X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fws%2Fdbsources%2FEBIAlfaFold.java;h=dd71ec329a9b58030acf76c1376a89cd0e442f8b;hb=7420ce36f2b43280ef610e3743960207e4c2dbe3;hp=b4cb614322276d6212a368722a07a3dae995bda1;hpb=023163e0fe8837c1ddb75eb30abc058f7747b5c2;p=jalview.git diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java index b4cb614..dd71ec3 100644 --- a/src/jalview/ws/dbsources/EBIAlfaFold.java +++ b/src/jalview/ws/dbsources/EBIAlfaFold.java @@ -21,31 +21,44 @@ */ package jalview.ws.dbsources; +import java.io.File; +import java.io.FileInputStream; +import java.io.FileNotFoundException; +import java.io.IOException; +import java.io.InputStream; +import java.util.ArrayList; +import java.util.List; +import java.util.Map; + +import org.json.simple.JSONArray; +import org.json.simple.JSONObject; +import org.json.simple.parser.ParseException; + +import com.stevesoft.pat.Regex; + import jalview.api.FeatureSettingsModelI; +import jalview.bin.Console; +import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.datamodel.ContactMatrixI; import jalview.datamodel.DBRefEntry; -import jalview.datamodel.DBRefSource; import jalview.datamodel.PDBEntry; -import jalview.datamodel.PDBEntry.Type; +import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; +import jalview.gui.Desktop; import jalview.io.DataSourceType; import jalview.io.FileFormat; import jalview.io.FileFormatI; import jalview.io.FormatAdapter; import jalview.io.PDBFeatureSettings; -import jalview.structure.StructureImportSettings; -import jalview.util.HttpUtils; +import jalview.structure.StructureMapping; +import jalview.structure.StructureSelectionManager; import jalview.util.MessageManager; -import jalview.ws.ebi.EBIFetchClient; +import jalview.util.Platform; +import jalview.ws.datamodel.alphafold.PAEContactMatrix; import jalview.ws.utils.UrlDownloadClient; -import java.io.File; -import java.util.ArrayList; -import java.util.List; - -import com.stevesoft.pat.Regex; - /** * @author JimP * @@ -58,6 +71,8 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy private static final int PDB_ID_LENGTH = 4; + private static String AF_VERSION = "3"; + public EBIAlfaFold() { super(); @@ -82,7 +97,9 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy @Override public Regex getAccessionValidator() { - return new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)"); + Regex validator = new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)"); + validator.setIgnoreCase(true); + return validator; } /* @@ -107,9 +124,24 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy return "1"; } - public static String getAlphaFoldCifDownloadUrl(String id) + public static String getAlphaFoldCifDownloadUrl(String id, String vnum) { - return "https://alphafold.ebi.ac.uk/files/" + id + "-model_v1.cif"; + if (vnum == null || vnum.length() == 0) + { + vnum = AF_VERSION; + } + return "https://alphafold.ebi.ac.uk/files/" + id + "-model_v" + vnum + + ".cif"; + } + + public static String getAlphaFoldPaeDownloadUrl(String id, String vnum) + { + if (vnum == null || vnum.length() == 0) + { + vnum = AF_VERSION; + } + return "https://alphafold.ebi.ac.uk/files/" + id + + "-predicted_aligned_error_v" + vnum + ".json"; } /* @@ -120,6 +152,12 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy @Override public AlignmentI getSequenceRecords(String queries) throws Exception { + return getSequenceRecords(queries, null); + } + + public AlignmentI getSequenceRecords(String queries, String retrievalUrl) + throws Exception + { AlignmentI pdbAlignment = null; String chain = null; String id = null; @@ -136,17 +174,23 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy if (!isValidReference(id)) { System.err.println( - "(AFClient) Ignoring invalid pdb query: '" + id + "'"); + "(AFClient) Ignoring invalid alphafold query: '" + id + "'"); stopQuery(); return null; } - String alphaFoldCif = getAlphaFoldCifDownloadUrl(id); + String alphaFoldCif = getAlphaFoldCifDownloadUrl(id, AF_VERSION); + if (retrievalUrl != null) + { + alphaFoldCif = retrievalUrl; + } 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) @@ -154,8 +198,8 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy return null; } - pdbAlignment = importDownloadedStructureFromUrl(alphaFoldCif, tmpFile, id, chain, getDbSource(),getDbVersion()); - + pdbAlignment = importDownloadedStructureFromUrl(alphaFoldCif, tmpFile, + id, chain, getDbSource(), getDbVersion()); if (pdbAlignment == null || pdbAlignment.getHeight() < 1) { @@ -163,6 +207,8 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy "exception.no_pdb_records_for_chain", new String[] { id, ((chain == null) ? "' '" : chain) })); } + // done during structure retrieval + // retrieve_AlphaFold_pAE(id, pdbAlignment, retrievalUrl); } catch (Exception ex) // Problem parsing PDB file { @@ -173,7 +219,273 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy } /** - * general purpose structure importer - designed to yield alignment useful for transfer of annotation to associated sequences + * 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) 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) 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 acfList = ssm.getSequenceMappings(); + + return true; + } + + /** + * general purpose structure importer - designed to yield alignment useful for + * transfer of annotation to associated sequences + * * @param alphaFoldCif * @param tmpFile * @param id @@ -183,8 +495,9 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy * @return * @throws Exception */ - public static AlignmentI importDownloadedStructureFromUrl(String alphaFoldCif, - File tmpFile, String id, String chain, String dbSource, String dbVersion) 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? @@ -236,6 +549,23 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy dbVersion, (chid == null ? id : id + chid)); // dbentry.setMap() pdbcs.addDBRef(dbentry); + // update any feature groups + List allsf = pdbcs.getFeatures() + .getAllFeatures(); + List newsf = new ArrayList(); + 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 @@ -279,13 +609,13 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy @Override public String getTestQuery() { - return "1QIP"; + return "AF-O15552-F1"; } @Override public String getDbName() { - return "PDB"; // getDbSource(); + return "ALPHAFOLD"; // getDbSource(); } @Override @@ -308,4 +638,5 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy { return new PDBFeatureSettings(); } + }