public ChemComp getChemComp(String recordName) {
String name = recordName.toUpperCase().trim();
InputStream inStream = this.getClass().getResourceAsStream("/chemcomp/" + name + ".cif.gz");
if (inStream == null) {
// System.out.println("Could not find chem comp: " + name + " ... using generic Chem Comp");
// could not find the chem comp definition for this in the jar file
logger.debug("Getting empty chem comp for " + recordName);
ChemComp cc = getEmptyChemComp();
cc.setId(name);
return cc;
}
MMcifParser parser = new SimpleMMcifParser();
ChemCompConsumer consumer = new ChemCompConsumer();
// The Consumer builds up the BioJava - structure object.
// you could also hook in your own and build up you own data model.
parser.addMMcifConsumer(consumer);
try {
parser.parse(new BufferedReader(new InputStreamReader(new GZIPInputStream(inStream))));
ChemicalComponentDictionary dict = consumer.getDictionary();
ChemComp chemComp = dict.getChemComp(name);
return chemComp;
} catch (IOException e) {
e.printStackTrace();
}
logger.warn("Problem when loading chem comp " + name);
ChemComp cc = getEmptyChemComp();
cc.setId(name);
return cc;
}
/** {@inheritDoc} */
public ChemComp getChemComp(String recordName) {
while (loading.get()) {
// another thread is still initializing the definitions
try {
// wait half a second
Thread.sleep(500);
} catch (InterruptedException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
}
return dict.getChemComp(recordName);
}
