X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraCommands.java;h=c9dbc1d7664b3ffd6b3fd55ac0687c8627de2f8d;hb=27f24d1f14b8e8704d72797286f7a6e5f60b2119;hp=3caaac3532367e30f3f2d11003cbdb23c9560437;hpb=0d1529f5a1f02b9cb959f0fe0d3e7f468723b83a;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java index 3caaac3..c9dbc1d 100644 --- a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java +++ b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java @@ -20,29 +20,29 @@ */ package jalview.ext.rbvi.chimera; +import java.awt.Color; +import java.util.ArrayList; +import java.util.Arrays; +import java.util.HashMap; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Map; + import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; import jalview.api.FeatureRenderer; -import jalview.api.SequenceRenderer; import jalview.datamodel.AlignmentI; -import jalview.datamodel.HiddenColumns; import jalview.datamodel.MappedFeatures; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceI; import jalview.gui.Desktop; -import jalview.renderer.seqfeatures.FeatureColourFinder; +import jalview.structure.AtomSpecModel; +import jalview.structure.StructureCommand; +import jalview.structure.StructureCommandI; +import jalview.structure.StructureCommandsBase; import jalview.structure.StructureMapping; -import jalview.structure.StructureMappingcommandSet; import jalview.structure.StructureSelectionManager; import jalview.util.ColorUtils; -import jalview.util.Comparison; - -import java.awt.Color; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.LinkedHashMap; -import java.util.List; -import java.util.Map; /** * Routines for generating Chimera commands for Jalview/Chimera binding @@ -50,274 +50,45 @@ import java.util.Map; * @author JimP * */ -public class ChimeraCommands +public class ChimeraCommands extends StructureCommandsBase { + private static final StructureCommand SHOW_BACKBONE = new StructureCommand( + "~display all;~ribbon;chain @CA|P"); public static final String NAMESPACE_PREFIX = "jv_"; - /** - * Constructs Chimera commands to colour residues as per the Jalview alignment - * - * @param ssm - * @param files - * @param sequence - * @param sr - * @param fr - * @param viewPanel - * @return - */ - public static StructureMappingcommandSet[] getColourBySequenceCommand( - StructureSelectionManager ssm, String[] files, - SequenceI[][] sequence, SequenceRenderer sr, - AlignmentViewPanel viewPanel) - { - Map colourMap = buildColoursMap(ssm, files, - sequence, sr, viewPanel); - - List colourCommands = buildColourCommands(colourMap); - - StructureMappingcommandSet cs = new StructureMappingcommandSet( - ChimeraCommands.class, null, - colourCommands.toArray(new String[colourCommands.size()])); - - return new StructureMappingcommandSet[] { cs }; - } - - /** - * 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 - * - * 
-   * 
 
-   * color colorname #modelnumber:range.chain 
-   * e.g. color #00ff00 #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
-   * 

-   *
- * - * @param colourMap - * @return - */ - protected static List buildColourCommands( - Map colourMap) - { - /* - * 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 (Object key : colourMap.keySet()) - { - Color colour = (Color) key; - String colourCode = ColorUtils.toTkCode(colour); - if (!firstColour) - { - sb.append("; "); - } - sb.append("color ").append(colourCode).append(" "); - firstColour = false; - final AtomSpecModel colourData = colourMap.get(colour); - sb.append(colourData.getAtomSpec()); - } - commands.add(sb.toString()); - return commands; - } + private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand( + "color white;color red ::ASP,GLU;color blue ::LYS,ARG;color yellow ::CYS"); - /** - * Traverses a map of { modelNumber, {chain, {list of from-to ranges} } } and - * builds a Chimera format atom spec - * - * @param modelAndChainRanges - */ - protected static String getAtomSpec( - Map>> modelAndChainRanges) - { - 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(":"); + private static final StructureCommandI COLOUR_BY_CHAIN = new StructureCommand( + "rainbow chain"); - 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(); - } + // Chimera clause to exclude alternate locations in atom selection + private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9"; - /** - * 
-   * Build a data structure which records contiguous subsequences for each colour. 
-   * From this 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)
-   *
- */ - protected static Map buildColoursMap( - StructureSelectionManager ssm, String[] files, - SequenceI[][] sequence, SequenceRenderer sr, - AlignmentViewPanel viewPanel) + @Override + public StructureCommandI getColourCommand(String atomSpec, Color colour) { - FeatureRenderer fr = viewPanel.getFeatureRenderer(); - FeatureColourFinder finder = new FeatureColourFinder(fr); - AlignViewportI viewport = viewPanel.getAlignViewport(); - HiddenColumns cs = viewport.getAlignment().getHiddenColumns(); - AlignmentI al = viewport.getAlignment(); - Map colourMap = new LinkedHashMap<>(); - Color lastColour = null; - - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) - { - 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++) - { - for (int sp, m = 0; m < mapping.length; m++) - { - final SequenceI seq = sequence[pdbfnum][s]; - if (mapping[m].getSequence() == seq - && (sp = al.findIndex(seq)) > -1) - { - SequenceI asp = al.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, finder); - - /* - * darker colour for hidden regions - */ - if (!cs.isVisible(r)) - { - colour = Color.GRAY; - } - - 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) - { - addAtomSpecRange(colourMap, lastColour, pdbfnum, startPos, - lastPos, lastChain); - } - startPos = pos; - } - lastColour = colour; - lastPos = pos; - lastChain = chain; - } - // final colour range - if (lastColour != null) - { - addAtomSpecRange(colourMap, lastColour, pdbfnum, startPos, - lastPos, lastChain); - } - // break; - } - } - } - } - return colourMap; + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/color.html + String colourCode = getColourString(colour); + return new StructureCommand("color " + colourCode + " " + atomSpec); } /** - * Helper method to add one contiguous range to the AtomSpec model for the given - * value (creating the model if necessary). As used by Jalview, {@code value} is - *
    - *
  • a colour, when building a 'colour structure by sequence' command
    • - *
  • a feature value, when building a 'set Chimera attributes from features' - * command
    • - *
+ * Returns a colour formatted suitable for use in viewer command syntax * - * @param map - * @param value - * @param model - * @param startPos - * @param endPos - * @param chain + * @param colour + * @return */ - protected static void addAtomSpecRange(Map map, - Object value, int model, int startPos, int endPos, String chain) + protected String getColourString(Color colour) { - /* - * Get/initialize map of data for the colour - */ - AtomSpecModel atomSpec = map.get(value); - if (atomSpec == null) - { - atomSpec = new AtomSpecModel(); - map.put(value, atomSpec); - } - - atomSpec.addRange(model, startPos, endPos, chain); + return ColorUtils.toTkCode(colour); } /** * Constructs and returns Chimera commands to set attributes on residues - * corresponding to features in Jalview. Attribute names are the Jalview - * feature type, with a "jv_" prefix. + * corresponding to features in Jalview. Attribute names are the Jalview feature + * type, with a "jv_" prefix. * * @param ssm * @param files @@ -325,20 +96,15 @@ public class ChimeraCommands * @param viewPanel * @return */ - public static StructureMappingcommandSet getSetAttributeCommandsForFeatures( + @Override + public List setAttributesForFeatures( StructureSelectionManager ssm, String[] files, SequenceI[][] seqs, AlignmentViewPanel viewPanel) { Map> featureMap = buildFeaturesMap( ssm, files, seqs, viewPanel); - List commands = buildSetAttributeCommands(featureMap); - - StructureMappingcommandSet cs = new StructureMappingcommandSet( - ChimeraCommands.class, null, - commands.toArray(new String[commands.size()])); - - return cs; + return setAttributes(featureMap); } /** @@ -353,7 +119,7 @@ public class ChimeraCommands * @param viewPanel * @return */ - protected static Map> buildFeaturesMap( + protected Map> buildFeaturesMap( StructureSelectionManager ssm, String[] files, SequenceI[][] seqs, AlignmentViewPanel viewPanel) { @@ -393,6 +159,8 @@ public class ChimeraCommands AlignmentI alignment = viewPanel.getAlignment(); for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) { + final int modelNumber = pdbfnum + getModelStartNo(); + String modelId = String.valueOf(modelNumber); StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); if (mapping == null || mapping.length < 1) @@ -416,12 +184,12 @@ public class ChimeraCommands if (!visibleFeatures.isEmpty()) { scanSequenceFeatures(visibleFeatures, structureMapping, seq, - theMap, pdbfnum); + theMap, modelId); } if (showLinkedFeatures) { scanComplementFeatures(complementRenderer, structureMapping, - seq, theMap, pdbfnum); + seq, theMap, modelId); } } } @@ -443,7 +211,8 @@ public class ChimeraCommands protected static void scanComplementFeatures( FeatureRenderer complementRenderer, StructureMapping structureMapping, SequenceI seq, - Map> theMap, int modelNumber) + Map> theMap, + String modelNumber) { /* * for each sequence residue mapped to a structure position... @@ -507,19 +276,19 @@ public class ChimeraCommands } /** - * Inspect features on the sequence; for each feature that is visible, determine - * its mapped ranges in the structure (if any) according to the given mapping, - * and add them to the map. + * Inspect features on the sequence; for each feature that is visible, + * determine its mapped ranges in the structure (if any) according to the + * given mapping, and add them to the map. * * @param visibleFeatures * @param mapping * @param seq * @param theMap - * @param modelNumber + * @param modelId */ protected static void scanSequenceFeatures(List visibleFeatures, StructureMapping mapping, SequenceI seq, - Map> theMap, int modelNumber) + Map> theMap, String modelId) { List sfs = seq.getFeatures().getPositionalFeatures( visibleFeatures.toArray(new String[visibleFeatures.size()])); @@ -559,7 +328,7 @@ public class ChimeraCommands } for (int[] range : mappedRanges) { - addAtomSpecRange(featureValues, value, modelNumber, range[0], + addAtomSpecRange(featureValues, value, modelId, range[0], range[1], mapping.getChain()); } } @@ -574,17 +343,17 @@ public class ChimeraCommands * * 
    * 
 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,...
+   * e.g. setattr r jv_chain <value> #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
    * 

    *
* * @param featureMap * @return */ - protected static List buildSetAttributeCommands( + protected List setAttributes( Map> featureMap) { - List commands = new ArrayList<>(); + List commands = new ArrayList<>(); for (String featureType : featureMap.keySet()) { String attributeName = makeAttributeName(featureType); @@ -603,13 +372,12 @@ public class ChimeraCommands * add a command to set the attribute on the mapped residues * Put values in single quotes, encoding any embedded single quotes */ - StringBuilder sb = new StringBuilder(128); + AtomSpecModel atomSpecModel = values.get(value); String featureValue = value.toString(); featureValue = featureValue.replaceAll("\\'", "'"); - sb.append("setattr r ").append(attributeName).append(" '") - .append(featureValue).append("' "); - sb.append(values.get(value).getAtomSpec()); - commands.add(sb.toString()); + StructureCommandI cmd = setAttribute(attributeName, featureValue, + atomSpecModel); + commands.add(cmd); } } @@ -617,16 +385,37 @@ public class ChimeraCommands } /** + * 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 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, false)); + 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 featureType * @return - * - * 
-   * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
-   *
+ * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html */ protected static String makeAttributeName(String featureType) { @@ -652,4 +441,231 @@ public class ChimeraCommands return attName; } + @Override + public StructureCommandI colourByChain() + { + return COLOUR_BY_CHAIN; + } + + @Override + public List colourByCharge() + { + return Arrays.asList(COLOUR_BY_CHARGE); + } + + @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() + { + // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/focus.html + return new StructureCommand("focus"); + } + + @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) + { + cmd.append(","); + } + cmd.append(showChainCmd); + first = false; + } + } + + /* + * 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) + { + /* + * 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, true); + String refSpecAlphaOnly = getAtomSpec(ref, true); + cmd.append("match ").append(atomSpecAlphaOnly).append(" ").append(refSpecAlphaOnly); + + /* + * show superposed residues as ribbon + */ + String atomSpec = getAtomSpec(spec, false); + String refSpec = getAtomSpec(ref, false); + 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. + * + * 
+   * #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 alphaOnly
+   * @return
+   * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
+   */
+  @Override
+  public String getAtomSpec(AtomSpecModel atomSpec, boolean alphaOnly)
+  {
+    StringBuilder sb = new StringBuilder(128);
+    boolean firstModel = true;
+    for (String model : atomSpec.getModels())
+    {
+      if (!firstModel)
+      {
+        sb.append("|");
+      }
+      firstModel = false;
+      appendModel(sb, model, atomSpec, alphaOnly);
+    }
+    return sb.toString();
+  }
+
+  /**
+   * A helper method to append an atomSpec string for atoms in the given model
+   * 
+   * @param sb
+   * @param model
+   * @param atomSpec
+   * @param alphaOnly
+   */
+  protected void appendModel(StringBuilder sb, String model,
+          AtomSpecModel atomSpec, boolean alphaOnly)
+  {
+    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 (alphaOnly)
+    {
+      /*
+       * 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);
+    }
+  }
+
+  @Override
+  public List showBackbone()
+  {
+    return Arrays.asList(SHOW_BACKBONE);
+  }
+
+  @Override
+  public StructureCommandI loadFile(String file)
+  {
+    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;
+  }
+
 }