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.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.Collections;
52 import java.util.Hashtable;
53 import java.util.LinkedHashMap;
54 import java.util.List;
57 import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
58 import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
59 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
60 import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
62 public abstract class JalviewChimeraBinding extends AAStructureBindingModel
64 public static final String CHIMERA_FEATURE_GROUP = "Chimera";
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";
78 private List<String> chainNames = new ArrayList<String>();
80 private Hashtable<String, String> chainFile = new Hashtable<String, String>();
83 * Object through which we talk to Chimera
85 private ChimeraManager viewer;
88 * Object which listens to Chimera notifications
90 private AbstractRequestHandler chimeraListener;
93 * set if chimera state is being restored from some source - instructs binding
94 * not to apply default display style when structure set is updated for first
97 private boolean loadingFromArchive = false;
100 * flag to indicate if the Chimera viewer should ignore sequence colouring
101 * events from the structure manager because the GUI is still setting up
103 private boolean loadingFinished = true;
105 public String fileLoadingError;
108 * Map of ChimeraModel objects keyed by PDB full local file name
110 private Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<String, List<ChimeraModel>>();
112 String lastHighlightCommand;
115 * incremented every time a load notification is successfully handled -
116 * lightweight mechanism for other threads to detect when they can start
117 * referring to new structures.
119 private long loadNotifiesHandled = 0;
122 * Open a PDB structure file in Chimera and set up mappings from Jalview.
124 * We check if the PDB model id is already loaded in Chimera, if so don't
125 * reopen it. This is the case if Chimera has opened a saved session file.
130 public boolean openFile(PDBEntry pe)
132 String file = pe.getFile();
135 List<ChimeraModel> modelsToMap = new ArrayList<ChimeraModel>();
136 List<ChimeraModel> oldList = viewer.getModelList();
137 boolean alreadyOpen = false;
140 * If Chimera already has this model, don't reopen it, but do remap it.
142 for (ChimeraModel open : oldList)
144 if (open.getModelName().equals(pe.getId()))
147 modelsToMap.add(open);
152 * If Chimera doesn't yet have this model, ask it to open it, and retrieve
153 * the model name(s) added by Chimera.
157 viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL);
158 List<ChimeraModel> newList = viewer.getModelList();
159 // JAL-1728 newList.removeAll(oldList) does not work
160 for (ChimeraModel cm : newList)
162 if (cm.getModelName().equals(pe.getId()))
169 chimeraMaps.put(file, modelsToMap);
171 if (getSsm() != null)
173 getSsm().addStructureViewerListener(this);
174 // ssm.addSelectionListener(this);
175 FeatureRenderer fr = getFeatureRenderer(null);
183 } catch (Exception q)
185 log("Exception when trying to open model " + file + "\n"
200 public JalviewChimeraBinding(StructureSelectionManager ssm,
201 PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol)
203 super(ssm, pdbentry, sequenceIs, protocol);
204 viewer = new ChimeraManager(
205 new ext.edu.ucsf.rbvi.strucviz2.StructureManager(true));
209 * Start a dedicated HttpServer to listen for Chimera notifications, and tell
210 * it to start listening
212 public void startChimeraListener()
216 chimeraListener = new ChimeraListener(this);
217 viewer.startListening(chimeraListener.getUri());
218 } catch (BindException e)
220 System.err.println("Failed to start Chimera listener: "
226 * Construct a title string for the viewer window based on the data Jalview
232 public String getViewerTitle(boolean verbose)
234 return getViewerTitle("Chimera", verbose);
238 * Tells Chimera to display only the specified chains
242 public void showChains(List<String> toshow)
245 * Construct a chimera command like
247 * ~display #*;~ribbon #*;ribbon :.A,:.B
249 StringBuilder cmd = new StringBuilder(64);
250 boolean first = true;
251 for (String chain : toshow)
253 int modelNumber = getModelNoForChain(chain);
254 String showChainCmd = modelNumber == -1 ? "" : modelNumber + ":."
255 + chain.split(":")[1];
260 cmd.append(showChainCmd);
265 * could append ";focus" to this command to resize the display to fill the
266 * window, but it looks more helpful not to (easier to relate chains to the
269 final String command = "~display #*; ~ribbon #*; ribbon :"
271 sendChimeraCommand(command, false);
275 * Close down the Jalview viewer and listener, and (optionally) the associated
278 public void closeViewer(boolean closeChimera)
280 getSsm().removeStructureViewerListener(this, this.getPdbFile());
283 viewer.exitChimera();
285 if (this.chimeraListener != null)
287 chimeraListener.shutdown();
288 chimeraListener = null;
292 releaseUIResources();
295 public void colourByChain()
297 colourBySequence = false;
298 sendAsynchronousCommand("rainbow chain", COLOURING_CHIMERA);
302 * Constructs and sends a Chimera command to colour by charge
304 * <li>Aspartic acid and Glutamic acid (negative charge) red</li>
305 * <li>Lysine and Arginine (positive charge) blue</li>
306 * <li>Cysteine - yellow</li>
307 * <li>all others - white</li>
310 public void colourByCharge()
312 colourBySequence = false;
313 String command = "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS";
314 sendAsynchronousCommand(command, COLOURING_CHIMERA);
318 * Construct and send a command to align structures against a reference
319 * structure, based on one or more sequence alignments
322 * an array of alignments to process
323 * @param _refStructure
324 * an array of corresponding reference structures (index into pdb
325 * file array); if a negative value is passed, the first PDB file
326 * mapped to an alignment sequence is used as the reference for
329 * an array of corresponding hidden columns for each alignment
331 public void superposeStructures(AlignmentI[] _alignment,
332 int[] _refStructure, ColumnSelection[] _hiddenCols)
334 StringBuilder allComs = new StringBuilder(128);
335 String[] files = getPdbFile();
337 if (!waitForFileLoad(files))
343 StringBuilder selectioncom = new StringBuilder(256);
344 for (int a = 0; a < _alignment.length; a++)
346 int refStructure = _refStructure[a];
347 AlignmentI alignment = _alignment[a];
348 ColumnSelection hiddenCols = _hiddenCols[a];
350 if (refStructure >= files.length)
352 System.err.println("Ignoring invalid reference structure value "
358 * 'matched' array will hold 'true' for visible alignment columns where
359 * all sequences have a residue with a mapping to the PDB structure
361 boolean matched[] = new boolean[alignment.getWidth()];
362 for (int m = 0; m < matched.length; m++)
364 matched[m] = (hiddenCols != null) ? hiddenCols.isVisible(m) : true;
367 SuperposeData[] structures = new SuperposeData[files.length];
368 for (int f = 0; f < files.length; f++)
370 structures[f] = new SuperposeData(alignment.getWidth());
374 * Calculate the superposable alignment columns ('matched'), and the
375 * corresponding structure residue positions (structures.pdbResNo)
377 int candidateRefStructure = findSuperposableResidues(alignment,
378 matched, structures);
379 if (refStructure < 0)
382 * If no reference structure was specified, pick the first one that has
383 * a mapping in the alignment
385 refStructure = candidateRefStructure;
389 for (boolean b : matched)
398 // TODO: bail out here because superposition illdefined?
402 * Generate select statements to select regions to superimpose structures
404 String[] selcom = new String[files.length];
405 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
407 String chainCd = "." + structures[pdbfnum].chain;
410 StringBuilder molsel = new StringBuilder();
411 for (int r = 0; r < matched.length; r++)
415 int pdbResNum = structures[pdbfnum].pdbResNo[r];
416 if (lpos != pdbResNum - 1)
419 * discontiguous - append last residue now
423 molsel.append(String.valueOf(lpos));
424 molsel.append(chainCd);
432 * extending a contiguous run
437 * start the range selection
439 molsel.append(String.valueOf(lpos));
449 * and terminate final selection
453 molsel.append(String.valueOf(lpos));
454 molsel.append(chainCd);
456 if (molsel.length() > 1)
458 selcom[pdbfnum] = molsel.toString();
459 selectioncom.append("#").append(String.valueOf(pdbfnum))
461 selectioncom.append(selcom[pdbfnum]);
462 selectioncom.append(" ");
463 if (pdbfnum < files.length - 1)
465 selectioncom.append("| ");
470 selcom[pdbfnum] = null;
474 StringBuilder command = new StringBuilder(256);
475 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
477 if (pdbfnum == refStructure || selcom[pdbfnum] == null
478 || selcom[refStructure] == null)
482 if (command.length() > 0)
488 * Form Chimera match command, from the 'new' structure to the
489 * 'reference' structure e.g. (50 residues, chain B/A, alphacarbons):
491 * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA
494 * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
496 command.append("match ").append(getModelSpec(pdbfnum)).append(":");
497 command.append(selcom[pdbfnum]);
498 command.append("@").append(
499 structures[pdbfnum].isRna ? PHOSPHORUS : ALPHACARBON);
500 // JAL-1757 exclude alternate CA locations
501 command.append(NO_ALTLOCS);
502 command.append(" ").append(getModelSpec(refStructure)).append(":");
503 command.append(selcom[refStructure]);
504 command.append("@").append(
505 structures[refStructure].isRna ? PHOSPHORUS : ALPHACARBON);
506 command.append(NO_ALTLOCS);
508 if (selectioncom.length() > 0)
512 System.out.println("Select regions:\n" + selectioncom.toString());
513 System.out.println("Superimpose command(s):\n"
514 + command.toString());
516 allComs.append("~display all; chain @CA|P; ribbon ")
517 .append(selectioncom.toString())
518 .append(";" + command.toString());
521 if (selectioncom.length() > 0)
523 // TODO: visually distinguish regions that were superposed
524 if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
526 selectioncom.setLength(selectioncom.length() - 1);
530 System.out.println("Select regions:\n" + selectioncom.toString());
532 allComs.append("; ~display all; chain @CA|P; ribbon ")
533 .append(selectioncom.toString()).append("; focus");
534 sendChimeraCommand(allComs.toString(), false);
540 * Helper method to construct model spec in Chimera format:
542 * <li>#0 (#1 etc) for a PDB file with no sub-models</li>
543 * <li>#0.1 (#1.1 etc) for a PDB file with sub-models</li>
545 * Note for now we only ever choose the first of multiple models. This
546 * corresponds to the hard-coded Jmol equivalent (compare {1.1}). Refactor in
547 * future if there is a need to select specific sub-models.
552 protected String getModelSpec(int pdbfnum)
554 if (pdbfnum < 0 || pdbfnum >= getPdbCount())
560 * For now, the test for having sub-models is whether multiple Chimera
561 * models are mapped for the PDB file; the models are returned as a response
562 * to the Chimera command 'list models type molecule', see
563 * ChimeraManager.getModelList().
565 List<ChimeraModel> maps = chimeraMaps.get(getPdbFile()[pdbfnum]);
566 boolean hasSubModels = maps != null && maps.size() > 1;
567 return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
571 * Launch Chimera, unless an instance linked to this object is already
572 * running. Returns true if chimera is successfully launched, or already
573 * running, else false.
577 public boolean launchChimera()
579 if (!viewer.isChimeraLaunched())
581 return viewer.launchChimera(StructureManager.getChimeraPaths());
583 if (viewer.isChimeraLaunched())
587 log("Failed to launch Chimera!");
592 * Answers true if the Chimera process is still running, false if ended or not
597 public boolean isChimeraRunning()
599 return viewer.isChimeraLaunched();
603 * Send a command to Chimera, and optionally log and return any responses.
605 * Does nothing, and returns null, if the command is the same as the last one
611 public List<String> sendChimeraCommand(final String command,
616 // ? thread running after viewer shut down
619 List<String> reply = null;
620 viewerCommandHistory(false);
621 if (true /*lastCommand == null || !lastCommand.equals(command)*/)
623 // trim command or it may never find a match in the replyLog!!
624 List<String> lastReply = viewer.sendChimeraCommand(command.trim(),
631 log("Response from command ('" + command + "') was:\n"
636 viewerCommandHistory(true);
642 * Send a Chimera command asynchronously in a new thread. If the progress
643 * message is not null, display this message while the command is executing.
648 protected abstract void sendAsynchronousCommand(String command,
652 * colour any structures associated with sequences in the given alignment
653 * using the getFeatureRenderer() and getSequenceRenderer() renderers but only
654 * if colourBySequence is enabled.
656 public void colourBySequence(boolean showFeatures,
657 jalview.api.AlignmentViewPanel alignmentv)
659 if (!colourBySequence || !loadingFinished)
663 if (getSsm() == null)
667 String[] files = getPdbFile();
669 SequenceRenderer sr = getSequenceRenderer(alignmentv);
671 FeatureRenderer fr = null;
674 fr = getFeatureRenderer(alignmentv);
676 AlignmentI alignment = alignmentv.getAlignment();
678 StructureMappingcommandSet colourBySequenceCommands = ChimeraCommands
679 .getColourBySequenceCommand(getSsm(), files, getSequence(), sr,
681 for (String command : colourBySequenceCommands.commands)
683 sendAsynchronousCommand(command, COLOURING_CHIMERA);
690 protected void executeWhenReady(String command)
693 sendChimeraCommand(command, false);
697 private void waitForChimera()
699 while (viewer != null && viewer.isBusy())
704 } catch (InterruptedException q)
710 // End StructureListener
711 // //////////////////////////
714 * returns the current featureRenderer that should be used to colour the
721 public abstract FeatureRenderer getFeatureRenderer(
722 AlignmentViewPanel alignment);
725 * instruct the Jalview binding to update the pdbentries vector if necessary
726 * prior to matching the viewer's contents to the list of structure files
727 * Jalview knows about.
729 public abstract void refreshPdbEntries();
731 // ////////////////////////////////
732 // /StructureListener
734 public synchronized String[] getPdbFile()
738 return new String[0];
741 return chimeraMaps.keySet().toArray(
742 modelFileNames = new String[chimeraMaps.size()]);
746 * returns the current sequenceRenderer that should be used to colour the
753 public abstract SequenceRenderer getSequenceRenderer(
754 AlignmentViewPanel alignment);
757 * Construct and send a command to highlight zero, one or more atoms. We do
758 * this by sending an "rlabel" command to show the residue label at that
762 public void highlightAtoms(List<AtomSpec> atoms)
764 if (atoms == null || atoms.size() == 0)
769 StringBuilder cmd = new StringBuilder(128);
770 boolean first = true;
771 boolean found = false;
773 for (AtomSpec atom : atoms)
775 int pdbResNum = atom.getPdbResNum();
776 String chain = atom.getChain();
777 String pdbfile = atom.getPdbFile();
778 List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
779 if (cms != null && !cms.isEmpty())
783 cmd.append("rlabel #").append(cms.get(0).getModelNumber())
791 cmd.append(pdbResNum);
792 if (!chain.equals(" "))
794 cmd.append(".").append(chain);
799 String command = cmd.toString();
802 * avoid repeated commands for the same residue
804 if (command.equals(lastHighlightCommand))
810 * unshow the label for the previous residue
812 if (lastHighlightCommand != null)
814 viewer.sendChimeraCommand("~" + lastHighlightCommand, false);
818 viewer.sendChimeraCommand(command, false);
820 this.lastHighlightCommand = command;
824 * Query Chimera for its current selection, and highlight it on the alignment
826 public void highlightChimeraSelection()
829 * Ask Chimera for its current selection
831 List<String> selection = viewer.getSelectedResidueSpecs();
834 * Parse model number, residue and chain for each selected position,
835 * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
837 List<AtomSpec> atomSpecs = convertStructureResiduesToAlignment(selection);
840 * Broadcast the selection (which may be empty, if the user just cleared all
843 getSsm().mouseOverStructure(atomSpecs);
847 * Converts a list of Chimera atomspecs to a list of AtomSpec representing the
848 * corresponding residues (if any) in Jalview
850 * @param structureSelection
853 protected List<AtomSpec> convertStructureResiduesToAlignment(
854 List<String> structureSelection)
856 List<AtomSpec> atomSpecs = new ArrayList<AtomSpec>();
857 for (String atomSpec : structureSelection)
861 AtomSpec spec = AtomSpec.fromChimeraAtomspec(atomSpec);
862 String pdbfilename = getPdbFileForModel(spec.getModelNumber());
863 spec.setPdbFile(pdbfilename);
865 } catch (IllegalArgumentException e)
867 System.err.println("Failed to parse atomspec: " + atomSpec);
877 protected String getPdbFileForModel(int modelId)
880 * Work out the pdbfilename from the model number
882 String pdbfilename = modelFileNames[0];
883 findfileloop: for (String pdbfile : this.chimeraMaps.keySet())
885 for (ChimeraModel cm : chimeraMaps.get(pdbfile))
887 if (cm.getModelNumber() == modelId)
889 pdbfilename = pdbfile;
897 private void log(String message)
899 System.err.println("## Chimera log: " + message);
902 private void viewerCommandHistory(boolean enable)
904 // log("(Not yet implemented) History "
905 // + ((debug || enable) ? "on" : "off"));
908 public long getLoadNotifiesHandled()
910 return loadNotifiesHandled;
913 public void setJalviewColourScheme(ColourSchemeI cs)
915 colourBySequence = false;
922 // Chimera expects RBG values in the range 0-1
923 final double normalise = 255D;
924 viewerCommandHistory(false);
925 StringBuilder command = new StringBuilder(128);
927 List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
929 for (String res : residueSet)
931 Color col = cs.findColour(res.charAt(0));
932 command.append("color " + col.getRed() / normalise + ","
933 + col.getGreen() / normalise + "," + col.getBlue()
934 / normalise + " ::" + res + ";");
937 sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
938 viewerCommandHistory(true);
942 * called when the binding thinks the UI needs to be refreshed after a Chimera
943 * state change. this could be because structures were loaded, or because an
944 * error has occurred.
946 public abstract void refreshGUI();
949 public void setLoadingFromArchive(boolean loadingFromArchive)
951 this.loadingFromArchive = loadingFromArchive;
956 * @return true if Chimeral is still restoring state or loading is still going
957 * on (see setFinsihedLoadingFromArchive)
960 public boolean isLoadingFromArchive()
962 return loadingFromArchive && !loadingFinished;
966 * modify flag which controls if sequence colouring events are honoured by the
967 * binding. Should be true for normal operation
969 * @param finishedLoading
972 public void setFinishedLoadingFromArchive(boolean finishedLoading)
974 loadingFinished = finishedLoading;
978 * Send the Chimera 'background solid <color>" command.
981 * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
985 public void setBackgroundColour(Color col)
987 viewerCommandHistory(false);
988 double normalise = 255D;
989 final String command = "background solid " + col.getRed() / normalise
990 + "," + col.getGreen() / normalise + "," + col.getBlue()
992 viewer.sendChimeraCommand(command, false);
993 viewerCommandHistory(true);
997 * Ask Chimera to save its session to the given file. Returns true if
998 * successful, else false.
1003 public boolean saveSession(String filepath)
1005 if (isChimeraRunning())
1007 List<String> reply = viewer.sendChimeraCommand("save " + filepath,
1009 if (reply.contains("Session written"))
1016 .error("Error saving Chimera session: " + reply.toString());
1023 * Ask Chimera to open a session file. Returns true if successful, else false.
1024 * The filename must have a .py extension for this command to work.
1029 public boolean openSession(String filepath)
1031 sendChimeraCommand("open " + filepath, true);
1032 // todo: test for failure - how?
1037 * Returns a list of chains mapped in this viewer. Note this list is not
1038 * currently scoped per structure.
1043 public List<String> getChainNames()
1049 * Send a 'focus' command to Chimera to recentre the visible display
1051 public void focusView()
1053 sendChimeraCommand("focus", false);
1057 * Send a 'show' command for all atoms in the currently selected columns
1059 * TODO: pull up to abstract structure viewer interface
1063 public void highlightSelection(AlignmentViewPanel vp)
1065 List<Integer> cols = vp.getAlignViewport().getColumnSelection()
1067 AlignmentI alignment = vp.getAlignment();
1068 StructureSelectionManager sm = getSsm();
1069 for (SequenceI seq : alignment.getSequences())
1072 * convert selected columns into sequence positions
1074 int[] positions = new int[cols.size()];
1076 for (Integer col : cols)
1078 positions[i++] = seq.findPosition(col);
1080 sm.highlightStructure(this, seq, positions);
1085 * Constructs and send commands to Chimera to set attributes on residues for
1086 * features visible in Jalview
1090 public void sendFeaturesToViewer(AlignmentViewPanel avp)
1092 // TODO refactor as required to pull up to an interface
1093 AlignmentI alignment = avp.getAlignment();
1094 FeatureRenderer fr = getFeatureRenderer(avp);
1097 * fr is null if feature display is turned off
1104 String[] files = getPdbFile();
1110 StructureMappingcommandSet commandSet = ChimeraCommands
1111 .getSetAttributeCommandsForFeatures(getSsm(), files,
1112 getSequence(), fr, alignment);
1113 String[] commands = commandSet.commands;
1114 if (commands.length > 10)
1116 sendCommandsByFile(commands);
1120 for (String command : commands)
1122 sendAsynchronousCommand(command, null);
1128 * Write commands to a temporary file, and send a command to Chimera to open
1129 * the file as a commands script. For use when sending a large number of
1130 * separate commands would overload the REST interface mechanism.
1134 protected void sendCommandsByFile(String[] commands)
1138 File tmp = File.createTempFile("chim", ".com");
1140 PrintWriter out = new PrintWriter(new FileOutputStream(tmp));
1141 for (String command : commands)
1143 out.println(command);
1147 String path = tmp.getAbsolutePath();
1148 sendAsynchronousCommand("open cmd:" + path, null);
1149 } catch (IOException e)
1152 .println("Sending commands to Chimera via file failed with "
1158 * Get Chimera residues which have the named attribute, find the mapped
1159 * positions in the Jalview sequence(s), and set as sequence features
1162 * @param alignmentPanel
1164 public void copyStructureAttributesToFeatures(String attName,
1165 AlignmentViewPanel alignmentPanel)
1167 // todo pull up to AAStructureBindingModel (and interface?)
1170 * ask Chimera to list residues with the attribute, reporting its value
1172 // this alternative command
1173 // list residues spec ':*/attName' attr attName
1174 // doesn't report 'None' values (which is good), but
1175 // fails for 'average.bfactor' (which is bad):
1177 String cmd = "list residues attr '" + attName + "'";
1178 List<String> residues = sendChimeraCommand(cmd, true);
1180 boolean featureAdded = createFeaturesForAttributes(attName, residues);
1183 alignmentPanel.getFeatureRenderer().featuresAdded();
1188 * Create features in Jalview for the given attribute name and structure
1192 * The residue list should be 0, 1 or more reply lines of the format:
1193 * residue id #0:5.A isHelix -155.000836316 index 5
1195 * residue id #0:6.A isHelix None
1202 protected boolean createFeaturesForAttributes(String attName,
1203 List<String> residues)
1205 boolean featureAdded = false;
1206 String featureGroup = getViewerFeatureGroup();
1208 for (String residue : residues)
1210 AtomSpec spec = null;
1211 String[] tokens = residue.split(" ");
1212 if (tokens.length < 5)
1216 String atomSpec = tokens[2];
1217 String attValue = tokens[4];
1220 * ignore 'None' (e.g. for phi) or 'False' (e.g. for isHelix)
1222 if ("None".equalsIgnoreCase(attValue)
1223 || "False".equalsIgnoreCase(attValue))
1230 spec = AtomSpec.fromChimeraAtomspec(atomSpec);
1231 } catch (IllegalArgumentException e)
1233 System.err.println("Problem parsing atomspec " + atomSpec);
1237 String chainId = spec.getChain();
1238 String description = attValue;
1239 float score = Float.NaN;
1242 score = Float.valueOf(attValue);
1243 description = chainId;
1244 } catch (NumberFormatException e)
1246 // was not a float value
1249 String pdbFile = getPdbFileForModel(spec.getModelNumber());
1250 spec.setPdbFile(pdbFile);
1252 List<AtomSpec> atoms = Collections.singletonList(spec);
1255 * locate the mapped position in the alignment (if any)
1257 SearchResults sr = getSsm()
1258 .findAlignmentPositionsForStructurePositions(atoms);
1261 * expect one matched alignment position, or none
1262 * (if the structure position is not mapped)
1264 for (SearchResultMatchI m : sr.getResults())
1266 SequenceI seq = m.getSequence();
1267 int start = m.getStart();
1268 int end = m.getEnd();
1269 SequenceFeature sf = new SequenceFeature(attName, description,
1270 start, end, score, featureGroup);
1271 // todo: should SequenceFeature have an explicit property for chain?
1272 // note: repeating the action shouldn't duplicate features
1273 featureAdded |= seq.addSequenceFeature(sf);
1276 return featureAdded;
1280 * Answers the feature group name to apply to features created in Jalview from
1281 * Chimera attributes
1285 protected String getViewerFeatureGroup()
1287 // todo pull up to interface
1288 return CHIMERA_FEATURE_GROUP;
1292 public Hashtable<String, String> getChainFile()
1297 public List<ChimeraModel> getChimeraModelByChain(String chain)
1299 return chimeraMaps.get(chainFile.get(chain));
1302 public int getModelNoForChain(String chain)
1304 List<ChimeraModel> foundModels = getChimeraModelByChain(chain);
1305 if (foundModels != null && !foundModels.isEmpty())
1307 return foundModels.get(0).getModelNumber();