package jalview.ws.dbsources;
import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
++import jalview.bin.Console;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ContactMatrix;
+import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
try
{
- File tmpFile = File.createTempFile(id, "cif");
+ File tmpFile = File.createTempFile(id, ".cif");
++ Console.debug("Retrieving structure file for "+id+" from "+alphaFoldCif);
UrlDownloadClient.download(alphaFoldCif, tmpFile);
+
+ // may not need this check ?
file = tmpFile.getAbsolutePath();
if (file == null)
{
{ id, ((chain == null) ? "' '" : chain) }));
}
+ // import PAE as contact matrix - assume this will work if there was a
+ // model
+ File pae = File.createTempFile(id, "pae_json");
+ String paeURL = getAlphaFoldPaeDownloadUrl(id);
- UrlDownloadClient.download(paeURL, pae);
++
++ if (retrievalUrl!=null) {
++ // manufacture the PAE url from a url like ...-model-vN.cif
++ paeURL = retrievalUrl.replace("model","predicted_aligned_error").replace(".cif",".json");
++ }
++ Console.debug("Downloading pae from " + paeURL
++ + " to " + pae.toString() + "");
++
++ try {
++ UrlDownloadClient.download(paeURL, pae);
+ if (!importPaeJSONAsContactMatrix(pdbAlignment, pae))
+ {
- Cache.log.debug("Couln't import contact matrix from " + paeURL
++ Console.warn("Couln't import contact matrix from " + paeURL
+ + " (stored in " + pae.toString() + ")");
+ }
++ } catch (Exception pae_ex) {
++ Console.debug("Couldn't download PAE",pae_ex);
++ }
+
} catch (Exception ex) // Problem parsing PDB file
{
stopQuery();
return pdbAlignment;
}
+ private boolean importPaeJSONAsContactMatrix(AlignmentI pdbAlignment,
+ File pae) throws Exception
+ {
+ FileInputStream pae_input = new FileInputStream(pae);
+
+ List<Object> pae_obj = (List<Object>) Platform
+ .parseJSON(pae_input);
+ if (pae_obj == null)
+ {
+ return false;
+ }
+ ContactMatrixI matrix = new PAEContactMatrix(
+ pdbAlignment.getSequenceAt(0), (Map<String, Object>)pae_obj.get(0));
+
+ pdbAlignment.getSequenceAt(0).addAlignmentAnnotation(pdbAlignment.addContactList(matrix));
+ return true;
+ }
+
+ /**
+ * general purpose structure importer - designed to yield alignment useful for transfer of annotation to associated sequences
+ * @param alphaFoldCif
+ * @param tmpFile
+ * @param id
+ * @param chain
+ * @param dbSource
+ * @param dbVersion
+ * @return
+ * @throws Exception
+ */
+ public static AlignmentI importDownloadedStructureFromUrl(String alphaFoldCif,
+ File tmpFile, String id, String chain, String dbSource, String dbVersion) throws Exception
+ {
+ String file = tmpFile.getAbsolutePath();
+ // todo get rid of Type and use FileFormatI instead?
+ FileFormatI fileFormat = FileFormat.MMCif;
+ AlignmentI pdbAlignment = new FormatAdapter().readFile(tmpFile,
+ DataSourceType.FILE, fileFormat);
+ if (pdbAlignment != null)
+ {
+ List<SequenceI> toremove = new ArrayList<SequenceI>();
+ for (SequenceI pdbcs : pdbAlignment.getSequences())
+ {
+ String chid = null;
+ // Mapping map=null;
+ for (PDBEntry pid : pdbcs.getAllPDBEntries())
+ {
+ if (pid.getFile() == file)
+ {
+ chid = pid.getChainCode();
+
+ }
+ }
+ if (chain == null || (chid != null && (chid.equals(chain)
+ || chid.trim().equals(chain.trim())
+ || (chain.trim().length() == 0 && chid.equals("_")))))
+ {
+ // FIXME seems to result in 'PDB|1QIP|1qip|A' - 1QIP is redundant.
+ // TODO: suggest simplify naming to 1qip|A as default name defined
+ pdbcs.setName(id + SEPARATOR + pdbcs.getName());
+ // Might need to add more metadata to the PDBEntry object
+ // like below
+ /*
+ * PDBEntry entry = new PDBEntry(); // Construct the PDBEntry
+ * entry.setId(id); if (entry.getProperty() == null)
+ * entry.setProperty(new Hashtable());
+ * entry.getProperty().put("chains", pdbchain.id + "=" +
+ * sq.getStart() + "-" + sq.getEnd());
+ * sq.getDatasetSequence().addPDBId(entry);
+ */
+ // Add PDB DB Refs
+ // We make a DBRefEtntry because we have obtained the PDB file from
+ // a
+ // verifiable source
+ // JBPNote - PDB DBRefEntry should also carry the chain and mapping
+ // information
+ if (dbSource != null)
+ {
+ DBRefEntry dbentry = new DBRefEntry(dbSource,
+
+ dbVersion, (chid == null ? id : id + chid));
+ // dbentry.setMap()
+ pdbcs.addDBRef(dbentry);
+ // update any feature groups
+ List<SequenceFeature> allsf = pdbcs.getFeatures().getAllFeatures();
+ List<SequenceFeature> newsf = new ArrayList<SequenceFeature>();
+ if (allsf!=null && allsf.size()>0)
+ {
+ for (SequenceFeature f:allsf)
+ {
+ if (file.equals(f.getFeatureGroup()))
+ {
+ f = new SequenceFeature(f, f.type, f.begin, f.end, id, f.score);
+ }
+ newsf.add(f);
+ }
+ pdbcs.setSequenceFeatures(newsf);
+ }
+ }
+ }
+ else
+ {
+ // mark this sequence to be removed from the alignment
+ // - since it's not from the right chain
+ toremove.add(pdbcs);
+ }
+ }
+ // now remove marked sequences
+ for (SequenceI pdbcs : toremove)
+ {
+ pdbAlignment.deleteSequence(pdbcs);
+ if (pdbcs.getAnnotation() != null)
+ {
+ for (AlignmentAnnotation aa : pdbcs.getAnnotation())
+ {
+ pdbAlignment.deleteAnnotation(aa);
+ }
+ }
+ }
+ }
+ return pdbAlignment;
+ }
+
/*
* (non-Javadoc)
*
git://source.jalview.org / jalview.git / commitdiff