public IRenderingElement generate(IAtomContainer ac, RendererModel model) {
if (generators == null) return EMPTY_ELEMENT;
if (use) {
ElementGroup group = new ElementGroup();
for (IGenerator generator : generators) {
group.add(generator.generate(ac, model));
}
return group;
} else return EMPTY_ELEMENT;
}
private IRenderingElement generate(IAtomContainer molecule, RendererModel model, int atomNum)
throws CDKException {
// tag the atom and bond ids
String molId = molecule.getProperty(MarkedElement.ID_KEY);
if (molId != null) {
int atomId = 0, bondid = 0;
for (IAtom atom : molecule.atoms())
setIfMissing(atom, MarkedElement.ID_KEY, molId + "atm" + ++atomId);
for (IBond bond : molecule.bonds())
setIfMissing(bond, MarkedElement.ID_KEY, molId + "bnd" + ++bondid);
}
if (annotateAtomNum) {
for (IAtom atom : molecule.atoms()) {
if (atom.getProperty(StandardGenerator.ANNOTATION_LABEL) != null)
throw new UnsupportedOperationException("Multiple annotation labels are not supported.");
atom.setProperty(StandardGenerator.ANNOTATION_LABEL, Integer.toString(atomNum++));
}
} else if (annotateAtomVal) {
for (IAtom atom : molecule.atoms()) {
if (atom.getProperty(StandardGenerator.ANNOTATION_LABEL) != null)
throw new UnsupportedOperationException("Multiple annotation labels are not supported.");
atom.setProperty(
StandardGenerator.ANNOTATION_LABEL, atom.getProperty(CDKConstants.COMMENT));
}
} else if (annotateAtomMap) {
for (IAtom atom : molecule.atoms()) {
if (atom.getProperty(StandardGenerator.ANNOTATION_LABEL) != null)
throw new UnsupportedOperationException("Multiple annotation labels are not supported.");
int mapidx = accessAtomMap(atom);
if (mapidx > 0) {
atom.setProperty(StandardGenerator.ANNOTATION_LABEL, Integer.toString(mapidx));
}
}
}
ElementGroup grp = new ElementGroup();
for (IGenerator<IAtomContainer> gen : gens) grp.add(gen.generate(molecule, model));
// cleanup
if (annotateAtomNum || annotateAtomMap) {
for (IAtom atom : molecule.atoms()) {
atom.removeProperty(StandardGenerator.ANNOTATION_LABEL);
}
}
return grp;
}
/**
* Create a depiction generator that will render atom labels using the specified AWT font.
*
* @param font the font to use to display
*/
public DepictionGenerator(Font font) {
gens.add(new BasicSceneGenerator());
gens.add(new StandardGenerator(this.font = font));
for (IGenerator<IAtomContainer> gen : gens) {
for (IGeneratorParameter<?> param : gen.getParameters()) {
params.put(param.getClass(), param);
}
}
for (IGeneratorParameter<?> param : new RendererModel().getRenderingParameters()) {
params.put(param.getClass(), param);
}
// default margin and separation is automatic
// since it depends on raster (px) vs vector (mm)
setParam(BasicSceneGenerator.Margin.class, AUTOMATIC);
setParam(RendererModel.Padding.class, AUTOMATIC);
}