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;
}
/** Load all {@link ChemComp} definitions into memory. */
private void loadAllChemComps() {
String fileName = getLocalFileName();
System.out.println("loading " + fileName);
InputStreamProvider isp = new InputStreamProvider();
try {
InputStream inStream = isp.getInputStream(fileName);
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);
parser.parse(new BufferedReader(new InputStreamReader(inStream)));
dict = consumer.getDictionary();
} catch (Exception e) {
e.printStackTrace();
}
}
