/**
* Read an IChemModel from a given file.
*
* @param file
* @param type
* @param panel
* @return
* @throws CDKException
* @throws FileNotFoundException
*/
public static IChemModel readFromFile(final File file, final String type,
final AbstractJChemPaintPanel panel) throws CDKException,
FileNotFoundException {
final String url = file.toURI().toString();
ISimpleChemObjectReader cor = null;
try {
cor = FileHandler.createReader(file.toURI().toURL(), url, type);
} catch (final MalformedURLException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
if (cor instanceof CMLReader) {
cor.setReader(new FileInputStream(file)); // hack
} else {
cor.setReader(new FileReader(file)); // hack
}
final IChemModel chemModel = JChemPaint.getChemModelFromReader(cor,
panel);
boolean avoidOverlap = true;
if (cor instanceof RGroupQueryReader) {
avoidOverlap = false;
}
JChemPaint.cleanUpChemModel(chemModel, avoidOverlap, panel);
return chemModel;
}
/** Returns true if another IMolecule can be read. */
public boolean hasNext() {
if (!nextAvailableIsKnown) {
hasNext = false;
// now try to parse the next Molecule
try {
if ((currentLine = input.readLine()) != null) {
currentFormat = (IChemFormat) MDLFormat.getInstance();
StringBuffer buffer = new StringBuffer();
while (currentLine != null && !currentLine.equals("M END")) {
// still in a molecule
buffer.append(currentLine);
buffer.append(System.getProperty("line.separator"));
currentLine = input.readLine();
// do MDL molfile version checking
if (currentLine.contains("V2000") || currentLine.contains("v2000")) {
currentFormat = (IChemFormat) MDLV2000Format.getInstance();
} else if (currentLine.contains("V3000") || currentLine.contains("v3000")) {
currentFormat = (IChemFormat) MDLV3000Format.getInstance();
}
}
buffer.append(currentLine);
buffer.append(System.getProperty("line.separator"));
logger.debug("MDL file part read: ", buffer);
ISimpleChemObjectReader reader = factory.createReader(currentFormat);
reader.setReader(new StringReader(buffer.toString()));
if (currentFormat instanceof MDLV2000Format) {
reader.addChemObjectIOListener(this);
((MDLV2000Reader) reader).customizeJob();
}
nextMolecule = (IMolecule) reader.read(builder.newInstance(IMolecule.class));
// note that a molecule may have 0 atoms, but still
// be useful (by having SD tags for example), so just
// check for null'ness rather than atom count
hasNext = nextMolecule != null;
// now read the data part
currentLine = input.readLine();
readDataBlockInto(nextMolecule);
} else {
hasNext = false;
}
} catch (Exception exception) {
logger.error("Error while reading next molecule: " + exception.getMessage());
logger.debug(exception);
hasNext = false;
}
if (!hasNext) nextMolecule = null;
nextAvailableIsKnown = true;
}
return hasNext;
}