public void removeProperty(Object description) {
logger.debug("Removing property: ", description);
super.removeProperty(description);
}
/**
* Returns an IChemModel, using the reader provided (picked).
*
* @param cor
* @param panel
* @return
* @throws CDKException
*/
public static IChemModel getChemModelFromReader(
final ISimpleChemObjectReader cor,
final AbstractJChemPaintPanel panel) throws CDKException {
panel.get2DHub().setRGroupHandler(null);
String error = null;
ChemModel chemModel = null;
IChemFile chemFile = null;
if (cor.accepts(IChemFile.class) && chemModel == null) {
// try to read a ChemFile
try {
chemFile = (IChemFile) cor.read((IChemObject) new ChemFile());
if (chemFile == null) {
error = "The object chemFile was empty unexpectedly!";
}
} catch (final Exception exception) {
error = "Error while reading file: " + exception.getMessage();
exception.printStackTrace();
}
}
if (error != null) {
throw new CDKException(error);
}
if (chemModel == null && chemFile != null) {
chemModel = (ChemModel) chemFile.getChemSequence(0).getChemModel(0);
}
if (cor.accepts(ChemModel.class) && chemModel == null) {
// try to read a ChemModel
try {
chemModel = (ChemModel) cor.read((IChemObject) new ChemModel());
if (chemModel == null) {
error = "The object chemModel was empty unexpectedly!";
}
} catch (final Exception exception) {
error = "Error while reading file: " + exception.getMessage();
exception.printStackTrace();
}
}
// Smiles reading
if (cor.accepts(AtomContainerSet.class) && chemModel == null) {
// try to read a AtomContainer set
try {
final IAtomContainerSet som = cor.read(new AtomContainerSet());
chemModel = new ChemModel();
chemModel.setMoleculeSet(som);
if (chemModel == null) {
error = "The object chemModel was empty unexpectedly!";
}
} catch (final Exception exception) {
error = "Error while reading file: " + exception.getMessage();
exception.printStackTrace();
}
}
// MDLV3000 reading
if (cor.accepts(AtomContainer.class) && chemModel == null) {
// try to read a AtomContainer
final IAtomContainer mol = cor.read(new AtomContainer());
if (mol != null) {
try {
final IAtomContainerSet newSet = new AtomContainerSet();
newSet.addAtomContainer(mol);
chemModel = new ChemModel();
chemModel.setMoleculeSet(newSet);
if (chemModel == null) {
error = "The object chemModel was empty unexpectedly!";
}
} catch (final Exception exception) {
error = "Error while reading file: "
+ exception.getMessage();
exception.printStackTrace();
}
}
}
// RGroupQuery reading
if (cor.accepts(RGroupQuery.class) && chemModel == null) {
final IRGroupQuery rgroupQuery = cor.read(new RGroupQuery());
if (rgroupQuery != null) {
try {
chemModel = new ChemModel();
final RGroupHandler rgHandler = new RGroupHandler(
rgroupQuery);
panel.get2DHub().setRGroupHandler(rgHandler);
chemModel.setMoleculeSet(rgHandler
.getMoleculeSet(chemModel));
rgHandler.layoutRgroup();
} catch (final Exception exception) {
error = "Error while reading file: "
+ exception.getMessage();
exception.printStackTrace();
}
}
}
if (error != null) {
throw new CDKException(error);
}
if (chemModel == null && chemFile != null) {
chemModel = (ChemModel) chemFile.getChemSequence(0).getChemModel(0);
}
// SmilesParser sets valencies, switch off by default.
if (cor instanceof SMILESReader) {
final IAtomContainer allinone = JChemPaintPanel
.getAllAtomContainersInOne(chemModel);
for (int k = 0; k < allinone.getAtomCount(); k++) {
allinone.getAtom(k).setValency(null);
}
}
return chemModel;
}
public void notifyChanged(IChemObjectChangeEvent evt) {
logger.debug("Notifying changed event: ", evt);
super.notifyChanged(evt);
}
public void setProperty(Object description, Object property) {
logger.debug("Setting property: ", description + "=" + property);
super.setProperty(description, property);
}
public void removeListener(IChemObjectListener col) {
logger.debug("Removing listener: ", col);
super.removeListener(col);
}
public void notifyChanged() {
logger.debug("Notifying changed");
super.notifyChanged();
}
public void setReactionSet(IReactionSet sor) {
logger.debug("Setting setOfReactions: ", sor);
super.setReactionSet(sor);
}
public void addListener(IChemObjectListener col) {
logger.debug("Adding listener: ", col);
super.addListener(col);
}
public void setRingSet(IRingSet ringSet) {
logger.debug("Setting ringSet: ", ringSet);
super.setRingSet(ringSet);
}
public void setCrystal(ICrystal crystal) {
logger.debug("Setting crystal: ", crystal);
super.setCrystal(crystal);
}
public void setMoleculeSet(IMoleculeSet setOfMolecules) {
logger.debug("Setting setOfMolecules: ", setOfMolecules);
super.setMoleculeSet(setOfMolecules);
}
public void setFlags(boolean[] flagsNew) {
logger.debug("Setting flags:", flagsNew.length);
super.setFlags(flagsNew);
}
public void setProperties(Map<Object, Object> properties) {
logger.debug("Setting properties: ", properties);
super.setProperties(properties);
}
public void setFlag(int flag_type, boolean flag_value) {
logger.debug("Setting flag: ", flag_type + "=" + flag_value);
super.setFlag(flag_type, flag_value);
}
public void setID(String identifier) {
logger.debug("Setting ID: ", identifier);
super.setID(identifier);
}