+ * get an alphafold pAE for the given id, and add it to sequence 0 in
+ * pdbAlignment (assuming it came from structurefile parser).
+ *
+ * @param id
+ * @param pdbAlignment
+ * @param retrievalUrl
+ * - URL of .mmcif from EBI-AlphaFold - will be used to generate the
+ * pAE URL automatically
+ * @throws IOException
+ * @throws Exception
+ */
+ public static void retrieve_AlphaFold_pAE(String id,
+ AlignmentI pdbAlignment, String retrievalUrl) throws IOException
+ {
+ // import PAE as contact matrix - assume this will work if there was a
+ // model
+ String paeURL = getAlphaFoldPaeDownloadUrl(id, AF_VERSION);
+
+ if (retrievalUrl != null)
+ {
+ // manufacture the PAE url from a url like ...-model-vN.cif
+ paeURL = retrievalUrl.replace("model", "predicted_aligned_error")
+ .replace(".cif", ".json");
+ }
+
+ File pae = null;
+ try
+ {
+ pae = File.createTempFile(id == null ? "af_pae" : id, "pae_json");
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ }
+ Console.debug("Downloading pae from " + paeURL + " to " + pae.toString()
+ + "");
+ UrlDownloadClient.download(paeURL, pae);
+ addAlphaFoldPAEToSequence(pdbAlignment, pae, 0, null);
+ }
+
+ public static void addAlphaFoldPAEToSequence(AlignmentI pdbAlignment,
+ File pae, int index, String seqId)
+ {
+ addAlphaFoldPAE(pdbAlignment, pae, index, seqId, false, false);
+ }
+
+ public static void addAlphaFoldPAEToStructure(AlignmentI pdbAlignment,
+ File pae, int index, String structIdOrFile, boolean isStructId)
+ {
+ addAlphaFoldPAE(pdbAlignment, pae, index, structIdOrFile, true,
+ isStructId);
+ }
+
+ public static void addAlphaFoldPAE(AlignmentI pdbAlignment, File pae,
+ int index, String id, boolean isStruct, boolean isStructId)
+ {
+ FileInputStream paeInput = null;
+ try
+ {
+ paeInput = new FileInputStream(pae);
+ } catch (FileNotFoundException e)
+ {
+ Console.error(
+ "Could not find pAE file '" + pae.getAbsolutePath() + "'", e);
+ return;
+ }
+
+ if (isStruct)
+ {
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ if (ssm != null)
+ {
+ String structFile = isStructId ? ssm.findFileForPDBId(id) : id;
+ Console.debug("##### AHA! structFile = " + structFile);
+ Console.debug("##### structFile "
+ + (ssm.isPDBFileRegistered(structFile) ? "IS " : "is NOT ")
+ + "registered.");
+
+ StructureMapping[] smArray = ssm.getMapping(structFile);
+ Console.debug("##### AHA! smArray obtained with " + smArray.length
+ + " elements");
+
+ try
+ {
+ if (!importPaeJSONAsContactMatrixToStructure(smArray, paeInput))
+ {
+ Console.warn("Could not import contact matrix from '"
+ + pae.getAbsolutePath() + "' to structure.");
+ }
+ } catch (IOException e1)
+ {
+ Console.error("Error when importing pAE file '"
+ + pae.getAbsolutePath() + "'", e1);
+ } catch (ParseException e2)
+ {
+ Console.error("Error when parsing pAE file '"
+ + pae.getAbsolutePath() + "'", e2);
+ }
+ }
+
+ }
+ else
+ {
+ // attach to sequence?!
+ try
+ {
+ if (!importPaeJSONAsContactMatrixToSequence(pdbAlignment, paeInput,
+ index, id))
+ {
+ Console.warn("Could not import contact matrix from '"
+ + pae.getAbsolutePath() + "' to sequence.");
+ }
+ } catch (IOException e1)
+ {
+ Console.error("Error when importing pAE file '"
+ + pae.getAbsolutePath() + "'", e1);
+ } catch (ParseException e2)
+ {
+ Console.error("Error when parsing pAE file '"
+ + pae.getAbsolutePath() + "'", e2);
+ }
+ }
+
+ }
+
+ /**
+ * parses the given pAE matrix and adds it to sequence 0 in the given
+ * alignment
+ *
+ * @param pdbAlignment
+ * @param pae_input
+ * @return true if there was a pAE matrix added
+ * @throws ParseException
+ * @throws IOException
+ * @throws Exception
+ */
+ public static boolean importPaeJSONAsContactMatrixToSequence(
+ AlignmentI pdbAlignment, InputStream pae_input)
+ throws IOException, ParseException
+ {
+ return importPaeJSONAsContactMatrixToSequence(pdbAlignment, pae_input,
+ 0, null);
+ }
+
+ public static boolean importPaeJSONAsContactMatrixToSequence(
+ AlignmentI pdbAlignment, InputStream pae_input, int index,
+ String seqId) throws IOException, ParseException
+ {
+ SequenceI sequence = null;
+ /* debugging */
+ SequenceI[] seqs = pdbAlignment.getSequencesArray();
+ if (seqs == null)
+ Console.debug("******* sequences is null");
+ else
+ {
+ for (int i = 0; i < seqs.length; i++)
+ {
+ SequenceI s = seqs[i];
+ }
+ }
+ /* end debug */
+ if (seqId == null)
+ {
+ int seqToGet = index > 0 ? index : 0;
+ sequence = pdbAlignment.getSequenceAt(seqToGet);
+ Console.debug("***** Got sequence at index " + seqToGet + ": "
+ + (sequence == null ? null : sequence.getName()));
+ }
+ if (sequence == null)
+ {
+ SequenceI[] sequences = pdbAlignment.findSequenceMatch(seqId);
+ if (sequences == null || sequences.length < 1)
+ {
+ Console.warn("Could not find sequence with id '" + seqId
+ + "' to attach pAE matrix to. Ignoring matrix.");
+ return false;
+ }
+ else
+ {
+ sequence = sequences[0]; // just use the first sequence with this seqId
+ }
+ }
+
+ JSONObject paeDict = parseJSONtoPAEContactMatrix(pae_input);
+ if (paeDict == null)
+ {
+ Console.debug("JSON file did not parse properly.");
+ return false;
+ }
+ ContactMatrixI matrix = new PAEContactMatrix(sequence,
+ (Map<String, Object>) paeDict);
+ ((PAEContactMatrix) matrix).makeGroups(5f, true);
+
+ AlignmentAnnotation cmannot = sequence.addContactList(matrix);
+ pdbAlignment.addAnnotation(cmannot);
+
+ return true;
+ }
+
+ public static JSONObject parseJSONtoPAEContactMatrix(
+ InputStream pae_input) throws IOException,ParseException
+ {
+ Object paeJson = Platform.parseJSON(pae_input);
+ JSONObject paeDict=null;
+ if (paeJson instanceof JSONObject)
+ {
+ Console.debug("***** paeJson is a JSONObject");
+ paeDict = (JSONObject) paeJson;
+ }
+ else if (paeJson instanceof JSONArray)
+ {
+ JSONArray jsonArray = (JSONArray) paeJson;
+ if (jsonArray.size() > 0)
+ paeDict = (JSONObject) jsonArray.get(0);
+ }
+
+ return paeDict;
+ }
+
+ public static boolean importPaeJSONAsContactMatrixToStructure(
+ StructureMapping[] smArray, InputStream paeInput)
+ throws IOException, ParseException
+ {
+ boolean someDone = false;
+ Console.debug("##### smArray.length=" + smArray.length);
+ for (StructureMapping sm : smArray)
+ {
+ Console.debug("##### sm[n]=" + sm.getPdbId());
+ boolean thisDone = importPaeJSONAsContactMatrixToStructure(sm,
+ paeInput);
+ Console.debug("##### thisDone = " + thisDone);
+ someDone |= thisDone;
+ }
+ return someDone;
+ }
+
+ public static boolean importPaeJSONAsContactMatrixToStructure(
+ StructureMapping sm, InputStream paeInput)
+ throws IOException, ParseException
+ {
+
+ JSONObject pae_obj = parseJSONtoPAEContactMatrix(paeInput);
+ if (pae_obj == null)
+ {
+ Console.debug("JSON file did not parse properly.");
+ return false;
+ }
+
+ ContactMatrixI matrix = new PAEContactMatrix(sm.getSequence(),
+ (Map<String, Object>) pae_obj);
+ ((PAEContactMatrix) matrix).makeGroups(5f, true);
+ AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
+ // sm.getSequence().addAlignmentAnnotation(cmannot);
+ sm.transfer(cmannot);
+ // return true;
+
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ List<AlignedCodonFrame> acfList = ssm.getSequenceMappings();
+
+ return true;
+ }
+
+ /**
+ * general purpose structure importer - designed to yield alignment useful for
+ * transfer of annotation to associated sequences
+ *