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.HiddenColumns;
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<>();
81 private Hashtable<String, String> chainFile = new Hashtable<>();
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<>();
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 reopen
126 * 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<>();
137 List<ChimeraModel> oldList = viewer.isChimeraX() ? new ArrayList<>()
138 : viewer.getModelList();
139 boolean alreadyOpen = false;
142 * If Chimera already has this model, don't reopen it, but do remap it.
144 for (ChimeraModel open : oldList)
146 if (open.getModelName().equals(pe.getId()))
149 modelsToMap.add(open);
154 * If Chimera doesn't yet have this model, ask it to open it, and retrieve
155 * the model name(s) added by Chimera.
159 viewer.openModel(file, pe.getId(), ModelType.PDB_MODEL);
160 if (viewer.isChimeraX())
163 * ChimeraX hack: force chimera model name to pdbId
165 int modelNumber = chimeraMaps.size() + 1;
166 String command = "setattr #" + modelNumber + " models name "
168 sendChimeraCommand(command, false);
169 modelsToMap.add(new ChimeraModel(pe.getId(), ModelType.PDB_MODEL,
175 * Chimera: query for actual models and find the one with
176 * matching model name - set in viewer.openModel()
178 List<ChimeraModel> newList = viewer.getModelList();
179 // JAL-1728 newList.removeAll(oldList) does not work
180 for (ChimeraModel cm : newList)
182 if (cm.getModelName().equals(pe.getId()))
190 chimeraMaps.put(file, modelsToMap);
192 if (getSsm() != null)
194 getSsm().addStructureViewerListener(this);
197 } catch (Exception q)
199 log("Exception when trying to open model " + file + "\n"
214 public JalviewChimeraBinding(StructureSelectionManager ssm,
215 PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
216 DataSourceType protocol)
218 super(ssm, pdbentry, sequenceIs, protocol);
219 viewer = new ChimeraManager(new StructureManager(true));
223 * Starts a thread that waits for the Chimera process to finish, so that we can
224 * then close the associated resources. This avoids leaving orphaned Chimera
225 * viewer panels in Jalview if the user closes Chimera.
227 protected void startChimeraProcessMonitor()
229 final Process p = viewer.getChimeraProcess();
230 chimeraMonitor = new Thread(new Runnable()
239 JalviewStructureDisplayI display = getViewer();
242 display.closeViewer(false);
244 } catch (InterruptedException e)
246 // exit thread if Chimera Viewer is closed in Jalview
250 chimeraMonitor.start();
254 * Start a dedicated HttpServer to listen for Chimera notifications, and tell it
257 public void startChimeraListener()
261 chimeraListener = new ChimeraListener(this);
262 viewer.startListening(chimeraListener.getUri());
263 } catch (BindException e)
266 "Failed to start Chimera listener: " + e.getMessage());
271 * Tells Chimera to display only the specified chains
275 public void showChains(List<String> toshow)
278 * Construct a chimera command like
280 * ~display #*;~ribbon #*;ribbon :.A,:.B
282 StringBuilder cmd = new StringBuilder(64);
283 boolean first = true;
284 for (String chain : toshow)
286 int modelNumber = getModelNoForChain(chain);
287 String showChainCmd = modelNumber == -1 ? ""
288 : modelNumber + ":." + chain.split(":")[1];
293 cmd.append(showChainCmd);
298 * could append ";focus" to this command to resize the display to fill the
299 * window, but it looks more helpful not to (easier to relate chains to the
302 final String command = "~display #*; ~ribbon #*; ribbon :"
304 sendChimeraCommand(command, false);
308 * Close down the Jalview viewer and listener, and (optionally) the associated
311 public void closeViewer(boolean closeChimera)
313 getSsm().removeStructureViewerListener(this, this.getStructureFiles());
316 viewer.exitChimera();
318 if (this.chimeraListener != null)
320 chimeraListener.shutdown();
321 chimeraListener = null;
325 if (chimeraMonitor != null)
327 chimeraMonitor.interrupt();
329 releaseUIResources();
333 public void colourByChain()
335 colourBySequence = false;
336 sendAsynchronousCommand("rainbow chain", COLOURING_CHIMERA);
340 * Constructs and sends a Chimera command to colour by charge
342 * <li>Aspartic acid and Glutamic acid (negative charge) red</li>
343 * <li>Lysine and Arginine (positive charge) blue</li>
344 * <li>Cysteine - yellow</li>
345 * <li>all others - white</li>
349 public void colourByCharge()
351 colourBySequence = false;
352 String command = "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS";
353 sendAsynchronousCommand(command, COLOURING_CHIMERA);
360 public String superposeStructures(AlignmentI[] _alignment,
361 int[] _refStructure, HiddenColumns[] _hiddenCols)
363 StringBuilder allComs = new StringBuilder(128);
364 String[] files = getStructureFiles();
366 if (!waitForFileLoad(files))
372 StringBuilder selectioncom = new StringBuilder(256);
373 for (int a = 0; a < _alignment.length; a++)
375 int refStructure = _refStructure[a];
376 AlignmentI alignment = _alignment[a];
377 HiddenColumns hiddenCols = _hiddenCols[a];
379 if (refStructure >= files.length)
381 System.err.println("Ignoring invalid reference structure value "
387 * 'matched' bit i will be set for visible alignment columns i where
388 * all sequences have a residue with a mapping to the PDB structure
390 BitSet matched = new BitSet();
391 for (int m = 0; m < alignment.getWidth(); m++)
393 if (hiddenCols == null || hiddenCols.isVisible(m))
399 SuperposeData[] structures = new SuperposeData[files.length];
400 for (int f = 0; f < files.length; f++)
402 structures[f] = new SuperposeData(alignment.getWidth());
406 * Calculate the superposable alignment columns ('matched'), and the
407 * corresponding structure residue positions (structures.pdbResNo)
409 int candidateRefStructure = findSuperposableResidues(alignment,
410 matched, structures);
411 if (refStructure < 0)
414 * If no reference structure was specified, pick the first one that has
415 * a mapping in the alignment
417 refStructure = candidateRefStructure;
420 int nmatched = matched.cardinality();
423 return MessageManager.formatMessage("label.insufficient_residues",
428 * Generate select statements to select regions to superimpose structures
430 String[] selcom = new String[files.length];
431 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
433 String chainCd = "." + structures[pdbfnum].chain;
436 StringBuilder molsel = new StringBuilder();
438 int nextColumnMatch = matched.nextSetBit(0);
439 while (nextColumnMatch != -1)
441 int pdbResNum = structures[pdbfnum].pdbResNo[nextColumnMatch];
442 if (lpos != pdbResNum - 1)
445 * discontiguous - append last residue now
449 molsel.append(String.valueOf(lpos));
450 molsel.append(chainCd);
458 * extending a contiguous run
463 * start the range selection
465 molsel.append(String.valueOf(lpos));
471 nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1);
475 * and terminate final selection
479 molsel.append(String.valueOf(lpos));
480 molsel.append(chainCd);
482 if (molsel.length() > 1)
484 selcom[pdbfnum] = molsel.toString();
485 selectioncom.append("#").append(String.valueOf(pdbfnum))
487 selectioncom.append(selcom[pdbfnum]);
488 selectioncom.append(" ");
489 if (pdbfnum < files.length - 1)
491 selectioncom.append("| ");
496 selcom[pdbfnum] = null;
500 StringBuilder command = new StringBuilder(256);
501 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
503 if (pdbfnum == refStructure || selcom[pdbfnum] == null
504 || selcom[refStructure] == null)
508 if (command.length() > 0)
514 * Form Chimera match command, from the 'new' structure to the
515 * 'reference' structure e.g. (50 residues, chain B/A, alphacarbons):
517 * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA
520 * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
522 command.append("match ").append(getModelSpec(pdbfnum)).append(":");
523 command.append(selcom[pdbfnum]);
524 command.append("@").append(
525 structures[pdbfnum].isRna ? PHOSPHORUS : ALPHACARBON);
526 // JAL-1757 exclude alternate CA locations
527 command.append(NO_ALTLOCS);
528 command.append(" ").append(getModelSpec(refStructure)).append(":");
529 command.append(selcom[refStructure]);
530 command.append("@").append(
531 structures[refStructure].isRna ? PHOSPHORUS : ALPHACARBON);
532 command.append(NO_ALTLOCS);
534 if (selectioncom.length() > 0)
538 System.out.println("Select regions:\n" + selectioncom.toString());
540 "Superimpose command(s):\n" + command.toString());
542 allComs.append("~display all; chain @CA|P; ribbon ")
543 .append(selectioncom.toString())
544 .append(";" + command.toString());
549 if (selectioncom.length() > 0)
551 // TODO: visually distinguish regions that were superposed
552 if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
554 selectioncom.setLength(selectioncom.length() - 1);
558 System.out.println("Select regions:\n" + selectioncom.toString());
560 allComs.append("; ~display all; chain @CA|P; ribbon ")
561 .append(selectioncom.toString()).append("; focus");
562 List<String> chimeraReplies = sendChimeraCommand(allComs.toString(),
564 for (String reply : chimeraReplies)
566 if (reply.toLowerCase().contains("unequal numbers of atoms"))
576 * Helper method to construct model spec in Chimera format:
578 * <li>#0 (#1 etc) for a PDB file with no sub-models</li>
579 * <li>#0.1 (#1.1 etc) for a PDB file with sub-models</li>
581 * Note for now we only ever choose the first of multiple models. This
582 * corresponds to the hard-coded Jmol equivalent (compare {1.1}). Refactor in
583 * future if there is a need to select specific sub-models.
588 protected String getModelSpec(int pdbfnum)
590 if (pdbfnum < 0 || pdbfnum >= getPdbCount())
596 * For now, the test for having sub-models is whether multiple Chimera
597 * models are mapped for the PDB file; the models are returned as a response
598 * to the Chimera command 'list models type molecule', see
599 * ChimeraManager.getModelList().
601 List<ChimeraModel> maps = chimeraMaps.get(getStructureFiles()[pdbfnum]);
602 boolean hasSubModels = maps != null && maps.size() > 1;
603 return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
607 * Launch Chimera, unless an instance linked to this object is already
608 * running. Returns true if Chimera is successfully launched, or already
609 * running, else false.
613 public boolean launchChimera()
615 if (viewer.isChimeraLaunched())
620 boolean launched = viewer
621 .launchChimera(StructureManager.getChimeraPaths());
624 startChimeraProcessMonitor();
628 log("Failed to launch Chimera!");
634 * Answers true if the Chimera process is still running, false if ended or not
639 public boolean isChimeraRunning()
641 return viewer.isChimeraLaunched();
645 * Send a command to Chimera, and optionally log and return any responses.
647 * Does nothing, and returns null, if the command is the same as the last one
653 public List<String> sendChimeraCommand(final String command,
658 // ? thread running after viewer shut down
661 List<String> reply = null;
662 viewerCommandHistory(false);
663 if (true /*lastCommand == null || !lastCommand.equals(command)*/)
665 // trim command or it may never find a match in the replyLog!!
666 List<String> lastReply = viewer.sendChimeraCommand(command.trim(),
673 log("Response from command ('" + command + "') was:\n"
678 viewerCommandHistory(true);
684 * Send a Chimera command asynchronously in a new thread. If the progress
685 * message is not null, display this message while the command is executing.
690 protected abstract void sendAsynchronousCommand(String command,
694 * Sends a set of colour commands to the structure viewer
696 * @param colourBySequenceCommands
699 protected void colourBySequence(
700 StructureMappingcommandSet[] colourBySequenceCommands)
702 for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
704 for (String command : cpdbbyseq.commands)
706 sendAsynchronousCommand(command, COLOURING_CHIMERA);
718 protected StructureMappingcommandSet[] getColourBySequenceCommands(
719 String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
721 return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
722 getSequence(), sr, viewPanel, viewer.isChimeraX());
728 protected void executeWhenReady(String command)
731 sendChimeraCommand(command, false);
735 private void waitForChimera()
737 while (viewer != null && viewer.isBusy())
742 } catch (InterruptedException q)
748 // End StructureListener
749 // //////////////////////////
752 * instruct the Jalview binding to update the pdbentries vector if necessary
753 * prior to matching the viewer's contents to the list of structure files
754 * Jalview knows about.
756 public abstract void refreshPdbEntries();
759 * map between index of model filename returned from getPdbFile and the first
760 * index of models from this file in the viewer. Note - this is not trimmed -
761 * use getPdbFile to get number of unique models.
763 private int _modelFileNameMap[];
765 // ////////////////////////////////
766 // /StructureListener
768 public synchronized String[] getStructureFiles()
772 return new String[0];
775 return chimeraMaps.keySet()
776 .toArray(modelFileNames = new String[chimeraMaps.size()]);
780 * Construct and send a command to highlight zero, one or more atoms. We do this
781 * by sending an "rlabel" command to show the residue label at that position.
784 public void highlightAtoms(List<AtomSpec> atoms)
786 if (atoms == null || atoms.size() == 0)
791 StringBuilder cmd = new StringBuilder(128);
792 boolean first = true;
793 boolean found = false;
795 for (AtomSpec atom : atoms)
797 int pdbResNum = atom.getPdbResNum();
798 String chain = atom.getChain();
799 String pdbfile = atom.getPdbFile();
800 List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
801 if (cms != null && !cms.isEmpty())
805 cmd.append("rlabel #").append(cms.get(0).getModelNumber())
813 cmd.append(pdbResNum);
814 if (!chain.equals(" "))
816 cmd.append(".").append(chain);
821 String command = cmd.toString();
824 * avoid repeated commands for the same residue
826 if (command.equals(lastHighlightCommand))
832 * unshow the label for the previous residue
834 if (lastHighlightCommand != null)
836 viewer.sendChimeraCommand("~" + lastHighlightCommand, false);
840 viewer.sendChimeraCommand(command, false);
842 this.lastHighlightCommand = command;
846 * Query Chimera for its current selection, and highlight it on the alignment
848 public void highlightChimeraSelection()
851 * Ask Chimera for its current selection
853 List<String> selection = viewer.getSelectedResidueSpecs();
856 * Parse model number, residue and chain for each selected position,
857 * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
859 List<AtomSpec> atomSpecs = convertStructureResiduesToAlignment(
863 * Broadcast the selection (which may be empty, if the user just cleared all
866 getSsm().mouseOverStructure(atomSpecs);
870 * Converts a list of Chimera atomspecs to a list of AtomSpec representing the
871 * corresponding residues (if any) in Jalview
873 * @param structureSelection
876 protected List<AtomSpec> convertStructureResiduesToAlignment(
877 List<String> structureSelection)
879 List<AtomSpec> atomSpecs = new ArrayList<>();
880 for (String atomSpec : structureSelection)
884 AtomSpec spec = AtomSpec.fromChimeraAtomspec(atomSpec);
885 String pdbfilename = getPdbFileForModel(spec.getModelNumber());
886 spec.setPdbFile(pdbfilename);
888 } catch (IllegalArgumentException e)
890 System.err.println("Failed to parse atomspec: " + atomSpec);
900 protected String getPdbFileForModel(int modelId)
903 * Work out the pdbfilename from the model number
905 String pdbfilename = modelFileNames[0];
906 findfileloop: for (String pdbfile : this.chimeraMaps.keySet())
908 for (ChimeraModel cm : chimeraMaps.get(pdbfile))
910 if (cm.getModelNumber() == modelId)
912 pdbfilename = pdbfile;
920 private void log(String message)
922 System.err.println("## Chimera log: " + message);
925 private void viewerCommandHistory(boolean enable)
927 // log("(Not yet implemented) History "
928 // + ((debug || enable) ? "on" : "off"));
931 public long getLoadNotifiesHandled()
933 return loadNotifiesHandled;
937 public void setJalviewColourScheme(ColourSchemeI cs)
939 colourBySequence = false;
946 // Chimera expects RBG values in the range 0-1
947 final double normalise = 255D;
948 viewerCommandHistory(false);
949 StringBuilder command = new StringBuilder(128);
951 List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
953 for (String resName : residueSet)
955 char res = resName.length() == 3
956 ? ResidueProperties.getSingleCharacterCode(resName)
958 Color col = cs.findColour(res, 0, null, null, 0f);
959 command.append("color " + col.getRed() / normalise + ","
960 + col.getGreen() / normalise + "," + col.getBlue() / normalise
961 + " ::" + resName + ";");
964 sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
965 viewerCommandHistory(true);
969 * called when the binding thinks the UI needs to be refreshed after a Chimera
970 * state change. this could be because structures were loaded, or because an
971 * error has occurred.
973 public abstract void refreshGUI();
976 public void setLoadingFromArchive(boolean loadingFromArchive)
978 this.loadingFromArchive = loadingFromArchive;
983 * @return true if Chimeral is still restoring state or loading is still going
984 * on (see setFinsihedLoadingFromArchive)
987 public boolean isLoadingFromArchive()
989 return loadingFromArchive && !loadingFinished;
993 * modify flag which controls if sequence colouring events are honoured by the
994 * binding. Should be true for normal operation
996 * @param finishedLoading
999 public void setFinishedLoadingFromArchive(boolean finishedLoading)
1001 loadingFinished = finishedLoading;
1005 * Send the Chimera 'background solid <color>" command.
1008 * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
1013 public void setBackgroundColour(Color col)
1015 viewerCommandHistory(false);
1016 double normalise = 255D;
1017 final String command = "background solid " + col.getRed() / normalise
1018 + "," + col.getGreen() / normalise + ","
1019 + col.getBlue() / normalise + ";";
1020 viewer.sendChimeraCommand(command, false);
1021 viewerCommandHistory(true);
1025 * Ask Chimera to save its session to the given file. Returns true if
1026 * successful, else false.
1031 public boolean saveSession(String filepath)
1033 if (isChimeraRunning())
1035 List<String> reply = viewer.sendChimeraCommand("save " + filepath,
1037 if (reply.contains("Session written"))
1044 .error("Error saving Chimera session: " + reply.toString());
1051 * Ask Chimera to open a session file. Returns true if successful, else false.
1052 * The filename must have a .py extension for this command to work.
1057 public boolean openSession(String filepath)
1059 sendChimeraCommand("open " + filepath, true);
1060 // todo: test for failure - how?
1065 * Returns a list of chains mapped in this viewer. Note this list is not
1066 * currently scoped per structure.
1071 public List<String> getChainNames()
1077 * Send a 'focus' command to Chimera to recentre the visible display
1079 public void focusView()
1081 sendChimeraCommand("focus", false);
1085 * Send a 'show' command for all atoms in the currently selected columns
1087 * TODO: pull up to abstract structure viewer interface
1091 public void highlightSelection(AlignmentViewPanel vp)
1093 List<Integer> cols = vp.getAlignViewport().getColumnSelection()
1095 AlignmentI alignment = vp.getAlignment();
1096 StructureSelectionManager sm = getSsm();
1097 for (SequenceI seq : alignment.getSequences())
1100 * convert selected columns into sequence positions
1102 int[] positions = new int[cols.size()];
1104 for (Integer col : cols)
1106 positions[i++] = seq.findPosition(col);
1108 sm.highlightStructure(this, seq, positions);
1113 * Constructs and send commands to Chimera to set attributes on residues for
1114 * features visible in Jalview
1119 public int sendFeaturesToViewer(AlignmentViewPanel avp)
1121 // TODO refactor as required to pull up to an interface
1122 AlignmentI alignment = avp.getAlignment();
1124 String[] files = getStructureFiles();
1130 StructureMappingcommandSet commandSet = ChimeraCommands
1131 .getSetAttributeCommandsForFeatures(getSsm(), files,
1132 getSequence(), avp, viewer.isChimeraX());
1133 String[] commands = commandSet.commands;
1134 if (commands.length > 10)
1136 sendCommandsByFile(commands);
1140 for (String command : commands)
1142 sendAsynchronousCommand(command, null);
1145 return commands.length;
1149 * Write commands to a temporary file, and send a command to Chimera to open the
1150 * file as a commands script. For use when sending a large number of separate
1151 * commands would overload the REST interface mechanism.
1155 protected void sendCommandsByFile(String[] commands)
1157 boolean toChimeraX = viewer.isChimeraX();
1160 File tmp = File.createTempFile("chim", toChimeraX ? ".cxc" : ".com");
1162 PrintWriter out = new PrintWriter(new FileOutputStream(tmp));
1163 for (String command : commands)
1165 out.println(command);
1169 String path = tmp.getAbsolutePath();
1170 String command = "open " + (toChimeraX ? "" : "cmd:") + path;
1171 sendAsynchronousCommand(command, null);
1172 } catch (IOException e)
1174 System.err.println("Sending commands to Chimera via file failed with "
1180 * Get Chimera residues which have the named attribute, find the mapped
1181 * positions in the Jalview sequence(s), and set as sequence features
1184 * @param alignmentPanel
1186 public void copyStructureAttributesToFeatures(String attName,
1187 AlignmentViewPanel alignmentPanel)
1189 // todo pull up to AAStructureBindingModel (and interface?)
1192 * ask Chimera to list residues with the attribute, reporting its value
1194 // this alternative command
1195 // list residues spec ':*/attName' attr attName
1196 // doesn't report 'None' values (which is good), but
1197 // fails for 'average.bfactor' (which is bad):
1199 String cmd = "list residues attr '" + attName + "'";
1200 List<String> residues = sendChimeraCommand(cmd, true);
1202 boolean featureAdded = createFeaturesForAttributes(attName, residues);
1205 alignmentPanel.getFeatureRenderer().featuresAdded();
1210 * Create features in Jalview for the given attribute name and structure
1214 * The residue list should be 0, 1 or more reply lines of the format:
1215 * residue id #0:5.A isHelix -155.000836316 index 5
1217 * residue id #0:6.A isHelix None
1224 protected boolean createFeaturesForAttributes(String attName,
1225 List<String> residues)
1227 boolean featureAdded = false;
1228 String featureGroup = getViewerFeatureGroup();
1230 for (String residue : residues)
1232 AtomSpec spec = null;
1233 String[] tokens = residue.split(" ");
1234 if (tokens.length < 5)
1238 String atomSpec = tokens[2];
1239 String attValue = tokens[4];
1242 * ignore 'None' (e.g. for phi) or 'False' (e.g. for isHelix)
1244 if ("None".equalsIgnoreCase(attValue)
1245 || "False".equalsIgnoreCase(attValue))
1252 spec = AtomSpec.fromChimeraAtomspec(atomSpec);
1253 } catch (IllegalArgumentException e)
1255 System.err.println("Problem parsing atomspec " + atomSpec);
1259 String chainId = spec.getChain();
1260 String description = attValue;
1261 float score = Float.NaN;
1264 score = Float.valueOf(attValue);
1265 description = chainId;
1266 } catch (NumberFormatException e)
1268 // was not a float value
1271 String pdbFile = getPdbFileForModel(spec.getModelNumber());
1272 spec.setPdbFile(pdbFile);
1274 List<AtomSpec> atoms = Collections.singletonList(spec);
1277 * locate the mapped position in the alignment (if any)
1279 SearchResultsI sr = getSsm()
1280 .findAlignmentPositionsForStructurePositions(atoms);
1283 * expect one matched alignment position, or none
1284 * (if the structure position is not mapped)
1286 for (SearchResultMatchI m : sr.getResults())
1288 SequenceI seq = m.getSequence();
1289 int start = m.getStart();
1290 int end = m.getEnd();
1291 SequenceFeature sf = new SequenceFeature(attName, description,
1292 start, end, score, featureGroup);
1293 // todo: should SequenceFeature have an explicit property for chain?
1294 // note: repeating the action shouldn't duplicate features
1295 featureAdded |= seq.addSequenceFeature(sf);
1298 return featureAdded;
1302 * Answers the feature group name to apply to features created in Jalview from
1303 * Chimera attributes
1307 protected String getViewerFeatureGroup()
1309 // todo pull up to interface
1310 return CHIMERA_FEATURE_GROUP;
1313 public Hashtable<String, String> getChainFile()
1318 public List<ChimeraModel> getChimeraModelByChain(String chain)
1320 return chimeraMaps.get(chainFile.get(chain));
1323 public int getModelNoForChain(String chain)
1325 List<ChimeraModel> foundModels = getChimeraModelByChain(chain);
1326 if (foundModels != null && !foundModels.isEmpty())
1328 return foundModels.get(0).getModelNumber();