boolean openRing(int rnum) { if (prev == null) { error = "Cannot open ring, no previous atom"; return false; } if (bond == null) { bond = new QueryBond(null); bond.setExpression(null); } bond.setAtom(prev, 0); rings[rnum] = addBond(prev, bond); numRingOpens++; bond = null; return true; }
boolean parseBondExpr() { bond = new QueryBond(mol.getBuilder()); bond.setExpression(new Expr(Expr.Type.NONE)); if (!parseBondExpr(bond.getExpression(), bond, '\0')) { error = "Invalid bond expression"; return false; } return true; }
continue; IQueryBond qbond = new QueryBond(beg, end, Expr.Type.TRUE); qry.addBond(qbond);
continue; IQueryBond qbond = new QueryBond(beg, end, Expr.Type.TRUE); qry.addBond(qbond);
explicitValence[atom1 - 1] = explicitValence[atom2 - 1] = Integer.MIN_VALUE; } else { newBond = new QueryBond(builder); IAtom[] bondAtoms = {a1, a2}; newBond.setAtoms(bondAtoms);
void append(IAtom atom) { if (curComponentId != 0) atom.setProperty(CDKConstants.REACTION_GROUP, curComponentId); mol.addAtom(atom); if (prev != null) { if (bond == null) { bond = new QueryBond(mol.getBuilder()); bond.setExpression(new Expr(SINGLE_OR_AROMATIC)); } bond.setAtom(prev, 0); bond.setAtom(atom, 1); addBond(prev, bond); addBond(atom, bond); } else local.put(atom, new LocalNbrs(true)); prev = atom; bond = null; }
explicitValence[atom1 - 1] = explicitValence[atom2 - 1] = Integer.MIN_VALUE; } else { newBond = new QueryBond(builder); IAtom[] bondAtoms = {a1, a2}; newBond.setAtoms(bondAtoms);
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; }
QueryBond qbond = new QueryBond((IAtom) mapping.get(bond.getBegin()), (IAtom) mapping.get(bond.getEnd()), expr);
break; case 5: // single or double bond = new QueryBond(bond.getBegin(), bond.getEnd(), Expr.Type.SINGLE_OR_DOUBLE); break; case 6: // single or aromatic bond = new QueryBond(bond.getBegin(), bond.getEnd(), Expr.Type.SINGLE_OR_AROMATIC); break; case 7: // double or aromatic bond = new QueryBond(bond.getBegin(), bond.getEnd(), Expr.Type.DOUBLE_OR_AROMATIC); break; case 8: // any bond = new QueryBond(bond.getBegin(), bond.getEnd(), Expr.Type.TRUE); break; default:
break; case 5: // single or double bond = new QueryBond(bond.getBegin(), bond.getEnd(), Expr.Type.SINGLE_OR_DOUBLE); break; case 6: // single or aromatic bond = new QueryBond(bond.getBegin(), bond.getEnd(), Expr.Type.SINGLE_OR_AROMATIC); break; case 7: // double or aromatic bond = new QueryBond(bond.getBegin(), bond.getEnd(), Expr.Type.DOUBLE_OR_AROMATIC); break; case 8: // any bond = new QueryBond(bond.getBegin(), bond.getEnd(), Expr.Type.TRUE); break; default:
&& bond.getOrder() == IBond.Order.SINGLE) { aminoAcid.removeBond(bondAtom0, bondAtom1); QueryBond qbond = new QueryBond(bondAtom0, bondAtom1, Expr.Type.SINGLE_OR_AROMATIC); aminoAcid.addBond(qbond); break;
&& bond.getOrder() == IBond.Order.SINGLE) { aminoAcid.removeBond(bondAtom0, bondAtom1); QueryBond qbond = new QueryBond(bondAtom0, bondAtom1, Expr.Type.SINGLE_OR_AROMATIC); aminoAcid.addBond(qbond); break;