*/
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.Date;
+import java.util.HashMap;
+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.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ContactMatrixI;
import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
+import jalview.datamodel.GroupSet;
import jalview.datamodel.PDBEntry;
-import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
-import jalview.datamodel.features.SequenceFeaturesI;
+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.StructureImportSettings.TFType;
+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
*
private static final int PDB_ID_LENGTH = 4;
+ private static String AF_VERSION = "3";
+
public EBIAlfaFold()
{
super();
return "1";
}
- public static String getAlphaFoldCifDownloadUrl(String id)
+ public static String getAlphaFoldCifDownloadUrl(String id, String vnum)
+ {
+ 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)
{
- 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
+ + "-predicted_aligned_error_v" + vnum + ".json";
}
/*
if (!isValidReference(id))
{
- System.err.println(
- "(AFClient) Ignoring invalid pdb query: '" + id + "'");
+ jalview.bin.Console.errPrintln(
+ "(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");
+ Console.debug("Retrieving structure file for " + id + " from "
+ + alphaFoldCif);
UrlDownloadClient.download(alphaFoldCif, tmpFile);
// may not need this check ?
{
return null;
}
+ // TODO Get the PAE file somewhere around here and remove from JmolParser
pdbAlignment = importDownloadedStructureFromUrl(alphaFoldCif, tmpFile,
id, chain, getDbSource(), getDbVersion());
"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
{
}
/**
+ * get an alphafold pAE for the given id and return the File object of the
+ * downloaded (temp) file
+ *
+ * @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 File fetchAlphaFoldPAE(String id, 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");
+ }
+
+ // check the cache
+ File pae = paeDownloadCache.get(paeURL);
+ if (pae != null && pae.exists() && (new Date().getTime()
+ - pae.lastModified()) < PAE_CACHE_STALE_TIME)
+ {
+ Console.debug(
+ "Using existing file in PAE cache for '" + paeURL + "'");
+ return pae;
+ }
+
+ 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()
+ + "");
+ try
+ {
+ UrlDownloadClient.download(paeURL, pae);
+ } catch (IOException e)
+ {
+ throw e;
+ }
+ // cache and it if successful
+ paeDownloadCache.put(paeURL, pae);
+ return pae;
+ }
+
+ /**
+ * 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
+ {
+ File pae = fetchAlphaFoldPAE(id, retrievalUrl);
+ addAlphaFoldPAE(pdbAlignment, pae, 0, null, false, false, null);
+ }
+
+ public static void addAlphaFoldPAE(AlignmentI pdbAlignment, File pae,
+ int index, String id, boolean isStruct, boolean isStructId,
+ String label)
+ {
+ FileInputStream paeInput = null;
+ try
+ {
+ paeInput = new FileInputStream(pae);
+ } catch (FileNotFoundException e)
+ {
+ Console.error(
+ "Could not find pAE file '" + pae.getAbsolutePath() + "'", e);
+ return;
+ }
+
+ if (isStruct)
+ {
+ // ###### WRITE A TEST for this bit of the logic addAlphaFoldPAE with
+ // different params.
+ StructureSelectionManager ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ if (ssm != null)
+ {
+ String structFilename = isStructId ? ssm.findFileForPDBId(id) : id;
+ addPAEToStructure(ssm, structFilename, pae, label);
+ }
+
+ }
+ else
+ {
+ // attach to sequence?!
+ try
+ {
+ if (!importPaeJSONAsContactMatrixToSequence(pdbAlignment, paeInput,
+ index, id, label))
+ {
+ 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);
+ }
+ }
+
+ }
+
+ public static void addPAEToStructure(StructureSelectionManager ssm,
+ String structFilename, File pae, String label)
+ {
+ FileInputStream paeInput = null;
+ try
+ {
+ paeInput = new FileInputStream(pae);
+ } catch (FileNotFoundException e)
+ {
+ Console.error(
+ "Could not find pAE file '" + pae.getAbsolutePath() + "'", e);
+ return;
+ }
+ if (ssm == null)
+ {
+ ssm = StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance);
+ }
+ if (ssm != null)
+ {
+ StructureMapping[] smArray = ssm.getMapping(structFilename);
+
+ try
+ {
+ if (!importPaeJSONAsContactMatrixToStructure(smArray, paeInput,
+ label))
+ {
+ 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);
+ }
+ }
+ }
+
+ /**
+ * 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, int index,
+ String seqId, String label) throws IOException, ParseException
+ {
+ SequenceI sequence = null;
+ if (seqId == null)
+ {
+ int seqToGet = index > 0 ? index : 0;
+ sequence = pdbAlignment.getSequenceAt(seqToGet);
+ }
+ 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
+ }
+ }
+ if (sequence == null)
+ {
+ return false;
+ }
+ return importPaeJSONAsContactMatrixToSequence(pdbAlignment, pae_input,
+ sequence, label);
+ }
+
+ public static boolean importPaeJSONAsContactMatrixToSequence(
+ AlignmentI pdbAlignment, InputStream pae_input,
+ SequenceI sequence, String label)
+ throws IOException, ParseException
+ {
+ 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);
+
+ AlignmentAnnotation cmannot = sequence.addContactList(matrix);
+ if (label != null)
+ cmannot.label = label;
+ 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)
+ {
+ paeDict = (JSONObject) paeJson;
+ }
+ else if (paeJson instanceof JSONArray)
+ {
+ JSONArray jsonArray = (JSONArray) paeJson;
+ if (jsonArray.size() > 0)
+ paeDict = (JSONObject) jsonArray.get(0);
+ }
+
+ return paeDict;
+ }
+
+ // ###### TEST THIS
+ public static boolean importPaeJSONAsContactMatrixToStructure(
+ StructureMapping[] smArray, InputStream paeInput, String label)
+ throws IOException, ParseException
+ {
+ boolean someDone = false;
+ for (StructureMapping sm : smArray)
+ {
+ boolean thisDone = importPaeJSONAsContactMatrixToStructure(sm,
+ paeInput, label);
+ someDone |= thisDone;
+ }
+ return someDone;
+ }
+
+ public static boolean importPaeJSONAsContactMatrixToStructure(
+ StructureMapping sm, InputStream paeInput, String label)
+ throws IOException, ParseException
+ {
+ JSONObject pae_obj = parseJSONtoPAEContactMatrix(paeInput);
+ if (pae_obj == null)
+ {
+ Console.debug("JSON file did not parse properly.");
+ return false;
+ }
+
+ SequenceI seq = sm.getSequence();
+ ContactMatrixI matrix = new PAEContactMatrix(seq,
+ (Map<String, Object>) pae_obj);
+ AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix);
+ /* this already happens in Sequence.addContactList()
+ seq.addAlignmentAnnotation(cmannot);
+ */
+ return true;
+ }
+
+ /**
* general purpose structure importer - designed to yield alignment useful for
* transfer of annotation to associated sequences
*
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);
+ TFType tempfacType = TFType.PLDDT;
+ AlignmentI pdbAlignment = new FormatAdapter().readFile(tmpFile, file,
+ DataSourceType.FILE, fileFormat, tempfacType);
+
if (pdbAlignment != null)
{
List<SequenceI> toremove = new ArrayList<SequenceI>();
if (pid.getFile() == file)
{
chid = pid.getChainCode();
-
}
}
if (chain == null || (chid != null && (chid.equals(chain)
@Override
public String getTestQuery()
{
- return "1QIP";
+ return "AF-O15552-F1";
}
@Override
public String getDbName()
{
- return "PDB"; // getDbSource();
+ return "ALPHAFOLD"; // getDbSource();
}
@Override
return new PDBFeatureSettings();
}
+ // days * 86400000
+ private static final long PAE_CACHE_STALE_TIME = 1 * 86400000;
+
+ private static Map<String, File> paeDownloadCache = new HashMap<>();
+
}
git://source.jalview.org / jalview.git / blobdiff