/**
* Clean up chemical model ,removing duplicates empty molecules etc
*
* @param chemModel
* @param avoidOverlap
* @throws CDKException
*/
public static void cleanUpChemModel(final IChemModel chemModel,
final boolean avoidOverlap, final AbstractJChemPaintPanel panel)
throws CDKException {
JChemPaint.setReactionIDs(chemModel);
JChemPaint.replaceReferencesWithClones(chemModel);
// check the model is not completely empty
if (ChemModelManipulator.getBondCount(chemModel) == 0
&& ChemModelManipulator.getAtomCount(chemModel) == 0) {
throw new CDKException(
"Structure does not have bonds or atoms. Cannot depict structure.");
}
JChemPaint.removeDuplicateAtomContainers(chemModel);
JChemPaint.checkCoordinates(chemModel);
JChemPaint.removeEmptyAtomContainers(chemModel);
if (avoidOverlap) {
try {
ControllerHub.avoidOverlap(chemModel);
} catch (final Exception e) {
JOptionPane.showMessageDialog(panel,
GT._("Structure could not be generated"));
throw new CDKException("Cannot depict structure");
}
}
// We update implicit Hs in any case
final CDKAtomTypeMatcher matcher = CDKAtomTypeMatcher
.getInstance(chemModel.getBuilder());
for (final IAtomContainer container : ChemModelManipulator
.getAllAtomContainers(chemModel)) {
for (final IAtom atom : container.atoms()) {
if (!(atom instanceof IPseudoAtom)) {
try {
final IAtomType type = matcher.findMatchingAtomType(
container, atom);
if (type != null
&& type.getFormalNeighbourCount() != null) {
final int connectedAtomCount = container
.getConnectedAtomsCount(atom);
atom.setImplicitHydrogenCount(type
.getFormalNeighbourCount()
- connectedAtomCount);
}
} catch (final CDKException e) {
e.printStackTrace();
}
}
}
}
}
private static void checkCoordinates(final IChemModel chemModel)
throws CDKException {
for (final IAtomContainer next : ChemModelManipulator
.getAllAtomContainers(chemModel)) {
if (!GeometryTools.get2DCoordinateCoverage(next).equals(
GeometryTools.CoordinateCoverage.FULL)) {
final String error = GT._("Not all atoms have 2D coordinates."
+ " JCP can only show full 2D specified structures."
+ " Shall we lay out the structure?");
final int answer = JOptionPane.showConfirmDialog(null, error,
"No 2D coordinates", JOptionPane.YES_NO_OPTION);
if (answer == JOptionPane.NO_OPTION) {
throw new CDKException(
GT._("Cannot display without 2D coordinates"));
} else {
// CreateCoordinatesForFileDialog frame =
// new CreateCoordinatesForFileDialog(chemModel);
// frame.pack();
// frame.show();
WaitDialog.showDialog();
final List<IAtomContainer> acs = ChemModelManipulator
.getAllAtomContainers(chemModel);
generate2dCoordinates(acs);
WaitDialog.hideDialog();
return;
}
}
}
/*
* Add implicit hydrogens (in ControllerParameters,
* autoUpdateImplicitHydrogens is true by default, so we need to do that
* anyway)
*/
final CDKHydrogenAdder hAdder = CDKHydrogenAdder.getInstance(chemModel
.getBuilder());
for (final IAtomContainer molecule : ChemModelManipulator
.getAllAtomContainers(chemModel)) {
if (molecule != null) {
try {
hAdder.addImplicitHydrogens(molecule);
} catch (final CDKException e) {
// do nothing
}
}
}
}