2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
7 * Jalview is free software: you can redistribute it and/or
8 * modify it under the terms of the GNU General Public License
9 * as published by the Free Software Foundation, either version 3
10 * of the License, or (at your option) any later version.
12 * Jalview is distributed in the hope that it will be useful, but
13 * WITHOUT ANY WARRANTY; without even the implied warranty
14 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
15 * PURPOSE. See the GNU General Public License for more details.
17 * You should have received a copy of the GNU General Public License
18 * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
19 * The Jalview Authors are detailed in the 'AUTHORS' file.
21 package jalview.ext.rbvi.chimera;
23 import jalview.api.AlignmentViewPanel;
24 import jalview.api.FeatureRenderer;
25 import jalview.api.SequenceRenderer;
26 import jalview.bin.Cache;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.ColumnSelection;
29 import jalview.datamodel.PDBEntry;
30 import jalview.datamodel.SearchResults;
31 import jalview.datamodel.SearchResults.Match;
32 import jalview.datamodel.SequenceFeature;
33 import jalview.datamodel.SequenceI;
34 import jalview.httpserver.AbstractRequestHandler;
35 import jalview.schemes.ColourSchemeI;
36 import jalview.schemes.ResidueProperties;
37 import jalview.structure.AtomSpec;
38 import jalview.structure.StructureMappingcommandSet;
39 import jalview.structure.StructureSelectionManager;
40 import jalview.structures.models.AAStructureBindingModel;
41 import jalview.util.MessageManager;
43 import java.awt.Color;
45 import java.io.FileOutputStream;
46 import java.io.IOException;
47 import java.io.PrintWriter;
48 import java.net.BindException;
49 import java.util.ArrayList;
50 import java.util.Collections;
51 import java.util.LinkedHashMap;
52 import java.util.List;
55 import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
56 import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
57 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
58 import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
60 public abstract class JalviewChimeraBinding extends AAStructureBindingModel
62 public static final String CHIMERA_FEATURE_GROUP = "Chimera";
64 private static final String CHIMERA_FEATURE_PREFIX = "chim_";
66 // Chimera clause to exclude alternate locations in atom selection
67 private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
69 private static final String COLOURING_CHIMERA = MessageManager
70 .getString("status.colouring_chimera");
72 private static final boolean debug = false;
74 private static final String PHOSPHORUS = "P";
76 private static final String ALPHACARBON = "CA";
79 * Object through which we talk to Chimera
81 private ChimeraManager viewer;
84 * Object which listens to Chimera notifications
86 private AbstractRequestHandler chimeraListener;
89 * set if chimera state is being restored from some source - instructs binding
90 * not to apply default display style when structure set is updated for first
93 private boolean loadingFromArchive = false;
96 * flag to indicate if the Chimera viewer should ignore sequence colouring
97 * events from the structure manager because the GUI is still setting up
99 private boolean loadingFinished = true;
101 public String fileLoadingError;
104 * Map of ChimeraModel objects keyed by PDB full local file name
106 private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<String, List<ChimeraModel>>();
108 String lastHighlightCommand;
111 * incremented every time a load notification is successfully handled -
112 * lightweight mechanism for other threads to detect when they can start
113 * referring to new structures.
115 private long loadNotifiesHandled = 0;
118 * Open a PDB structure file in Chimera and set up mappings from Jalview.
120 * We check if the PDB model id is already loaded in Chimera, if so don't
121 * reopen it. This is the case if Chimera has opened a saved session file.
126 public boolean openFile(PDBEntry pe)
128 String file = pe.getFile();
131 List<ChimeraModel> modelsToMap = new ArrayList<ChimeraModel>();
132 List<ChimeraModel> oldList = viewer.getModelList();
133 boolean alreadyOpen = false;
136 * If Chimera already has this model, don't reopen it, but do remap it.
138 for (ChimeraModel open : oldList)
140 if (open.getModelName().equals(pe.getId()))
143 modelsToMap.add(open);
148 * If Chimera doesn't yet have this model, ask it to open it, and retrieve
149 * the model name(s) added by Chimera.
153 viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL);
154 List<ChimeraModel> newList = viewer.getModelList();
155 // JAL-1728 newList.removeAll(oldList) does not work
156 for (ChimeraModel cm : newList)
158 if (cm.getModelName().equals(pe.getId()))
165 chimeraMaps.put(file, modelsToMap);
167 if (getSsm() != null)
169 getSsm().addStructureViewerListener(this);
170 // ssm.addSelectionListener(this);
171 FeatureRenderer fr = getFeatureRenderer(null);
179 } catch (Exception q)
181 log("Exception when trying to open model " + file + "\n"
197 public JalviewChimeraBinding(StructureSelectionManager ssm,
198 PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
201 super(ssm, pdbentry, sequenceIs, chains, protocol);
202 viewer = new ChimeraManager(
203 new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
207 * Start a dedicated HttpServer to listen for Chimera notifications, and tell
208 * it to start listening
210 public void startChimeraListener()
214 chimeraListener = new ChimeraListener(this);
215 viewer.startListening(chimeraListener.getUri());
216 } catch (BindException e)
218 System.err.println("Failed to start Chimera listener: "
224 * Construct a title string for the viewer window based on the data Jalview
230 public String getViewerTitle(boolean verbose)
232 return getViewerTitle(CHIMERA_FEATURE_GROUP, verbose);
236 * Tells Chimera to display only the specified chains
240 public void showChains(List<String> toshow)
243 * Construct a chimera command like
245 * ~display #*;~ribbon #*;ribbon :.A,:.B
247 StringBuilder cmd = new StringBuilder(64);
248 boolean first = true;
249 for (String chain : toshow)
255 cmd.append(":.").append(chain);
260 * could append ";focus" to this command to resize the display to fill the
261 * window, but it looks more helpful not to (easier to relate chains to the
264 final String command = "~display #*; ~ribbon #*; ribbon "
266 sendChimeraCommand(command, false);
270 * Close down the Jalview viewer and listener, and (optionally) the associated
273 public void closeViewer(boolean closeChimera)
275 getSsm().removeStructureViewerListener(this, this.getPdbFile());
278 viewer.exitChimera();
280 if (this.chimeraListener != null)
282 chimeraListener.shutdown();
283 chimeraListener = null;
287 releaseUIResources();
290 public void colourByChain()
292 colourBySequence = false;
293 sendAsynchronousCommand("rainbow chain", COLOURING_CHIMERA);
297 * Constructs and sends a Chimera command to colour by charge
299 * <li>Aspartic acid and Glutamic acid (negative charge) red</li>
300 * <li>Lysine and Arginine (positive charge) blue</li>
301 * <li>Cysteine - yellow</li>
302 * <li>all others - white</li>
305 public void colourByCharge()
307 colourBySequence = false;
308 String command = "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS";
309 sendAsynchronousCommand(command, COLOURING_CHIMERA);
313 * Construct and send a command to align structures against a reference
314 * structure, based on one or more sequence alignments
317 * an array of alignments to process
318 * @param _refStructure
319 * an array of corresponding reference structures (index into pdb
320 * file array); if a negative value is passed, the first PDB file
321 * mapped to an alignment sequence is used as the reference for
324 * an array of corresponding hidden columns for each alignment
326 public void superposeStructures(AlignmentI[] _alignment,
327 int[] _refStructure, ColumnSelection[] _hiddenCols)
329 StringBuilder allComs = new StringBuilder(128);
330 String[] files = getPdbFile();
332 if (!waitForFileLoad(files))
338 StringBuilder selectioncom = new StringBuilder(256);
339 for (int a = 0; a < _alignment.length; a++)
341 int refStructure = _refStructure[a];
342 AlignmentI alignment = _alignment[a];
343 ColumnSelection hiddenCols = _hiddenCols[a];
345 if (refStructure >= files.length)
347 System.err.println("Ignoring invalid reference structure value "
353 * 'matched' array will hold 'true' for visible alignment columns where
354 * all sequences have a residue with a mapping to the PDB structure
356 boolean matched[] = new boolean[alignment.getWidth()];
357 for (int m = 0; m < matched.length; m++)
359 matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
362 SuperposeData[] structures = new SuperposeData[files.length];
363 for (int f = 0; f < files.length; f++)
365 structures[f] = new SuperposeData(alignment.getWidth());
369 * Calculate the superposable alignment columns ('matched'), and the
370 * corresponding structure residue positions (structures.pdbResNo)
372 int candidateRefStructure = findSuperposableResidues(alignment,
373 matched, structures);
374 if (refStructure < 0)
377 * If no reference structure was specified, pick the first one that has
378 * a mapping in the alignment
380 refStructure = candidateRefStructure;
384 for (boolean b : matched)
393 // TODO: bail out here because superposition illdefined?
397 * Generate select statements to select regions to superimpose structures
399 String[] selcom = new String[files.length];
400 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
402 String chainCd = "." + structures[pdbfnum].chain;
405 StringBuilder molsel = new StringBuilder();
406 for (int r = 0; r < matched.length; r++)
410 int pdbResNum = structures[pdbfnum].pdbResNo[r];
411 if (lpos != pdbResNum - 1)
414 * discontiguous - append last residue now
418 molsel.append(String.valueOf(lpos));
419 molsel.append(chainCd);
427 * extending a contiguous run
432 * start the range selection
434 molsel.append(String.valueOf(lpos));
444 * and terminate final selection
448 molsel.append(String.valueOf(lpos));
449 molsel.append(chainCd);
451 if (molsel.length() > 1)
453 selcom[pdbfnum] = molsel.toString();
454 selectioncom.append("#").append(String.valueOf(pdbfnum))
456 selectioncom.append(selcom[pdbfnum]);
457 selectioncom.append(" ");
458 if (pdbfnum < files.length - 1)
460 selectioncom.append("| ");
465 selcom[pdbfnum] = null;
469 StringBuilder command = new StringBuilder(256);
470 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
472 if (pdbfnum == refStructure || selcom[pdbfnum] == null
473 || selcom[refStructure] == null)
477 if (command.length() > 0)
483 * Form Chimera match command, from the 'new' structure to the
484 * 'reference' structure e.g. (50 residues, chain B/A, alphacarbons):
486 * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA
489 * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
491 command.append("match ").append(getModelSpec(pdbfnum)).append(":");
492 command.append(selcom[pdbfnum]);
493 command.append("@").append(
494 structures[pdbfnum].isRna ? PHOSPHORUS : ALPHACARBON);
495 // JAL-1757 exclude alternate CA locations
496 command.append(NO_ALTLOCS);
497 command.append(" ").append(getModelSpec(refStructure)).append(":");
498 command.append(selcom[refStructure]);
499 command.append("@").append(
500 structures[refStructure].isRna ? PHOSPHORUS : ALPHACARBON);
501 command.append(NO_ALTLOCS);
503 if (selectioncom.length() > 0)
507 System.out.println("Select regions:\n" + selectioncom.toString());
508 System.out.println("Superimpose command(s):\n"
509 + command.toString());
511 allComs.append("~display all; chain @CA|P; ribbon ")
512 .append(selectioncom.toString())
513 .append(";" + command.toString());
516 if (selectioncom.length() > 0)
518 // TODO: visually distinguish regions that were superposed
519 if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
521 selectioncom.setLength(selectioncom.length() - 1);
525 System.out.println("Select regions:\n" + selectioncom.toString());
527 allComs.append("; ~display all; chain @CA|P; ribbon ")
528 .append(selectioncom.toString()).append("; focus");
529 sendChimeraCommand(allComs.toString(), false);
535 * Helper method to construct model spec in Chimera format:
537 * <li>#0 (#1 etc) for a PDB file with no sub-models</li>
538 * <li>#0.1 (#1.1 etc) for a PDB file with sub-models</li>
540 * Note for now we only ever choose the first of multiple models. This
541 * corresponds to the hard-coded Jmol equivalent (compare {1.1}). Refactor in
542 * future if there is a need to select specific sub-models.
547 protected String getModelSpec(int pdbfnum)
549 if (pdbfnum < 0 || pdbfnum >= getPdbCount())
555 * For now, the test for having sub-models is whether multiple Chimera
556 * models are mapped for the PDB file; the models are returned as a response
557 * to the Chimera command 'list models type molecule', see
558 * ChimeraManager.getModelList().
560 List<ChimeraModel> maps = chimeraMaps.get(getPdbFile()[pdbfnum]);
561 boolean hasSubModels = maps != null && maps.size() > 1;
562 return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
566 * Launch Chimera, unless an instance linked to this object is already
567 * running. Returns true if chimera is successfully launched, or already
568 * running, else false.
572 public boolean launchChimera()
574 if (!viewer.isChimeraLaunched())
576 return viewer.launchChimera(StructureManager.getChimeraPaths());
578 if (viewer.isChimeraLaunched())
582 log("Failed to launch Chimera!");
587 * Answers true if the Chimera process is still running, false if ended or not
592 public boolean isChimeraRunning()
594 return viewer.isChimeraLaunched();
598 * Send a command to Chimera, and optionally log and return any responses.
600 * Does nothing, and returns null, if the command is the same as the last one
606 public List<String> sendChimeraCommand(final String command,
611 // ? thread running after viewer shut down
614 List<String> reply = null;
615 viewerCommandHistory(false);
616 if (true /*lastCommand == null || !lastCommand.equals(command)*/)
618 // trim command or it may never find a match in the replyLog!!
619 List<String> lastReply = viewer.sendChimeraCommand(command.trim(),
626 log("Response from command ('" + command + "') was:\n"
631 viewerCommandHistory(true);
637 * Send a Chimera command asynchronously in a new thread. If the progress
638 * message is not null, display this message while the command is executing.
643 protected abstract void sendAsynchronousCommand(String command,
647 * colour any structures associated with sequences in the given alignment
648 * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
649 * if colourBySequence is enabled.
651 public void colourBySequence(boolean showFeatures,
652 jalview.api.AlignmentViewPanel alignmentv)
654 if (!colourBySequence || !loadingFinished)
658 if (getSsm() == null)
662 String[] files = getPdbFile();
664 SequenceRenderer sr = getSequenceRenderer(alignmentv);
666 FeatureRenderer fr = null;
669 fr = getFeatureRenderer(alignmentv);
671 AlignmentI alignment = alignmentv.getAlignment();
673 StructureMappingcommandSet colourBySequenceCommands = ChimeraCommands
674 .getColourBySequenceCommand(getSsm(), files, getSequence(), sr,
676 for (String command : colourBySequenceCommands.commands)
678 sendAsynchronousCommand(command, COLOURING_CHIMERA);
685 protected void executeWhenReady(String command)
688 sendChimeraCommand(command, false);
692 private void waitForChimera()
694 while (viewer != null && viewer.isBusy())
699 } catch (InterruptedException q)
705 // End StructureListener
706 // //////////////////////////
709 * returns the current featureRenderer that should be used to colour the
716 public abstract FeatureRenderer getFeatureRenderer(
717 AlignmentViewPanel alignment);
720 * instruct the Jalview binding to update the pdbentries vector if necessary
721 * prior to matching the viewer's contents to the list of structure files
722 * Jalview knows about.
724 public abstract void refreshPdbEntries();
726 private int getModelNum(String modelFileName)
728 String[] mfn = getPdbFile();
733 for (int i = 0; i < mfn.length; i++)
735 if (mfn[i].equalsIgnoreCase(modelFileName))
744 * map between index of model filename returned from getPdbFile and the first
745 * index of models from this file in the viewer. Note - this is not trimmed -
746 * use getPdbFile to get number of unique models.
748 private int _modelFileNameMap[];
750 // ////////////////////////////////
751 // /StructureListener
753 public synchronized String[] getPdbFile()
757 return new String[0];
759 // if (modelFileNames == null)
761 // Collection<ChimeraModel> chimodels = viewer.getChimeraModels();
762 // _modelFileNameMap = new int[chimodels.size()];
764 // for (ChimeraModel chimodel : chimodels)
766 // String mdlName = chimodel.getModelName();
768 // modelFileNames = new String[j];
769 // // System.arraycopy(mset, 0, modelFileNames, 0, j);
772 return chimeraMaps.keySet().toArray(
773 modelFileNames = new String[chimeraMaps.size()]);
777 * returns the current sequenceRenderer that should be used to colour the
784 public abstract SequenceRenderer getSequenceRenderer(
785 AlignmentViewPanel alignment);
788 * Construct and send a command to highlight zero, one or more atoms. We do
789 * this by sending an "rlabel" command to show the residue label at that
793 public void highlightAtoms(List<AtomSpec> atoms)
795 if (atoms == null || atoms.size() == 0)
800 StringBuilder cmd = new StringBuilder(128);
801 boolean first = true;
802 boolean found = false;
804 for (AtomSpec atom : atoms)
806 int pdbResNum = atom.getPdbResNum();
807 String chain = atom.getChain();
808 String pdbfile = atom.getPdbFile();
809 List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
810 if (cms != null && !cms.isEmpty())
814 cmd.append("rlabel #").append(cms.get(0).getModelNumber())
822 cmd.append(pdbResNum);
823 if (!chain.equals(" "))
825 cmd.append(".").append(chain);
830 String command = cmd.toString();
833 * avoid repeated commands for the same residue
835 if (command.equals(lastHighlightCommand))
841 * unshow the label for the previous residue
843 if (lastHighlightCommand != null)
845 viewer.sendChimeraCommand("~" + lastHighlightCommand, false);
849 viewer.sendChimeraCommand(command, false);
851 this.lastHighlightCommand = command;
855 * Query Chimera for its current selection, and highlight it on the alignment
857 public void highlightChimeraSelection()
860 * Ask Chimera for its current selection
862 List<String> selection = viewer.getSelectedResidueSpecs();
865 * Parse model number, residue and chain for each selected position,
866 * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
868 List<AtomSpec> atomSpecs = convertStructureResiduesToAlignment(selection);
871 * Broadcast the selection (which may be empty, if the user just cleared all
874 getSsm().mouseOverStructure(atomSpecs);
878 * Converts a list of Chimera atomspecs to a list of AtomSpec representing the
879 * corresponding residues (if any) in Jalview
881 * @param structureSelection
884 protected List<AtomSpec> convertStructureResiduesToAlignment(
885 List<String> structureSelection)
887 List<AtomSpec> atomSpecs = new ArrayList<AtomSpec>();
888 for (String atomSpec : structureSelection)
892 AtomSpec spec = AtomSpec.fromChimeraAtomspec(atomSpec);
893 String pdbfilename = getPdbFileForModel(spec.getModelNumber());
894 spec.setPdbFile(pdbfilename);
896 } catch (IllegalArgumentException e)
898 System.err.println("Failed to parse atomspec: " + atomSpec);
908 protected String getPdbFileForModel(int modelId)
911 * Work out the pdbfilename from the model number
913 String pdbfilename = modelFileNames[0];
914 findfileloop: for (String pdbfile : this.chimeraMaps.keySet())
916 for (ChimeraModel cm : chimeraMaps.get(pdbfile))
918 if (cm.getModelNumber() == modelId)
920 pdbfilename = pdbfile;
928 private void log(String message)
930 System.err.println("## Chimera log: " + message);
933 private void viewerCommandHistory(boolean enable)
935 // log("(Not yet implemented) History "
936 // + ((debug || enable) ? "on" : "off"));
939 public long getLoadNotifiesHandled()
941 return loadNotifiesHandled;
944 public void setJalviewColourScheme(ColourSchemeI cs)
946 colourBySequence = false;
953 // Chimera expects RBG values in the range 0-1
954 final double normalise = 255D;
955 viewerCommandHistory(false);
956 StringBuilder command = new StringBuilder(128);
958 List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
960 for (String res : residueSet)
962 Color col = cs.findColour(res.charAt(0));
963 command.append("color " + col.getRed() / normalise + ","
964 + col.getGreen() / normalise + "," + col.getBlue()
965 / normalise + " ::" + res + ";");
968 sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
969 viewerCommandHistory(true);
973 * called when the binding thinks the UI needs to be refreshed after a Chimera
974 * state change. this could be because structures were loaded, or because an
975 * error has occurred.
977 public abstract void refreshGUI();
980 public void setLoadingFromArchive(boolean loadingFromArchive)
982 this.loadingFromArchive = loadingFromArchive;
987 * @return true if Chimeral is still restoring state or loading is still going
988 * on (see setFinsihedLoadingFromArchive)
991 public boolean isLoadingFromArchive()
993 return loadingFromArchive && !loadingFinished;
997 * modify flag which controls if sequence colouring events are honoured by the
998 * binding. Should be true for normal operation
1000 * @param finishedLoading
1003 public void setFinishedLoadingFromArchive(boolean finishedLoading)
1005 loadingFinished = finishedLoading;
1009 * Send the Chimera 'background solid <color>" command.
1012 * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
1016 public void setBackgroundColour(Color col)
1018 viewerCommandHistory(false);
1019 double normalise = 255D;
1020 final String command = "background solid " + col.getRed() / normalise
1021 + "," + col.getGreen() / normalise + "," + col.getBlue()
1023 viewer.sendChimeraCommand(command, false);
1024 viewerCommandHistory(true);
1028 * Ask Chimera to save its session to the given file. Returns true if
1029 * successful, else false.
1034 public boolean saveSession(String filepath)
1036 if (isChimeraRunning())
1038 List<String> reply = viewer.sendChimeraCommand("save " + filepath,
1040 if (reply.contains("Session written"))
1047 .error("Error saving Chimera session: " + reply.toString());
1054 * Ask Chimera to open a session file. Returns true if successful, else false.
1055 * The filename must have a .py extension for this command to work.
1060 public boolean openSession(String filepath)
1062 sendChimeraCommand("open " + filepath, true);
1063 // todo: test for failure - how?
1068 * Returns a list of chains mapped in this viewer. Note this list is not
1069 * currently scoped per structure.
1073 public List<String> getChainNames()
1075 List<String> names = new ArrayList<String>();
1076 String[][] allNames = getChains();
1077 if (allNames != null)
1079 for (String[] chainsForPdb : allNames)
1081 if (chainsForPdb != null)
1083 for (String chain : chainsForPdb)
1085 if (chain != null && !names.contains(chain))
1097 * Send a 'focus' command to Chimera to recentre the visible display
1099 public void focusView()
1101 sendChimeraCommand("focus", false);
1105 * Send a 'show' command for all atoms in the currently selected columns
1107 * TODO: pull up to abstract structure viewer interface
1111 public void highlightSelection(AlignmentViewPanel vp)
1113 List<Integer> cols = vp.getAlignViewport().getColumnSelection()
1115 AlignmentI alignment = vp.getAlignment();
1116 StructureSelectionManager sm = getSsm();
1117 for (SequenceI seq : alignment.getSequences())
1120 * convert selected columns into sequence positions
1122 int[] positions = new int[cols.size()];
1124 for (Integer col : cols)
1126 positions[i++] = seq.findPosition(col);
1128 sm.highlightStructure(this, seq, positions);
1133 * Constructs and send commands to Chimera to set attributes on residues for
1134 * features visible in Jalview
1138 public void sendFeaturesToViewer(AlignmentViewPanel avp)
1140 // TODO refactor as required to pull up to an interface
1141 AlignmentI alignment = avp.getAlignment();
1142 FeatureRenderer fr = getFeatureRenderer(avp);
1145 * fr is null if feature display is turned off
1152 String[] files = getPdbFile();
1158 StructureMappingcommandSet commandSet = ChimeraCommands
1159 .getSetAttributeCommandsForFeatures(getSsm(), files,
1160 getSequence(), fr, alignment);
1161 String[] commands = commandSet.commands;
1162 if (commands.length > 10)
1164 sendCommandsByFile(commands);
1168 for (String command : commands)
1170 sendAsynchronousCommand(command, null);
1176 * Write commands to a temporary file, and send a command to Chimera to open
1177 * the file as a commands script. For use when sending a large number of
1178 * separate commands would overload the REST interface mechanism.
1182 protected void sendCommandsByFile(String[] commands)
1186 File tmp = File.createTempFile("chim", ".com");
1188 PrintWriter out = new PrintWriter(new FileOutputStream(tmp));
1189 for (String command : commands)
1191 out.println(command);
1195 String path = tmp.getAbsolutePath();
1196 sendAsynchronousCommand("open cmd:" + path, null);
1197 } catch (IOException e)
1200 .println("Sending commands to Chimera via file failed with "
1206 * Get Chimera residues which have the named attribute, find the mapped
1207 * positions in the Jalview sequence(s), and set as sequence features
1210 * @param alignmentPanel
1212 public void copyStructureAttributesToFeatures(String attName,
1213 AlignmentViewPanel alignmentPanel)
1215 // todo pull up to AAStructureBindingModel (and interface?)
1218 * ask Chimera to list residues with the attribute, reporting its value
1220 // this alternative command
1221 // list residues spec ':*/attName' attr attName
1222 // doesn't report 'None' values (which is good), but
1223 // fails for 'average.bfactor' (which is bad):
1225 String cmd = "list residues attr '" + attName + "'";
1226 List<String> residues = sendChimeraCommand(cmd, true);
1229 * TODO check if Jalview already has this feature name, if so give it a
1230 * distinguishing prefix e.g. chim_
1232 FeatureRenderer fr = alignmentPanel.getFeatureRenderer();
1233 // todo should getRenderOrder be in api.FeatureRenderer?
1234 // FIXME this is empty if feature display is turned off
1235 List<String> existingFeatures = ((jalview.gui.FeatureRenderer) fr)
1237 if (existingFeatures.contains(attName))
1239 attName = getStructureFeaturePrefix() + attName;
1243 * Expect 0, 1 or more reply lines of the format (chi2 is attName):
1244 * residue id #0:5.A chi2 -155.000836316 index 5
1246 * residue id #0:6.A chi3 None
1248 * We assume here that attributes on structure do not naturally convert
1249 * to ranges on sequence, i.e. we just set one feature per mapped position.
1251 * To conflate positions, would need to first build a map
1252 * Map<String value, Map<Sequence seq, List<Integer position>>>
1253 * and then traverse it to find feature ranges.
1255 boolean featureAdded = false;
1256 for (String residue : residues)
1258 AtomSpec spec = null;
1259 String[] tokens = residue.split(" ");
1260 if (tokens.length < 5)
1264 String atomSpec = tokens[2];
1265 String attValue = tokens[4];
1266 if ("None".equals(attValue))
1272 spec = AtomSpec.fromChimeraAtomspec(atomSpec);
1273 } catch (IllegalArgumentException e)
1275 System.err.println("Problem parsing atomspec " + atomSpec);
1278 String pdbFile = getPdbFileForModel(spec.getModelNumber());
1279 spec.setPdbFile(pdbFile);
1281 List<AtomSpec> atoms = Collections.singletonList(spec);
1282 SearchResults sr = getSsm()
1283 .findAlignmentPositionsForStructurePositions(atoms);
1286 * expect one matched alignment position, or none
1287 * (if the structure position is not mapped)
1289 for (Match m : sr.getResults())
1291 SequenceI seq = m.getSequence();
1292 int start = m.getStart();
1293 int end = m.getEnd();
1295 float score = Float.NaN;
1298 score = Float.valueOf(attValue);
1299 } catch (NumberFormatException e)
1301 // was not a float value
1303 String featureGroup = getViewerFeatureGroup();
1304 SequenceFeature sf = new SequenceFeature(attName, attValue, start,
1305 end, score, featureGroup);
1306 // note: repeating the action shouldn't duplicate features
1307 featureAdded |= seq.addSequenceFeature(sf);
1317 * Answers a 'namespace' prefix to use for features created in Jalview from
1318 * attributes in the structure viewer
1322 protected String getStructureFeaturePrefix()
1324 // TODO pull up as abstract
1325 return CHIMERA_FEATURE_PREFIX;
1329 * Answers the feature group name to apply to features created in Jalview from
1330 * Chimera attributes
1334 protected String getViewerFeatureGroup()
1336 // todo pull up to interface
1337 return CHIMERA_FEATURE_GROUP;