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
}
}
}
}
/**
* 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();
}
}
}
}
}
public void doInit() {
String version = JCPPropertyHandler.getInstance(true).getVersion();
String s1 = "JChemPaint " + version + "\n";
s1 += GT._("An open-source editor for 2D chemical structures.");
String s2 = GT._("An OpenScience project.")+"\n";
s2 += GT._("See 'http://jchempaint.github.com' for more information.");
getContentPane().setLayout(new BorderLayout());
getContentPane().setBackground(Color.white);
JLabel label1 = new JLabel();
try {
JCPPropertyHandler jcpph = JCPPropertyHandler.getInstance(true);
URL url = jcpph.getResource("jcplogo" + JCPAction.imageSuffix);
ImageIcon icon = new ImageIcon(url);
//ImageIcon icon = new ImageIcon(../resources/);
label1 = new JLabel(icon);
} catch (Exception exception) {
logger.error("Cannot add JCP logo: " + exception.getMessage());
logger.debug(exception);
}
label1.setBackground(Color.white);
Border lb = BorderFactory.createLineBorder(Color.white, 5);
JTextArea jtf1 = new JTextArea(s1);
jtf1.setBorder(lb);
jtf1.setEditable(false);
JTextArea jtf2 = new JTextArea(s2);
jtf2.setEditable(false);
jtf2.setBorder(lb);
getContentPane().add("Center", label1);
getContentPane().add("North", jtf1);
getContentPane().add("South", jtf2);
pack();
setVisible(true);
}
public static void showInstance(final File inFile, final String type,
final AbstractJChemPaintPanel jcpPanel, final boolean debug) {
try {
final IChemModel chemModel = JChemPaint.readFromFile(inFile, type,
jcpPanel);
final String name = inFile.getName();
final JChemPaintPanel p = JChemPaint.showInstance(chemModel, name,
debug);
p.setCurrentWorkDirectory(inFile.getParentFile());
p.setLastOpenedFile(inFile);
p.setIsAlreadyAFile(inFile);
} catch (final CDKException ex) {
JOptionPane.showMessageDialog(jcpPanel, ex.getMessage());
return;
} catch (final FileNotFoundException e) {
JOptionPane.showMessageDialog(jcpPanel, GT._("File does not exist")
+ ": " + inFile.getPath());
return;
}
}
public static void showEmptyInstance(final boolean debug) {
final IChemModel chemModel = emptyModel();
showInstance(chemModel, GT._("Untitled") + " " + instancecounter++,
debug);
}
@SuppressWarnings("static-access")
public static void main(String[] args) {
try {
final String vers = System.getProperty("java.version");
final String requiredJVM = "1.5.0";
final Package self = Package
.getPackage("org.openscience.jchempaint");
String version = GT._("Could not determine JCP version");
if (self != null) {
version = JCPPropertyHandler.getInstance(true).getVersion();
}
if (vers.compareTo(requiredJVM) < 0) {
System.err
.println(GT
._("WARNING: JChemPaint {0} must be run with a Java VM version {1} or higher.",
new String[] { version, requiredJVM }));
System.err.println(GT._("Your JVM version is {0}", vers));
System.exit(1);
}
final Options options = new Options();
options.addOption("h", "help", false, GT._("gives this help page"));
options.addOption("v", "version", false,
GT._("gives JChemPaints version number"));
options.addOption("d", "debug", false,
"switches on various debug options");
options.addOption(OptionBuilder.withArgName("property=value")
.hasArg().withValueSeparator()
.withDescription(GT._("supported options are given below"))
.create("D"));
CommandLine line = null;
try {
final CommandLineParser parser = new PosixParser();
line = parser.parse(options, args);
} catch (final UnrecognizedOptionException exception) {
System.err.println(exception.getMessage());
System.exit(-1);
} catch (final ParseException exception) {
System.err.println("Unexpected exception: "
+ exception.toString());
}
if (line.hasOption("v")) {
System.out.println("JChemPaint v." + version + "\n");
System.exit(0);
}
if (line.hasOption("h")) {
System.out.println("JChemPaint v." + version + "\n");
final HelpFormatter formatter = new HelpFormatter();
formatter.printHelp("JChemPaint", options);
// now report on the -D options
System.out.println();
System.out
.println("The -D options are as follows (defaults in parathesis):");
System.out.println(" cdk.debugging [true|false] (false)");
System.out.println(" cdk.debug.stdout [true|false] (false)");
System.out
.println(" user.language [ar|ca|cs|de|en|es|hu|nb|nl|pl|pt|ru|th] (en)");
System.out
.println(" user.language [ar|ca|cs|de|hu|nb|nl|pl|pt_BR|ru|th] (EN)");
System.exit(0);
}
boolean debug = false;
if (line.hasOption("d")) {
debug = true;
}
// Set Look&Feel
final Properties props = JCPPropertyHandler.getInstance(true)
.getJCPProperties();
try {
UIManager.setLookAndFeel(props.getProperty("LookAndFeelClass"));
} catch (final Throwable e) {
final String sys = UIManager.getSystemLookAndFeelClassName();
UIManager.setLookAndFeel(sys);
props.setProperty("LookAndFeelClass", sys);
}
// Language
props.setProperty("General.language",
System.getProperty("user.language", "en"));
// Process command line arguments
String modelFilename = "";
args = line.getArgs();
if (args.length > 0) {
modelFilename = args[0];
final File file = new File(modelFilename);
if (!file.exists()) {
System.err.println(GT._("File does not exist") + ": "
+ modelFilename);
System.exit(-1);
}
showInstance(file, null, null, debug);
} else {
showEmptyInstance(debug);
}
} catch (final Throwable t) {
System.err.println("uncaught exception: " + t);
t.printStackTrace(System.err);
}
}
/**
* Inserts a molecule into the current set, usually from Combobox or Insert
* field, with possible shifting of the existing set.
*
* @param chemPaintPanel
* @param molecule
* @param generateCoordinates
* @param shiftPanel
* @throws CDKException
*/
public static void generateModel(
final AbstractJChemPaintPanel chemPaintPanel,
IAtomContainer molecule, final boolean generateCoordinates,
final boolean shiftPasted) throws CDKException {
if (molecule == null) {
return;
}
final IChemModel chemModel = chemPaintPanel.getChemModel();
IAtomContainerSet moleculeSet = chemModel.getMoleculeSet();
if (moleculeSet == null) {
moleculeSet = new AtomContainerSet();
}
// On copy & paste on top of an existing drawn structure, prevent the
// pasted section to be drawn exactly on top or to far away from the
// original by shifting it to a fixed position next to it.
if (shiftPasted) {
double maxXCurr = Double.NEGATIVE_INFINITY;
double minXPaste = Double.POSITIVE_INFINITY;
for (final IAtomContainer atc : moleculeSet.atomContainers()) {
// Detect the right border of the current structure..
for (final IAtom atom : atc.atoms()) {
if (atom.getPoint2d().x > maxXCurr) {
maxXCurr = atom.getPoint2d().x;
}
}
// Detect the left border of the pasted structure..
for (final IAtom atom : molecule.atoms()) {
if (atom.getPoint2d().x < minXPaste) {
minXPaste = atom.getPoint2d().x;
}
}
}
if (maxXCurr != Double.NEGATIVE_INFINITY
&& minXPaste != Double.POSITIVE_INFINITY) {
// Shift the pasted structure to be nicely next to the existing
// one.
final int MARGIN = 1;
final double SHIFT = maxXCurr - minXPaste;
for (final IAtom atom : molecule.atoms()) {
atom.setPoint2d(new Point2d(atom.getPoint2d().x + MARGIN
+ SHIFT, atom.getPoint2d().y));
}
}
}
if (generateCoordinates) {
// now generate 2D coordinates
final StructureDiagramGenerator sdg = new StructureDiagramGenerator();
sdg.setTemplateHandler(new TemplateHandler(moleculeSet.getBuilder()));
try {
sdg.setMolecule(molecule);
sdg.generateCoordinates(new Vector2d(0, 1));
molecule = sdg.getMolecule();
} catch (final Exception exc) {
JOptionPane.showMessageDialog(chemPaintPanel,
GT._("Structure could not be generated"));
throw new CDKException("Cannot depict structure");
}
}
if (moleculeSet.getAtomContainer(0).getAtomCount() == 0) {
moleculeSet.getAtomContainer(0).add(molecule);
} else {
moleculeSet.addAtomContainer(molecule);
}
final IUndoRedoFactory undoRedoFactory = chemPaintPanel.get2DHub()
.getUndoRedoFactory();
final UndoRedoHandler undoRedoHandler = chemPaintPanel.get2DHub()
.getUndoRedoHandler();
if (undoRedoFactory != null) {
final IUndoRedoable undoredo = undoRedoFactory
.getAddAtomsAndBondsEdit(chemPaintPanel.get2DHub()
.getIChemModel(), molecule, null, "Paste",
chemPaintPanel.get2DHub());
undoRedoHandler.postEdit(undoredo);
}
chemPaintPanel.getChemModel().setMoleculeSet(moleculeSet);
chemPaintPanel.updateUndoRedoControls();
chemPaintPanel.get2DHub().updateView();
}