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<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);
177 } catch (Exception q)
179 log("Exception when trying to open model " + file + "\n"
194 public JalviewChimeraBinding(StructureSelectionManager ssm,
195 PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol)
197 super(ssm, pdbentry, sequenceIs, protocol);
198 viewer = new ChimeraManager(new StructureManager(true));
202 * Starts a thread that waits for the Chimera process to finish, so that we
203 * can then close the associated resources. This avoids leaving orphaned
204 * Chimera viewer panels in Jalview if the user closes Chimera.
206 protected void startChimeraProcessMonitor()
208 final Process p = viewer.getChimeraProcess();
209 chimeraMonitor = new Thread(new Runnable()
218 JalviewStructureDisplayI display = getViewer();
221 display.closeViewer(false);
223 } catch (InterruptedException e)
225 // exit thread if Chimera Viewer is closed in Jalview
229 chimeraMonitor.start();
233 * Start a dedicated HttpServer to listen for Chimera notifications, and tell
234 * it to start listening
236 public void startChimeraListener()
240 chimeraListener = new ChimeraListener(this);
241 viewer.startListening(chimeraListener.getUri());
242 } catch (BindException e)
244 System.err.println("Failed to start Chimera listener: "
250 * Tells Chimera to display only the specified chains
254 public void showChains(List<String> toshow)
257 * Construct a chimera command like
259 * ~display #*;~ribbon #*;ribbon :.A,:.B
261 StringBuilder cmd = new StringBuilder(64);
262 boolean first = true;
263 for (String chain : toshow)
265 int modelNumber = getModelNoForChain(chain);
266 String showChainCmd = modelNumber == -1 ? "" : modelNumber + ":."
267 + chain.split(":")[1];
272 cmd.append(showChainCmd);
277 * could append ";focus" to this command to resize the display to fill the
278 * window, but it looks more helpful not to (easier to relate chains to the
281 final String command = "~display #*; ~ribbon #*; ribbon :"
283 sendChimeraCommand(command, false);
287 * Close down the Jalview viewer and listener, and (optionally) the associated
290 public void closeViewer(boolean closeChimera)
292 getSsm().removeStructureViewerListener(this, this.getStructureFiles());
295 viewer.exitChimera();
297 if (this.chimeraListener != null)
299 chimeraListener.shutdown();
300 chimeraListener = null;
304 if (chimeraMonitor != null)
306 chimeraMonitor.interrupt();
308 releaseUIResources();
312 public void colourByChain()
314 colourBySequence = false;
315 sendAsynchronousCommand("rainbow chain", COLOURING_CHIMERA);
319 * Constructs and sends a Chimera command to colour by charge
321 * <li>Aspartic acid and Glutamic acid (negative charge) red</li>
322 * <li>Lysine and Arginine (positive charge) blue</li>
323 * <li>Cysteine - yellow</li>
324 * <li>all others - white</li>
328 public void colourByCharge()
330 colourBySequence = false;
331 String command = "color white;color red ::ASP;color red ::GLU;color blue ::LYS;color blue ::ARG;color yellow ::CYS";
332 sendAsynchronousCommand(command, COLOURING_CHIMERA);
339 public String superposeStructures(AlignmentI[] _alignment,
340 int[] _refStructure, HiddenColumns[] _hiddenCols)
342 StringBuilder allComs = new StringBuilder(128);
343 String[] files = getStructureFiles();
345 if (!waitForFileLoad(files))
351 StringBuilder selectioncom = new StringBuilder(256);
352 for (int a = 0; a < _alignment.length; a++)
354 int refStructure = _refStructure[a];
355 AlignmentI alignment = _alignment[a];
356 HiddenColumns hiddenCols = _hiddenCols[a];
358 if (refStructure >= files.length)
360 System.err.println("Ignoring invalid reference structure value "
366 * 'matched' bit i will be set for visible alignment columns i where
367 * all sequences have a residue with a mapping to the PDB structure
369 BitSet matched = new BitSet();
370 for (int m = 0; m < alignment.getWidth(); m++)
372 if (hiddenCols == null || hiddenCols.isVisible(m))
378 SuperposeData[] structures = new SuperposeData[files.length];
379 for (int f = 0; f < files.length; f++)
381 structures[f] = new SuperposeData(alignment.getWidth());
385 * Calculate the superposable alignment columns ('matched'), and the
386 * corresponding structure residue positions (structures.pdbResNo)
388 int candidateRefStructure = findSuperposableResidues(alignment,
389 matched, structures);
390 if (refStructure < 0)
393 * If no reference structure was specified, pick the first one that has
394 * a mapping in the alignment
396 refStructure = candidateRefStructure;
399 int nmatched = matched.cardinality();
402 return MessageManager.formatMessage("label.insufficient_residues",
407 * Generate select statements to select regions to superimpose structures
409 String[] selcom = new String[files.length];
410 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
412 String chainCd = "." + structures[pdbfnum].chain;
415 StringBuilder molsel = new StringBuilder();
417 int nextColumnMatch = matched.nextSetBit(0);
418 while (nextColumnMatch != -1)
420 int pdbResNum = structures[pdbfnum].pdbResNo[nextColumnMatch];
421 if (lpos != pdbResNum - 1)
424 * discontiguous - append last residue now
428 molsel.append(String.valueOf(lpos));
429 molsel.append(chainCd);
437 * extending a contiguous run
442 * start the range selection
444 molsel.append(String.valueOf(lpos));
450 nextColumnMatch = matched.nextSetBit(nextColumnMatch + 1);
454 * and terminate final selection
458 molsel.append(String.valueOf(lpos));
459 molsel.append(chainCd);
461 if (molsel.length() > 1)
463 selcom[pdbfnum] = molsel.toString();
464 selectioncom.append("#").append(String.valueOf(pdbfnum))
466 selectioncom.append(selcom[pdbfnum]);
467 selectioncom.append(" ");
468 if (pdbfnum < files.length - 1)
470 selectioncom.append("| ");
475 selcom[pdbfnum] = null;
479 StringBuilder command = new StringBuilder(256);
480 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
482 if (pdbfnum == refStructure || selcom[pdbfnum] == null
483 || selcom[refStructure] == null)
487 if (command.length() > 0)
493 * Form Chimera match command, from the 'new' structure to the
494 * 'reference' structure e.g. (50 residues, chain B/A, alphacarbons):
496 * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA
499 * https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
501 command.append("match ").append(getModelSpec(pdbfnum)).append(":");
502 command.append(selcom[pdbfnum]);
503 command.append("@").append(
504 structures[pdbfnum].isRna ? PHOSPHORUS : ALPHACARBON);
505 // JAL-1757 exclude alternate CA locations
506 command.append(NO_ALTLOCS);
507 command.append(" ").append(getModelSpec(refStructure)).append(":");
508 command.append(selcom[refStructure]);
509 command.append("@").append(
510 structures[refStructure].isRna ? PHOSPHORUS : ALPHACARBON);
511 command.append(NO_ALTLOCS);
513 if (selectioncom.length() > 0)
517 System.out.println("Select regions:\n" + selectioncom.toString());
518 System.out.println("Superimpose command(s):\n"
519 + command.toString());
521 allComs.append("~display all; chain @CA|P; ribbon ")
522 .append(selectioncom.toString())
523 .append(";" + command.toString());
528 if (selectioncom.length() > 0)
530 // TODO: visually distinguish regions that were superposed
531 if (selectioncom.substring(selectioncom.length() - 1).equals("|"))
533 selectioncom.setLength(selectioncom.length() - 1);
537 System.out.println("Select regions:\n" + selectioncom.toString());
539 allComs.append("; ~display all; chain @CA|P; ribbon ")
540 .append(selectioncom.toString()).append("; focus");
541 List<String> chimeraReplies = sendChimeraCommand(allComs.toString(),
543 for (String reply : chimeraReplies)
545 if (reply.toLowerCase().contains("unequal numbers of atoms"))
555 * Helper method to construct model spec in Chimera format:
557 * <li>#0 (#1 etc) for a PDB file with no sub-models</li>
558 * <li>#0.1 (#1.1 etc) for a PDB file with sub-models</li>
560 * Note for now we only ever choose the first of multiple models. This
561 * corresponds to the hard-coded Jmol equivalent (compare {1.1}). Refactor in
562 * future if there is a need to select specific sub-models.
567 protected String getModelSpec(int pdbfnum)
569 if (pdbfnum < 0 || pdbfnum >= getPdbCount())
575 * For now, the test for having sub-models is whether multiple Chimera
576 * models are mapped for the PDB file; the models are returned as a response
577 * to the Chimera command 'list models type molecule', see
578 * ChimeraManager.getModelList().
580 List<ChimeraModel> maps = chimeraMaps.get(getStructureFiles()[pdbfnum]);
581 boolean hasSubModels = maps != null && maps.size() > 1;
582 return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
586 * Launch Chimera, unless an instance linked to this object is already
587 * running. Returns true if Chimera is successfully launched, or already
588 * running, else false.
592 public boolean launchChimera()
594 if (viewer.isChimeraLaunched())
599 boolean launched = viewer.launchChimera(StructureManager
603 startChimeraProcessMonitor();
607 log("Failed to launch Chimera!");
613 * Answers true if the Chimera process is still running, false if ended or not
618 public boolean isChimeraRunning()
620 return viewer.isChimeraLaunched();
624 * Send a command to Chimera, and optionally log and return any responses.
626 * Does nothing, and returns null, if the command is the same as the last one
632 public List<String> sendChimeraCommand(final String command,
637 // ? thread running after viewer shut down
640 List<String> reply = null;
641 viewerCommandHistory(false);
642 if (true /*lastCommand == null || !lastCommand.equals(command)*/)
644 // trim command or it may never find a match in the replyLog!!
645 List<String> lastReply = viewer.sendChimeraCommand(command.trim(),
652 log("Response from command ('" + command + "') was:\n"
657 viewerCommandHistory(true);
663 * Send a Chimera command asynchronously in a new thread. If the progress
664 * message is not null, display this message while the command is executing.
669 protected abstract void sendAsynchronousCommand(String command,
673 * Sends a set of colour commands to the structure viewer
675 * @param colourBySequenceCommands
678 protected void colourBySequence(
679 StructureMappingcommandSet[] colourBySequenceCommands)
681 for (StructureMappingcommandSet cpdbbyseq : colourBySequenceCommands)
683 for (String command : cpdbbyseq.commands)
685 sendAsynchronousCommand(command, COLOURING_CHIMERA);
697 protected StructureMappingcommandSet[] getColourBySequenceCommands(
698 String[] files, SequenceRenderer sr, AlignmentViewPanel viewPanel)
700 return ChimeraCommands.getColourBySequenceCommand(getSsm(), files,
701 getSequence(), sr, viewPanel);
707 protected void executeWhenReady(String command)
710 sendChimeraCommand(command, false);
714 private void waitForChimera()
716 while (viewer != null && viewer.isBusy())
721 } catch (InterruptedException q)
727 // End StructureListener
728 // //////////////////////////
731 * instruct the Jalview binding to update the pdbentries vector if necessary
732 * prior to matching the viewer's contents to the list of structure files
733 * Jalview knows about.
735 public abstract void refreshPdbEntries();
738 * map between index of model filename returned from getPdbFile and the first
739 * index of models from this file in the viewer. Note - this is not trimmed -
740 * use getPdbFile to get number of unique models.
742 private int _modelFileNameMap[];
745 // ////////////////////////////////
746 // /StructureListener
748 public synchronized String[] getStructureFiles()
752 return new String[0];
755 return chimeraMaps.keySet().toArray(
756 modelFileNames = new String[chimeraMaps.size()]);
760 * Construct and send a command to highlight zero, one or more atoms. We do
761 * this by sending an "rlabel" command to show the residue label at that
765 public void highlightAtoms(List<AtomSpec> atoms)
767 if (atoms == null || atoms.size() == 0)
772 StringBuilder cmd = new StringBuilder(128);
773 boolean first = true;
774 boolean found = false;
776 for (AtomSpec atom : atoms)
778 int pdbResNum = atom.getPdbResNum();
779 String chain = atom.getChain();
780 String pdbfile = atom.getPdbFile();
781 List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
782 if (cms != null && !cms.isEmpty())
786 cmd.append("rlabel #").append(cms.get(0).getModelNumber())
794 cmd.append(pdbResNum);
795 if (!chain.equals(" "))
797 cmd.append(".").append(chain);
802 String command = cmd.toString();
805 * avoid repeated commands for the same residue
807 if (command.equals(lastHighlightCommand))
813 * unshow the label for the previous residue
815 if (lastHighlightCommand != null)
817 viewer.sendChimeraCommand("~" + lastHighlightCommand, false);
821 viewer.sendChimeraCommand(command, false);
823 this.lastHighlightCommand = command;
827 * Query Chimera for its current selection, and highlight it on the alignment
829 public void highlightChimeraSelection()
832 * Ask Chimera for its current selection
834 List<String> selection = viewer.getSelectedResidueSpecs();
837 * Parse model number, residue and chain for each selected position,
838 * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
840 List<AtomSpec> atomSpecs = convertStructureResiduesToAlignment(selection);
843 * Broadcast the selection (which may be empty, if the user just cleared all
846 getSsm().mouseOverStructure(atomSpecs);
850 * Converts a list of Chimera atomspecs to a list of AtomSpec representing the
851 * corresponding residues (if any) in Jalview
853 * @param structureSelection
856 protected List<AtomSpec> convertStructureResiduesToAlignment(
857 List<String> structureSelection)
859 List<AtomSpec> atomSpecs = new ArrayList<AtomSpec>();
860 for (String atomSpec : structureSelection)
864 AtomSpec spec = AtomSpec.fromChimeraAtomspec(atomSpec);
865 String pdbfilename = getPdbFileForModel(spec.getModelNumber());
866 spec.setPdbFile(pdbfilename);
868 } catch (IllegalArgumentException e)
870 System.err.println("Failed to parse atomspec: " + atomSpec);
880 protected String getPdbFileForModel(int modelId)
883 * Work out the pdbfilename from the model number
885 String pdbfilename = modelFileNames[0];
886 findfileloop: for (String pdbfile : this.chimeraMaps.keySet())
888 for (ChimeraModel cm : chimeraMaps.get(pdbfile))
890 if (cm.getModelNumber() == modelId)
892 pdbfilename = pdbfile;
900 private void log(String message)
902 System.err.println("## Chimera log: " + message);
905 private void viewerCommandHistory(boolean enable)
907 // log("(Not yet implemented) History "
908 // + ((debug || enable) ? "on" : "off"));
911 public long getLoadNotifiesHandled()
913 return loadNotifiesHandled;
917 public void setJalviewColourScheme(ColourSchemeI cs)
919 colourBySequence = false;
926 // Chimera expects RBG values in the range 0-1
927 final double normalise = 255D;
928 viewerCommandHistory(false);
929 StringBuilder command = new StringBuilder(128);
931 List<String> residueSet = ResidueProperties.getResidues(isNucleotide(),
933 for (String resName : residueSet)
935 char res = resName.length() == 3 ? ResidueProperties
936 .getSingleCharacterCode(resName) : resName.charAt(0);
937 Color col = cs.findColour(res, 0, null, null, 0f);
938 command.append("color " + col.getRed() / normalise + ","
939 + col.getGreen() / normalise + "," + col.getBlue()
940 / normalise + " ::" + resName + ";");
943 sendAsynchronousCommand(command.toString(), COLOURING_CHIMERA);
944 viewerCommandHistory(true);
948 * called when the binding thinks the UI needs to be refreshed after a Chimera
949 * state change. this could be because structures were loaded, or because an
950 * error has occurred.
952 public abstract void refreshGUI();
955 public void setLoadingFromArchive(boolean loadingFromArchive)
957 this.loadingFromArchive = loadingFromArchive;
962 * @return true if Chimeral is still restoring state or loading is still going
963 * on (see setFinsihedLoadingFromArchive)
966 public boolean isLoadingFromArchive()
968 return loadingFromArchive && !loadingFinished;
972 * modify flag which controls if sequence colouring events are honoured by the
973 * binding. Should be true for normal operation
975 * @param finishedLoading
978 public void setFinishedLoadingFromArchive(boolean finishedLoading)
980 loadingFinished = finishedLoading;
984 * Send the Chimera 'background solid <color>" command.
987 * ://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/background
992 public void setBackgroundColour(Color col)
994 viewerCommandHistory(false);
995 double normalise = 255D;
996 final String command = "background solid " + col.getRed() / normalise
997 + "," + col.getGreen() / normalise + "," + col.getBlue()
999 viewer.sendChimeraCommand(command, false);
1000 viewerCommandHistory(true);
1004 * Ask Chimera to save its session to the given file. Returns true if
1005 * successful, else false.
1010 public boolean saveSession(String filepath)
1012 if (isChimeraRunning())
1014 List<String> reply = viewer.sendChimeraCommand("save " + filepath,
1016 if (reply.contains("Session written"))
1023 .error("Error saving Chimera session: " + reply.toString());
1030 * Ask Chimera to open a session file. Returns true if successful, else false.
1031 * The filename must have a .py extension for this command to work.
1036 public boolean openSession(String filepath)
1038 sendChimeraCommand("open " + filepath, true);
1039 // todo: test for failure - how?
1044 * Returns a list of chains mapped in this viewer. Note this list is not
1045 * currently scoped per structure.
1050 public List<String> getChainNames()
1056 * Send a 'focus' command to Chimera to recentre the visible display
1058 public void focusView()
1060 sendChimeraCommand("focus", false);
1064 * Send a 'show' command for all atoms in the currently selected columns
1066 * TODO: pull up to abstract structure viewer interface
1070 public void highlightSelection(AlignmentViewPanel vp)
1072 List<Integer> cols = vp.getAlignViewport().getColumnSelection()
1074 AlignmentI alignment = vp.getAlignment();
1075 StructureSelectionManager sm = getSsm();
1076 for (SequenceI seq : alignment.getSequences())
1079 * convert selected columns into sequence positions
1081 int[] positions = new int[cols.size()];
1083 for (Integer col : cols)
1085 positions[i++] = seq.findPosition(col);
1087 sm.highlightStructure(this, seq, positions);
1092 * Constructs and send commands to Chimera to set attributes on residues for
1093 * features visible in Jalview
1098 public int sendFeaturesToViewer(AlignmentViewPanel avp)
1100 // TODO refactor as required to pull up to an interface
1101 AlignmentI alignment = avp.getAlignment();
1103 String[] files = getStructureFiles();
1109 StructureMappingcommandSet commandSet = ChimeraCommands
1110 .getSetAttributeCommandsForFeatures(getSsm(), files,
1111 getSequence(), avp);
1112 String[] commands = commandSet.commands;
1113 if (commands.length > 10)
1115 sendCommandsByFile(commands);
1119 for (String command : commands)
1121 sendAsynchronousCommand(command, null);
1124 return commands.length;
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 SearchResultsI 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();