X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommands.java;h=d3dd6250a3e51a7c13383c13dee4954b2d6f109e;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=857dbcc162cdbc768f6260b92434c9e1ea6be7cb;hpb=4994aa94fd62af0058f2db96f0ea6c4ca1abe80b;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java index 857dbcc..d3dd625 100644 --- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java +++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java @@ -20,6 +20,8 @@ */ package jalview.ext.rbvi.chimera; +import java.util.Locale; + import java.awt.Color; import java.util.ArrayList; import java.util.Arrays; @@ -30,6 +32,7 @@ import jalview.structure.AtomSpecModel; import jalview.structure.StructureCommand; import jalview.structure.StructureCommandI; import jalview.structure.StructureCommandsBase; +import jalview.structure.StructureCommandsI.AtomSpecType; import jalview.util.ColorUtils; /** @@ -40,13 +43,28 @@ import jalview.util.ColorUtils; */ public class ChimeraCommands extends StructureCommandsBase { - private static final StructureCommand CLOSE_CHIMERA = new StructureCommand("stop really"); + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/focus.html + private static final StructureCommand FOCUS_VIEW = new StructureCommand( + "focus"); + + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listresattr + private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand( + "list resattr"); - private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand("listen stop selection"); + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/stop.html + private static final StructureCommand CLOSE_CHIMERA = new StructureCommand( + "stop really"); - private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand("listen stop models"); + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html + private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand( + "listen stop selection"); - private static final StructureCommand GET_SELECTION = new StructureCommand("list selection level residue"); + private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand( + "listen stop models"); + + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listselection + private static final StructureCommand GET_SELECTION = new StructureCommand( + "list selection level residue"); private static final StructureCommand SHOW_BACKBONE = new StructureCommand( "~display all;~ribbon;chain @CA|P"); @@ -54,6 +72,7 @@ public class ChimeraCommands extends StructureCommandsBase private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand( "color white;color red ::ASP,GLU;color blue ::LYS,ARG;color yellow ::CYS"); + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/rainbow.html private static final StructureCommandI COLOUR_BY_CHAIN = new StructureCommand( "rainbow chain"); @@ -143,13 +162,12 @@ public class ChimeraCommands extends StructureCommandsBase * @return */ protected StructureCommandI setAttribute(String attributeName, - String attributeValue, - AtomSpecModel atomSpecModel) + String attributeValue, AtomSpecModel atomSpecModel) { StringBuilder sb = new StringBuilder(128); sb.append("setattr res ").append(attributeName).append(" '") .append(attributeValue).append("' "); - sb.append(getAtomSpec(atomSpecModel, false)); + sb.append(getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY)); return new StructureCommand(sb.toString()); } @@ -171,7 +189,7 @@ public class ChimeraCommands extends StructureCommandsBase * Chimera treats an attribute name ending in 'color' as colour-valued; * Jalview doesn't, so prevent this by appending an underscore */ - if (attName.toUpperCase().endsWith("COLOR")) + if (attName.toUpperCase(Locale.ROOT).endsWith("COLOR")) { attName += "_"; } @@ -207,8 +225,7 @@ public class ChimeraCommands extends StructureCommandsBase @Override public StructureCommandI focusView() { - // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/focus.html - return new StructureCommand("focus"); + return FOCUS_VIEW; } @Override @@ -248,7 +265,7 @@ public class ChimeraCommands extends StructureCommandsBase @Override public List superposeStructures(AtomSpecModel ref, - AtomSpecModel spec) + AtomSpecModel spec, AtomSpecType backbone) { /* * Form Chimera match command to match spec to ref @@ -259,15 +276,16 @@ public class ChimeraCommands extends StructureCommandsBase * @see https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html */ StringBuilder cmd = new StringBuilder(); - String atomSpecAlphaOnly = getAtomSpec(spec, true); - String refSpecAlphaOnly = getAtomSpec(ref, true); - cmd.append("match ").append(atomSpecAlphaOnly).append(" ").append(refSpecAlphaOnly); + String atomSpecAlphaOnly = getAtomSpec(spec, backbone); + String refSpecAlphaOnly = getAtomSpec(ref, backbone); + cmd.append("match ").append(atomSpecAlphaOnly).append(" ") + .append(refSpecAlphaOnly); /* * show superposed residues as ribbon */ - String atomSpec = getAtomSpec(spec, false); - String refSpec = getAtomSpec(ref, false); + String atomSpec = getAtomSpec(spec, AtomSpecType.RESIDUE_ONLY); + String refSpec = getAtomSpec(ref, AtomSpecType.RESIDUE_ONLY); cmd.append("; ribbon "); cmd.append(atomSpec).append("|").append(refSpec).append("; focus"); @@ -308,12 +326,12 @@ public class ChimeraCommands extends StructureCommandsBase * 
    * 
    * @param model
-   * @param alphaOnly
+   * @param specType
    * @return
    * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
    */
   @Override
-  public String getAtomSpec(AtomSpecModel atomSpec, boolean alphaOnly)
+  public String getAtomSpec(AtomSpecModel atomSpec, AtomSpecType specType)
   {
     StringBuilder sb = new StringBuilder(128);
     boolean firstModel = true;
@@ -324,7 +342,7 @@ public class ChimeraCommands extends StructureCommandsBase
         sb.append("|");
       }
       firstModel = false;
-      appendModel(sb, model, atomSpec, alphaOnly);
+      appendModel(sb, model, atomSpec, specType);
     }
     return sb.toString();
   }
@@ -338,7 +356,7 @@ public class ChimeraCommands extends StructureCommandsBase
    * @param alphaOnly
    */
   protected void appendModel(StringBuilder sb, String model,
-          AtomSpecModel atomSpec, boolean alphaOnly)
+          AtomSpecModel atomSpec, AtomSpecType specType)
   {
     sb.append("#").append(model).append(":");
 
@@ -356,15 +374,18 @@ public class ChimeraCommands extends StructureCommandsBase
         firstPositionForModel = false;
       }
     }
-    if (alphaOnly)
+    if (specType == AtomSpecType.ALPHA)
     {
       /*
        * restrict to alpha carbon, no alternative locations
        * (needed to ensuring matching atom counts for superposition)
        */
-      // TODO @P instead if RNA - add nucleotide flag to AtomSpecModel?
       sb.append("@CA").append(NO_ALTLOCS);
     }
+    if (specType == AtomSpecType.PHOSPHATE)
+    {
+      sb.append("@P").append(NO_ALTLOCS);
+    }
   }
 
   @Override
@@ -379,33 +400,6 @@ public class ChimeraCommands extends StructureCommandsBase
     return new StructureCommand("open " + file);
   }
 
-  /**
-   * Overrides the default method to concatenate colour commands into one
-   */
-  @Override
-  public List colourBySequence(
-          Map colourMap)
-  {
-    List commands = new ArrayList<>();
-    StringBuilder sb = new StringBuilder(colourMap.size() * 20);
-    boolean first = true;
-    for (Object key : colourMap.keySet())
-    {
-      Color colour = (Color) key;
-      final AtomSpecModel colourData = colourMap.get(colour);
-      StructureCommandI command = getColourCommand(colourData, colour);
-      if (!first)
-      {
-        sb.append(getCommandSeparator());
-      }
-      first = false;
-      sb.append(command.getCommand());
-    }
-
-    commands.add(new StructureCommand(sb.toString()));
-    return commands;
-  }
-
   @Override
   public StructureCommandI openSession(String filepath)
   {
@@ -417,7 +411,6 @@ public class ChimeraCommands extends StructureCommandsBase
   @Override
   public StructureCommandI closeViewer()
   {
-    // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/stop.html
     return CLOSE_CHIMERA;
   }
 
@@ -427,14 +420,14 @@ public class ChimeraCommands extends StructureCommandsBase
     // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
     List cmds = new ArrayList<>();
     cmds.add(new StructureCommand("listen start models url " + uri));
-    cmds.add(new StructureCommand("listen start select prefix SelectionChanged url " + uri));
+    cmds.add(new StructureCommand(
+            "listen start select prefix SelectionChanged url " + uri));
     return cmds;
   }
 
   @Override
   public List stopNotifications()
   {
-    // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
     List cmds = new ArrayList<>();
     cmds.add(STOP_NOTIFY_MODELS);
     cmds.add(STOP_NOTIFY_SELECTION);
@@ -447,4 +440,20 @@ public class ChimeraCommands extends StructureCommandsBase
     return GET_SELECTION;
   }
 
+  @Override
+  public StructureCommandI listResidueAttributes()
+  {
+    return LIST_RESIDUE_ATTRIBUTES;
+  }
+
+  @Override
+  public StructureCommandI getResidueAttributes(String attName)
+  {
+    // this alternative command
+    // list residues spec ':*/attName' attr attName
+    // doesn't report 'None' values (which is good), but
+    // fails for 'average.bfactor' (which is bad):
+    return new StructureCommand("list residues attr '" + attName + "'");
+  }
+
 }