X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommands.java;h=d3dd6250a3e51a7c13383c13dee4954b2d6f109e;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=93262aa98b97b16b125794691abb79be1f98c1d5;hpb=c0d803f0d4b7374d93f91055007a9a1f16f8c8dd;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java index 93262aa..d3dd625 100644 --- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java +++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java @@ -20,422 +20,440 @@ */ package jalview.ext.rbvi.chimera; -import jalview.api.FeatureRenderer; -import jalview.api.SequenceRenderer; -import jalview.datamodel.AlignmentI; -import jalview.datamodel.SequenceFeature; -import jalview.datamodel.SequenceI; -import jalview.structure.StructureMapping; -import jalview.structure.StructureMappingcommandSet; -import jalview.structure.StructureSelectionManager; -import jalview.util.ColorUtils; -import jalview.util.Comparison; +import java.util.Locale; import java.awt.Color; import java.util.ArrayList; -import java.util.HashMap; -import java.util.LinkedHashMap; +import java.util.Arrays; import java.util.List; import java.util.Map; +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; + /** * Routines for generating Chimera commands for Jalview/Chimera binding * * @author JimP * */ -public class ChimeraCommands +public class ChimeraCommands extends StructureCommandsBase { + // 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"); + + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/stop.html + private static final StructureCommand CLOSE_CHIMERA = new StructureCommand( + "stop really"); + + // 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 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"); + + 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"); + + // Chimera clause to exclude alternate locations in atom selection + private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9"; + + @Override + public StructureCommandI colourResidues(String atomSpec, Color colour) + { + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/color.html + String colourCode = getColourString(colour); + return new StructureCommand("color " + colourCode + " " + atomSpec); + } /** - * utility to construct the commands to colour chains by the given alignment - * for passing to Chimera - * - * @returns Object[] { Object[] { , + * Returns a colour formatted suitable for use in viewer command syntax * + * @param colour + * @return */ - public static StructureMappingcommandSet getColourBySequenceCommand( - StructureSelectionManager ssm, String[] files, - SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, - AlignmentI alignment) + protected String getColourString(Color colour) { - Map colourMap = buildColoursMap( - ssm, files, sequence, sr, fr, alignment); - - List colourCommands = buildColourCommands(colourMap); - - StructureMappingcommandSet cs = new StructureMappingcommandSet( - ChimeraCommands.class, null, - colourCommands.toArray(new String[colourCommands.size()])); - - return cs; + return ColorUtils.toTkCode(colour); } /** - * Traverse the map of colours/models/chains/positions to construct a list of - * 'color' commands (one per distinct colour used). The format of each command - * is + * Traverse the map of features/values/models/chains/positions to construct a + * list of 'setattr' commands (one per distinct feature type and value). + *

+ * The format of each command is * * 

-   * 
 
-   * color colorname #modelnumber:range.chain 
-   * e.g. color #00ff00 #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
+   * 
 setattr r  " " #modelnumber:range.chain 
+   * e.g. setattr r jv_chain <value> #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
    * 

    *
* - * @param colourMap + * @param featureMap * @return */ - protected static List buildColourCommands( - Map colourMap) + @Override + public List setAttributes( + Map> featureMap) { - /* - * This version concatenates all commands into a single String (semi-colon - * delimited). If length limit issues arise, refactor to return one color - * command per colour. - */ - List commands = new ArrayList(); - StringBuilder sb = new StringBuilder(256); - boolean firstColour = true; - for (Color colour : colourMap.keySet()) + List commands = new ArrayList<>(); + for (String featureType : featureMap.keySet()) { - String colourCode = ColorUtils.toTkCode(colour); - if (!firstColour) + String attributeName = makeAttributeName(featureType); + + /* + * clear down existing attributes for this feature + */ + // 'problem' - sets attribute to None on all residues - overkill? + // commands.add("~setattr r " + attributeName + " :*"); + + Map values = featureMap.get(featureType); + for (Object value : values.keySet()) { - sb.append("; "); + /* + * 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("\\'", "'"); + StructureCommandI cmd = setAttribute(attributeName, featureValue, + atomSpecModel); + commands.add(cmd); } - sb.append("color ").append(colourCode).append(" "); - firstColour = false; - final AtomSpecModel colourData = colourMap - .get(colour); - sb.append(colourData.getAtomSpec()); } - commands.add(sb.toString()); + return commands; } /** - * Traverses a map of { modelNumber, {chain, {list of from-to ranges} } } and - * builds a Chimera format atom spec + * Returns a viewer command to set the given residue attribute value on + * residues specified by the AtomSpecModel, for example + * + * 
+   * setatr res jv_chain 'primary' #1:12-34,48-55.B
+   *
* - * @param modelAndChainRanges + * @param attributeName + * @param attributeValue + * @param atomSpecModel + * @return */ - protected static String getAtomSpec( - Map>> modelAndChainRanges) + protected StructureCommandI setAttribute(String attributeName, + String attributeValue, AtomSpecModel atomSpecModel) { StringBuilder sb = new StringBuilder(128); - boolean firstModelForColour = true; - for (Integer model : modelAndChainRanges.keySet()) - { - boolean firstPositionForModel = true; - if (!firstModelForColour) - { - sb.append("|"); - } - firstModelForColour = false; - sb.append("#").append(model).append(":"); - - final Map> modelData = modelAndChainRanges - .get(model); - for (String chain : modelData.keySet()) - { - boolean hasChain = !"".equals(chain.trim()); - for (int[] range : modelData.get(chain)) - { - if (!firstPositionForModel) - { - sb.append(","); - } - if (range[0] == range[1]) - { - sb.append(range[0]); - } - else - { - sb.append(range[0]).append("-").append(range[1]); - } - if (hasChain) - { - sb.append(".").append(chain); - } - firstPositionForModel = false; - } - } - } - return sb.toString(); + sb.append("setattr res ").append(attributeName).append(" '") + .append(attributeValue).append("' "); + sb.append(getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY)); + return new StructureCommand(sb.toString()); } /** - * 
-   * Build a data structure which maps contiguous subsequences for each colour. 
-   * This generates a data structure from which we can easily generate the 
-   * Chimera command for colour by sequence.
-   * Color
-   *     Model number
-   *         Chain
-   *             list of start/end ranges
-   * Ordering is by order of addition (for colours and positions), natural ordering (for models and chains)
-   *
+ * Makes a prefixed and valid Chimera attribute name. A jv_ prefix is applied + * for a 'Jalview' namespace, and any non-alphanumeric character is converted + * to an underscore. + * + * @param featureType + * @return + * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html */ - protected static Map buildColoursMap( - StructureSelectionManager ssm, String[] files, - SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, - AlignmentI alignment) + @Override + protected String makeAttributeName(String featureType) { - Map colourMap = new LinkedHashMap(); - Color lastColour = null; - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) + String attName = super.makeAttributeName(featureType); + + /* + * Chimera treats an attribute name ending in 'color' as colour-valued; + * Jalview doesn't, so prevent this by appending an underscore + */ + if (attName.toUpperCase(Locale.ROOT).endsWith("COLOR")) { - StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); + attName += "_"; + } - if (mapping == null || mapping.length < 1) - { - continue; - } + return attName; + } + + @Override + public StructureCommandI colourByChain() + { + return COLOUR_BY_CHAIN; + } + + @Override + public List colourByCharge() + { + return Arrays.asList(COLOUR_BY_CHARGE); + } - int startPos = -1, lastPos = -1; - String lastChain = ""; - for (int s = 0; s < sequence[pdbfnum].length; s++) + @Override + public String getResidueSpec(String residue) + { + return "::" + residue; + } + + @Override + public StructureCommandI setBackgroundColour(Color col) + { + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/set.html#bgcolor + return new StructureCommand("set bgColor " + ColorUtils.toTkCode(col)); + } + + @Override + public StructureCommandI focusView() + { + return FOCUS_VIEW; + } + + @Override + public List showChains(List toShow) + { + /* + * Construct a chimera command like + * + * ~display #*;~ribbon #*;ribbon :.A,:.B + */ + StringBuilder cmd = new StringBuilder(64); + boolean first = true; + for (String chain : toShow) + { + String[] tokens = chain.split(":"); + if (tokens.length == 2) { - for (int sp, m = 0; m < mapping.length; m++) + String showChainCmd = tokens[0] + ":." + tokens[1]; + if (!first) { - final SequenceI seq = sequence[pdbfnum][s]; - if (mapping[m].getSequence() == seq - && (sp = alignment.findIndex(seq)) > -1) - { - SequenceI asp = alignment.getSequenceAt(sp); - for (int r = 0; r < asp.getLength(); r++) - { - // no mapping to gaps in sequence - if (Comparison.isGap(asp.getCharAt(r))) - { - continue; - } - int pos = mapping[m].getPDBResNum(asp.findPosition(r)); - - if (pos < 1 || pos == lastPos) - { - continue; - } - - Color colour = sr.getResidueColour(seq, r, fr); - final String chain = mapping[m].getChain(); - - /* - * Just keep incrementing the end position for this colour range - * _unless_ colour, PDB model or chain has changed, or there is a - * gap in the mapped residue sequence - */ - final boolean newColour = !colour.equals(lastColour); - final boolean nonContig = lastPos + 1 != pos; - final boolean newChain = !chain.equals(lastChain); - if (newColour || nonContig || newChain) - { - if (startPos != -1) - { - addColourRange(colourMap, lastColour, pdbfnum, startPos, - lastPos, lastChain); - } - startPos = pos; - } - lastColour = colour; - lastPos = pos; - lastChain = chain; - } - // final colour range - if (lastColour != null) - { - addColourRange(colourMap, lastColour, pdbfnum, startPos, - lastPos, lastChain); - } - // break; - } + cmd.append(","); } + cmd.append(showChainCmd); + first = false; } } - return colourMap; + + /* + * could append ";focus" to this command to resize the display to fill the + * window, but it looks more helpful not to (easier to relate chains to the + * whole) + */ + final String command = "~display #*; ~ribbon #*; ribbon :" + + cmd.toString(); + return Arrays.asList(new StructureCommand(command)); } - /** - * Helper method to add one contiguous colour range to the colour map. - * - * @param colourMap - * @param colour - * @param model - * @param startPos - * @param endPos - * @param chain - */ - protected static void addColourRange( -Map colourMap, - Color colour, int model, int startPos, int endPos, String chain) + @Override + public List superposeStructures(AtomSpecModel ref, + AtomSpecModel spec, AtomSpecType backbone) { - // refactor for reuse as addRange /* - * Get/initialize map of data for the colour + * Form Chimera match command to match spec to ref + * (the first set of atoms are moved on to the second) + * + * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA + * + * @see https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html */ - AtomSpecModel colourData = colourMap.get(colour); - if (colourData == null) - { - colourData = new AtomSpecModel(); - colourMap.put(colour, colourData); - } + StringBuilder cmd = new StringBuilder(); + 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, AtomSpecType.RESIDUE_ONLY); + String refSpec = getAtomSpec(ref, AtomSpecType.RESIDUE_ONLY); + cmd.append("; ribbon "); + cmd.append(atomSpec).append("|").append(refSpec).append("; focus"); - colourData.addRange(model, startPos, endPos, chain); + return Arrays.asList(new StructureCommand(cmd.toString())); } - /** - * Constructs and returns a set of Chimera commands to set attributes on - * residues corresponding to features in Jalview. - * - * @param ssm - * @param files - * @param seqs - * @param fr - * @param alignment - * @return - */ - public static StructureMappingcommandSet getSetAttributeCommandsForFeatures( - StructureSelectionManager ssm, String[] files, - SequenceI[][] seqs, FeatureRenderer fr, AlignmentI alignment) + @Override + public StructureCommandI openCommandFile(String path) { - Map>>> featureMap = buildFeaturesMap( - ssm, files, seqs, fr, alignment); - - List colourCommands = buildSetAttributeCommands(featureMap); - - StructureMappingcommandSet cs = new StructureMappingcommandSet( - ChimeraCommands.class, null, - colourCommands.toArray(new String[colourCommands.size()])); + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html + return new StructureCommand("open cmd:" + path); + } - return cs; + @Override + public StructureCommandI saveSession(String filepath) + { + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/save.html + return new StructureCommand("save " + filepath); } /** + * Returns the range(s) modelled by {@code atomSpec} formatted as a Chimera + * atomspec string, e.g. + * * 
-   * Helper method to build a map of 
-   * { featureType, {modelNumber, {chain, {list of from-to ranges} } } }
+   * #0:15.A,28.A,54.A,70-72.A|#1:2.A,6.A,11.A,13-14.A
    *
* - * @param ssm - * @param files - * @param seqs - * @param fr - * @param alignment + * where + *
    + *
  • #0 is a model number
    • + *
  • 15 or 70-72 is a residue number, or range of residue numbers
    • + *
  • .A is a chain identifier
    • + *
  • residue ranges are separated by comma
    • + *
  • atomspecs for distinct models are separated by | (or)
    • + *
+ * + * 
+   * 
+   * @param model
+   * @param specType
    * @return
+   * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
    */
-  protected static Map>>> buildFeaturesMap(
-          StructureSelectionManager ssm, String[] files,
-          SequenceI[][] seqs, FeatureRenderer fr, AlignmentI alignment)
+  @Override
+  public String getAtomSpec(AtomSpecModel atomSpec, AtomSpecType specType)
   {
-    Map>>> theMap = new HashMap>>>();
-
-    List visibleFeatures = fr.getDisplayedFeatureTypes();
-    if (visibleFeatures.isEmpty())
-    {
-      return theMap;
-    }
-    
-    /*
-     * traverse mappings to structures 
-     */
-    for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
+    StringBuilder sb = new StringBuilder(128);
+    boolean firstModel = true;
+    for (String model : atomSpec.getModels())
     {
-      StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
-
-      if (mapping == null || mapping.length < 1)
+      if (!firstModel)
       {
-        continue;
-      }
-
-      int lastPos = -1;
-      for (int seqNo = 0; seqNo < seqs[pdbfnum].length; seqNo++)
-      {
-        for (int m = 0; m < mapping.length; m++)
-        {
-          final SequenceI seq = seqs[pdbfnum][seqNo];
-          int sp = alignment.findIndex(seq);
-          if (mapping[m].getSequence() == seq && sp > -1)
-          {
-            SequenceI asp = alignment.getSequenceAt(sp);
-
-            /*
-             * traverse each sequence for its mapped positions
-             */
-            for (int r = 0; r < asp.getLength(); r++)
-            {
-              // no mapping to gaps in sequence
-              if (Comparison.isGap(asp.getCharAt(r)))
-              {
-                continue;
-              }
-              int residuePos = asp.findPosition(r);
-              int pos = mapping[m].getPDBResNum(residuePos);
-
-              if (pos < 1 || pos == lastPos)
-              {
-                continue;
-              }
-              final String chain = mapping[m].getChain();
-
-              /*
-               * record any features at this position, with the model, chain
-               * and residue number they map to
-               */
-              List features = fr.findFeaturesAtRes(asp,
-                      residuePos);
-              for (SequenceFeature feature : features)
-              {
-                if (!visibleFeatures.contains(feature))
-                {
-                  continue;
-                }
-              }
-            }
-          }
-        }
-      }
+        sb.append("|");
       }
-    return theMap;
+      firstModel = false;
+      appendModel(sb, model, atomSpec, specType);
+    }
+    return sb.toString();
   }
 
   /**
-   * Traverse the map of features/models/chains/positions to construct a list of
-   * 'setattr' commands (one per feature type). The format of each command is
-   * 
-   * 
-   * 
 setattr r  " " #modelnumber:range.chain 
-   * e.g. setattr r jv:chain " " #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
-   * 

-   * 

-   * 

-   * Note we are not (currently) setting attribute values, only the type
-   * (presence) of each attribute. This is to avoid overloading the Chimera REST
-   * interface by sending too many distinct commands. Analysis by feature values
-   * may still be performed in Jalview, on selections created in Chimera.
+   * A helper method to append an atomSpec string for atoms in the given model
    * 
-   * @param featureMap
-   * @return
-   * @see http 
-   *      ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec
-   *      .html
+   * @param sb
+   * @param model
+   * @param atomSpec
+   * @param alphaOnly
    */
-  protected static List buildSetAttributeCommands(
-          Map>>> featureMap)
+  protected void appendModel(StringBuilder sb, String model,
+          AtomSpecModel atomSpec, AtomSpecType specType)
   {
-    List commands = new ArrayList();
-    for (String featureType : featureMap.keySet())
+    sb.append("#").append(model).append(":");
+
+    boolean firstPositionForModel = true;
+
+    for (String chain : atomSpec.getChains(model))
+    {
+      chain = " ".equals(chain) ? chain : chain.trim();
+
+      List rangeList = atomSpec.getRanges(model, chain);
+      for (int[] range : rangeList)
+      {
+        appendRange(sb, range[0], range[1], chain, firstPositionForModel,
+                false);
+        firstPositionForModel = false;
+      }
+    }
+    if (specType == AtomSpecType.ALPHA)
+    {
+      /*
+       * restrict to alpha carbon, no alternative locations
+       * (needed to ensuring matching atom counts for superposition)
+       */
+      sb.append("@CA").append(NO_ALTLOCS);
+    }
+    if (specType == AtomSpecType.PHOSPHATE)
     {
-      StringBuilder sb = new StringBuilder(128);
-      featureType = featureType.replace(" ", "_");
-      sb.append("setattr r jv:").append(featureType).append(" \" \" ");
-      final Map>> featureData = featureMap
-              .get(featureType);
-      sb.append(getAtomSpec(featureData));
-      commands.add(sb.toString());
+      sb.append("@P").append(NO_ALTLOCS);
     }
+  }
 
-    return commands;
+  @Override
+  public List showBackbone()
+  {
+    return Arrays.asList(SHOW_BACKBONE);
+  }
+
+  @Override
+  public StructureCommandI loadFile(String file)
+  {
+    return new StructureCommand("open " + file);
+  }
+
+  @Override
+  public StructureCommandI openSession(String filepath)
+  {
+    // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html
+    // this version of the command has no dependency on file extension
+    return new StructureCommand("open chimera:" + filepath);
+  }
+
+  @Override
+  public StructureCommandI closeViewer()
+  {
+    return CLOSE_CHIMERA;
+  }
+
+  @Override
+  public List startNotifications(String uri)
+  {
+    // 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));
+    return cmds;
+  }
+
+  @Override
+  public List stopNotifications()
+  {
+    List cmds = new ArrayList<>();
+    cmds.add(STOP_NOTIFY_MODELS);
+    cmds.add(STOP_NOTIFY_SELECTION);
+    return cmds;
+  }
+
+  @Override
+  public StructureCommandI getSelectedResidues()
+  {
+    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 + "'");
   }
 
 }