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.SequenceRenderer;
25 import jalview.api.structures.JalviewStructureDisplayI;
26 import jalview.bin.Cache;
27 import jalview.datamodel.AlignmentI;
28 import jalview.datamodel.ColumnSelection;
29 import jalview.datamodel.PDBEntry;
30 import jalview.datamodel.SearchResultMatchI;
31 import jalview.datamodel.SearchResultsI;
32 import jalview.datamodel.SequenceFeature;
33 import jalview.datamodel.SequenceI;
34 import jalview.httpserver.AbstractRequestHandler;
35 import jalview.io.DataSourceType;
36 import jalview.schemes.ColourSchemeI;
37 import jalview.schemes.ResidueProperties;
38 import jalview.structure.AtomSpec;
39 import jalview.structure.StructureMappingcommandSet;
40 import jalview.structure.StructureSelectionManager;
41 import jalview.structures.models.AAStructureBindingModel;
42 import jalview.util.MessageManager;
44 import java.awt.Color;
46 import java.io.FileOutputStream;
47 import java.io.IOException;
48 import java.io.PrintWriter;
49 import java.net.BindException;
50 import java.util.ArrayList;
51 import java.util.BitSet;
52 import java.util.Collections;
53 import java.util.Hashtable;
54 import java.util.LinkedHashMap;
55 import java.util.List;
58 import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
59 import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
60 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
61 import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
63 public abstract class JalviewChimeraBinding extends AAStructureBindingModel
65 public static final String CHIMERA_FEATURE_GROUP = "Chimera";
67 // Chimera clause to exclude alternate locations in atom selection
68 private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
70 private static final String COLOURING_CHIMERA = MessageManager
71 .getString("status.colouring_chimera");
73 private static final boolean debug = false;
75 private static final String PHOSPHORUS = "P";
77 private static final String ALPHACARBON = "CA";
79 private List<String> chainNames = new ArrayList<String>();
81 private Hashtable<String, String> chainFile = new Hashtable<String, String>();
84 * Object through which we talk to Chimera
86 private ChimeraManager viewer;
89 * Object which listens to Chimera notifications
91 private AbstractRequestHandler chimeraListener;
94 * set if chimera state is being restored from some source - instructs binding
95 * not to apply default display style when structure set is updated for first
98 private boolean loadingFromArchive = false;
101 * flag to indicate if the Chimera viewer should ignore sequence colouring
102 * events from the structure manager because the GUI is still setting up
104 private boolean loadingFinished = true;
107 * Map of ChimeraModel objects keyed by PDB full local file name
109 private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<String, List<ChimeraModel>>();
111 String lastHighlightCommand;
114 * incremented every time a load notification is successfully handled -
115 * lightweight mechanism for other threads to detect when they can start
116 * referring to new structures.
118 private long loadNotifiesHandled = 0;
120 private Thread chimeraMonitor;
123 * Open a PDB structure file in Chimera and set up mappings from Jalview.
125 * We check if the PDB model id is already loaded in Chimera, if so don't
126 * reopen it. This is the case if Chimera has opened a saved session file.
131 public boolean openFile(PDBEntry pe)
133 String file = pe.getFile();
136 List<ChimeraModel> modelsToMap = new ArrayList<ChimeraModel>();
137 List<ChimeraModel> oldList = viewer.getModelList();
138 boolean alreadyOpen = false;
141 * If Chimera already has this model, don't reopen it, but do remap it.
143 for (ChimeraModel open : oldList)
145 if (open.getModelName().equals(pe.getId()))
148 modelsToMap.add(open);
153 * If Chimera doesn't yet have this model, ask it to open it, and retrieve
154 * the model name(s) added by Chimera.
158 viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL);
159 List<ChimeraModel> newList = viewer.getModelList();
160 // JAL-1728 newList.removeAll(oldList) does not work
161 for (ChimeraModel cm : newList)
163 if (cm.getModelName().equals(pe.getId()))
170 chimeraMaps.put(file, modelsToMap);
172 if (getSsm() != null)
174 getSsm().addStructureViewerListener(this);
175 // ssm.addSelectionListener(this);
179 } catch (Exception q)
181 log("Exception when trying to open model " + file + "\n"
196 public JalviewChimeraBinding(StructureSelectionManager ssm,
197 PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol)
199 super(ssm, pdbentry, sequenceIs, protocol);
200 viewer = new ChimeraManager(new StructureManager(true));
204 * Starts a thread that waits for the Chimera process to finish, so that we
205 * can then close the associated resources. This avoids leaving orphaned
206 * Chimera viewer panels in Jalview if the user closes Chimera.
208 protected void startChimeraProcessMonitor()
210 final Process p = viewer.getChimeraProcess();
211 chimeraMonitor = new Thread(new Runnable()
220 JalviewStructureDisplayI display = getViewer();
223 display.closeViewer(false);
225 } catch (InterruptedException e)
227 // exit thread if Chimera Viewer is closed in Jalview
231 chimeraMonitor.start();
235 * Start a dedicated HttpServer to listen for Chimera notifications, and tell
236 * it to start listening
238 public void startChimeraListener()
242 chimeraListener = new ChimeraListener(this);
243 viewer.startListening(chimeraListener.getUri());
244 } catch (BindException e)
246 System.err.println("Failed to start Chimera listener: "
252 * Tells Chimera to display only the specified chains
256 public void showChains(List<String> toshow)
259 * Construct a chimera command like
261 * ~display #*;~ribbon #*;ribbon :.A,:.B
263 StringBuilder cmd = new StringBuilder(64);
264 boolean first = true;
265 for (String chain : toshow)
267 int modelNumber = getModelNoForChain(chain);
268 String showChainCmd = modelNumber == -1 ? "" : modelNumber + ":."
269 + chain.split(":")[1];
274 cmd.append(showChainCmd);
279 * could append ";focus" to this command to resize the display to fill the
280 * window, but it looks more helpful not to (easier to relate chains to the
283 final String command = "~display #*; ~ribbon #*; ribbon :"
285 sendChimeraCommand(command, false);
289 * Close down the Jalview viewer and listener, and (optionally) the associated
292 public void closeViewer(boolean closeChimera)
294 getSsm().removeStructureViewerListener(this, this.getStructureFiles());
297 viewer.exitChimera();
299 if (this.chimeraListener != null)
301 chimeraListener.shutdown();
302 chimeraListener = null;
306 if (chimeraMonitor != null)
308 chimeraMonitor.interrupt();
310 releaseUIResources();
314 public void colourByChain()
316 colourBySequence = false;
317 sendAsynchronousCommand("rainbow chain", COLOURING_CHIMERA);
321 * Constructs and sends a Chimera command to colour by charge
323 * <li>Aspartic acid and Glutamic acid (negative charge) red</li>
324 * <li>Lysine and Arginine (positive charge) blue</li>
325 * <li>Cysteine - yellow</li>
326 * <li>all others - white</li>
330 public void colourByCharge()
332 colourBySequence = false;
333 String command = "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS";
334 sendAsynchronousCommand(command, COLOURING_CHIMERA);
341 public String superposeStructures(AlignmentI[] _alignment,
342 int[] _refStructure, ColumnSelection[] _hiddenCols)
344 StringBuilder allComs = new StringBuilder(128);
345 String[] files = getStructureFiles();
347 if (!waitForFileLoad(files))
353 StringBuilder selectioncom = new StringBuilder(256);
354 for (int a = 0; a < _alignment.length; a++)
356 int refStructure = _refStructure[a];
357 AlignmentI alignment = _alignment[a];
358 ColumnSelection hiddenCols = _hiddenCols[a];
360 if (refStructure >= files.length)
362 System.err.println("Ignoring invalid reference structure value "
368 * 'matched' bit i will be set for visible alignment columns i where
369 * all sequences have a residue with a mapping to the PDB structure
371 BitSet matched = new BitSet();
372 for (int m = 0; m < alignment.getWidth(); m++)
374 if (hiddenCols == null || hiddenCols.isVisible(m))
380 SuperposeData[] structures = new SuperposeData[files.length];
381 for (int f = 0; f < files.length; f++)
383 structures[f] = new SuperposeData(alignment.getWidth());
387 * Calculate the superposable alignment columns ('matched'), and the
388 * corresponding structure residue positions (structures.pdbResNo)
390 int candidateRefStructure = findSuperposableResidues(alignment,
391 matched, structures);
392 if (refStructure < 0)
395 * If no reference structure was specified, pick the first one that has
396 * a mapping in the alignment
398 refStructure = candidateRefStructure;
401 int nmatched = matched.cardinality();
404 return MessageManager.formatMessage("label.insufficient_residues",
409 * Generate select statements to select regions to superimpose structures
411 String[] selcom = new String[files.length];
412 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
414 String chainCd = "." + structures[pdbfnum].chain;
417 StringBuilder molsel = new StringBuilder();
419 int nextColumnMatch = matched.nextSetBit(0);
420 while (nextColumnMatch != -1)
422 int pdbResNum = structures[pdbfnum].pdbResNo[nextColumnMatch];
423 if (lpos != pdbResNum - 1)
426 * discontiguous - append last residue now
430 molsel.append(String.valueOf(lpos));
431 molsel.append(chainCd);
439 * extending a contiguous run
444 * start the range selection
446 molsel.append(String.valueOf(lpos));
452 nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1);
456 * and terminate final selection
460 molsel.append(String.valueOf(lpos));
461 molsel.append(chainCd);
463 if (molsel.length() > 1)
465 selcom[pdbfnum] = molsel.toString();
466 selectioncom.append("#").append(String.valueOf(pdbfnum))
468 selectioncom.append(selcom[pdbfnum]);
469 selectioncom.append(" ");
470 if (pdbfnum < files.length - 1)
472 selectioncom.append("| ");
477 selcom[pdbfnum] = null;
481 StringBuilder command = new StringBuilder(256);
482 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
484 if (pdbfnum == refStructure || selcom[pdbfnum] == null
485 || selcom[refStructure] == null)
489 if (command.length() > 0)
495 * Form Chimera match command, from the 'new' structure to the
496 * 'reference' structure e.g. (50 residues, chain B/A, alphacarbons):
498 * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA
501 * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
503 command.append("match ").append(getModelSpec(pdbfnum)).append(":");
504 command.append(selcom[pdbfnum]);
505 command.append("@").append(
506 structures[pdbfnum].isRna ? PHOSPHORUS : ALPHACARBON);
507 // JAL-1757 exclude alternate CA locations
508 command.append(NO_ALTLOCS);
509 command.append(" ").append(getModelSpec(refStructure)).append(":");
510 command.append(selcom[refStructure]);
511 command.append("@").append(
512 structures[refStructure].isRna ? PHOSPHORUS : ALPHACARBON);
513 command.append(NO_ALTLOCS);
515 if (selectioncom.length() > 0)
519 System.out.println("Select regions:\n" + selectioncom.toString());
520 System.out.println("Superimpose command(s):\n"
521 + command.toString());
523 allComs.append("~display all; chain @CA|P; ribbon ")
524 .append(selectioncom.toString())
525 .append(";" + command.toString());
530 if (selectioncom.length() > 0)
532 // TODO: visually distinguish regions that were superposed
533 if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
535 selectioncom.setLength(selectioncom.length() - 1);
539 System.out.println("Select regions:\n" + selectioncom.toString());
541 allComs.append("; ~display all; chain @CA|P; ribbon ")
542 .append(selectioncom.toString()).append("; focus");
543 List<String> chimeraReplies = sendChimeraCommand(allComs.toString(),
545 for (String reply : chimeraReplies)
547 if (reply.toLowerCase().contains("unequal numbers of atoms"))
557 * Helper method to construct model spec in Chimera format:
559 * <li>#0 (#1 etc) for a PDB file with no sub-models</li>
560 * <li>#0.1 (#1.1 etc) for a PDB file with sub-models</li>
562 * Note for now we only ever choose the first of multiple models. This
563 * corresponds to the hard-coded Jmol equivalent (compare {1.1}). Refactor in
564 * future if there is a need to select specific sub-models.
569 protected String getModelSpec(int pdbfnum)
571 if (pdbfnum < 0 || pdbfnum >= getPdbCount())
577 * For now, the test for having sub-models is whether multiple Chimera
578 * models are mapped for the PDB file; the models are returned as a response
579 * to the Chimera command 'list models type molecule', see
580 * ChimeraManager.getModelList().
582 List<ChimeraModel> maps = chimeraMaps.get(getStructureFiles()[pdbfnum]);
583 boolean hasSubModels = maps != null && maps.size() > 1;
584 return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
588 * Launch Chimera, unless an instance linked to this object is already
589 * running. Returns true if Chimera is successfully launched, or already
590 * running, else false.
594 public boolean launchChimera()
596 if (viewer.isChimeraLaunched())
601 boolean launched = viewer.launchChimera(StructureManager
605 startChimeraProcessMonitor();
609 log("Failed to launch Chimera!");
615 * Answers true if the Chimera process is still running, false if ended or not
620 public boolean isChimeraRunning()
622 return viewer.isChimeraLaunched();
626 * Send a command to Chimera, and optionally log and return any responses.
628 * Does nothing, and returns null, if the command is the same as the last one
634 public List<String> sendChimeraCommand(final String command,
639 // ? thread running after viewer shut down
642 List<String> reply = null;
643 viewerCommandHistory(false);
644 if (true /*lastCommand == null || !lastCommand.equals(command)*/)
646 // trim command or it may never find a match in the replyLog!!
647 List<String> lastReply = viewer.sendChimeraCommand(command.trim(),
654 log("Response from command ('" + command + "') was:\n"
659 viewerCommandHistory(true);
665 * Send a Chimera command asynchronously in a new thread. If the progress
666 * message is not null, display this message while the command is executing.
671 protected abstract void sendAsynchronousCommand(String command,
675 * Sends a set of colour commands to the structure viewer
677 * @param colourBySequenceCommands
680 protected void colourBySequence(
681 StructureMappingcommandSet[] colourBySequenceCommands)
683 for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
685 for (String command : cpdbbyseq.commands)
687 sendAsynchronousCommand(command, COLOURING_CHIMERA);
699 protected StructureMappingcommandSet[] getColourBySequenceCommands(
700 String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
702 return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
703 getSequence(), sr, viewPanel);
709 protected void executeWhenReady(String command)
712 sendChimeraCommand(command, false);
716 private void waitForChimera()
718 while (viewer != null && viewer.isBusy())
723 } catch (InterruptedException q)
729 // End StructureListener
730 // //////////////////////////
733 * instruct the Jalview binding to update the pdbentries vector if necessary
734 * prior to matching the viewer's contents to the list of structure files
735 * Jalview knows about.
737 public abstract void refreshPdbEntries();
740 * map between index of model filename returned from getPdbFile and the first
741 * index of models from this file in the viewer. Note - this is not trimmed -
742 * use getPdbFile to get number of unique models.
744 private int _modelFileNameMap[];
747 // ////////////////////////////////
748 // /StructureListener
750 public synchronized String[] getStructureFiles()
754 return new String[0];
757 return chimeraMaps.keySet().toArray(
758 modelFileNames = new String[chimeraMaps.size()]);
762 * Construct and send a command to highlight zero, one or more atoms. We do
763 * this by sending an "rlabel" command to show the residue label at that
767 public void highlightAtoms(List<AtomSpec> atoms)
769 if (atoms == null || atoms.size() == 0)
774 StringBuilder cmd = new StringBuilder(128);
775 boolean first = true;
776 boolean found = false;
778 for (AtomSpec atom : atoms)
780 int pdbResNum = atom.getPdbResNum();
781 String chain = atom.getChain();
782 String pdbfile = atom.getPdbFile();
783 List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
784 if (cms != null && !cms.isEmpty())
788 cmd.append("rlabel #").append(cms.get(0).getModelNumber())
796 cmd.append(pdbResNum);
797 if (!chain.equals(" "))
799 cmd.append(".").append(chain);
804 String command = cmd.toString();
807 * avoid repeated commands for the same residue
809 if (command.equals(lastHighlightCommand))
815 * unshow the label for the previous residue
817 if (lastHighlightCommand != null)
819 viewer.sendChimeraCommand("~" + lastHighlightCommand, false);
823 viewer.sendChimeraCommand(command, false);
825 this.lastHighlightCommand = command;
829 * Query Chimera for its current selection, and highlight it on the alignment
831 public void highlightChimeraSelection()
834 * Ask Chimera for its current selection
836 List<String> selection = viewer.getSelectedResidueSpecs();
839 * Parse model number, residue and chain for each selected position,
840 * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
842 List<AtomSpec> atomSpecs = convertStructureResiduesToAlignment(selection);
845 * Broadcast the selection (which may be empty, if the user just cleared all
848 getSsm().mouseOverStructure(atomSpecs);
852 * Converts a list of Chimera atomspecs to a list of AtomSpec representing the
853 * corresponding residues (if any) in Jalview
855 * @param structureSelection
858 protected List<AtomSpec> convertStructureResiduesToAlignment(
859 List<String> structureSelection)
861 List<AtomSpec> atomSpecs = new ArrayList<AtomSpec>();
862 for (String atomSpec : structureSelection)
866 AtomSpec spec = AtomSpec.fromChimeraAtomspec(atomSpec);
867 String pdbfilename = getPdbFileForModel(spec.getModelNumber());
868 spec.setPdbFile(pdbfilename);
870 } catch (IllegalArgumentException e)
872 System.err.println("Failed to parse atomspec: " + atomSpec);
882 protected String getPdbFileForModel(int modelId)
885 * Work out the pdbfilename from the model number
887 String pdbfilename = modelFileNames[0];
888 findfileloop: for (String pdbfile : this.chimeraMaps.keySet())
890 for (ChimeraModel cm : chimeraMaps.get(pdbfile))
892 if (cm.getModelNumber() == modelId)
894 pdbfilename = pdbfile;
902 private void log(String message)
904 System.err.println("## Chimera log: " + message);
907 private void viewerCommandHistory(boolean enable)
909 // log("(Not yet implemented) History "
910 // + ((debug || enable) ? "on" : "off"));
913 public long getLoadNotifiesHandled()
915 return loadNotifiesHandled;
919 public void setJalviewColourScheme(ColourSchemeI cs)
921 colourBySequence = false;
928 // Chimera expects RBG values in the range 0-1
929 final double normalise = 255D;
930 viewerCommandHistory(false);
931 StringBuilder command = new StringBuilder(128);
933 List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
935 for (String resName : residueSet)
937 char res = resName.length() == 3 ? ResidueProperties
938 .getSingleCharacterCode(resName) : resName.charAt(0);
939 Color col = cs.findColour(res, 0, null, null, 0f);
940 command.append("color " + col.getRed() / normalise + ","
941 + col.getGreen() / normalise + "," + col.getBlue()
942 / normalise + " ::" + resName + ";");
945 sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
946 viewerCommandHistory(true);
950 * called when the binding thinks the UI needs to be refreshed after a Chimera
951 * state change. this could be because structures were loaded, or because an
952 * error has occurred.
954 public abstract void refreshGUI();
957 public void setLoadingFromArchive(boolean loadingFromArchive)
959 this.loadingFromArchive = loadingFromArchive;
964 * @return true if Chimeral is still restoring state or loading is still going
965 * on (see setFinsihedLoadingFromArchive)
968 public boolean isLoadingFromArchive()
970 return loadingFromArchive && !loadingFinished;
974 * modify flag which controls if sequence colouring events are honoured by the
975 * binding. Should be true for normal operation
977 * @param finishedLoading
980 public void setFinishedLoadingFromArchive(boolean finishedLoading)
982 loadingFinished = finishedLoading;
986 * Send the Chimera 'background solid <color>" command.
989 * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
994 public void setBackgroundColour(Color col)
996 viewerCommandHistory(false);
997 double normalise = 255D;
998 final String command = "background solid " + col.getRed() / normalise
999 + "," + col.getGreen() / normalise + "," + col.getBlue()
1001 viewer.sendChimeraCommand(command, false);
1002 viewerCommandHistory(true);
1006 * Ask Chimera to save its session to the given file. Returns true if
1007 * successful, else false.
1012 public boolean saveSession(String filepath)
1014 if (isChimeraRunning())
1016 List<String> reply = viewer.sendChimeraCommand("save " + filepath,
1018 if (reply.contains("Session written"))
1025 .error("Error saving Chimera session: " + reply.toString());
1032 * Ask Chimera to open a session file. Returns true if successful, else false.
1033 * The filename must have a .py extension for this command to work.
1038 public boolean openSession(String filepath)
1040 sendChimeraCommand("open " + filepath, true);
1041 // todo: test for failure - how?
1046 * Returns a list of chains mapped in this viewer. Note this list is not
1047 * currently scoped per structure.
1052 public List<String> getChainNames()
1058 * Send a 'focus' command to Chimera to recentre the visible display
1060 public void focusView()
1062 sendChimeraCommand("focus", false);
1066 * Send a 'show' command for all atoms in the currently selected columns
1068 * TODO: pull up to abstract structure viewer interface
1072 public void highlightSelection(AlignmentViewPanel vp)
1074 List<Integer> cols = vp.getAlignViewport().getColumnSelection()
1076 AlignmentI alignment = vp.getAlignment();
1077 StructureSelectionManager sm = getSsm();
1078 for (SequenceI seq : alignment.getSequences())
1081 * convert selected columns into sequence positions
1083 int[] positions = new int[cols.size()];
1085 for (Integer col : cols)
1087 positions[i++] = seq.findPosition(col);
1089 sm.highlightStructure(this, seq, positions);
1094 * Constructs and send commands to Chimera to set attributes on residues for
1095 * features visible in Jalview
1100 public int sendFeaturesToViewer(AlignmentViewPanel avp)
1102 // TODO refactor as required to pull up to an interface
1103 AlignmentI alignment = avp.getAlignment();
1105 String[] files = getStructureFiles();
1111 StructureMappingcommandSet commandSet = ChimeraCommands
1112 .getSetAttributeCommandsForFeatures(getSsm(), files,
1113 getSequence(), avp);
1114 String[] commands = commandSet.commands;
1115 if (commands.length > 10)
1117 sendCommandsByFile(commands);
1121 for (String command : commands)
1123 sendAsynchronousCommand(command, null);
1126 return commands.length;
1130 * Write commands to a temporary file, and send a command to Chimera to open
1131 * the file as a commands script. For use when sending a large number of
1132 * separate commands would overload the REST interface mechanism.
1136 protected void sendCommandsByFile(String[] commands)
1140 File tmp = File.createTempFile("chim", ".com");
1142 PrintWriter out = new PrintWriter(new FileOutputStream(tmp));
1143 for (String command : commands)
1145 out.println(command);
1149 String path = tmp.getAbsolutePath();
1150 sendAsynchronousCommand("open cmd:" + path, null);
1151 } catch (IOException e)
1154 .println("Sending commands to Chimera via file failed with "
1160 * Get Chimera residues which have the named attribute, find the mapped
1161 * positions in the Jalview sequence(s), and set as sequence features
1164 * @param alignmentPanel
1166 public void copyStructureAttributesToFeatures(String attName,
1167 AlignmentViewPanel alignmentPanel)
1169 // todo pull up to AAStructureBindingModel (and interface?)
1172 * ask Chimera to list residues with the attribute, reporting its value
1174 // this alternative command
1175 // list residues spec ':*/attName' attr attName
1176 // doesn't report 'None' values (which is good), but
1177 // fails for 'average.bfactor' (which is bad):
1179 String cmd = "list residues attr '" + attName + "'";
1180 List<String> residues = sendChimeraCommand(cmd, true);
1182 boolean featureAdded = createFeaturesForAttributes(attName, residues);
1185 alignmentPanel.getFeatureRenderer().featuresAdded();
1190 * Create features in Jalview for the given attribute name and structure
1194 * The residue list should be 0, 1 or more reply lines of the format:
1195 * residue id #0:5.A isHelix -155.000836316 index 5
1197 * residue id #0:6.A isHelix None
1204 protected boolean createFeaturesForAttributes(String attName,
1205 List<String> residues)
1207 boolean featureAdded = false;
1208 String featureGroup = getViewerFeatureGroup();
1210 for (String residue : residues)
1212 AtomSpec spec = null;
1213 String[] tokens = residue.split(" ");
1214 if (tokens.length < 5)
1218 String atomSpec = tokens[2];
1219 String attValue = tokens[4];
1222 * ignore 'None' (e.g. for phi) or 'False' (e.g. for isHelix)
1224 if ("None".equalsIgnoreCase(attValue)
1225 || "False".equalsIgnoreCase(attValue))
1232 spec = AtomSpec.fromChimeraAtomspec(atomSpec);
1233 } catch (IllegalArgumentException e)
1235 System.err.println("Problem parsing atomspec " + atomSpec);
1239 String chainId = spec.getChain();
1240 String description = attValue;
1241 float score = Float.NaN;
1244 score = Float.valueOf(attValue);
1245 description = chainId;
1246 } catch (NumberFormatException e)
1248 // was not a float value
1251 String pdbFile = getPdbFileForModel(spec.getModelNumber());
1252 spec.setPdbFile(pdbFile);
1254 List<AtomSpec> atoms = Collections.singletonList(spec);
1257 * locate the mapped position in the alignment (if any)
1259 SearchResultsI sr = getSsm()
1260 .findAlignmentPositionsForStructurePositions(atoms);
1263 * expect one matched alignment position, or none
1264 * (if the structure position is not mapped)
1266 for (SearchResultMatchI m : sr.getResults())
1268 SequenceI seq = m.getSequence();
1269 int start = m.getStart();
1270 int end = m.getEnd();
1271 SequenceFeature sf = new SequenceFeature(attName, description,
1272 start, end, score, featureGroup);
1273 // todo: should SequenceFeature have an explicit property for chain?
1274 // note: repeating the action shouldn't duplicate features
1275 featureAdded |= seq.addSequenceFeature(sf);
1278 return featureAdded;
1282 * Answers the feature group name to apply to features created in Jalview from
1283 * Chimera attributes
1287 protected String getViewerFeatureGroup()
1289 // todo pull up to interface
1290 return CHIMERA_FEATURE_GROUP;
1294 public Hashtable<String, String> getChainFile()
1299 public List<ChimeraModel> getChimeraModelByChain(String chain)
1301 return chimeraMaps.get(chainFile.get(chain));
1304 public int getModelNoForChain(String chain)
1306 List<ChimeraModel> foundModels = getChimeraModelByChain(chain);
1307 if (foundModels != null && !foundModels.isEmpty())
1309 return foundModels.get(0).getModelNumber();