@Override
public IAtomContainer getStructure(ChemSpiderIdentifier identifier) {
try {
StringPreference key = ServicePreferences.getInstance().getPreference("CHEM_SPIDER_KEY");
if (key.get().isEmpty()) {
System.err.println("No ChemSpider key available: please input the key via preferences!");
return BUILDER.newInstance(IAtomContainer.class);
}
CompoundInfo info =
service.getCompoundInfo(Integer.parseInt(identifier.getAccession()), key.get());
InChIGeneratorFactory inchiFactory = InChIGeneratorFactory.getInstance();
InChIToStructure inchi2structure = inchiFactory.getInChIToStructure(info.getInChI(), BUILDER);
return inchi2structure.getAtomContainer();
} catch (CDKException e) {
e
.printStackTrace(); // To change body of catch statement use File | Settings | File
// Templates.
} catch (RemoteException e) {
e
.printStackTrace(); // To change body of catch statement use File | Settings | File
// Templates.
}
return BUILDER.newInstance(IAtomContainer.class);
}
private static String nextAccession() {
StringPreference format =
ResourcePreferences.getInstance().getPreference("BASIC_PROT_ID_FORMAT");
IncrementalPreference ticker =
ResourcePreferences.getInstance().getPreference("BASIC_GENE_ID_TICK");
return String.format(format.get(), ticker.get());
}