/**
* Procedure required by the CDOInterface. This function is only supposed to be called by the JCFL
* library
*/
public void endObject(String objectType) {
logger.debug("END: " + objectType);
if (objectType.equals("Molecule")) {
eventReader.fireFrameRead();
clearData();
} else if (objectType.equals("Atom")) {
currentMolecule.addAtom(currentAtom);
} else if (objectType.equals("Bond")) {
logger.debug("Bond(" + bond_id + "): " + bond_a1 + ", " + bond_a2 + ", " + bond_order);
if (bond_a1 > currentMolecule.getAtomCount() || bond_a2 > currentMolecule.getAtomCount()) {
logger.error(
"Cannot add bond between at least one non-existant atom: "
+ bond_a1
+ " and "
+ bond_a2);
} else {
IAtom a1 = currentMolecule.getAtom(bond_a1);
IAtom a2 = currentMolecule.getAtom(bond_a2);
IBond b = builder.newBond(a1, a2, bond_order);
if (bond_id != null) b.setID(bond_id);
if (bond_stereo != -99) {
b.setStereo(bond_stereo);
}
currentMolecule.addBond(b);
}
}
}
public Object clone() throws CloneNotSupportedException {
Object clone = null;
try {
clone = super.clone();
} catch (Exception exception) {
logger.error("Could not clone DebugAtomContainer: " + exception.getMessage(), exception);
logger.debug(exception);
}
return clone;
}
/**
* Procedure required by the CDOInterface. This function is only supposed to be called by the JCFL
* library
*/
public void startObject(String objectType) {
logger.debug("START:" + objectType);
if (objectType.equals("Molecule")) {
currentMolecule = builder.newAtomContainer();
atomEnumeration = new Hashtable<String, Integer>();
} else if (objectType.equals("Atom")) {
currentAtom = builder.newAtom("H");
logger.debug("Atom # " + numberOfAtoms);
numberOfAtoms++;
} else if (objectType.equals("Bond")) {
bond_id = null;
bond_stereo = -99;
}
}
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;
}
public boolean getFlag(int flag_type) {
logger.debug("Setting flag: ", flag_type + "=" + super.getFlag(flag_type));
return super.getFlag(flag_type);
}
public void setID(String identifier) {
logger.debug("Setting ID: ", identifier);
super.setID(identifier);
}
public void setFlag(int flag_type, boolean flag_value) {
logger.debug("Setting flag: ", flag_type + "=" + flag_value);
super.setFlag(flag_type, flag_value);
}
public boolean contains(IBond bond) {
logger.debug("Contains bond: ", bond);
return super.contains(bond);
}
public String getID() {
logger.debug("Getting ID: ", super.getID());
return super.getID();
}
public boolean[] getFlags() {
logger.debug("Getting flags:", super.getFlags().length);
return super.getFlags();
}
public boolean contains(ISingleElectron ec) {
logger.debug("Contains single electron: ", ec);
return super.contains(ec);
}
public void notifyChanged(IChemObjectChangeEvent evt) {
logger.debug("Notifying changed event: ", evt);
super.notifyChanged(evt);
}
public void addAtomParity(IAtomParity parity) {
logger.debug("Adding atom parity: ", parity);
super.addAtomParity(parity);
}
public void removeListener(IChemObjectListener col) {
logger.debug("Removing listener: ", col);
super.removeListener(col);
}
public void notifyChanged() {
logger.debug("Notifying changed");
super.notifyChanged();
}
public int getListenerCount() {
logger.debug("Getting listener count: ", super.getListenerCount());
return super.getListenerCount();
}
public void addListener(IChemObjectListener col) {
logger.debug("Adding listener: ", col);
super.addListener(col);
}
public boolean contains(IElectronContainer electronContainer) {
logger.debug("Contains electron container: ", electronContainer);
return super.contains(electronContainer);
}
public void setProperties(Map<Object, Object> properties) {
logger.debug("Setting properties: ", properties);
super.setProperties(properties);
}
public void setAtoms(IAtom[] atoms) {
logger.debug("Setting atoms: ", atoms.length);
super.setAtoms(atoms);
}
public void setFlags(boolean[] flagsNew) {
logger.debug("Setting flags:", flagsNew.length);
super.setFlags(flagsNew);
}
public IAtom getAtom(int number) {
logger.debug("Getting atom at: ", number);
return super.getAtom(number);
}
public void setProperty(Object description, Object property) {
logger.debug("Setting property: ", description + "=" + property);
super.setProperty(description, property);
}
public boolean contains(ILonePair ec) {
logger.debug("Contains lone pair: ", ec);
return super.contains(ec);
}
public IAtomParity getAtomParity(IAtom atom) {
logger.debug("Getting atom parity: ", atom);
return super.getAtomParity(atom);
}
public void removeProperty(Object description) {
logger.debug("Removing property: ", description);
super.removeProperty(description);
}
public void setAtom(int number, IAtom atom) {
logger.debug("Setting atom at: pos=" + number, " atom=" + atom);
super.setAtom(number, atom);
}
public Object getProperty(Object description) {
logger.debug("Getting property: ", description + "=" + super.getProperty(description));
return super.getProperty(description);
}
public IBond getBond(int number) {
logger.debug("Getting bond at: ", number);
return super.getBond(number);
}
public Map<Object, Object> getProperties() {
logger.debug("Getting properties");
return super.getProperties();
}