/**
* Sets the given cml. Does not update other fields like for example smiles
*
* @param cml
*/
public void setCML(String cml) {
InputStream inputStream = new ByteArrayInputStream(cml.getBytes());
CMLReader cmlReader = new CMLReader(inputStream);
try {
IChemFile readFile = (IChemFile) cmlReader.read(new ChemFile());
setAtomContainer((AtomContainer) ChemFileManipulator.getAllAtomContainers(readFile).get(0));
} catch (CDKException e) {
throw new RuntimeException("failed to read atomContainer", e);
}
}
/**
* Creates a new DBMolecule that is an exact copy of the given instance including the same id.
*
* @param dBMolecule
*/
public DBMolecule(DBMolecule dBMolecule) {
super(dBMolecule);
setAtomContainer(dBMolecule.getMolecule());
fingerPrint = (BitSet) dBMolecule.getFingerPrint().clone();
persistedFingerPrint = makePersistedFingerPrint(fingerPrint);
smiles = dBMolecule.toSMILES();
annotations = new ArrayList<Annotation>(dBMolecule.getAnnotations());
}
public IAtomContainer getAtomContainer() {
if (atomContainer == null) {
InputStream in = FileStoreKeeper.FILE_STORE.retrieve(fileStoreKey);
CMLReader cmlReader = new CMLReader(in);
try {
IChemFile readFile = (IChemFile) cmlReader.read(new ChemFile());
setAtomContainer((AtomContainer) ChemFileManipulator.getAllAtomContainers(readFile).get(0));
} catch (CDKException e) {
throw new RuntimeException("failed to read atomContainer", e);
}
}
return atomContainer;
}
public DBMolecule(String name, ICDKMolecule cdkMolecule) throws BioclipseException {
super();
this.name = name;
try {
fingerPrint =
cdkMolecule.getFingerprint(
net.bioclipse.core.domain.IMolecule.Property.USE_CACHED_OR_CALCULATED);
} catch (BioclipseException e) {
logger.error("Could not create fingerprint for molecule", e);
}
persistedFingerPrint = makePersistedFingerPrint(fingerPrint);
setAtomContainer(cdkMolecule.getAtomContainer());
smiles = "";
annotations = new ArrayList<Annotation>();
}