private static void replaceReferencesWithClones(final IChemModel chemModel)
throws CDKException {
// we make references in products/reactants clones, since same compounds
// in different reactions need separate layout (different positions etc)
if (chemModel.getReactionSet() != null) {
for (final IReaction reaction : chemModel.getReactionSet()
.reactions()) {
int i = 0;
final IAtomContainerSet products = reaction.getProducts();
for (final IAtomContainer product : products.atomContainers()) {
try {
products.replaceAtomContainer(i, product.clone());
} catch (final CloneNotSupportedException e) {
}
i++;
}
i = 0;
final IAtomContainerSet reactants = reaction.getReactants();
for (final IAtomContainer reactant : reactants.atomContainers()) {
try {
reactants.replaceAtomContainer(i, reactant.clone());
} catch (final CloneNotSupportedException e) {
}
i++;
}
}
}
}
/**
* Takes an object which subclasses IChemObject, e.g.Molecule, and will read this (from file,
* database, internet etc). If the specific implementation does not support a specific IChemObject
* it will throw an Exception.
*
* @param object The object that subclasses IChemObject
* @return The IChemObject read
* @exception CDKException
*/
public IChemObject read(IChemObject object) throws CDKException {
if (object instanceof IReaction) {
return (IChemObject) readReaction(object.getBuilder());
} else if (object instanceof IReactionSet) {
IReactionSet reactionSet = object.getBuilder().newReactionSet();
reactionSet.addReaction(readReaction(object.getBuilder()));
return reactionSet;
} else if (object instanceof IChemModel) {
IChemModel model = object.getBuilder().newChemModel();
IReactionSet reactionSet = object.getBuilder().newReactionSet();
reactionSet.addReaction(readReaction(object.getBuilder()));
model.setReactionSet(reactionSet);
return model;
} else if (object instanceof IChemFile) {
IChemFile chemFile = object.getBuilder().newChemFile();
IChemSequence sequence = object.getBuilder().newChemSequence();
sequence.addChemModel((IChemModel) read(object.getBuilder().newChemModel()));
chemFile.addChemSequence(sequence);
return chemFile;
} else {
throw new CDKException(
"Only supported are Reaction and ChemModel, and not "
+ object.getClass().getName()
+ ".");
}
}
public static IChemModel emptyModel() {
final IChemModel chemModel = DefaultChemObjectBuilder.getInstance()
.newInstance(IChemModel.class);
chemModel.setMoleculeSet(chemModel.getBuilder().newInstance(
IAtomContainerSet.class));
chemModel.getMoleculeSet().addAtomContainer(
chemModel.getBuilder().newInstance(IAtomContainer.class));
return chemModel;
}
private IChemModel readChemModel(IChemModel chemModel) throws CDKException {
IAtomContainerSet setOfMolecules = chemModel.getMoleculeSet();
if (setOfMolecules == null) {
setOfMolecules = chemModel.getBuilder().newInstance(IAtomContainerSet.class);
}
IAtomContainer m = readAtomContainer(chemModel.getBuilder().newInstance(IAtomContainer.class));
if (m != null && m instanceof IAtomContainer) {
setOfMolecules.addAtomContainer((IAtomContainer) m);
}
chemModel.setMoleculeSet(setOfMolecules);
return chemModel;
}
@TestMethod("testReadReactions1")
public <T extends IChemObject> T read(T object) throws CDKException {
if (object instanceof IReaction) {
return (T) readReaction(object.getBuilder());
} else if (object instanceof IChemModel) {
IChemModel model = object.getBuilder().newInstance(IChemModel.class);
IReactionSet reactionSet = object.getBuilder().newInstance(IReactionSet.class);
reactionSet.addReaction(readReaction(object.getBuilder()));
model.setReactionSet(reactionSet);
return (T) model;
} else {
throw new CDKException(
"Only supported are Reaction and ChemModel, and not "
+ object.getClass().getName()
+ ".");
}
}
private IChemFile readChemFile() throws CDKException {
IChemSequence seq = file.getBuilder().newChemSequence();
IChemModel model = file.getBuilder().newChemModel();
IMoleculeSet containerSet = file.getBuilder().newMoleculeSet();
IMolecule container = file.getBuilder().newMolecule();
int lineNumber = 0;
try {
String line = input.readLine();
while (input.ready() && line != null) {
logger.debug((lineNumber++) + ": ", line);
String command = null;
if (isCommand(line)) {
command = getCommand(line);
int lineCount = getContentLinesCount(line);
if ("ATOMS".equals(command)) {
processAtomsBlock(lineCount, container);
} else if ("BONDS".equals(command)) {
processBondsBlock(lineCount, container);
} else if ("IDENT".equals(command)) {
processIdentBlock(lineCount, container);
} else if ("NAME".equals(command)) {
processNameBlock(lineCount, container);
} else {
// skip lines
logger.warn("Dropping block: ", command);
for (int i = 0; i < lineCount; i++) input.readLine();
}
} else {
logger.warn("Unexpected content at line: ", lineNumber);
}
line = input.readLine();
}
containerSet.addAtomContainer(container);
model.setMoleculeSet(containerSet);
seq.addChemModel(model);
file.addChemSequence(seq);
} catch (Exception exception) {
String message = "Error while parsing CTX file: " + exception.getMessage();
logger.error(message);
logger.debug(exception);
throw new CDKException(message, exception);
}
return file;
}
private static void removeDuplicateAtomContainers(final IChemModel chemModel) {
// we remove molecules which are in AtomContainerSet as well as in a
// reaction
final IReactionSet reactionSet = chemModel.getReactionSet();
final IAtomContainerSet moleculeSet = chemModel.getMoleculeSet();
if (reactionSet != null && moleculeSet != null) {
final List<IAtomContainer> aclist = ReactionSetManipulator
.getAllAtomContainers(reactionSet);
for (int i = moleculeSet.getAtomContainerCount() - 1; i >= 0; i--) {
for (int k = 0; k < aclist.size(); k++) {
final String label = moleculeSet.getAtomContainer(i)
.getID();
if (aclist.get(k).getID().equals(label)) {
chemModel.getMoleculeSet().removeAtomContainer(i);
break;
}
}
}
}
}
private static void setReactionIDs(final IChemModel chemModel) {
// we give all reactions an ID, in case they have none
// IDs are needed for handling in JCP
final IReactionSet reactionSet = chemModel.getReactionSet();
if (reactionSet != null) {
int i = 0;
for (final IReaction reaction : reactionSet.reactions()) {
if (reaction.getID() == null) {
reaction.setID("Reaction " + ++i);
}
}
}
}
private IReaction checkForXReactionFile(IChemFile chemFile, int numberOfReactions) {
Assert.assertNotNull(chemFile);
Assert.assertEquals(chemFile.getChemSequenceCount(), 1);
org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
Assert.assertNotNull(seq);
Assert.assertEquals(seq.getChemModelCount(), 1);
org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
Assert.assertNotNull(model);
IReactionSet reactionSet = model.getReactionSet();
Assert.assertNotNull(reactionSet);
Assert.assertEquals(reactionSet.getReactionCount(), numberOfReactions);
IReaction reaction = null;
for (int i = 0; i < numberOfReactions; i++) {
reaction = reactionSet.getReaction(i);
Assert.assertNotNull(reaction);
}
return reaction;
}
private IMolecule checkForXMoleculeFile(IChemFile chemFile, int numberOfMolecules) {
Assert.assertNotNull(chemFile);
Assert.assertEquals(chemFile.getChemSequenceCount(), 1);
org.openscience.cdk.interfaces.IChemSequence seq = chemFile.getChemSequence(0);
Assert.assertNotNull(seq);
Assert.assertEquals(seq.getChemModelCount(), 1);
org.openscience.cdk.interfaces.IChemModel model = seq.getChemModel(0);
Assert.assertNotNull(model);
org.openscience.cdk.interfaces.IMoleculeSet moleculeSet = model.getMoleculeSet();
Assert.assertNotNull(moleculeSet);
Assert.assertEquals(moleculeSet.getMoleculeCount(), numberOfMolecules);
IMolecule mol = null;
for (int i = 0; i < numberOfMolecules; i++) {
mol = moleculeSet.getMolecule(i);
Assert.assertNotNull(mol);
}
return mol;
}
/**
* 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
}
}
}
}
public static JChemPaintPanel showInstance(final IChemModel chemModel,
final String title, final boolean debug) {
final JFrame f = new JFrame(title + " - JChemPaint");
chemModel.setID(title);
f.addWindowListener(new JChemPaintPanel.AppCloser());
f.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE);
final JChemPaintPanel p = new JChemPaintPanel(chemModel,
GUI_APPLICATION, debug, null, new ArrayList<String>());
p.updateStatusBar();
f.setPreferredSize(new Dimension(800, 494)); // 1.618
f.add(p);
f.pack();
final Point point = GraphicsEnvironment.getLocalGraphicsEnvironment()
.getCenterPoint();
final int w2 = f.getWidth() / 2;
final int h2 = f.getHeight() / 2;
f.setLocation(point.x - w2, point.y - h2);
f.setVisible(true);
frameList.add(f);
return p;
}
private static void removeEmptyAtomContainers(final IChemModel chemModel) {
final IAtomContainerSet moleculeSet = chemModel.getMoleculeSet();
if (moleculeSet != null && moleculeSet.getAtomContainerCount() == 0) {
chemModel.setMoleculeSet(null);
}
}
/**
* 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();
}
/**
* Read a ChemFile from a file in MDL SDF format.
*
* @return The ChemFile that was read from the MDL file.
*/
private IChemFile readChemFile(IChemFile chemFile) throws CDKException {
IChemSequence chemSequence = chemFile.getBuilder().newInstance(IChemSequence.class);
IChemModel chemModel = chemFile.getBuilder().newInstance(IChemModel.class);
IAtomContainerSet setOfMolecules = chemFile.getBuilder().newInstance(IAtomContainerSet.class);
IAtomContainer m = readAtomContainer(chemFile.getBuilder().newInstance(IAtomContainer.class));
if (m != null && m instanceof IAtomContainer) {
setOfMolecules.addAtomContainer((IAtomContainer) m);
}
chemModel.setMoleculeSet(setOfMolecules);
chemSequence.addChemModel(chemModel);
setOfMolecules = chemFile.getBuilder().newInstance(IAtomContainerSet.class);
chemModel = chemFile.getBuilder().newInstance(IChemModel.class);
String str;
try {
String line;
while ((line = input.readLine()) != null) {
logger.debug("line: ", line);
// apparently, this is a SDF file, continue with
// reading mol files
str = new String(line);
if (str.equals("$$$$")) {
m = readAtomContainer(chemFile.getBuilder().newInstance(IAtomContainer.class));
if (m != null && m instanceof IAtomContainer) {
setOfMolecules.addAtomContainer((IAtomContainer) m);
chemModel.setMoleculeSet(setOfMolecules);
chemSequence.addChemModel(chemModel);
setOfMolecules = chemFile.getBuilder().newInstance(IAtomContainerSet.class);
chemModel = chemFile.getBuilder().newInstance(IChemModel.class);
}
} else {
// here the stuff between 'M END' and '$$$$'
if (m != null) {
// ok, the first lines should start with '>'
String fieldName = null;
if (str.startsWith("> ")) {
// ok, should extract the field name
str.substring(2); // String content =
int index = str.indexOf("<");
if (index != -1) {
int index2 = str.substring(index).indexOf(">");
if (index2 != -1) {
fieldName = str.substring(index + 1, index + index2);
}
}
}
if (line == null) {
throw new CDKException("Expecting data line here, but found null!");
}
StringBuilder data = new StringBuilder();
int dataLineCount = 0;
boolean lineIsContinued = false;
while ((line = input.readLine()) != null) {
if (line.equals(" ") && dataLineCount == 0) {
// apparently a file can have a field whose value is a single space. Moronic
// we check for it *before* trimming it. ideally we should check for any length
// of whitespace
// In adition some SD files have the blank line after the value line contain
// a space, rather than being a true blank line. So we only store a blank value
// line if it's the first line after the key line
data.append(line);
lineIsContinued = false;
dataLineCount++;
if (!lineIsContinued && dataLineCount > 1)
data.append(System.getProperty("line.separator"));
continue;
}
line = line.trim();
if (line.length() == 0) break;
if (line.equals("$$$$")) {
logger.error("Expecting data line here, but found end of molecule: ", line);
break;
}
logger.debug("data line: ", line);
lineIsContinued = false; // reset property
dataLineCount++;
// preserve newlines, unless the line is exactly 80 chars;
// in that case it is assumed to continue on the next line.
// See MDL documentation.
if (!lineIsContinued && dataLineCount > 1)
data.append(System.getProperty("line.separator"));
// add the data line
data.append(line);
// check if the line will be continued on the next line
if (line.length() == 80) lineIsContinued = true;
}
if (fieldName != null) {
logger.info("fieldName, data: ", fieldName, ", ", data);
m.setProperty(fieldName, data.toString());
}
}
}
}
} catch (CDKException cdkexc) {
throw cdkexc;
} catch (Exception exception) {
String error = "Error while parsing SDF";
logger.error(error);
logger.debug(exception);
throw new CDKException(error, exception);
}
try {
input.close();
} catch (Exception exc) {
String error = "Error while closing file: " + exc.getMessage();
logger.error(error);
throw new CDKException(error, exc);
}
chemFile.addChemSequence(chemSequence);
return chemFile;
}
