X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fpymol%2FPymolCommands.java;h=ed64c006002f22a161bf2582ea46e6ae8af8dabf;hb=f9062df1303c1ff071075256cf4b7ad7c9db9658;hp=115efa15f7408d0f4ed070020e36824537acf608;hpb=1dd1e3cd8272449af3fe4dfa3f69239ca4ae471b;p=jalview.git

diff --git a/src/jalview/ext/pymol/PymolCommands.java b/src/jalview/ext/pymol/PymolCommands.java
index 115efa1..ed64c00 100644
--- a/src/jalview/ext/pymol/PymolCommands.java
+++ b/src/jalview/ext/pymol/PymolCommands.java
@@ -2,7 +2,9 @@ package jalview.ext.pymol;
 
 import java.awt.Color;
 import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
+import java.util.Map;
 
 import jalview.structure.AtomSpecModel;
 import jalview.structure.StructureCommand;
@@ -21,23 +23,31 @@ import jalview.structure.StructureCommandsBase;
  */
 public class PymolCommands extends StructureCommandsBase
 {
-  private static final StructureCommand COLOUR_BY_CHAIN = new StructureCommand("spectrum", "chain");
+  // 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");
 
-  private static final List<StructureCommandI> COLOR_BY_CHARGE = new ArrayList<>();
+  // https://pymolwiki.org/index.php/Quit
+  private static final StructureCommand CLOSE_PYMOL = new StructureCommand(
+          "quit");
 
-  private static final List<StructureCommandI> SHOW_BACKBONE = new ArrayList<>();
+  // not currently documented on
+  // https://pymolwiki.org/index.php/Category:Commands
+  private static final StructureCommand COLOUR_BY_CHAIN = new StructureCommand(
+          "spectrum", "chain");
 
-  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"));
-  }
+  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()
@@ -74,8 +84,7 @@ public class PymolCommands extends StructureCommandsBase
   @Override
   public StructureCommandI focusView()
   {
-    // TODO what?
-    return null;
+    return FOCUS_VIEW;
   }
 
   @Override
@@ -90,26 +99,29 @@ 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
+    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));
 
@@ -143,7 +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;
@@ -174,10 +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();
@@ -190,7 +206,7 @@ public class PymolCommands extends StructureCommandsBase
   }
 
   @Override
-  protected StructureCommandI getColourCommand(String atomSpec, Color colour)
+  protected StructureCommandI colourResidues(String atomSpec, Color colour)
   {
     // https://pymolwiki.org/index.php/Color
     return new StructureCommand("color", getColourString(colour), atomSpec);
@@ -209,4 +225,117 @@ public class PymolCommands extends StructureCommandsBase
     return new StructureCommand("load", file);
   }
 
+  /**
+   * Overrides the default implementation (which generates concatenated
+   * commands) to generate one per colour (because the XML-RPC interface to
+   * PyMOL only accepts one command at a time)
+   * 
+   * @param colourMap
+   * @return
+   */
+  @Override
+  public List<StructureCommandI> colourBySequence(
+          Map<Object, AtomSpecModel> colourMap)
+  {
+    List<StructureCommandI> commands = new ArrayList<>();
+    for (Object key : colourMap.keySet())
+    {
+      Color colour = (Color) key;
+      final AtomSpecModel colourData = colourMap.get(colour);
+      commands.add(getColourCommand(colourData, colour));
+    }
+
+    return commands;
+  }
+
+  /**
+   * Returns a viewer command to set the given atom property value on atoms
+   * specified by the AtomSpecModel, for example
+   * 
+   * <pre>
+   * iterate 4zho//B/12-34,48-55/CA,jv_chain='primary'
+   * </pre>
+   * 
+   * @param attributeName
+   * @param attributeValue
+   * @param atomSpecModel
+   * @return
+   */
+  protected StructureCommandI setAttribute(String attributeName,
+          String attributeValue, AtomSpecModel atomSpecModel)
+  {
+    StringBuilder sb = new StringBuilder(128);
+    sb.append("p.").append(attributeName).append("='")
+            .append(attributeValue).append("'");
+    String atomSpec = getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY);
+    return new StructureCommand("iterate", atomSpec, sb.toString());
+  }
+
+  /**
+   * Traverse the map of features/values/models/chains/positions to construct a
+   * list of 'set property' commands (one per distinct feature type and value).
+   * The values are stored in the 'p' dictionary of user-defined properties of
+   * each atom.
+   * <p>
+   * The format of each command is
+   * 
+   * <pre>
+   * <blockquote> iterate atomspec, p.featureName='value' 
+   * e.g. iterate 4zho//A/23,28-29/CA, p.jv_Metal='Fe'
+   * </blockquote>
+   * </pre>
+   * 
+   * @param featureMap
+   * @return
+   */
+  @Override
+  public List<StructureCommandI> setAttributes(
+          Map<String, Map<Object, AtomSpecModel>> featureMap)
+  {
+    List<StructureCommandI> commands = new ArrayList<>();
+    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())
+      {
+        /*
+         * for each distinct value recorded for this feature type,
+         * add a command to set the attribute on the mapped residues
+         * Put values in single quotes, encoding any embedded single quotes
+         */
+        AtomSpecModel atomSpecModel = values.get(value);
+        String featureValue = value.toString();
+        featureValue = featureValue.replaceAll("\\'", "&#39;");
+        StructureCommandI cmd = setAttribute(attributeName, featureValue,
+                atomSpecModel);
+        commands.add(cmd);
+      }
+    }
+
+    return commands;
+  }
+
+  @Override
+  public StructureCommandI openSession(String filepath)
+  {
+    // https://pymolwiki.org/index.php/Load
+    // 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;
+  }
+
 }