Merge branch 'features/r2_11_2_alphafold/JAL-2349_JAL-3855' into develop

[jalview.git] / src / jalview / ws / dbsources / EBIAlfaFold.java

diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java
index e3687bd..7c72f4b 100644 (file)
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -22,8 +22,12 @@
 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;
@@ -36,15 +40,23 @@ import jalview.io.FileFormat;
 import jalview.io.FileFormatI;
 import jalview.io.FormatAdapter;
 import jalview.io.PDBFeatureSettings;
+import jalview.javascript.json.JSON;
 import jalview.structure.StructureImportSettings;
 import jalview.util.HttpUtils;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.datamodel.alphafold.PAEContactMatrix;
 import jalview.ws.ebi.EBIFetchClient;
 import jalview.ws.utils.UrlDownloadClient;
 
+import java.io.BufferedReader;
 import java.io.File;
+import java.io.FileInputStream;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Map;
+
+import org.jmol.adapter.readers.simple.JSONReader;
 
 import com.stevesoft.pat.Regex;
 
@@ -116,6 +128,12 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     return "https://alphafold.ebi.ac.uk/files/" + id + "-model_v1.cif";
   }
 
+  public static String getAlphaFoldPaeDownloadUrl(String id)
+  {
+    return "https://alphafold.ebi.ac.uk/files/" + id
+            + "-predicted_aligned_error_v1.json";
+  }
+
   /*
    * (non-Javadoc)
    * 
@@ -146,7 +164,7 @@ 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;
     }
@@ -159,6 +177,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     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 ?
@@ -178,6 +197,29 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
                 { 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);
+      
+      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))
+      {
+        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();
@@ -186,6 +228,24 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
     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
@@ -313,13 +373,13 @@ 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