public static IChemModel readFromFileReader(final URL fileURL,
final String url, final String type,
final AbstractJChemPaintPanel panel) throws CDKException {
IChemModel chemModel = null;
WaitDialog.showDialog();
// InChI workaround - guessing for InChI results into an INChIReader
// (this does not work, we'd need an INChIPlainTextReader..)
// Instead here we use STDInChIReader, to be consistent throughout JCP
// using the nestedVm based classes.
try {
ISimpleChemObjectReader cor = null;
if (url.endsWith("txt")) {
// chemModel = StdInChIReader.readInChI(fileURL);
} else {
cor = FileHandler.createReader(fileURL, url, type);
chemModel = JChemPaint.getChemModelFromReader(cor, panel);
}
boolean avoidOverlap = true;
if (cor instanceof RGroupQueryReader) {
avoidOverlap = false;
}
JChemPaint.cleanUpChemModel(chemModel, avoidOverlap, panel);
} finally {
WaitDialog.hideDialog();
}
return chemModel;
}
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
}
}
}
}