@Override
public SortedSet<String> getDomainNames(String name) throws IOException, StructureException {
if (name.length() < 4)
throw new IllegalArgumentException("Can't interpret IDs that are shorter than 4 residues!");
if (serializedCache != null) {
if (serializedCache.containsKey(name)) {
return serializedCache.get(name);
}
}
StructureName n = new StructureName(name);
List<ScopDomain> scopDomains = scop.getDomainsForPDB(n.getPdbId());
String chainID = n.getChainId();
if (scopDomains == null || scopDomains.size() == 0) {
SortedSet<String> data = getPDPDomains(n);
cache(name, data);
return data;
} else {
SortedSet<String> r = new TreeSet<String>();
for (ScopDomain d : scopDomains) {
StructureName s = new StructureName(d.getScopId());
if (chainID == null) {
r.add(s.getIdentifier());
} else if (s.getChainId().equalsIgnoreCase(n.getChainId())) {
// SCOP IDS are case insensitive...
r.add(s.getIdentifier());
}
}
cache(name, r);
return r;
}
}
/**
* Returns the representation of a {@link ScopDomain} as a BioJava {@link Structure} object.
*
* @param scopId a SCOP Id
* @param scopDatabase A {@link ScopDatabase} to use
* @return a Structure object
* @throws IOException
* @throws StructureException
*/
public Structure getStructureForDomain(String scopId, ScopDatabase scopDatabase)
throws IOException, StructureException {
ScopDomain domain = scopDatabase.getDomainByScopID(scopId);
return getStructureForDomain(domain, scopDatabase);
}
/**
* Returns the representation of a {@link ScopDomain} as a BioJava {@link Structure} object.
*
* @param domain a SCOP domain
* @param scopDatabase A {@link ScopDatabase} to use
* @param strictLigandHandling If set to false, hetero-atoms are included if and only if they
* belong to a chain to which the SCOP domain belongs; if set to true, hetero-atoms are
* included if and only if they are strictly within the definition (residue numbers) of the
* SCOP domain
* @return a Structure object
* @throws IOException
* @throws StructureException
*/
public Structure getStructureForDomain(
ScopDomain domain, ScopDatabase scopDatabase, boolean strictLigandHandling)
throws IOException, StructureException {
String pdbId = domain.getPdbId();
Structure fullStructure = getStructureForPdbId(pdbId);
Structure structure = domain.reduce(fullStructure);
// TODO It would be better to move all of this into the reduce method,
// but that would require ligand handling properties in StructureIdentifiers
// because ligands sometimes occur after TER records in PDB files, we may need to add some
// ligands back in
// specifically, we add a ligand if and only if it occurs within the domain
AtomPositionMap map = null;
List<ResidueRangeAndLength> rrs = null;
if (strictLigandHandling) {
map =
new AtomPositionMap(
StructureTools.getAllAtomArray(fullStructure), AtomPositionMap.ANYTHING_MATCHER);
rrs = ResidueRangeAndLength.parseMultiple(domain.getRanges(), map);
}
for (Chain chain : fullStructure.getChains()) {
if (!structure.hasChain(chain.getChainID())) {
continue; // we can't do anything with a chain our domain
}
// doesn't contain
Chain newChain = structure.getChainByPDB(chain.getChainID());
List<Group> ligands = StructureTools.filterLigands(chain.getAtomGroups());
for (Group group : ligands) {
boolean shouldContain = true;
if (strictLigandHandling) {
shouldContain = false; // whether the ligand occurs within the domain
for (ResidueRange rr : rrs) {
if (rr.contains(group.getResidueNumber(), map)) {
shouldContain = true;
}
}
}
boolean alreadyContains =
newChain.getAtomGroups().contains(group); // we don't want to add duplicate
// ligands
if (shouldContain && !alreadyContains) {
newChain.addGroup(group);
}
}
}
// build a more meaningful description for the new structure
StringBuilder header = new StringBuilder();
header.append(domain.getClassificationId());
if (scopDatabase != null) {
int sf = domain.getSuperfamilyId();
ScopDescription description = scopDatabase.getScopDescriptionBySunid(sf);
if (description != null) {
header.append(" | ");
header.append(description.getDescription());
}
}
structure.getPDBHeader().setDescription(header.toString());
return structure;
}