X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommands.java;h=6d4caa220bb32d991fc3b65da2a6a574dc046ce6;hb=f9062df1303c1ff071075256cf4b7ad7c9db9658;hp=a551ca26a8f55131e4a3e3376b132ab3404909d7;hpb=d787bb9555e6ad57ae4e10a89f842345ff05ec77;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java index a551ca2..6d4caa2 100644 --- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java +++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java @@ -20,22 +20,20 @@ */ package jalview.ext.rbvi.chimera; -import jalview.api.FeatureRenderer; -import jalview.api.SequenceRenderer; -import jalview.datamodel.AlignmentI; -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.LinkedHashMap; +import java.util.Arrays; import java.util.List; import java.util.Map; -import java.util.TreeMap; + +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 @@ -43,251 +41,412 @@ import java.util.TreeMap; * @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); + } + + /** + * Returns a colour formatted suitable for use in viewer command syntax + * + * @param colour + * @return + */ + protected String getColourString(Color colour) + { + return ColorUtils.toTkCode(colour); + } /** - * utility to construct the commands to colour chains by the given alignment - * for passing to Chimera + * 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 * - * @returns Object[] { Object[] { , + * 

+   * 
 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 featureMap + * @return */ - public static StructureMappingcommandSet[] getColourBySequenceCommand( - StructureSelectionManager ssm, String[] files, - SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr, - AlignmentI alignment) + @Override + public List setAttributes( + Map> featureMap) { - Map>>> colourMap = buildColoursMap( - ssm, files, sequence, sr, fr, alignment); + List commands = new ArrayList<>(); + for (String featureType : featureMap.keySet()) + { + String attributeName = makeAttributeName(featureType); - List colourCommands = buildColourCommands(colourMap); + /* + * clear down existing attributes for this feature + */ + // 'problem' - sets attribute to None on all residues - overkill? + // commands.add("~setattr r " + attributeName + " :*"); - StructureMappingcommandSet cs = new StructureMappingcommandSet( - ChimeraCommands.class, null, - colourCommands.toArray(new String[0])); + Map 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("\\'", "'"); + StructureCommandI cmd = setAttribute(attributeName, featureValue, + atomSpecModel); + commands.add(cmd); + } + } - return new StructureMappingcommandSet[] { cs }; + return commands; } /** - * 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 + * Returns a viewer command to set the given residue attribute value on + * residues specified by the AtomSpecModel, for example * - *
color colorname #modelnumber:range.chain e.g. color #00ff00 - * #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,... + * 
+   * setatr res jv_chain 'primary' #1:12-34,48-55.B
+   *
* - * @see http - * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec - * .html + * @param attributeName + * @param attributeValue + * @param atomSpecModel + * @return + */ + protected StructureCommandI setAttribute(String attributeName, + String attributeValue, + AtomSpecModel atomSpecModel) + { + StringBuilder sb = new StringBuilder(128); + sb.append("setattr res ").append(attributeName).append(" '") + .append(attributeValue).append("' "); + sb.append(getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY)); + return new StructureCommand(sb.toString()); + } + + /** + * 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 colourMap + * @param featureType * @return + * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html */ - protected static List buildColourCommands( - Map>>> colourMap) + @Override + protected String makeAttributeName(String featureType) { + String attName = super.makeAttributeName(featureType); + /* - * 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. + * Chimera treats an attribute name ending in 'color' as colour-valued; + * Jalview doesn't, so prevent this by appending an underscore */ - List commands = new ArrayList(); - StringBuilder sb = new StringBuilder(256); - boolean firstColour = true; - for (Color colour : colourMap.keySet()) + if (attName.toUpperCase(Locale.ROOT).endsWith("COLOR")) { - String colourCode = ColorUtils.toTkCode(colour); - if (!firstColour) - { - sb.append("; "); - } - sb.append("color ").append(colourCode).append(" "); - firstColour = false; - boolean firstModelForColour = true; - final Map>> colourData = colourMap - .get(colour); - for (Integer model : colourData.keySet()) - { - boolean firstPositionForModel = true; - if (!firstModelForColour) - { - sb.append("|"); - } - firstModelForColour = false; - sb.append("#").append(model).append(":"); + attName += "_"; + } + + return attName; + } + + @Override + public StructureCommandI colourByChain() + { + return COLOUR_BY_CHAIN; + } + + @Override + public List colourByCharge() + { + return Arrays.asList(COLOUR_BY_CHARGE); + } - final Map> modelData = colourData.get(model); - for (String chain : modelData.keySet()) + @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) + { + String showChainCmd = tokens[0] + ":." + tokens[1]; + if (!first) { - 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; - } + cmd.append(","); } + cmd.append(showChainCmd); + first = false; } } - commands.add(sb.toString()); - return commands; + + /* + * 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)); + } + + @Override + public List superposeStructures(AtomSpecModel ref, + AtomSpecModel spec, AtomSpecType backbone) + { + /* + * 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 + */ + 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"); + + return Arrays.asList(new StructureCommand(cmd.toString())); + } + + @Override + public StructureCommandI openCommandFile(String path) + { + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html + return new StructureCommand("open cmd:" + path); + } + + @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. + * * 
-   * 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)
+   * #0:15.A,28.A,54.A,70-72.A|#1:2.A,6.A,11.A,13-14.A
    *
+ * + * 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>>> buildColoursMap(
-          StructureSelectionManager ssm, String[] files,
-          SequenceI[][] sequence, SequenceRenderer sr, FeatureRenderer fr,
-          AlignmentI alignment)
+  @Override
+  public String getAtomSpec(AtomSpecModel atomSpec, AtomSpecType specType)
   {
-    Map>>> colourMap = new LinkedHashMap>>>();
-    Color lastColour = null;
-    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)
-      {
-        continue;
-      }
-
-      int startPos = -1, lastPos = -1;
-      String lastChain = "";
-      for (int s = 0; s < sequence[pdbfnum].length; s++)
+      if (!firstModel)
       {
-        for (int sp, m = 0; m < mapping.length; m++)
-        {
-          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;
-          }
-        }
+        sb.append("|");
       }
+      firstModel = false;
+      appendModel(sb, model, atomSpec, specType);
     }
-    return colourMap;
+    return sb.toString();
   }
 
   /**
-   * Helper method to add one contiguous colour range to the colour map.
+   * A helper method to append an atomSpec string for atoms in the given model
    * 
-   * @param colourMap
-   * @param colour
+   * @param sb
    * @param model
-   * @param startPos
-   * @param endPos
-   * @param chain
+   * @param atomSpec
+   * @param alphaOnly
    */
-  protected static void addColourRange(
-          Map>>> colourMap,
-          Color colour, int model, int startPos, int endPos, String chain)
+  protected void appendModel(StringBuilder sb, String model,
+          AtomSpecModel atomSpec, AtomSpecType specType)
   {
-    /*
-     * Get/initialize map of data for the colour
-     */
-    Map>> colourData = colourMap
-            .get(colour);
-    if (colourData == null)
+    sb.append("#").append(model).append(":");
+
+    boolean firstPositionForModel = true;
+
+    for (String chain : atomSpec.getChains(model))
     {
-      colourMap
-              .put(colour,
-                      colourData = new TreeMap>>());
-    }
+      chain = " ".equals(chain) ? chain : chain.trim();
 
-    /*
-     * Get/initialize map of data for the colour and model
-     */
-    Map> modelData = colourData.get(model);
-    if (modelData == null)
+      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)
     {
-      colourData.put(model, modelData = new TreeMap>());
+      /*
+       * restrict to alpha carbon, no alternative locations
+       * (needed to ensuring matching atom counts for superposition)
+       */
+      sb.append("@CA").append(NO_ALTLOCS);
     }
-
-    /*
-     * Get/initialize map of data for colour, model and chain
-     */
-    List chainData = modelData.get(chain);
-    if (chainData == null)
+    if (specType == AtomSpecType.PHOSPHATE)
     {
-      modelData.put(chain, chainData = new ArrayList());
+      sb.append("@P").append(NO_ALTLOCS);
     }
+  }
 
-    /*
-     * Add the start/end positions
-     */
-    chainData.add(new int[] { startPos, endPos });
+  @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 + "'");
   }
 
 }