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.SearchResultMatchI;
31 import jalview.datamodel.SearchResults;
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.Hashtable;
52 import java.util.LinkedHashMap;
53 import java.util.List;
56 import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
57 import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
58 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
59 import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
61 public abstract class JalviewChimeraBinding extends AAStructureBindingModel
63 public static final String CHIMERA_FEATURE_GROUP = "Chimera";
65 // Chimera clause to exclude alternate locations in atom selection
66 private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
68 private static final String COLOURING_CHIMERA = MessageManager
69 .getString("status.colouring_chimera");
71 private static final boolean debug = false;
73 private static final String PHOSPHORUS = "P";
75 private static final String ALPHACARBON = "CA";
77 private List<String> chainNames = new ArrayList<String>();
79 private Hashtable<String, String> chainFile = new Hashtable<String, String>();
82 * Object through which we talk to Chimera
84 private ChimeraManager viewer;
87 * Object which listens to Chimera notifications
89 private AbstractRequestHandler chimeraListener;
92 * set if chimera state is being restored from some source - instructs binding
93 * not to apply default display style when structure set is updated for first
96 private boolean loadingFromArchive = false;
99 * flag to indicate if the Chimera viewer should ignore sequence colouring
100 * events from the structure manager because the GUI is still setting up
102 private boolean loadingFinished = true;
104 public String fileLoadingError;
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;
121 * Open a PDB structure file in Chimera and set up mappings from Jalview.
123 * We check if the PDB model id is already loaded in Chimera, if so don't
124 * reopen it. This is the case if Chimera has opened a saved session file.
129 public boolean openFile(PDBEntry pe)
131 String file = pe.getFile();
134 List<ChimeraModel> modelsToMap = new ArrayList<ChimeraModel>();
135 List<ChimeraModel> oldList = viewer.getModelList();
136 boolean alreadyOpen = false;
139 * If Chimera already has this model, don't reopen it, but do remap it.
141 for (ChimeraModel open : oldList)
143 if (open.getModelName().equals(pe.getId()))
146 modelsToMap.add(open);
151 * If Chimera doesn't yet have this model, ask it to open it, and retrieve
152 * the model name(s) added by Chimera.
156 viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL);
157 List<ChimeraModel> newList = viewer.getModelList();
158 // JAL-1728 newList.removeAll(oldList) does not work
159 for (ChimeraModel cm : newList)
161 if (cm.getModelName().equals(pe.getId()))
168 chimeraMaps.put(file, modelsToMap);
170 if (getSsm() != null)
172 getSsm().addStructureViewerListener(this);
173 // ssm.addSelectionListener(this);
174 FeatureRenderer fr = getFeatureRenderer(null);
182 } catch (Exception q)
184 log("Exception when trying to open model " + file + "\n"
199 public JalviewChimeraBinding(StructureSelectionManager ssm,
200 PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String protocol)
202 super(ssm, pdbentry, sequenceIs, protocol);
203 viewer = new ChimeraManager(
204 new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
208 * Start a dedicated HttpServer to listen for Chimera notifications, and tell
209 * it to start listening
211 public void startChimeraListener()
215 chimeraListener = new ChimeraListener(this);
216 viewer.startListening(chimeraListener.getUri());
217 } catch (BindException e)
219 System.err.println("Failed to start Chimera listener: "
225 * Construct a title string for the viewer window based on the data Jalview
231 public String getViewerTitle(boolean verbose)
233 return getViewerTitle("Chimera", verbose);
237 * Tells Chimera to display only the specified chains
241 public void showChains(List<String> toshow)
244 * Construct a chimera command like
246 * ~display #*;~ribbon #*;ribbon :.A,:.B
248 StringBuilder cmd = new StringBuilder(64);
249 boolean first = true;
250 for (String chain : toshow)
252 int modelNumber = getModelNoForChain(chain);
253 String showChainCmd = modelNumber == -1 ? "" : modelNumber + ":."
254 + chain.split(":")[1];
259 cmd.append(showChainCmd);
264 * could append ";focus" to this command to resize the display to fill the
265 * window, but it looks more helpful not to (easier to relate chains to the
268 final String command = "~display #*; ~ribbon #*; ribbon :"
270 sendChimeraCommand(command, false);
274 * Close down the Jalview viewer and listener, and (optionally) the associated
277 public void closeViewer(boolean closeChimera)
279 getSsm().removeStructureViewerListener(this, this.getPdbFile());
282 viewer.exitChimera();
284 if (this.chimeraListener != null)
286 chimeraListener.shutdown();
287 chimeraListener = null;
291 releaseUIResources();
294 public void colourByChain()
296 colourBySequence = false;
297 sendAsynchronousCommand("rainbow chain", COLOURING_CHIMERA);
301 * Constructs and sends a Chimera command to colour by charge
303 * <li>Aspartic acid and Glutamic acid (negative charge) red</li>
304 * <li>Lysine and Arginine (positive charge) blue</li>
305 * <li>Cysteine - yellow</li>
306 * <li>all others - white</li>
309 public void colourByCharge()
311 colourBySequence = false;
312 String command = "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS";
313 sendAsynchronousCommand(command, COLOURING_CHIMERA);
317 * Construct and send a command to align structures against a reference
318 * structure, based on one or more sequence alignments
321 * an array of alignments to process
322 * @param _refStructure
323 * an array of corresponding reference structures (index into pdb
324 * file array); if a negative value is passed, the first PDB file
325 * mapped to an alignment sequence is used as the reference for
328 * an array of corresponding hidden columns for each alignment
330 public void superposeStructures(AlignmentI[] _alignment,
331 int[] _refStructure, ColumnSelection[] _hiddenCols)
333 StringBuilder allComs = new StringBuilder(128);
334 String[] files = getPdbFile();
336 if (!waitForFileLoad(files))
342 StringBuilder selectioncom = new StringBuilder(256);
343 for (int a = 0; a < _alignment.length; a++)
345 int refStructure = _refStructure[a];
346 AlignmentI alignment = _alignment[a];
347 ColumnSelection hiddenCols = _hiddenCols[a];
349 if (refStructure >= files.length)
351 System.err.println("Ignoring invalid reference structure value "
357 * 'matched' array will hold 'true' for visible alignment columns where
358 * all sequences have a residue with a mapping to the PDB structure
360 boolean matched[] = new boolean[alignment.getWidth()];
361 for (int m = 0; m < matched.length; m++)
363 matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
366 SuperposeData[] structures = new SuperposeData[files.length];
367 for (int f = 0; f < files.length; f++)
369 structures[f] = new SuperposeData(alignment.getWidth());
373 * Calculate the superposable alignment columns ('matched'), and the
374 * corresponding structure residue positions (structures.pdbResNo)
376 int candidateRefStructure = findSuperposableResidues(alignment,
377 matched, structures);
378 if (refStructure < 0)
381 * If no reference structure was specified, pick the first one that has
382 * a mapping in the alignment
384 refStructure = candidateRefStructure;
388 for (boolean b : matched)
397 // TODO: bail out here because superposition illdefined?
401 * Generate select statements to select regions to superimpose structures
403 String[] selcom = new String[files.length];
404 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
406 String chainCd = "." + structures[pdbfnum].chain;
409 StringBuilder molsel = new StringBuilder();
410 for (int r = 0; r < matched.length; r++)
414 int pdbResNum = structures[pdbfnum].pdbResNo[r];
415 if (lpos != pdbResNum - 1)
418 * discontiguous - append last residue now
422 molsel.append(String.valueOf(lpos));
423 molsel.append(chainCd);
431 * extending a contiguous run
436 * start the range selection
438 molsel.append(String.valueOf(lpos));
448 * and terminate final selection
452 molsel.append(String.valueOf(lpos));
453 molsel.append(chainCd);
455 if (molsel.length() > 1)
457 selcom[pdbfnum] = molsel.toString();
458 selectioncom.append("#").append(String.valueOf(pdbfnum))
460 selectioncom.append(selcom[pdbfnum]);
461 selectioncom.append(" ");
462 if (pdbfnum < files.length - 1)
464 selectioncom.append("| ");
469 selcom[pdbfnum] = null;
473 StringBuilder command = new StringBuilder(256);
474 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
476 if (pdbfnum == refStructure || selcom[pdbfnum] == null
477 || selcom[refStructure] == null)
481 if (command.length() > 0)
487 * Form Chimera match command, from the 'new' structure to the
488 * 'reference' structure e.g. (50 residues, chain B/A, alphacarbons):
490 * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA
493 * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
495 command.append("match ").append(getModelSpec(pdbfnum)).append(":");
496 command.append(selcom[pdbfnum]);
497 command.append("@").append(
498 structures[pdbfnum].isRna ? PHOSPHORUS : ALPHACARBON);
499 // JAL-1757 exclude alternate CA locations
500 command.append(NO_ALTLOCS);
501 command.append(" ").append(getModelSpec(refStructure)).append(":");
502 command.append(selcom[refStructure]);
503 command.append("@").append(
504 structures[refStructure].isRna ? PHOSPHORUS : ALPHACARBON);
505 command.append(NO_ALTLOCS);
507 if (selectioncom.length() > 0)
511 System.out.println("Select regions:\n" + selectioncom.toString());
512 System.out.println("Superimpose command(s):\n"
513 + command.toString());
515 allComs.append("~display all; chain @CA|P; ribbon ")
516 .append(selectioncom.toString())
517 .append(";" + command.toString());
520 if (selectioncom.length() > 0)
522 // TODO: visually distinguish regions that were superposed
523 if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
525 selectioncom.setLength(selectioncom.length() - 1);
529 System.out.println("Select regions:\n" + selectioncom.toString());
531 allComs.append("; ~display all; chain @CA|P; ribbon ")
532 .append(selectioncom.toString()).append("; focus");
533 sendChimeraCommand(allComs.toString(), false);
539 * Helper method to construct model spec in Chimera format:
541 * <li>#0 (#1 etc) for a PDB file with no sub-models</li>
542 * <li>#0.1 (#1.1 etc) for a PDB file with sub-models</li>
544 * Note for now we only ever choose the first of multiple models. This
545 * corresponds to the hard-coded Jmol equivalent (compare {1.1}). Refactor in
546 * future if there is a need to select specific sub-models.
551 protected String getModelSpec(int pdbfnum)
553 if (pdbfnum < 0 || pdbfnum >= getPdbCount())
559 * For now, the test for having sub-models is whether multiple Chimera
560 * models are mapped for the PDB file; the models are returned as a response
561 * to the Chimera command 'list models type molecule', see
562 * ChimeraManager.getModelList().
564 List<ChimeraModel> maps = chimeraMaps.get(getPdbFile()[pdbfnum]);
565 boolean hasSubModels = maps != null && maps.size() > 1;
566 return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
570 * Launch Chimera, unless an instance linked to this object is already
571 * running. Returns true if chimera is successfully launched, or already
572 * running, else false.
576 public boolean launchChimera()
578 if (!viewer.isChimeraLaunched())
580 return viewer.launchChimera(StructureManager.getChimeraPaths());
582 if (viewer.isChimeraLaunched())
586 log("Failed to launch Chimera!");
591 * Answers true if the Chimera process is still running, false if ended or not
596 public boolean isChimeraRunning()
598 return viewer.isChimeraLaunched();
602 * Send a command to Chimera, and optionally log and return any responses.
604 * Does nothing, and returns null, if the command is the same as the last one
610 public List<String> sendChimeraCommand(final String command,
615 // ? thread running after viewer shut down
618 List<String> reply = null;
619 viewerCommandHistory(false);
620 if (true /*lastCommand == null || !lastCommand.equals(command)*/)
622 // trim command or it may never find a match in the replyLog!!
623 List<String> lastReply = viewer.sendChimeraCommand(command.trim(),
630 log("Response from command ('" + command + "') was:\n"
635 viewerCommandHistory(true);
641 * Send a Chimera command asynchronously in a new thread. If the progress
642 * message is not null, display this message while the command is executing.
647 protected abstract void sendAsynchronousCommand(String command,
651 * colour any structures associated with sequences in the given alignment
652 * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
653 * if colourBySequence is enabled.
655 public void colourBySequence(boolean showFeatures,
656 jalview.api.AlignmentViewPanel alignmentv)
658 if (!colourBySequence || !loadingFinished)
662 if (getSsm() == null)
666 String[] files = getPdbFile();
668 SequenceRenderer sr = getSequenceRenderer(alignmentv);
670 FeatureRenderer fr = null;
673 fr = getFeatureRenderer(alignmentv);
675 AlignmentI alignment = alignmentv.getAlignment();
677 StructureMappingcommandSet colourBySequenceCommands = ChimeraCommands
678 .getColourBySequenceCommand(getSsm(), files, getSequence(), sr,
680 for (String command : colourBySequenceCommands.commands)
682 sendAsynchronousCommand(command, COLOURING_CHIMERA);
689 protected void executeWhenReady(String command)
692 sendChimeraCommand(command, false);
696 private void waitForChimera()
698 while (viewer != null && viewer.isBusy())
703 } catch (InterruptedException q)
709 // End StructureListener
710 // //////////////////////////
713 * returns the current featureRenderer that should be used to colour the
720 public abstract FeatureRenderer getFeatureRenderer(
721 AlignmentViewPanel alignment);
724 * instruct the Jalview binding to update the pdbentries vector if necessary
725 * prior to matching the viewer's contents to the list of structure files
726 * Jalview knows about.
728 public abstract void refreshPdbEntries();
730 // ////////////////////////////////
731 // /StructureListener
733 public synchronized String[] getPdbFile()
737 return new String[0];
740 return chimeraMaps.keySet().toArray(
741 modelFileNames = new String[chimeraMaps.size()]);
745 * returns the current sequenceRenderer that should be used to colour the
752 public abstract SequenceRenderer getSequenceRenderer(
753 AlignmentViewPanel alignment);
756 * Construct and send a command to highlight zero, one or more atoms. We do
757 * this by sending an "rlabel" command to show the residue label at that
761 public void highlightAtoms(List<AtomSpec> atoms)
763 if (atoms == null || atoms.size() == 0)
768 StringBuilder cmd = new StringBuilder(128);
769 boolean first = true;
770 boolean found = false;
772 for (AtomSpec atom : atoms)
774 int pdbResNum = atom.getPdbResNum();
775 String chain = atom.getChain();
776 String pdbfile = atom.getPdbFile();
777 List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
778 if (cms != null && !cms.isEmpty())
782 cmd.append("rlabel #").append(cms.get(0).getModelNumber())
790 cmd.append(pdbResNum);
791 if (!chain.equals(" "))
793 cmd.append(".").append(chain);
798 String command = cmd.toString();
801 * avoid repeated commands for the same residue
803 if (command.equals(lastHighlightCommand))
809 * unshow the label for the previous residue
811 if (lastHighlightCommand != null)
813 viewer.sendChimeraCommand("~" + lastHighlightCommand, false);
817 viewer.sendChimeraCommand(command, false);
819 this.lastHighlightCommand = command;
823 * Query Chimera for its current selection, and highlight it on the alignment
825 public void highlightChimeraSelection()
828 * Ask Chimera for its current selection
830 List<String> selection = viewer.getSelectedResidueSpecs();
833 * Parse model number, residue and chain for each selected position,
834 * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
836 List<AtomSpec> atomSpecs = convertStructureResiduesToAlignment(selection);
839 * Broadcast the selection (which may be empty, if the user just cleared all
842 getSsm().mouseOverStructure(atomSpecs);
846 * Converts a list of Chimera atomspecs to a list of AtomSpec representing the
847 * corresponding residues (if any) in Jalview
849 * @param structureSelection
852 protected List<AtomSpec> convertStructureResiduesToAlignment(
853 List<String> structureSelection)
855 List<AtomSpec> atomSpecs = new ArrayList<AtomSpec>();
856 for (String atomSpec : structureSelection)
860 AtomSpec spec = AtomSpec.fromChimeraAtomspec(atomSpec);
861 String pdbfilename = getPdbFileForModel(spec.getModelNumber());
862 spec.setPdbFile(pdbfilename);
864 } catch (IllegalArgumentException e)
866 System.err.println("Failed to parse atomspec: " + atomSpec);
876 protected String getPdbFileForModel(int modelId)
879 * Work out the pdbfilename from the model number
881 String pdbfilename = modelFileNames[0];
882 findfileloop: for (String pdbfile : this.chimeraMaps.keySet())
884 for (ChimeraModel cm : chimeraMaps.get(pdbfile))
886 if (cm.getModelNumber() == modelId)
888 pdbfilename = pdbfile;
896 private void log(String message)
898 System.err.println("## Chimera log: " + message);
901 private void viewerCommandHistory(boolean enable)
903 // log("(Not yet implemented) History "
904 // + ((debug || enable) ? "on" : "off"));
907 public long getLoadNotifiesHandled()
909 return loadNotifiesHandled;
912 public void setJalviewColourScheme(ColourSchemeI cs)
914 colourBySequence = false;
921 // Chimera expects RBG values in the range 0-1
922 final double normalise = 255D;
923 viewerCommandHistory(false);
924 StringBuilder command = new StringBuilder(128);
926 List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
928 for (String res : residueSet)
930 Color col = cs.findColour(res.charAt(0));
931 command.append("color " + col.getRed() / normalise + ","
932 + col.getGreen() / normalise + "," + col.getBlue()
933 / normalise + " ::" + res + ";");
936 sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
937 viewerCommandHistory(true);
941 * called when the binding thinks the UI needs to be refreshed after a Chimera
942 * state change. this could be because structures were loaded, or because an
943 * error has occurred.
945 public abstract void refreshGUI();
948 public void setLoadingFromArchive(boolean loadingFromArchive)
950 this.loadingFromArchive = loadingFromArchive;
955 * @return true if Chimeral is still restoring state or loading is still going
956 * on (see setFinsihedLoadingFromArchive)
959 public boolean isLoadingFromArchive()
961 return loadingFromArchive && !loadingFinished;
965 * modify flag which controls if sequence colouring events are honoured by the
966 * binding. Should be true for normal operation
968 * @param finishedLoading
971 public void setFinishedLoadingFromArchive(boolean finishedLoading)
973 loadingFinished = finishedLoading;
977 * Send the Chimera 'background solid <color>" command.
980 * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
984 public void setBackgroundColour(Color col)
986 viewerCommandHistory(false);
987 double normalise = 255D;
988 final String command = "background solid " + col.getRed() / normalise
989 + "," + col.getGreen() / normalise + "," + col.getBlue()
991 viewer.sendChimeraCommand(command, false);
992 viewerCommandHistory(true);
996 * Ask Chimera to save its session to the given file. Returns true if
997 * successful, else false.
1002 public boolean saveSession(String filepath)
1004 if (isChimeraRunning())
1006 List<String> reply = viewer.sendChimeraCommand("save " + filepath,
1008 if (reply.contains("Session written"))
1015 .error("Error saving Chimera session: " + reply.toString());
1022 * Ask Chimera to open a session file. Returns true if successful, else false.
1023 * The filename must have a .py extension for this command to work.
1028 public boolean openSession(String filepath)
1030 sendChimeraCommand("open " + filepath, true);
1031 // todo: test for failure - how?
1036 * Returns a list of chains mapped in this viewer. Note this list is not
1037 * currently scoped per structure.
1042 public List<String> getChainNames()
1048 * Send a 'focus' command to Chimera to recentre the visible display
1050 public void focusView()
1052 sendChimeraCommand("focus", false);
1056 * Send a 'show' command for all atoms in the currently selected columns
1058 * TODO: pull up to abstract structure viewer interface
1062 public void highlightSelection(AlignmentViewPanel vp)
1064 List<Integer> cols = vp.getAlignViewport().getColumnSelection()
1066 AlignmentI alignment = vp.getAlignment();
1067 StructureSelectionManager sm = getSsm();
1068 for (SequenceI seq : alignment.getSequences())
1071 * convert selected columns into sequence positions
1073 int[] positions = new int[cols.size()];
1075 for (Integer col : cols)
1077 positions[i++] = seq.findPosition(col);
1079 sm.highlightStructure(this, seq, positions);
1084 * Constructs and send commands to Chimera to set attributes on residues for
1085 * features visible in Jalview
1089 public void sendFeaturesToViewer(AlignmentViewPanel avp)
1091 // TODO refactor as required to pull up to an interface
1092 AlignmentI alignment = avp.getAlignment();
1093 FeatureRenderer fr = getFeatureRenderer(avp);
1096 * fr is null if feature display is turned off
1103 String[] files = getPdbFile();
1109 StructureMappingcommandSet commandSet = ChimeraCommands
1110 .getSetAttributeCommandsForFeatures(getSsm(), files,
1111 getSequence(), fr, alignment);
1112 String[] commands = commandSet.commands;
1113 if (commands.length > 10)
1115 sendCommandsByFile(commands);
1119 for (String command : commands)
1121 sendAsynchronousCommand(command, null);
1127 * Write commands to a temporary file, and send a command to Chimera to open
1128 * the file as a commands script. For use when sending a large number of
1129 * separate commands would overload the REST interface mechanism.
1133 protected void sendCommandsByFile(String[] commands)
1137 File tmp = File.createTempFile("chim", ".com");
1139 PrintWriter out = new PrintWriter(new FileOutputStream(tmp));
1140 for (String command : commands)
1142 out.println(command);
1146 String path = tmp.getAbsolutePath();
1147 sendAsynchronousCommand("open cmd:" + path, null);
1148 } catch (IOException e)
1151 .println("Sending commands to Chimera via file failed with "
1157 * Get Chimera residues which have the named attribute, find the mapped
1158 * positions in the Jalview sequence(s), and set as sequence features
1161 * @param alignmentPanel
1163 public void copyStructureAttributesToFeatures(String attName,
1164 AlignmentViewPanel alignmentPanel)
1166 // todo pull up to AAStructureBindingModel (and interface?)
1169 * ask Chimera to list residues with the attribute, reporting its value
1171 // this alternative command
1172 // list residues spec ':*/attName' attr attName
1173 // doesn't report 'None' values (which is good), but
1174 // fails for 'average.bfactor' (which is bad):
1176 String cmd = "list residues attr '" + attName + "'";
1177 List<String> residues = sendChimeraCommand(cmd, true);
1179 boolean featureAdded = createFeaturesForAttributes(attName, residues);
1182 alignmentPanel.getFeatureRenderer().featuresAdded();
1187 * Create features in Jalview for the given attribute name and structure
1191 * The residue list should be 0, 1 or more reply lines of the format:
1192 * residue id #0:5.A isHelix -155.000836316 index 5
1194 * residue id #0:6.A isHelix None
1201 protected boolean createFeaturesForAttributes(String attName,
1202 List<String> residues)
1204 boolean featureAdded = false;
1205 String featureGroup = getViewerFeatureGroup();
1207 for (String residue : residues)
1209 AtomSpec spec = null;
1210 String[] tokens = residue.split(" ");
1211 if (tokens.length < 5)
1215 String atomSpec = tokens[2];
1216 String attValue = tokens[4];
1219 * ignore 'None' (e.g. for phi) or 'False' (e.g. for isHelix)
1221 if ("None".equalsIgnoreCase(attValue)
1222 || "False".equalsIgnoreCase(attValue))
1229 spec = AtomSpec.fromChimeraAtomspec(atomSpec);
1230 } catch (IllegalArgumentException e)
1232 System.err.println("Problem parsing atomspec " + atomSpec);
1236 String chainId = spec.getChain();
1237 String description = attValue;
1238 float score = Float.NaN;
1241 score = Float.valueOf(attValue);
1242 description = chainId;
1243 } catch (NumberFormatException e)
1245 // was not a float value
1248 String pdbFile = getPdbFileForModel(spec.getModelNumber());
1249 spec.setPdbFile(pdbFile);
1251 List<AtomSpec> atoms = Collections.singletonList(spec);
1254 * locate the mapped position in the alignment (if any)
1256 SearchResults sr = getSsm()
1257 .findAlignmentPositionsForStructurePositions(atoms);
1260 * expect one matched alignment position, or none
1261 * (if the structure position is not mapped)
1263 for (SearchResultMatchI m : sr.getResults())
1265 SequenceI seq = m.getSequence();
1266 int start = m.getStart();
1267 int end = m.getEnd();
1268 SequenceFeature sf = new SequenceFeature(attName, description,
1269 start, end, score, featureGroup);
1270 // todo: should SequenceFeature have an explicit property for chain?
1271 // note: repeating the action shouldn't duplicate features
1272 featureAdded |= seq.addSequenceFeature(sf);
1275 return featureAdded;
1279 * Answers the feature group name to apply to features created in Jalview from
1280 * Chimera attributes
1284 protected String getViewerFeatureGroup()
1286 // todo pull up to interface
1287 return CHIMERA_FEATURE_GROUP;
1291 public Hashtable<String, String> getChainFile()
1296 public List<ChimeraModel> getChimeraModelByChain(String chain)
1298 return chimeraMaps.get(chainFile.get(chain));
1301 public int getModelNoForChain(String chain)
1303 List<ChimeraModel> foundModels = getChimeraModelByChain(chain);
1304 if (foundModels != null && !foundModels.isEmpty())
1306 return foundModels.get(0).getModelNumber();