public void loadStructureIO() {
try {
Structure s1 = StructureIO.getStructure("1gav");
System.out.println(s1.getPDBCode() + " asym unit has nr atoms:");
System.out.println(StructureTools.getNrAtoms(s1));
Structure s2 = StructureIO.getBiologicalAssembly("1gav");
System.out.println(s2.getPDBCode() + " biological assembly has nr atoms:");
System.out.println(StructureTools.getNrAtoms(s2));
} catch (Exception e) {
e.printStackTrace();
}
}
private static char getOneLetter(Group g) {
try {
Character c = StructureTools.get1LetterCode(g.getPDBName());
return c;
} catch (Exception e) {
return 'X';
}
}
/**
* Constructs a new AsaCalculator. Subsequently call {@link #calculateAsas()} or {@link
* #getGroupAsas()} to calculate the ASAs Only non-Hydrogen atoms are considered in the
* calculation.
*
* @param structure
* @param probe
* @param nSpherePoints
* @param nThreads
* @param hetAtoms if true HET residues are considered, if false they aren't, equivalent to
* NACCESS' -h option
* @see StructureTools.getAllNonHAtomArray
*/
public AsaCalculator(
Structure structure, double probe, int nSpherePoints, int nThreads, boolean hetAtoms) {
this.atoms = StructureTools.getAllNonHAtomArray(structure, hetAtoms);
this.probe = probe;
this.nThreads = nThreads;
// initialising the radii by looking them up through AtomRadii
radii = new double[atoms.length];
for (int i = 0; i < atoms.length; i++) {
radii[i] = getRadius(atoms[i]);
}
// initialising the sphere points to sample
spherePoints = generateSpherePoints(nSpherePoints);
cons = 4.0 * Math.PI / (double) nSpherePoints;
}
public void run() {
AtomCache cache = new AtomCache(config);
StructureAlignment algorithm = null;
if (parent != null) algorithm = parent.getStructureAlignment();
else {
algorithm = customAlgorithm;
}
String serverLocation = FarmJobParameters.DEFAULT_SERVER_URL;
if (representatives == null) {
SortedSet<String> repre = JFatCatClient.getRepresentatives(serverLocation, 40);
System.out.println("got " + repre.size() + " representatives for comparison");
representatives = repre;
}
String header = "# algorithm:" + algorithm.getAlgorithmName();
String legend =
"# name1\tname2\tscore\tprobability\trmsd\tlen1\tlen2\tcov1\tcov2\t%ID\tDescription\t ";
if (algorithm.getAlgorithmName().equalsIgnoreCase(CeMain.algorithmName)
|| algorithm.getAlgorithmName().equalsIgnoreCase(CeSideChainMain.algorithmName)) {
legend = "# name1\tname2\tscore\tz-score\trmsd\tlen1\tlen2\tcov1\tcov2\t%ID\tDescription\t ";
}
File outFileF = new File(outFile);
if (!outFileF.isDirectory()) {
System.err.println(
outFileF.getAbsolutePath()
+ " is not a directory, can't create result files in there... ");
interrupt();
cleanup();
}
if (name1 == null) name1 = "CUSTOM";
SynchronizedOutFile out;
resultList = new File(outFileF, "results_" + name1 + ".out");
try {
out = new SynchronizedOutFile(resultList);
out.write(header);
out.write(AFPChain.newline);
out.write(legend);
out.write(AFPChain.newline);
if (name1.equals("CUSTOM")) {
String config1 = "#param:file1=" + parent.getDBSearch().getPDBUploadPanel().getFilePath1();
out.write(config1);
out.write(AFPChain.newline);
String config2 = "#param:chain1=" + parent.getDBSearch().getPDBUploadPanel().getChain1();
out.write(config2);
out.write(AFPChain.newline);
}
if (algorithm.getAlgorithmName().startsWith("jCE")) {
ConfigStrucAligParams params = algorithm.getParameters();
if (params instanceof CeParameters) {
CeParameters ceParams = (CeParameters) params;
if (ceParams.getScoringStrategy() != CeParameters.DEFAULT_SCORING_STRATEGY) {
String scoring = "#param:scoring=" + ceParams.getScoringStrategy();
out.write(scoring);
out.write(AFPChain.newline);
}
}
}
} catch (Exception e) {
System.err.println("Error while loading representative structure " + name1);
e.printStackTrace();
interrupt();
cleanup();
return;
}
DomainProvider domainProvider = DomainProviderFactory.getDomainProvider();
ConcurrencyTools.setThreadPoolSize(nrCPUs);
Atom[] ca1 = StructureTools.getAtomCAArray(structure1);
int nrJobs = 0;
for (String repre : representatives) {
if (domainSplit) {
SortedSet<String> domainNames = domainProvider.getDomainNames(repre);
// System.out.println(repre +" got domains: " +domainNames);
if (domainNames == null || domainNames.size() == 0) {
// no domains found, use whole chain.
submit(name1, repre, ca1, algorithm, outFileF, out, cache);
nrJobs++;
continue;
}
// System.out.println("got " + domainNames.size() + " for " + repre);
for (String domain : domainNames) {
submit(name1, domain, ca1, algorithm, outFileF, out, cache);
nrJobs++;
}
} else {
submit(name1, repre, ca1, algorithm, outFileF, out, cache);
nrJobs++;
}
}
ThreadPoolExecutor pool = ConcurrencyTools.getThreadPool();
System.out.println(pool.getPoolSize());
long startTime = System.currentTimeMillis();
try {
while (pool.getCompletedTaskCount() < nrJobs - 1) {
// long now = System.currentTimeMillis();
// System.out.println( pool.getCompletedTaskCount() + " " + (now-startTime)/1000 + " " +
// pool.getPoolSize() + " " + pool.getActiveCount() + " " + pool.getTaskCount() );
// if ((now-startTime)/1000 > 60) {
//
// interrupt();
// System.out.println("completed: " + pool.getCompletedTaskCount());
// }
if (interrupted.get()) break;
Thread.sleep(2000);
}
out.close();
} catch (Exception e) {
e.printStackTrace();
interrupt();
cleanup();
}
if (domainProvider instanceof RemoteDomainProvider) {
RemoteDomainProvider remote = (RemoteDomainProvider) domainProvider;
remote.flushCache();
}
long now = System.currentTimeMillis();
System.out.println("Calculation took : " + (now - startTime) / 1000 + " sec.");
System.out.println(
pool.getCompletedTaskCount()
+ " "
+ pool.getPoolSize()
+ " "
+ pool.getActiveCount()
+ " "
+ pool.getTaskCount());
// if ((now-startTime)/1000 > 30) {
// try {
// out.flush();
// out.close();
// } catch (Exception e) {
// e.printStackTrace();
// }
if (parent != null) {
parent.notifyCalcFinished();
DBResultTable table = new DBResultTable();
table.show(resultList, config);
}
}
/**
* Identify a set of modifications in a a list of chains.
*
* @param chains query {@link Chain}s.
* @param potentialModifications query {@link ProteinModification}s.
*/
public void identify(
final List<Chain> chains, final Set<ProteinModification> potentialModifications) {
if (chains == null) {
throw new IllegalArgumentException("Null structure.");
}
if (potentialModifications == null) {
throw new IllegalArgumentException("Null potentialModifications.");
}
reset();
if (potentialModifications.isEmpty()) {
return;
}
Map<String, Chain> mapChainIdChain = new HashMap<String, Chain>(chains.size());
residues = new ArrayList<Group>();
List<Group> ligands = new ArrayList<Group>();
Map<Component, Set<Group>> mapCompGroups = new HashMap<Component, Set<Group>>();
for (Chain chain : chains) {
mapChainIdChain.put(chain.getChainID(), chain);
List<Group> ress = StructureUtil.getAminoAcids(chain);
// List<Group> ligs = chain.getAtomLigands();
List<Group> ligs = StructureTools.filterLigands(chain.getAtomGroups());
residues.addAll(ress);
residues.removeAll(ligs);
ligands.addAll(ligs);
addModificationGroups(potentialModifications, ress, ligs, mapCompGroups);
}
if (residues.isEmpty()) {
String pdbId = "?";
if (chains.size() > 0) {
Structure struc = chains.get(0).getParent();
if (struc != null) pdbId = struc.getPDBCode();
}
System.err.println(
"WARNING: no amino acids found for "
+ pdbId
+ ". Either you did not parse the PDB file with alignSEQRES records, or this record does not contain any amino acids.");
}
List<ModifiedCompound> modComps = new ArrayList<ModifiedCompound>();
for (ProteinModification mod : potentialModifications) {
ModificationCondition condition = mod.getCondition();
List<Component> components = condition.getComponents();
if (!mapCompGroups.keySet().containsAll(components)) {
// not all components exist for this mod.
continue;
}
int sizeComps = components.size();
if (sizeComps == 1) {
processCrosslink1(mapCompGroups, modComps, mod, components);
} else {
processMultiCrosslink(mapCompGroups, modComps, mod, condition);
}
}
if (recordAdditionalAttachments) {
// identify additional groups that are not directly attached to amino acids.
for (ModifiedCompound mc : modComps) {
identifyAdditionalAttachments(mc, ligands, mapChainIdChain);
}
}
mergeModComps(modComps);
identifiedModifiedCompounds.addAll(modComps);
// record unidentifiable linkage
if (recordUnidentifiableModifiedCompounds) {
recordUnidentifiableAtomLinkages(modComps, ligands);
recordUnidentifiableModifiedResidues(modComps);
}
}
