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); }