/** * Handler for MODEL Record Format * <pre> * COLUMNS DATA TYPE FIELD DEFINITION * ---------------------------------------------------------------------- * 1 - 6 Record name "MODEL " * 11 - 14 Integer serial Model serial number. * </pre> */ private void pdb_MODEL_Handler(String line) { if (params.isHeaderOnly()) return; // new model: we start a new molecule startOfMolecule = true; startOfModel = true; }
if (params.isHeaderOnly()) return;
if (params.isHeaderOnly()) return;
if (params.isHeaderOnly()) return;
if (params.isHeaderOnly()) return;
private void pdb_REMARK_800_Handler(String line){ if (params.isHeaderOnly()) return;
if (params.isHeaderOnly()) return;
if (params.isHeaderOnly()) return;
return ; if (params.isHeaderOnly()) { return;
@Override public void newStructSite(StructSite structSite) { if (params.isHeaderOnly()) { return; } // Simply implement the method. List<Site> sites = structure.getSites(); if (sites == null) sites = new ArrayList<Site>(); Site site = null; for (Site asite : sites) { if (asite.getSiteID().equals(structSite.getId())) { site = asite; // Prevent duplicate siteIds } } boolean addSite = false; if (site == null) { site = new Site(); addSite = true; } site.setSiteID(structSite.getId()); site.setDescription(structSite.getDetails()); // site.setPdbxEvidenceCode(structSite.getPdbxEvidenceCode()); // TODO - add addition fields in Sites if (addSite) sites.add(site); structure.setSites(sites); }
if ( params.isParseSecStruc() && !params.isHeaderOnly()) setSecStruc();
if ( params.isAlignSeqRes() && !params.isHeaderOnly() && !seqResChains.isEmpty()){ logger.debug("Parsing mode align_seqres, will parse SEQRES and align to ATOM sequence"); SeqRes2AtomAligner aligner = new SeqRes2AtomAligner(); SeqRes2AtomAligner.storeUnAlignedSeqRes(structure, seqResChains, params.isHeaderOnly()); if (!params.isHeaderOnly()) {
if ( params.isHeaderOnly()) return;
currentModel.add(currentChain); } else if (!params.isHeaderOnly()){ logger.warn("current chain is null at end of document."); if ( params.isAlignSeqRes() && !params.isHeaderOnly() ){ logger.debug("Parsing mode align_seqres, will parse SEQRES and align to ATOM sequence"); alignSeqRes(); } else { logger.debug("Parsing mode unalign_seqres, will parse SEQRES but not align it to ATOM sequence"); SeqRes2AtomAligner.storeUnAlignedSeqRes(structure, seqResChains, params.isHeaderOnly()); if (!params.isHeaderOnly()) { if ( params.shouldCreateAtomBonds()) { addBonds(); if (!params.isHeaderOnly()) {
@Override public void newAtomSite(AtomSite atom) { if (params.isHeaderOnly()) return;