qbond.setOrder(bond.getOrder()); if (optset.contains(Expr.Type.SINGLE_OR_AROMATIC) || optset.contains(Expr.Type.DOUBLE_OR_AROMATIC) ||
public static QueryAtomContainer createSymbolChargeIDQueryContainer(IAtomContainer container) { QueryAtomContainer queryContainer = new QueryAtomContainer(container.getBuilder()); for (int i = 0; i < container.getAtomCount(); i++) { queryContainer.addAtom(new SymbolChargeIDQueryAtom(container.getAtom(i))); } Iterator<IBond> bonds = container.bonds().iterator(); while (bonds.hasNext()) { IBond bond = bonds.next(); int index1 = container.indexOf(bond.getBegin()); int index2 = container.indexOf(bond.getEnd()); if (bond.isAromatic()) { QueryBond qbond = new QueryBond(queryContainer.getAtom(index1), queryContainer.getAtom(index2), Expr.Type.IS_AROMATIC); queryContainer.addBond(qbond); } else { QueryBond qbond = new QueryBond(queryContainer.getAtom(index1), queryContainer.getAtom(index2), Expr.Type.ORDER, bond.getOrder().numeric()); qbond.setOrder(bond.getOrder()); // backwards compatibility queryContainer.addBond(qbond); } } return queryContainer; }