/**
* 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());
}
}
/**
* If the molecule has display shortcuts (abbreviations or multiple group sgroups) certain parts
* of the structure are hidden from display. This method marks the parts to hide and in the case
* of abbreviations, remaps atom symbols. Appart from additional property flags, the molecule is
* unchanged by this method.
*
* @param container molecule input
* @param symbolRemap a map that will hold symbol remapping
*/
static void prepareDisplayShortcuts(IAtomContainer container, Map<IAtom, String> symbolRemap) {
List<Sgroup> sgroups = container.getProperty(CDKConstants.CTAB_SGROUPS);
if (sgroups == null || sgroups.isEmpty()) return;
// select abbreviations that should be contracted
for (Sgroup sgroup : sgroups) {
if (sgroup.getType() == SgroupType.CtabAbbreviation) {
Boolean expansion = sgroup.getValue(SgroupKey.CtabExpansion);
// abbreviation is displayed as expanded
if (expansion != null && expansion == Boolean.TRUE) continue;
// no or empty label, skip it
if (sgroup.getSubscript() == null || sgroup.getSubscript().isEmpty()) continue;
contractAbbreviation(container, symbolRemap, sgroup);
} else if (sgroup.getType() == SgroupType.CtabMultipleGroup) {
hideMultipleParts(container, sgroup);
}
}
}
private IRenderingElement generateAbbreviationSgroup(Sgroup sgroup) {
String label = sgroup.getSubscript();
// already handled by symbol remapping
if (sgroup.getBonds().size() > 0 || label == null || label.isEmpty()) {
return new ElementGroup();
}
// we're showing a label where there were no atoms before, we put it in the
// middle of all of those which were hidden
final Point2d labelCoords = GeometryUtil.get2DCenter(sgroup.getAtoms());
ElementGroup group = new ElementGroup();
for (Shape outline :
atomGenerator
.generatePseudoSymbol(label, HydrogenPosition.Right)
.resize(1 / scale, 1 / -scale)
.getOutlines()) group.add(GeneralPath.shapeOf(outline, foreground));
return MarkedElement.markupAtom(group, null);
}