X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Frbvi%2Fchimera%2FChimeraXCommands.java;h=f1a8b5fd64051001d6ba4c634d1aba63c3d2385b;hb=4994aa94fd62af0058f2db96f0ea6c4ca1abe80b;hp=3947bb010155ccb8c7e9fec5504653c86959ba47;hpb=2ab7b9b152018bb808693218ad88dc3778166492;p=jalview.git diff --git a/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java b/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java index 3947bb0..f1a8b5f 100644 --- a/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java +++ b/src/jalview/ext/rbvi/chimera/ChimeraXCommands.java @@ -20,608 +20,249 @@ */ package jalview.ext.rbvi.chimera; -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.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.Arrays; import java.util.List; -import java.util.Map; -import java.util.Map.Entry; + +import jalview.structure.AtomSpecModel; +import jalview.structure.StructureCommand; +import jalview.structure.StructureCommandI; +import jalview.util.ColorUtils; /** * Routines for generating ChimeraX commands for Jalview/ChimeraX binding */ public class ChimeraXCommands extends ChimeraCommands { - public static final String NAMESPACE_PREFIX = "jv_"; - - private static final String CMD_COLOUR_BY_CHARGE = "color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow"; + private static final StructureCommand CLOSE_CHIMERAX = new StructureCommand("exit"); - /** - * 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(":"); - - 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(); - } + private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand("info notify stop selection jalview"); - /** - * 
-   * 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) - { - 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; + private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand("info notify stop models jalview"); - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) - { - StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); + private static final StructureCommand GET_SELECTION = new StructureCommand("info selection level residue"); - if (mapping == null || mapping.length < 1) - { - continue; - } + private static final StructureCommand SHOW_BACKBONE = new StructureCommand( + "~display all;~ribbon;show @CA|P atoms"); - 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)); + private static final StructureCommand FOCUS_VIEW = new StructureCommand( + "view"); - if (pos < 1 || pos == lastPos) - { - continue; - } + private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand( + "color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow"); - Color colour = sr.getResidueColour(seq, r, finder); + @Override + public List colourByCharge() + { + return Arrays.asList(COLOUR_BY_CHARGE); + } - /* - * darker colour for hidden regions - */ - if (!cs.isVisible(r)) - { - colour = Color.GRAY; - } + @Override + public String getResidueSpec(String residue) + { + return ":" + residue; + } - final String chain = mapping[m].getChain(); + @Override + public StructureCommandI colourResidues(String atomSpec, Color colour) + { + // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html + String colourCode = getColourString(colour); - /* - * 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; + return new StructureCommand("color " + atomSpec + " " + colourCode); } - /** - * 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
    • - *
- * - * @param map - * @param value - * @param model - * @param startPos - * @param endPos - * @param chain - */ - protected static void addAtomSpecRange(Map map, - Object value, int model, int startPos, int endPos, String chain) + @Override + public StructureCommandI focusView() { - /* - * 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); + // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/view.html + return FOCUS_VIEW; } /** - * 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. + * {@inheritDoc} * - * @param ssm - * @param files - * @param seqs - * @param viewPanel * @return */ - public static StructureMappingcommandSet getSetAttributeCommandsForFeatures( - StructureSelectionManager ssm, String[] files, SequenceI[][] seqs, - AlignmentViewPanel viewPanel) + @Override + public int getModelStartNo() { - Map> featureMap = buildFeaturesMap( - ssm, files, seqs, viewPanel); - - List commands = buildSetAttributeCommands(featureMap); - - StructureMappingcommandSet cs = new StructureMappingcommandSet( - ChimeraXCommands.class, null, - commands.toArray(new String[commands.size()])); - - return cs; + return 1; } /** + * Returns a viewer command to set the given residue attribute value on + * residues specified by the AtomSpecModel, for example + * * 
-   * Helper method to build a map of 
-   *   { featureType, { feature value, AtomSpecModel } }
+   * setattr #0/A:3-9,14-20,39-43 res jv_strand 'strand' create true
    *
* - * @param ssm - * @param files - * @param seqs - * @param viewPanel + * @param attributeName + * @param attributeValue + * @param atomSpecModel * @return */ - protected static Map> buildFeaturesMap( - StructureSelectionManager ssm, String[] files, SequenceI[][] seqs, - AlignmentViewPanel viewPanel) + @Override + protected StructureCommandI setAttribute(String attributeName, + String attributeValue, AtomSpecModel atomSpecModel) { - Map> theMap = new LinkedHashMap<>(); - - FeatureRenderer fr = viewPanel.getFeatureRenderer(); - if (fr == null) - { - return theMap; - } - - AlignViewportI viewport = viewPanel.getAlignViewport(); - List visibleFeatures = fr.getDisplayedFeatureTypes(); - - /* - * if alignment is showing features from complement, we also transfer - * these features to the corresponding mapped structure residues - */ - boolean showLinkedFeatures = viewport.isShowComplementFeatures(); - List complementFeatures = new ArrayList<>(); - FeatureRenderer complementRenderer = null; - if (showLinkedFeatures) - { - AlignViewportI comp = fr.getViewport().getCodingComplement(); - if (comp != null) - { - complementRenderer = Desktop.getAlignFrameFor(comp) - .getFeatureRenderer(); - complementFeatures = complementRenderer.getDisplayedFeatureTypes(); - } - } - if (visibleFeatures.isEmpty() && complementFeatures.isEmpty()) - { - return theMap; - } - - AlignmentI alignment = viewPanel.getAlignment(); - for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) - { - StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); - - if (mapping == null || mapping.length < 1) - { - continue; - } - - 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); - StructureMapping structureMapping = mapping[m]; - if (structureMapping.getSequence() == seq && sp > -1) - { - /* - * found a sequence with a mapping to a structure; - * now scan its features - */ - if (!visibleFeatures.isEmpty()) - { - scanSequenceFeatures(visibleFeatures, structureMapping, seq, - theMap, pdbfnum); - } - if (showLinkedFeatures) - { - scanComplementFeatures(complementRenderer, structureMapping, - seq, theMap, pdbfnum); - } - } - } - } - } - return theMap; + StringBuilder sb = new StringBuilder(128); + sb.append("setattr ").append(getAtomSpec(atomSpecModel, false)); + sb.append(" res ").append(attributeName).append(" '") + .append(attributeValue).append("'"); + sb.append(" create true"); + return new StructureCommand(sb.toString()); } - /** - * Scans visible features in mapped positions of the CDS/peptide complement, and - * adds any found to the map of attribute values/structure positions - * - * @param complementRenderer - * @param structureMapping - * @param seq - * @param theMap - * @param modelNumber - */ - protected static void scanComplementFeatures( - FeatureRenderer complementRenderer, - StructureMapping structureMapping, SequenceI seq, - Map> theMap, int modelNumber) + @Override + public StructureCommandI openCommandFile(String path) { - /* - * for each sequence residue mapped to a structure position... - */ - for (int seqPos : structureMapping.getMapping().keySet()) - { - /* - * find visible complementary features at mapped position(s) - */ - MappedFeatures mf = complementRenderer - .findComplementFeaturesAtResidue(seq, seqPos); - if (mf != null) - { - for (SequenceFeature sf : mf.features) - { - String type = sf.getType(); - - /* - * Don't copy features which originated from Chimera - */ - if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP - .equals(sf.getFeatureGroup())) - { - continue; - } - - /* - * record feature 'value' (score/description/type) as at the - * corresponding structure position - */ - List mappedRanges = structureMapping - .getPDBResNumRanges(seqPos, seqPos); + // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html + return new StructureCommand("open " + path); + } - if (!mappedRanges.isEmpty()) - { - String value = sf.getDescription(); - if (value == null || value.length() == 0) - { - value = type; - } - float score = sf.getScore(); - if (score != 0f && !Float.isNaN(score)) - { - value = Float.toString(score); - } - Map featureValues = theMap.get(type); - if (featureValues == null) - { - featureValues = new HashMap<>(); - theMap.put(type, featureValues); - } - for (int[] range : mappedRanges) - { - addAtomSpecRange(featureValues, value, modelNumber, range[0], - range[1], structureMapping.getChain()); - } - } - } - } - } + @Override + public StructureCommandI saveSession(String filepath) + { + // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html + // note ChimeraX will append ".cxs" to the filepath! + return new StructureCommand("save " + filepath + " format session"); } /** - * 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. + * Returns the range(s) formatted as a ChimeraX atomspec, for example + *

+ * #1/A:2-20,30-40/B:10-20|#2/A:12-30 * - * @param visibleFeatures - * @param mapping - * @param seq - * @param theMap - * @param modelNumber + * @return */ - protected static void scanSequenceFeatures(List visibleFeatures, - StructureMapping mapping, SequenceI seq, - Map> theMap, int modelNumber) + @Override + public String getAtomSpec(AtomSpecModel atomSpec, boolean alphaOnly) { - List sfs = seq.getFeatures().getPositionalFeatures( - visibleFeatures.toArray(new String[visibleFeatures.size()])); - for (SequenceFeature sf : sfs) + StringBuilder sb = new StringBuilder(128); + boolean firstModel = true; + for (String model : atomSpec.getModels()) { - String type = sf.getType(); - - /* - * Don't copy features which originated from Chimera - */ - if (JalviewChimeraBinding.CHIMERA_FEATURE_GROUP - .equals(sf.getFeatureGroup())) + if (!firstModel) { - continue; + sb.append("|"); } - - List mappedRanges = mapping.getPDBResNumRanges(sf.getBegin(), - sf.getEnd()); - - if (!mappedRanges.isEmpty()) + firstModel = false; + appendModel(sb, model, atomSpec); + if (alphaOnly) { - String value = sf.getDescription(); - if (value == null || value.length() == 0) - { - value = type; - } - float score = sf.getScore(); - if (score != 0f && !Float.isNaN(score)) - { - value = Float.toString(score); - } - Map featureValues = theMap.get(type); - if (featureValues == null) - { - featureValues = new HashMap<>(); - theMap.put(type, featureValues); - } - for (int[] range : mappedRanges) - { - addAtomSpecRange(featureValues, value, modelNumber, range[0], - range[1], mapping.getChain()); - } + // TODO @P if RNA - add nucleotide flag to AtomSpecModel? + sb.append("@CA"); } + // todo: is there ChimeraX syntax to exclude altlocs? } + return sb.toString(); } /** - * 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 + * A helper method to append an atomSpec string for atoms in the given model * - * 

-   * 
 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,...
-   * 

-   *
- * - * @param featureMap - * @return + * @param sb + * @param model + * @param atomSpec */ - protected static List buildSetAttributeCommands( - Map> featureMap) + protected void appendModel(StringBuilder sb, String model, + AtomSpecModel atomSpec) { - List commands = new ArrayList<>(); - for (String featureType : featureMap.keySet()) - { - 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 + " :*"); + sb.append("#").append(model); - Map values = featureMap.get(featureType); - for (Object value : values.keySet()) + for (String chain : atomSpec.getChains(model)) + { + boolean firstPositionForChain = true; + sb.append("/").append(chain.trim()).append(":"); + List rangeList = atomSpec.getRanges(model, chain); + boolean first = true; + for (int[] range : rangeList) { - /* - * 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 - */ - StringBuilder sb = new StringBuilder(128); - 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()); + if (!first) + { + sb.append(","); + } + first = false; + appendRange(sb, range[0], range[1], chain, firstPositionForChain, + true); } } + } - return commands; + @Override + public List showBackbone() + { + return Arrays.asList(SHOW_BACKBONE); } - /** - * 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 String makeAttributeName(String featureType) + @Override + public List superposeStructures(AtomSpecModel ref, + AtomSpecModel spec) { - StringBuilder sb = new StringBuilder(); - if (featureType != null) - { - for (char c : featureType.toCharArray()) - { - sb.append(Character.isLetterOrDigit(c) ? c : '_'); - } - } - String attName = NAMESPACE_PREFIX + sb.toString(); + /* + * Form ChimeraX match command to match spec to ref + * + * match #1/A:2-94 toAtoms #2/A:1-93 + * + * @see https://www.cgl.ucsf.edu/chimerax/docs/user/commands/align.html + */ + StringBuilder cmd = new StringBuilder(); + String atomSpec = getAtomSpec(spec, true); + String refSpec = getAtomSpec(ref, true); + cmd.append("align ").append(atomSpec).append(" toAtoms ") + .append(refSpec); /* - * Chimera treats an attribute name ending in 'color' as colour-valued; - * Jalview doesn't, so prevent this by appending an underscore + * show superposed residues as ribbon, others as chain */ - if (attName.toUpperCase().endsWith("COLOR")) - { - attName += "_"; - } + cmd.append("; ribbon "); + cmd.append(getAtomSpec(spec, false)).append("|"); + cmd.append(getAtomSpec(ref, false)).append("; view"); - return attName; + return Arrays.asList(new StructureCommand(cmd.toString())); } @Override - public String colourByCharge() + public StructureCommandI openSession(String filepath) { - return CMD_COLOUR_BY_CHARGE; + // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html#composite + // this version of the command has no dependency on file extension + return new StructureCommand("open " + filepath + " format session"); } @Override - public String colourByResidues(Map colours) + public StructureCommandI closeViewer() { - StringBuilder cmd = new StringBuilder(12 * colours.size()); - - /* - * concatenate commands like - * color :VAL #4949b6 - */ - for (Entry entry : colours.entrySet()) - { - String colorSpec = ColorUtils.toTkCode(entry.getValue()); - String resCode = entry.getKey(); - cmd.append("color :").append(resCode).append(" ").append(colorSpec) - .append(CMD_SEPARATOR); - } - return cmd.toString(); + // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/exit.html + return CLOSE_CHIMERAX; } @Override - public String setBackgroundColour(Color col) + public List startNotifications(String uri) { - return "set bgColor " + ColorUtils.toTkCode(col); + // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#notify + List cmds = new ArrayList<>(); + cmds.add(new StructureCommand("info notify start models prefix ModelChanged jalview url " + uri)); + cmds.add(new StructureCommand("info notify start selection jalview prefix SelectionChanged url " + uri)); + return cmds; } @Override - protected String getColourCommand(AtomSpecModel colourData, - String colourCode) + public List stopNotifications() { - return "color " + colourData.getAtomSpecX() + " " + colourCode; + // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#notify + List cmds = new ArrayList<>(); + cmds.add(STOP_NOTIFY_MODELS); + cmds.add(STOP_NOTIFY_SELECTION); + return cmds; } @Override - public String focusView() + public StructureCommandI getSelectedResidues() { - return "view"; + return GET_SELECTION; } - }