From d46c8cbd1a5282ede9a0a94471f23ca002cf7df6 Mon Sep 17 00:00:00 2001
From: Jim Procter <j.procter@dundee.ac.uk>
Date: Tue, 14 Sep 2021 15:51:39 +0100
Subject: [PATCH] JAL-3855 detect an alphafold model and import its
 temperature factor as reliability

---
 src/jalview/ext/jmol/JmolParser.java |   25 +++++++++++++++++++++++--
 src/mc_view/PDBChain.java            |   18 +++++++++++++++---
 src/mc_view/PDBfile.java             |    3 ++-
 test/mc_view/PDBChainTest.java       |    2 +-
 4 files changed, 41 insertions(+), 7 deletions(-)

diff --git a/src/jalview/ext/jmol/JmolParser.java b/src/jalview/ext/jmol/JmolParser.java
index a9c5f5c..ae8ff7a 100644
--- a/src/jalview/ext/jmol/JmolParser.java
+++ b/src/jalview/ext/jmol/JmolParser.java
@@ -45,6 +45,8 @@ import org.jmol.c.STR;
 import org.jmol.modelset.ModelSet;
 import org.jmol.viewer.Viewer;
 
+import com.stevesoft.pat.Regex;
+
 import mc_view.Atom;
 import mc_view.PDBChain;
 import mc_view.Residue;
@@ -59,6 +61,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener
 {
   Viewer viewer = null;
 
+  private boolean alphaFoldModel;
+
   public JmolParser(boolean immediate, Object inFile,
           DataSourceType sourceType) throws IOException
   {
@@ -148,16 +152,26 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     }
     return viewer;
   }
+  
+  public static Regex getNewAlphafoldValidator()
+  {
+    Regex validator =  new Regex("(AF-[A-Z]+[0-9]+[A-Z0-9]+-F1)");
+    validator.setIgnoreCase(true);
+    return validator;
+  }
+
 
   public void transformJmolModelToJalview(ModelSet ms) throws IOException
   {
     try
     {
+      Regex alphaFold = getNewAlphafoldValidator();
       String lastID = "";
       List<SequenceI> rna = new ArrayList<SequenceI>();
       List<SequenceI> prot = new ArrayList<SequenceI>();
       PDBChain tmpchain;
       String pdbId = (String) ms.getInfo(0, "title");
+      String isMMCIF = (String) ms.getInfo(0, "fileType");
 
       if (pdbId == null)
       {
@@ -168,6 +182,8 @@ public class JmolParser extends StructureFile implements JmolStatusListener
       {
         setId(pdbId);
         setPDBIdAvailable(true);
+        alphaFoldModel = alphaFold.search(pdbId) && isMMCIF!=null && isMMCIF.equalsIgnoreCase("mmcif");  
+
       }
       List<Atom> significantAtoms = convertSignificantAtoms(ms);
       for (Atom tmpatom : significantAtoms)
@@ -183,7 +199,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
           tmpchain.atoms.addElement(tmpatom);
         } else
         {
-          tmpchain = new PDBChain(getId(), tmpatom.chain);
+          tmpchain = new PDBChain(getId(), tmpatom.chain,isAlphafoldModel());
           getChains().add(tmpchain);
           tmpchain.atoms.addElement(tmpatom);
         }
@@ -225,6 +241,11 @@ public class JmolParser extends StructureFile implements JmolStatusListener
     }
   }
 
+  private boolean isAlphafoldModel()
+  {
+    return alphaFoldModel;
+  }
+
   private List<Atom> convertSignificantAtoms(ModelSet ms)
   {
     List<Atom> significantAtoms = new ArrayList<Atom>();
@@ -351,7 +372,7 @@ public class JmolParser extends StructureFile implements JmolStatusListener
 
   /**
    * Helper method that adds an AlignmentAnnotation for secondary structure to
-   * the sequence, provided at least one secondary structure prediction has been
+   * the sequence, provided at least one secondary structure assignment has been
    * made
    * 
    * @param modelTitle
diff --git a/src/mc_view/PDBChain.java b/src/mc_view/PDBChain.java
index a3c8bee..60c289e 100755
--- a/src/mc_view/PDBChain.java
+++ b/src/mc_view/PDBChain.java
@@ -78,10 +78,11 @@ public class PDBChain
 
   public String pdbid = "";
 
-  public PDBChain(String thePdbid, String theId)
+  public PDBChain(String thePdbid, String theId, boolean isAlphaFoldModel)
   {
     this.pdbid = thePdbid == null ? thePdbid : thePdbid.toLowerCase();
     this.id = theId;
+    this.alphaFoldModel = isAlphaFoldModel;
   }
 
   /**
@@ -91,6 +92,8 @@ public class PDBChain
 
   public Mapping shadowMap;
 
+  private boolean alphaFoldModel;
+
   public void setNewlineString(String nl)
   {
     newline = nl;
@@ -490,15 +493,24 @@ public class PDBChain
         min = Math.min(min, annots[i].value);
         resAnnotation.setElementAt(null, i);
       }
-
+      String tfacName = "Temperature Factor";
+      if (isAlphaFoldModel())
+      {
+        tfacName = "Alphafold Reliability";
+      }
       AlignmentAnnotation tfactorann = new AlignmentAnnotation(
-              "Temperature Factor", "Temperature Factor for " + pdbid + id,
+              tfacName, tfacName + " for " + pdbid + id,
               annots, min, max, AlignmentAnnotation.LINE_GRAPH);
       tfactorann.setSequenceRef(sequence);
       sequence.addAlignmentAnnotation(tfactorann);
     }
   }
 
+  private boolean isAlphaFoldModel()
+  {
+    return alphaFoldModel;
+  }
+
   /**
    * Colour start/end of bonds by charge
    * <ul>
diff --git a/src/mc_view/PDBfile.java b/src/mc_view/PDBfile.java
index 04eda42..24e0435 100755
--- a/src/mc_view/PDBfile.java
+++ b/src/mc_view/PDBfile.java
@@ -154,7 +154,8 @@ public class PDBfile extends StructureFile
             tmpchain.atoms.addElement(tmpatom);
           } else
           {
-            tmpchain = new PDBChain(getId(), tmpatom.chain);
+            // PDBfile never handles alphafold models, so false
+            tmpchain = new PDBChain(getId(), tmpatom.chain, false);
             getChains().add(tmpchain);
             tmpchain.atoms.addElement(tmpatom);
           }
diff --git a/test/mc_view/PDBChainTest.java b/test/mc_view/PDBChainTest.java
index 0f748ce..14ec1e7 100644
--- a/test/mc_view/PDBChainTest.java
+++ b/test/mc_view/PDBChainTest.java
@@ -68,7 +68,7 @@ public class PDBChainTest
   {
     System.out.println("setup");
     StructureImportSettings.setShowSeqFeatures(true);
-    c = new PDBChain("1GAQ", "A");
+    c = new PDBChain("1GAQ", "A", false);
   }
 
   @Test(groups = { "Functional" })
-- 
1.7.10.2