From: Jim Procter <j.procter@dundee.ac.uk>
Date: Sat, 15 Oct 2022 10:11:34 +0000 (+0100)
Subject: JAL-3855 import pAE when StructureSelectionManager parses an alphaFold structure... 
X-Git-Tag: Release_2_11_3_0~23^2~47
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=356ec810340821d8b1b1701aae913b3a58778335

JAL-3855 import pAE when StructureSelectionManager parses an alphaFold structure. Works but AlignmentI holding the contact matrices prevents transfer.
---

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index 661ed33..ec123f4 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 +281,21 @@ 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);
+          ;
+        } catch (Throwable t)
+        {
+          Console.error("Couldn't get the pAE for " + pdbId, t);
+        }
+      }
     } catch (OutOfMemoryError er)
     {
       System.out.println(
diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java
index fa867cd..0e148ff 100644
--- a/src/jalview/ws/dbsources/EBIAlfaFold.java
+++ b/src/jalview/ws/dbsources/EBIAlfaFold.java
@@ -274,6 +274,9 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy
             pdbAlignment.getSequenceAt(0),
             (Map<String, Object>) pae_obj.get(0));
 
+    // THIS IS NOT GOING TO WORK !!!
+    // ?? StructureFile assumes sequenceI holds all data, so AlignmentAnnotation
+    // needs to hold the contact matrix data.
     pdbAlignment.getSequenceAt(0)
             .addAlignmentAnnotation(pdbAlignment.addContactList(matrix));
     return true;