3 * Copyright (c) 2006 The Regents of the University of California.
6 * Redistribution and use in source and binary forms, with or without
7 * modification, are permitted provided that the following conditions
9 * 1. Redistributions of source code must retain the above copyright
10 * notice, this list of conditions, and the following disclaimer.
11 * 2. Redistributions in binary form must reproduce the above
12 * copyright notice, this list of conditions, and the following
13 * disclaimer in the documentation and/or other materials provided
14 * with the distribution.
15 * 3. Redistributions must acknowledge that this software was
16 * originally developed by the UCSF Computer Graphics Laboratory
17 * under support by the NIH National Center for Research Resources,
20 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDER "AS IS" AND ANY
21 * EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
22 * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
23 * PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS BE LIABLE
24 * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
25 * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
26 * OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR
27 * BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
28 * WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
29 * OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
30 * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
33 package ext.edu.ucsf.rbvi.strucviz2;
35 import java.awt.Color;
36 import java.io.BufferedReader;
38 import java.io.IOException;
39 import java.io.InputStream;
40 import java.io.InputStreamReader;
41 import java.nio.file.Paths;
42 import java.util.ArrayList;
43 import java.util.Collection;
44 import java.util.HashMap;
45 import java.util.List;
48 import org.apache.http.NameValuePair;
49 import org.apache.http.message.BasicNameValuePair;
50 import org.slf4j.Logger;
51 import org.slf4j.LoggerFactory;
53 import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
54 import ext.edu.ucsf.rbvi.strucviz2.port.ListenerThreads;
55 import jalview.ws.HttpClientUtils;
58 * This object maintains the Chimera communication information.
60 public class ChimeraManager
62 private static final int REST_REPLY_TIMEOUT_MS = 15000;
64 private static final int CONNECTION_TIMEOUT_MS = 100;
66 private static final boolean debug = false;
68 private int chimeraRestPort;
70 private Process chimera;
72 private ListenerThreads chimeraListenerThread;
74 private Map<Integer, ChimeraModel> currentModelsMap;
76 private Logger logger = LoggerFactory
77 .getLogger(ext.edu.ucsf.rbvi.strucviz2.ChimeraManager.class);
79 private StructureManager structureManager;
81 public ChimeraManager(StructureManager structureManager)
83 this.structureManager = structureManager;
85 chimeraListenerThread = null;
86 currentModelsMap = new HashMap<>();
90 public List<ChimeraModel> getChimeraModels(String modelName)
92 List<ChimeraModel> models = getChimeraModels(modelName,
94 models.addAll(getChimeraModels(modelName, ModelType.SMILES));
98 public List<ChimeraModel> getChimeraModels(String modelName,
101 List<ChimeraModel> models = new ArrayList<>();
102 for (ChimeraModel model : currentModelsMap.values())
104 if (modelName.equals(model.getModelName())
105 && modelType.equals(model.getModelType()))
113 public Map<String, List<ChimeraModel>> getChimeraModelsMap()
115 Map<String, List<ChimeraModel>> models = new HashMap<>();
116 for (ChimeraModel model : currentModelsMap.values())
118 String modelName = model.getModelName();
119 if (!models.containsKey(modelName))
121 models.put(modelName, new ArrayList<ChimeraModel>());
123 if (!models.get(modelName).contains(model))
125 models.get(modelName).add(model);
131 public ChimeraModel getChimeraModel(Integer modelNumber,
132 Integer subModelNumber)
134 Integer key = ChimUtils.makeModelKey(modelNumber, subModelNumber);
135 if (currentModelsMap.containsKey(key))
137 return currentModelsMap.get(key);
142 public ChimeraModel getChimeraModel()
144 return currentModelsMap.values().iterator().next();
147 public Collection<ChimeraModel> getChimeraModels()
149 // this method is invoked by the model navigator dialog
150 return currentModelsMap.values();
153 public int getChimeraModelsCount(boolean smiles)
155 // this method is invokes by the model navigator dialog
156 int counter = currentModelsMap.size();
162 for (ChimeraModel model : currentModelsMap.values())
164 if (model.getModelType() == ModelType.SMILES)
172 public boolean hasChimeraModel(Integer modelNubmer)
174 return hasChimeraModel(modelNubmer, 0);
177 public boolean hasChimeraModel(Integer modelNubmer, Integer subModelNumber)
179 return currentModelsMap.containsKey(ChimUtils.makeModelKey(modelNubmer,
183 public void addChimeraModel(Integer modelNumber, Integer subModelNumber,
186 currentModelsMap.put(
187 ChimUtils.makeModelKey(modelNumber, subModelNumber), model);
190 public void removeChimeraModel(Integer modelNumber, Integer subModelNumber)
192 int modelKey = ChimUtils.makeModelKey(modelNumber, subModelNumber);
193 if (currentModelsMap.containsKey(modelKey))
195 currentModelsMap.remove(modelKey);
199 public List<ChimeraModel> openModel(String modelPath, ModelType type)
201 return openModel(modelPath, getFileNameFromPath(modelPath), type);
205 * Overloaded method to allow Jalview to pass in a model name.
212 public List<ChimeraModel> openModel(String modelPath, String modelName,
215 logger.info("chimera open " + modelPath);
217 List<ChimeraModel> modelList = getModelList();
218 List<String> response = null;
219 // TODO: [Optional] Handle modbase models
220 if (type == ModelType.MODBASE_MODEL)
222 response = sendChimeraCommand("open modbase:" + modelPath, true);
223 // } else if (type == ModelType.SMILES) {
224 // response = sendChimeraCommand("open smiles:" + modelName, true);
225 // modelName = "smiles:" + modelName;
229 response = sendChimeraCommand("open " + modelPath, true);
231 if (response == null)
233 // something went wrong
234 logger.warn("Could not open " + modelPath);
238 // patch for Jalview - set model name in Chimera
239 // TODO: find a variant that works for sub-models
240 for (ChimeraModel newModel : getModelList())
242 if (!modelList.contains(newModel))
244 newModel.setModelName(modelName);
246 "setattr M name " + modelName + " #"
247 + newModel.getModelNumber(), false);
248 modelList.add(newModel);
252 // assign color and residues to open models
253 for (ChimeraModel chimeraModel : modelList)
256 Color modelColor = isChimeraX() ? null : getModelColor(chimeraModel);
257 if (modelColor != null)
259 chimeraModel.setModelColor(modelColor);
262 // Get our properties (default color scheme, etc.)
263 // Make the molecule look decent
264 // chimeraSend("repr stick "+newModel.toSpec());
266 // Create the information we need for the navigator
267 if (type != ModelType.SMILES && !isChimeraX())
269 addResidues(chimeraModel);
273 sendChimeraCommand("focus", false);
274 // startListening(); // see ChimeraListener
279 * Refactored method to extract the last (or only) element delimited by file
285 private String getFileNameFromPath(String modelPath)
287 String modelName = modelPath;
288 if (modelPath == null)
292 // TODO: [Optional] Convert path to name in a better way
293 if (modelPath.lastIndexOf(File.separator) > 0)
295 modelName = modelPath
296 .substring(modelPath.lastIndexOf(File.separator) + 1);
298 else if (modelPath.lastIndexOf("/") > 0)
300 modelName = modelPath.substring(modelPath.lastIndexOf("/") + 1);
305 public void closeModel(ChimeraModel model)
307 // int model = structure.modelNumber();
308 // int subModel = structure.subModelNumber();
309 // Integer modelKey = makeModelKey(model, subModel);
311 logger.info("chimera close model " + model.getModelName());
312 if (currentModelsMap.containsKey(ChimUtils.makeModelKey(
313 model.getModelNumber(), model.getSubModelNumber())))
315 sendChimeraCommand("close " + model.toSpec(), false);
316 // currentModelNamesMap.remove(model.getModelName());
317 currentModelsMap.remove(ChimUtils.makeModelKey(
318 model.getModelNumber(), model.getSubModelNumber()));
319 // selectionList.remove(chimeraModel);
323 logger.warn("Could not find model " + model.getModelName()
329 public void startListening()
331 sendChimeraCommand("listen start models; listen start selection", false);
334 public void stopListening()
336 // TODO send this command when viewer connection is closed in Jalview
337 String command = isChimeraX
338 ? "info notify stop models jalview; info notify stop selection jalview"
339 : "listen stop models ; listen stop selection ";
340 sendChimeraCommand(command, false);
344 * Tell Chimera we are listening on the given URI
348 public void startListening(String uri)
351 * listen for model changes
353 String command = isChimeraX
354 ? ("info notify start models prefix ModelChanged jalview url "
356 : ("listen start models url " + uri);
357 sendChimeraCommand(command, false);
360 * listen for selection changes
363 ? ("info notify start selection jalview prefix SelectionChanged url "
365 : ("listen start select prefix SelectionChanged url " + uri);
366 sendChimeraCommand(command, false);
370 * Select something in Chimera
373 * the selection command to pass to Chimera
375 public void select(String command)
377 sendChimeraCommand("listen stop selection; " + command
378 + "; listen start selection", false);
383 sendChimeraCommand("focus", false);
386 public void clearOnChimeraExit()
389 currentModelsMap.clear();
390 this.chimeraRestPort = 0;
391 structureManager.clearOnChimeraExit();
394 public void exitChimera()
396 if (isChimeraLaunched() && chimera != null)
398 sendChimeraCommand("stop really", false);
401 // TODO is this too violent? could it force close the process
402 // before it has done an orderly shutdown?
404 } catch (Exception ex)
409 clearOnChimeraExit();
412 public Map<Integer, ChimeraModel> getSelectedModels()
414 Map<Integer, ChimeraModel> selectedModelsMap = new HashMap<>();
415 List<String> chimeraReply = sendChimeraCommand(
416 "list selection level molecule", true);
417 if (chimeraReply != null)
419 for (String modelLine : chimeraReply)
421 ChimeraModel chimeraModel = new ChimeraModel(modelLine);
422 Integer modelKey = ChimUtils.makeModelKey(
423 chimeraModel.getModelNumber(),
424 chimeraModel.getSubModelNumber());
425 selectedModelsMap.put(modelKey, chimeraModel);
428 return selectedModelsMap;
432 * Sends a 'list selection level residue' command to Chimera and returns the
433 * list of selected atomspecs
437 public List<String> getSelectedResidueSpecs()
439 List<String> selectedResidues = new ArrayList<>();
441 // in fact 'listinfo' (undocumented) works in ChimeraX
442 String command = (isChimeraX
444 : "list") + " selection level residue";
445 List<String> chimeraReply = sendChimeraCommand(command, true);
446 if (chimeraReply != null)
449 * expect 0, 1 or more lines of the format either
451 * residue id #0:43.A type GLY
453 * residue id /A:89 name THR index 88
454 * We are only interested in the atomspec (third token of the reply)
456 for (String inputLine : chimeraReply)
458 String[] inputLineParts = inputLine.split("\\s+");
459 if (inputLineParts.length >= 5)
461 selectedResidues.add(inputLineParts[2]);
465 return selectedResidues;
468 public void getSelectedResidues(
469 Map<Integer, ChimeraModel> selectedModelsMap)
471 List<String> chimeraReply = sendChimeraCommand(
472 "list selection level residue", true);
473 if (chimeraReply != null)
475 for (String inputLine : chimeraReply)
477 ChimeraResidue r = new ChimeraResidue(inputLine);
478 Integer modelKey = ChimUtils.makeModelKey(r.getModelNumber(),
479 r.getSubModelNumber());
480 if (selectedModelsMap.containsKey(modelKey))
482 ChimeraModel model = selectedModelsMap.get(modelKey);
490 * Return the list of ChimeraModels currently open. Warning: if smiles model
491 * name too long, only part of it with "..." is printed.
494 * @return List of ChimeraModel's
496 // TODO: [Optional] Handle smiles names in a better way in Chimera?
497 public List<ChimeraModel> getModelList()
499 List<ChimeraModel> modelList = new ArrayList<>();
500 String command = "list models type "
501 + (isChimeraX ? "AtomicStructure" : "molecule");
502 List<String> list = sendChimeraCommand(command, true);
505 for (String modelLine : list)
509 ChimeraModel chimeraModel = new ChimeraModel(modelLine);
510 modelList.add(chimeraModel);
511 } catch (NullPointerException e)
521 * Return the list of depiction presets available from within Chimera. Chimera
522 * will return the list as a series of lines with the format: Preset type
523 * number "description"
525 * @return list of presets
527 public List<String> getPresets()
529 ArrayList<String> presetList = new ArrayList<>();
530 List<String> output = sendChimeraCommand("preset list", true);
533 for (String preset : output)
535 preset = preset.substring(7); // Skip over the "Preset"
536 preset = preset.replaceFirst("\"", "(");
537 preset = preset.replaceFirst("\"", ")");
538 // string now looks like: type number (description)
539 presetList.add(preset);
545 public boolean isChimeraLaunched()
547 boolean launched = false;
553 // if we get here, process has ended
554 } catch (IllegalThreadStateException e)
556 // ok - not yet terminated
564 * Launch Chimera, unless an instance linked to this object is already
565 * running. Returns true if chimera is successfully launched, or already
566 * running, else false.
568 * @param chimeraPaths
571 public boolean launchChimera(List<String> chimeraPaths)
573 // Do nothing if Chimera is already launched
574 if (isChimeraLaunched())
579 // Try to launch Chimera (eventually using one of the possible paths)
580 String error = "Error message: ";
581 String workingPath = "";
582 // iterate over possible paths for starting Chimera
583 for (String chimeraPath : chimeraPaths)
587 // ensure symbolic links are resolved
588 chimeraPath = Paths.get(chimeraPath).toRealPath().toString();
589 isChimeraX = chimeraPath.toLowerCase().contains("chimerax");
590 File path = new File(chimeraPath);
591 // uncomment the next line to simulate Chimera not installed
592 // path = new File(chimeraPath + "x");
593 if (!path.canExecute())
595 error += "File '" + path + "' does not exist.\n";
598 List<String> args = new ArrayList<>();
599 args.add(chimeraPath);
600 // shows Chimera output window but suppresses REST responses:
601 // args.add("--debug");
605 args.add("remote rest start");
610 args.add("RESTServer");
612 ProcessBuilder pb = new ProcessBuilder(args);
613 chimera = pb.start();
615 workingPath = chimeraPath;
617 } catch (Exception e)
619 // Chimera could not be started using this path
620 error += e.getMessage();
623 // If no error, then Chimera was launched successfully
624 if (error.length() == 0)
626 this.chimeraRestPort = getPortNumber();
627 System.out.println("Chimera REST API started on port "
629 // structureManager.initChimTable();
630 structureManager.setChimeraPathProperty(workingPath);
631 // TODO: [Optional] Check Chimera version and show a warning if below 1.8
632 // Ask Chimera to give us updates
633 // startListening(); // later - see ChimeraListener
634 return (chimeraRestPort > 0);
637 // Tell the user that Chimera could not be started because of an error
643 * Read and return the port number returned in the reply to --start RESTServer
645 private int getPortNumber()
648 InputStream readChan = chimera.getInputStream();
649 BufferedReader lineReader = new BufferedReader(new InputStreamReader(
651 StringBuilder responses = new StringBuilder();
654 String response = lineReader.readLine();
655 while (response != null)
657 responses.append("\n" + response);
658 // expect: REST server on host 127.0.0.1 port port_number
659 // ChimeraX is the same except "REST server started on host..."
660 if (response.startsWith("REST server"))
662 String[] tokens = response.split(" ");
663 for (int i = 0; i < tokens.length - 1; i++)
665 if ("port".equals(tokens[i]))
667 port = Integer.parseInt(tokens[i + 1]);
674 break; // hack for hanging readLine()
676 response = lineReader.readLine();
678 } catch (Exception e)
680 logger.error("Failed to get REST port number from " + responses
681 + ": " + e.getMessage());
687 } catch (IOException e2)
694 .println("Failed to start Chimera with REST service, response was: "
697 logger.info("Chimera REST service listening on port " + chimeraRestPort);
702 * Determine the color that Chimera is using for this model.
705 * the ChimeraModel we want to get the Color for
706 * @return the default model Color for this model in Chimera
708 public Color getModelColor(ChimeraModel model)
710 List<String> colorLines = sendChimeraCommand(
711 "list model spec " + model.toSpec() + " attribute color", true);
712 if (colorLines == null || colorLines.size() == 0)
716 return ChimUtils.parseModelColor(colorLines.get(0));
721 * Get information about the residues associated with a model. This uses the
722 * Chimera listr command. We don't return the resulting residues, but we add
723 * the residues to the model.
726 * the ChimeraModel to get residue information for
729 public void addResidues(ChimeraModel model)
731 int modelNumber = model.getModelNumber();
732 int subModelNumber = model.getSubModelNumber();
733 // Get the list -- it will be in the reply log
734 List<String> reply = sendChimeraCommand(
735 "list residues spec " + model.toSpec(), true);
740 for (String inputLine : reply)
742 ChimeraResidue r = new ChimeraResidue(inputLine);
743 if (r.getModelNumber() == modelNumber
744 || r.getSubModelNumber() == subModelNumber)
751 public List<String> getAttrList()
753 List<String> attributes = new ArrayList<>();
754 String command = (isChimeraX ? "info " : "list ") + "resattr";
755 final List<String> reply = sendChimeraCommand(command, true);
758 for (String inputLine : reply)
760 String[] lineParts = inputLine.split("\\s");
761 if (lineParts.length == 2 && lineParts[0].equals("resattr"))
763 attributes.add(lineParts[1]);
770 public Map<ChimeraResidue, Object> getAttrValues(String aCommand,
773 Map<ChimeraResidue, Object> values = new HashMap<>();
774 final List<String> reply = sendChimeraCommand("list residue spec "
775 + model.toSpec() + " attribute " + aCommand, true);
778 for (String inputLine : reply)
780 String[] lineParts = inputLine.split("\\s");
781 if (lineParts.length == 5)
783 ChimeraResidue residue = ChimUtils
784 .getResidue(lineParts[2], model);
785 String value = lineParts[4];
788 if (value.equals("None"))
792 if (value.equals("True") || value.equals("False"))
794 values.put(residue, Boolean.valueOf(value));
799 Double doubleValue = Double.valueOf(value);
800 values.put(residue, doubleValue);
801 } catch (NumberFormatException ex)
803 values.put(residue, value);
812 private volatile boolean busy = false;
814 private boolean isChimeraX;
817 * Send a command to Chimera.
820 * Command string to be send.
822 * Flag indicating whether the method should return the reply from
824 * @return List of Strings corresponding to the lines in the Chimera reply or
827 public List<String> sendChimeraCommand(String command, boolean reply)
829 System.out.println("chimeradebug>> " + command);
830 if (!isChimeraLaunched() || command == null
831 || "".equals(command.trim()))
835 // TODO do we need a maximum wait time before aborting?
841 } catch (InterruptedException q)
846 long startTime = System.currentTimeMillis();
849 return sendRestCommand(command);
853 * Make sure busy flag is reset come what may!
858 System.out.println("Chimera command took "
859 + (System.currentTimeMillis() - startTime) + "ms: "
867 * Sends the command to Chimera's REST API, and returns any response lines.
872 protected List<String> sendRestCommand(String command)
874 String restUrl = "http://127.0.0.1:" + this.chimeraRestPort + "/run";
875 List<NameValuePair> commands = new ArrayList<>(1);
876 String method = isChimeraX() ? "GET" : "POST";
877 if ("GET".equals(method))
879 command = command.replace(" ", "+").replace("#", "%23")
880 .replace("|", "%7C").replace(";", "%3B");
882 commands.add(new BasicNameValuePair("command", command));
884 List<String> reply = new ArrayList<>();
885 BufferedReader response = null;
888 response = "GET".equals(method)
889 ? HttpClientUtils.doHttpGet(restUrl, commands,
890 CONNECTION_TIMEOUT_MS, REST_REPLY_TIMEOUT_MS)
891 : HttpClientUtils.doHttpUrlPost(restUrl, commands,
892 CONNECTION_TIMEOUT_MS, REST_REPLY_TIMEOUT_MS);
894 while ((line = response.readLine()) != null)
898 } catch (Exception e)
900 logger.error("REST call '" + command + "' failed: " + e.getMessage());
903 if (response != null)
908 } catch (IOException e)
917 * Send a command to stdin of Chimera process, and optionally read any
924 protected List<String> sendStdinCommand(String command, boolean readReply)
926 chimeraListenerThread.clearResponse(command);
927 String text = command.concat("\n");
931 chimera.getOutputStream().write(text.getBytes());
932 chimera.getOutputStream().flush();
933 } catch (IOException e)
935 // logger.info("Unable to execute command: " + text);
936 // logger.info("Exiting...");
937 logger.warn("Unable to execute command: " + text);
938 logger.warn("Exiting...");
939 clearOnChimeraExit();
946 List<String> rsp = chimeraListenerThread.getResponse(command);
950 public StructureManager getStructureManager()
952 return structureManager;
955 public boolean isBusy()
960 public Process getChimeraProcess()
965 public boolean isChimeraX()
970 public void setChimeraX(boolean b)