond[2]);
IAtom[] ends = ExtendedCisTrans.findTerminalAtoms(container, middle); IBond[] bonds = elem.getCarriers().toArray(new IBond[2]);
IAtom[] ends = ExtendedCisTrans.findTerminalAtoms(org, focus); IAtom u = ends[0]; IAtom v = ends[1];