/**
* Identify a set of modifications in a structure.
*
* @param structure query {@link Structure}.
* @param potentialModifications query {@link ProteinModification}s.
*/
public void identify(
final Structure structure, final Set<ProteinModification> potentialModifications) {
if (structure == null) {
throw new IllegalArgumentException("Null structure.");
}
identify(structure.getChains(), potentialModifications);
}
public static void main(String[] args) {
try {
FileParsingParameters params = new FileParsingParameters();
params.setParseSecStruc(true);
AtomCache cache = new AtomCache();
cache.setFileParsingParams(params);
Structure s = cache.getStructure("4hhb");
for (Chain c : s.getChains()) {
for (Group g : c.getAtomGroups()) {
if (g instanceof AminoAcid) {
AminoAcid aa = (AminoAcid) g;
Map<String, String> sec = aa.getSecStruc();
System.out.println(
c.getChainID()
+ " "
+ g.getResidueNumber()
+ " "
+ g.getPDBName()
+ " "
+ " "
+ sec);
}
}
}
} catch (Exception e) {
e.printStackTrace();
}
}