X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fpymol%2FPymolCommands.java;h=b69d3e390c4007d0141da778d972da55e187518f;hb=966baa18c09b8fb041b874acdb8a850ad143d205;hp=bba11a1bcd2d5f2fe343dfbda0af00857b083330;hpb=7720585dc8cc56cdad2486b330ed37ddd0133531;p=jalview.git

diff --git a/src/jalview/ext/pymol/PymolCommands.java b/src/jalview/ext/pymol/PymolCommands.java
index bba11a1..b69d3e3 100644
--- a/src/jalview/ext/pymol/PymolCommands.java
+++ b/src/jalview/ext/pymol/PymolCommands.java
@@ -2,6 +2,7 @@ package jalview.ext.pymol;
 
 import java.awt.Color;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
 import java.util.Map;
 
@@ -22,23 +23,31 @@ import jalview.structure.StructureCommandsBase;
  */
 public class PymolCommands extends StructureCommandsBase
 {
-  private static final StructureCommand COLOUR_BY_CHAIN = new StructureCommand("spectrum", "chain");
-
-  private static final List<StructureCommandI> COLOR_BY_CHARGE = new ArrayList<>();
-
-  private static final List<StructureCommandI> SHOW_BACKBONE = new ArrayList<>();
-
-  static {
-    COLOR_BY_CHARGE.add(new StructureCommand("color", "white", "*"));
-    COLOR_BY_CHARGE
-            .add(new StructureCommand("color", "red", "resn ASP resn GLU"));
-    COLOR_BY_CHARGE.add(
-            new StructureCommand("color", "blue", "resn LYS resn ARG"));
-    COLOR_BY_CHARGE
-            .add(new StructureCommand("color", "yellow", "resn CYS"));
-    SHOW_BACKBONE.add(new StructureCommand("hide", "everything"));
-    SHOW_BACKBONE.add(new StructureCommand("show", "ribbon"));
-  }
+  // https://pymol.org/dokuwiki/doku.php?id=command:zoom
+  // not currently documented on
+  // https://pymolwiki.org/index.php/Category:Commands
+  private static final StructureCommand FOCUS_VIEW = new StructureCommand(
+          "zoom");
+
+  // https://pymolwiki.org/index.php/Quit
+  private static final StructureCommand CLOSE_PYMOL = new StructureCommand(
+          "quit");
+
+  // not currently documented on
+  // https://pymolwiki.org/index.php/Category:Commands
+  private static final StructureCommand COLOUR_BY_CHAIN = new StructureCommand(
+          "spectrum", "chain");
+
+  private static final List<StructureCommandI> COLOR_BY_CHARGE = Arrays
+          .asList(new StructureCommand("color", "white", "*"),
+                  new StructureCommand("color", "red", "resn ASP resn GLU"),
+                  new StructureCommand("color", "blue",
+                          "resn LYS resn ARG"),
+                  new StructureCommand("color", "yellow", "resn CYS"));
+
+  private static final List<StructureCommandI> SHOW_BACKBONE = Arrays
+          .asList(new StructureCommand("hide", "everything"),
+                  new StructureCommand("show", "ribbon"));
 
   @Override
   public StructureCommandI colourByChain()
@@ -75,8 +84,7 @@ public class PymolCommands extends StructureCommandsBase
   @Override
   public StructureCommandI focusView()
   {
-    // TODO what?
-    return null;
+    return FOCUS_VIEW;
   }
 
   @Override
@@ -91,26 +99,32 @@ public class PymolCommands extends StructureCommandsBase
     {
       chains.append(" chain ").append(chain);
     }
-    commands.add(new StructureCommand("show", "cartoon", chains.toString()));
+    commands.add(
+            new StructureCommand("show", "cartoon", chains.toString()));
     return commands;
   }
 
   @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
+    // crashes when undo is enabled on 2.5.2 (incentive)
+    commands.add(new StructureCommand("undo_disable"));
+    commands.add(new StructureCommand("pair_fit", 
+            atomSpec2AlphaOnly, refAtomsAlphaOnly));
+    commands.add(new StructureCommand("undo_enable"));
+    
     /*
      * 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));
 
@@ -144,7 +158,7 @@ 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;
@@ -175,10 +189,14 @@ 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();
@@ -229,7 +247,7 @@ public class PymolCommands extends StructureCommandsBase
       final AtomSpecModel colourData = colourMap.get(colour);
       commands.add(getColourCommand(colourData, colour));
     }
-  
+
     return commands;
   }
 
@@ -247,13 +265,12 @@ public class PymolCommands extends StructureCommandsBase
    * @return
    */
   protected StructureCommandI setAttribute(String attributeName,
-          String attributeValue,
-          AtomSpecModel atomSpecModel)
+          String attributeValue, AtomSpecModel atomSpecModel)
   {
     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());
   }
 
@@ -282,13 +299,13 @@ public class PymolCommands extends StructureCommandsBase
     for (String featureType : featureMap.keySet())
     {
       String attributeName = makeAttributeName(featureType);
-  
+
       /*
        * todo: clear down existing attributes for this feature?
        */
       // commands.add(new StructureCommand("iterate", "all",
       // "p."+attributeName+"='None'"); //?
-  
+
       Map<Object, AtomSpecModel> values = featureMap.get(featureType);
       for (Object value : values.keySet())
       {
@@ -305,7 +322,7 @@ public class PymolCommands extends StructureCommandsBase
         commands.add(cmd);
       }
     }
-  
+
     return commands;
   }
 
@@ -313,7 +330,15 @@ public class PymolCommands extends StructureCommandsBase
   public StructureCommandI openSession(String filepath)
   {
     // https://pymolwiki.org/index.php/Load
-    return new StructureCommand("load", "", "0", "pse");
+    // this version of the command has no dependency on file extension
+    return new StructureCommand("load", filepath, "", "0", "pse");
+  }
+
+  @Override
+  public StructureCommandI closeViewer()
+  {
+    // https://pymolwiki.org/index.php/Quit
+    return CLOSE_PYMOL;
   }
 
 }