X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fjmol%2FJmolParser.java;h=269fc31519b159d52450f4fbe49742743a698fb2;hb=51ff7ec3b6914f3c69b35e91e69d10c88aaf5270;hp=661ed33b780e6fe089382c80c949b5f96de1062f;hpb=0d3cbb0cb96f079d5dd499301ba8733297a22c91;p=jalview.git

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index 661ed33..269fc31 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -37,6 +37,8 @@ import org.jmol.viewer.Viewer;
 
 import com.stevesoft.pat.Regex;
 
+import jalview.bin.Console;
+import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.PDBEntry;
@@ -49,6 +51,7 @@ import jalview.io.StructureFile;
 import jalview.schemes.ResidueProperties;
 import jalview.util.Format;
 import jalview.util.MessageManager;
+import jalview.ws.dbsources.EBIAlfaFold;
 import mc_view.Atom;
 import mc_view.PDBChain;
 import mc_view.Residue;
@@ -278,6 +281,28 @@ public class JmolParser extends StructureFile implements JmolStatusListener
           createAnnotation(chainseq, chain, ms.at);
         }
       }
+      if (isAlphafoldModel())
+      {
+        // TODO - work out how to handle different ways that pAE is provided
+        //
+        try
+        {
+          Console.info("retrieving pAE for " + pdbId);
+          Alignment al = new Alignment(prot.toArray(new SequenceI[0]));
+          EBIAlfaFold.retrieve_AlphaFold_pAE(pdbId, al, null);
+          if (al.getAlignmentAnnotation() != null)
+          {
+            for (AlignmentAnnotation alann : al.getAlignmentAnnotation())
+            {
+              annotations.add(alann);
+            }
+          }
+          ;
+        } catch (Throwable t)
+        {
+          Console.error("Couldn't get the pAE for " + pdbId, t);
+        }
+      }
     } catch (OutOfMemoryError er)
     {
       System.out.println(