Merge branch 'develop' into feature/r2_11_2/JAL-3808_gff2_exonerate

[jalview.git] / src / jalview / ext / pymol / PymolCommands.java

diff --git a/src/jalview/ext/pymol/PymolCommands.java b/src/jalview/ext/pymol/PymolCommands.java
index 36957f5..ed64c00 100644 (file)
--- a/src/jalview/ext/pymol/PymolCommands.java
+++ b/src/jalview/ext/pymol/PymolCommands.java
@@ -106,20 +106,22 @@ public class PymolCommands extends StructureCommandsBase
 
   @Override
   public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
-          AtomSpecModel atomSpec)
+          AtomSpecModel atomSpec, AtomSpecType specType)
   {
+             
     // https://pymolwiki.org/index.php/Super
     List<StructureCommandI> commands = new ArrayList<>();
-    String refAtomsAlphaOnly = getAtomSpec(refAtoms, true);
-    String atomSpec2AlphaOnly = getAtomSpec(atomSpec, true);
-    commands.add(new StructureCommand("super", refAtomsAlphaOnly,
-            atomSpec2AlphaOnly));
+    String refAtomsAlphaOnly = "("+getAtomSpec(refAtoms, specType)+" and (altloc '' or altloc 'a'))";
+    String atomSpec2AlphaOnly = "("+getAtomSpec(atomSpec, specType)+" and (altloc '' or altloc 'a'))";
+    // pair_fit mobile -> reference
+    commands.add(new StructureCommand("pair_fit", 
+            atomSpec2AlphaOnly, refAtomsAlphaOnly));
 
     /*
      * and show superposed residues as cartoon
      */
-    String refAtomsAll = getAtomSpec(refAtoms, false);
-    String atomSpec2All = getAtomSpec(atomSpec, false);
+    String refAtomsAll = getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY);
+    String atomSpec2All = getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY);
     commands.add(new StructureCommand("show", "cartoon",
             refAtomsAll + " " + atomSpec2All));
 
@@ -153,7 +155,7 @@ public class PymolCommands extends StructureCommandsBase
    * @see https://pymolwiki.org/index.php/Selection_Macros
    */
   @Override
-  public String getAtomSpec(AtomSpecModel model, boolean alphaOnly)
+  public String getAtomSpec(AtomSpecModel model, AtomSpecType specType)
   {
     StringBuilder sb = new StringBuilder(64);
     boolean first = true;
@@ -184,10 +186,14 @@ public class PymolCommands extends StructureCommandsBase
           }
         }
         sb.append("/");
-        if (alphaOnly)
+        if (specType == AtomSpecType.ALPHA)
         {
           sb.append("CA");
         }
+        if (specType == AtomSpecType.PHOSPHATE)
+        {
+          sb.append("P");
+        }
       }
     }
     return sb.toString();
@@ -261,7 +267,7 @@ public class PymolCommands extends StructureCommandsBase
     StringBuilder sb = new StringBuilder(128);
     sb.append("p.").append(attributeName).append("='")
             .append(attributeValue).append("'");
-    String atomSpec = getAtomSpec(atomSpecModel, false);
+    String atomSpec = getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY);
     return new StructureCommand("iterate", atomSpec, sb.toString());
   }