/**
* Hide the atoms and bonds of a contracted abbreviation. If the abbreviations is attached we
* remap the attachment symbol to display the name. If there are no attachments the symbol we be
* added later ({@see #generateSgroups}).
*
* @param container molecule
* @param sgroup abbreviation group display shortcut
*/
private static void contractAbbreviation(
IAtomContainer container, Map<IAtom, String> symbolRemap, Sgroup sgroup) {
final Set<IBond> crossing = sgroup.getBonds();
final Set<IAtom> atoms = sgroup.getAtoms();
// only do 0,1 attachments for now
if (crossing.size() > 1) return;
for (IAtom atom : atoms) {
StandardGenerator.hide(atom);
}
for (IBond bond : container.bonds()) {
if (atoms.contains(bond.getAtom(0)) || atoms.contains(bond.getAtom(1)))
StandardGenerator.hide(bond);
}
for (IBond bond : crossing) {
StandardGenerator.unhide(bond);
IAtom a1 = bond.getAtom(0);
IAtom a2 = bond.getAtom(1);
StandardGenerator.unhide(a1);
if (atoms.contains(a1)) symbolRemap.put(a1, sgroup.getSubscript());
StandardGenerator.unhide(a2);
if (atoms.contains(a2)) symbolRemap.put(a2, sgroup.getSubscript());
}
}
/**
* Hide the repeated atoms and bonds of a multiple group. We hide al atoms that belong to the
* group unless they are defined in the parent atom list. Any bond to those atoms that is not a
* crossing bond or one connecting atoms in the parent list is hidden.
*
* @param container molecule
* @param sgroup multiple group display shortcut
*/
private static void hideMultipleParts(IAtomContainer container, Sgroup sgroup) {
final Set<IBond> crossing = sgroup.getBonds();
final Set<IAtom> atoms = sgroup.getAtoms();
final Set<IAtom> parentAtoms = sgroup.getValue(SgroupKey.CtabParentAtomList);
for (IBond bond : container.bonds()) {
if (parentAtoms.contains(bond.getAtom(0)) && parentAtoms.contains(bond.getAtom(1))) continue;
if (atoms.contains(bond.getAtom(0)) || atoms.contains(bond.getAtom(1)))
StandardGenerator.hide(bond);
}
for (IAtom atom : atoms) {
if (!parentAtoms.contains(atom)) StandardGenerator.hide(atom);
}
for (IBond bond : crossing) {
StandardGenerator.unhide(bond);
}
}