/**
* Return the symmetric repeats as structure identifiers, if the result is symmetric and it was
* refined, return null otherwise.
*
* @return List of StructureIdentifiers or null if not defined
* @throws StructureException
*/
public List<StructureIdentifier> getRepeatsID() throws StructureException {
if (!isRefined()) return null;
List<StructureIdentifier> repeats = new ArrayList<StructureIdentifier>(symmOrder);
String pdbId = structureId.toCanonical().getPdbId();
Block align = multipleAlignment.getBlocks().get(0);
for (int su = 0; su < symmOrder; su++) {
// Get the start and end residues of the repeat
ResidueNumber res1 = atoms[align.getStartResidue(su)].getGroup().getResidueNumber();
ResidueNumber res2 = atoms[align.getFinalResidue(su)].getGroup().getResidueNumber();
ResidueRange range = new ResidueRange(res1.getChainId(), res1, res2);
StructureIdentifier id = new SubstructureIdentifier(pdbId, Arrays.asList(range));
repeats.add(id);
}
return repeats;
}
/**
* Get the structure corresponding to the given {@link StructureIdentifier}. Equivalent to calling
* {@link StructureIdentifier#loadStructure(AtomCache)} followed by {@link
* StructureIdentifier#reduce(Structure)}.
*
* <p>Note that this method should not be used in StructureIdentifier implementations to avoid
* circular calls.
*
* @param strucId
* @return
* @throws IOException
* @throws StructureException
*/
public Structure getStructure(StructureIdentifier strucId)
throws IOException, StructureException {
Structure s = strucId.loadStructure(this);
Structure r = strucId.reduce(s);
r.setStructureIdentifier(strucId);
return r;
// if (name.length() < 4) {
// throw new IllegalArgumentException("Can't interpret IDs that are shorter than 4
// characters!");
// }
//
// Structure n = null;
//
// boolean useChainNr = false;
// boolean useDomainInfo = false;
// String range = null;
// int chainNr = -1;
//
//
// StructureName structureName = new StructureName(name);
//
// String pdbId = null;
// String chainId = null;
//
// if (name.length() == 4) {
//
// pdbId = name;
// Structure s;
// if (useMmCif) {
// s = loadStructureFromCifByPdbId(pdbId);
// } else {
// s = loadStructureFromPdbByPdbId(pdbId);
// }
// return s;
// } else if (structureName.isScopName()) {
//
// // return based on SCOP domain ID
// return getStructureFromSCOPDomain(name);
// } else if (structureName.isCathID()) {
// return getStructureForCathDomain(structureName, CathFactory.getCathDatabase());
// } else if (name.length() == 6) {
// // name is PDB.CHAINID style (e.g. 4hhb.A)
//
// pdbId = name.substring(0, 4);
// if (name.substring(4, 5).equals(CHAIN_SPLIT_SYMBOL)) {
// chainId = name.substring(5, 6);
// } else if (name.substring(4, 5).equals(CHAIN_NR_SYMBOL)) {
//
// useChainNr = true;
// chainNr = Integer.parseInt(name.substring(5, 6));
// }
//
// } else if (name.startsWith("file:/") || name.startsWith("http:/")) {
// // this is a URL
//
// URL url = new URL(name);
// return getStructureFromURL(url);
//
//
// } else if (structureName.isPDPDomain()) {
//
// // this is a PDP domain definition
//
// return getPDPStructure(name);
//
// } else if (name.startsWith(BIOL_ASSEMBLY_IDENTIFIER)) {
//
// return getBioAssembly(name);
//
// } else if (name.length() > 6 && !name.startsWith(PDP_DOMAIN_IDENTIFIER)
// && (name.contains(CHAIN_NR_SYMBOL) || name.contains(UNDERSCORE))
// && !(name.startsWith("file:/") || name.startsWith("http:/"))
//
// ) {
//
// // this is a name + range
//
// pdbId = name.substring(0, 4);
// // this ID has domain split information...
// useDomainInfo = true;
// range = name.substring(5);
//
// }
//
// // System.out.println("got: >" + name + "< " + pdbId + " " + chainId + " useChainNr:" +
// useChainNr + " "
// // +chainNr + " useDomainInfo:" + useDomainInfo + " " + range);
//
// if (pdbId == null) {
//
// return null;
// }
//
// while (checkLoading(pdbId)) {
// // waiting for loading to be finished...
//
// try {
// Thread.sleep(100);
// } catch (InterruptedException e) {
// logger.error(e.getMessage());
// }
//
// }
//
// // long start = System.currentTimeMillis();
//
// Structure s;
// if (useMmCif) {
// s = loadStructureFromCifByPdbId(pdbId);
// } else {
// s = loadStructureFromPdbByPdbId(pdbId);
// }
//
// // long end = System.currentTimeMillis();
// // System.out.println("time to load " + pdbId + " " + (end-start) + "\t size :" +
// // StructureTools.getNrAtoms(s) + "\t cached: " + cache.size());
//
// if (chainId == null && chainNr < 0 && range == null) {
// // we only want the 1st model in this case
// n = StructureTools.getReducedStructure(s, -1);
// } else {
//
// if (useChainNr) {
// // System.out.println("using ChainNr");
// n = StructureTools.getReducedStructure(s, chainNr);
// } else if (useDomainInfo) {
// // System.out.println("calling getSubRanges");
// n = StructureTools.getSubRanges(s, range);
// } else {
// // System.out.println("reducing Chain Id " + chainId);
// n = StructureTools.getReducedStructure(s, chainId);
// }
// }
//
//
//
// n.setName(name);
// return n;
}