@Override public void newDatabasePDBrevRecord(DatabasePdbrevRecord record) { PDBHeader header = structure.getPDBHeader(); if ( header == null) { header = new PDBHeader(); structure.setPDBHeader(header); } List<DatabasePdbrevRecord> revRecords = header.getRevisionRecords(); if ( revRecords == null) { revRecords = new ArrayList<DatabasePdbrevRecord>(); header.setRevisionRecords(revRecords); } revRecords.add(record); }
@Override public void newPdbxDatabaseStatus(PdbxDatabaseStatus status) { // the deposition date field is only available in mmCIF 5.0 if (status.getRecvd_initial_deposition_date() == null) { // skip this method for older mmCIF versions return; } SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd",Locale.US); PDBHeader header = structure.getPDBHeader(); if (header == null) { header = new PDBHeader(); } try { Date depositionDate = dateFormat.parse(status.getRecvd_initial_deposition_date()); header.setDepDate(depositionDate); } catch (ParseException e){ logger.warn("Could not parse date string '{}', deposition date will be unavailable", status.getRecvd_initial_deposition_date()); } structure.setPDBHeader(header); }
Chain c1 = structure1.findChain(chain); tmp1.setPDBCode(structure1.getPDBCode()); tmp1.setPDBHeader(structure1.getPDBHeader()); tmp1.setPDBCode(structure1.getPDBCode()); tmp1.addChain(c1);
@Override public void newPdbxAuditRevisionHistory(PdbxAuditRevisionHistory history) { SimpleDateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd",Locale.US); PDBHeader header = structure.getPDBHeader(); if ( header == null) { header = new PDBHeader(); } // first entry in revision history is the release date if (history.getOrdinal().equals("1")){ try { Date releaseDate = dateFormat.parse(history.getRevision_date()); header.setRelDate(releaseDate); } catch (ParseException e){ logger.warn("Could not parse date string '{}', release date will be unavailable", history.getRevision_date()); } } else { // all other dates are revision dates; // since this method may be called multiple times, // the last revision date will "stick" try { Date revisionDate = dateFormat.parse(history.getRevision_date()); header.setModDate(revisionDate); } catch (ParseException e){ logger.warn("Could not parse date string '{}', revision date will be unavailable", history.getRevision_date()); } } structure.setPDBHeader(header); }
structure.setPDBHeader(header);
Chain c1 = structure1.findChain(chain); tmp1.setPDBCode(structure1.getPDBCode()); tmp1.setPDBHeader(structure1.getPDBHeader()); tmp1.setPDBCode(structure1.getPDBCode()); tmp1.addChain(c1);
@Override public void setStruct(Struct struct) { PDBHeader header = structure.getPDBHeader(); if ( header == null) header = new PDBHeader(); header.setTitle(struct.getTitle()); header.setIdCode(struct.getEntry_id()); //header.setDescription(struct.getPdbx_descriptor()); //header.setClassification(struct.getPdbx_descriptor()); //header.setDescription(struct.getPdbx_descriptor()); structure.setPDBHeader(header); structure.setPDBCode(struct.getEntry_id()); }
structure.setPDBHeader(pdbHeader); structure.setCrystallographicInfo(crystallographicInfo);
public static Structure toMultimodelStructure(MultipleAlignment multAln, List<Atom[]> transformedAtoms) throws StructureException { PDBHeader header = new PDBHeader(); String title = multAln.getEnsemble().getAlgorithmName() + " V." + multAln.getEnsemble().getVersion() + " : "; for (StructureIdentifier name : multAln.getEnsemble() .getStructureIdentifiers()) { title += name.getIdentifier() + " "; } Structure artificial = getAlignedStructure(transformedAtoms); artificial.setPDBHeader(header); header.setTitle(title); return artificial; }
n.setName(getName()); n.setPDBHeader(pdbHeader); n.setDBRefs(this.getDBRefs()); n.setSites(getSites());
@Override protected void initCoords() { try { if (ca1 == null || ca2 == null) { if (structure != null) setStructure(structure); else { // System.err.println("could not find anything to // display!"); return; } } Structure artificial = AlignmentTools.getAlignedStructure(ca1, ca2); PDBHeader header = new PDBHeader(); String title = afpChain.getAlgorithmName() + " V." + afpChain.getVersion() + " : " + afpChain.getName1() + " vs. " + afpChain.getName2(); header.setTitle(title); artificial.setPDBHeader(header); setStructure(artificial); } catch (StructureException e) { e.printStackTrace(); } }
/** * Remove all models from a Structure and keep only the first * * @param s * original Structure * @return a structure that contains only the first model * @since 3.0.5 */ public static Structure removeModels(Structure s) { if (s.nrModels() == 1) return s; Structure n = new StructureImpl(); // go through whole substructure and clone ... // copy structure data n.setPDBCode(s.getPDBCode()); n.setName(s.getName()); // TODO: do deep copying of data! n.setPDBHeader(s.getPDBHeader()); n.setDBRefs(s.getDBRefs()); n.setSites(s.getSites()); n.setChains(s.getModel(0)); return n; }
newS.setPDBHeader(s.getPDBHeader()); newS.setName(s.getName()); newS.setSSBonds(s.getSSBonds());
newS.setPDBHeader(s.getPDBHeader()); newS.setName(this.toString()); newS.setDBRefs(s.getDBRefs());
s.setPDBHeader(orig.getPDBHeader()); for ( Chain c : orig.getChains()){