/** * Adds a ElectronContainer to this AtomContainer. * *@param electronContainer The ElectronContainer to added to this container */ @Override public void addElectronContainer(IElectronContainer electronContainer) { if (electronContainer instanceof IBond) this.addBond((IBond) electronContainer); if (electronContainer instanceof ILonePair) this.addLonePair((ILonePair) electronContainer); if (electronContainer instanceof ISingleElectron) this.addSingleElectron((ISingleElectron) electronContainer); }
/** * Adds a bond to this container. * *@param atom1 Id of the first atom of the Bond in [0,..] *@param atom2 Id of the second atom of the Bond in [0,..] *@param order Bondorder */ @Override public void addBond(int atom1, int atom2, IBond.Order order) { IBond bond = getBuilder().newInstance(IBond.class, getAtom(atom1), getAtom(atom2), order); if (bondCount >= bonds.length) { growBondArray(); } addBond(bond); /* * no notifyChanged() here because addBond(bond) does it already */ }
/** * Adds a bond to this container. * *@param atom1 Id of the first atom of the Bond in [0,..] *@param atom2 Id of the second atom of the Bond in [0,..] *@param order Bondorder *@param stereo Stereochemical orientation */ @Override public void addBond(int atom1, int atom2, IBond.Order order, IBond.Stereo stereo) { IBond bond = getBuilder().newInstance(IBond.class, getAtom(atom1), getAtom(atom2), order, stereo); if (contains(bond)) { return; } if (bondCount >= bonds.length) { growBondArray(); } addBond(bond); /* * no notifyChanged() here because addBond(bond) does it already */ }
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; }
query.addBond(qbond);
addBond(atomContainer.getBond(f));
aminoAcid.removeBond(bondAtom0, bondAtom1); QueryBond qbond = new QueryBond(bondAtom0, bondAtom1, Expr.Type.SINGLE_OR_AROMATIC); aminoAcid.addBond(qbond); break;
aminoAcid.removeBond(bondAtom0, bondAtom1); QueryBond qbond = new QueryBond(bondAtom0, bondAtom1, Expr.Type.SINGLE_OR_AROMATIC); aminoAcid.addBond(qbond); break;