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 jalview.ws.HttpClientUtils;
37 import java.awt.Color;
38 import java.io.BufferedReader;
40 import java.io.IOException;
41 import java.io.InputStream;
42 import java.io.InputStreamReader;
43 import java.nio.file.Paths;
44 import java.util.ArrayList;
45 import java.util.Collection;
46 import java.util.HashMap;
47 import java.util.List;
50 import org.apache.http.NameValuePair;
51 import org.apache.http.message.BasicNameValuePair;
52 import org.slf4j.Logger;
53 import org.slf4j.LoggerFactory;
55 import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
56 import ext.edu.ucsf.rbvi.strucviz2.port.ListenerThreads;
59 * This object maintains the Chimera communication information.
61 public class ChimeraManager
63 private static final int REST_REPLY_TIMEOUT_MS = 15000;
65 private static final int CONNECTION_TIMEOUT_MS = 100;
67 private static final boolean debug = false;
69 private int chimeraRestPort;
71 private Process chimera;
73 private ListenerThreads chimeraListenerThread;
75 private Map<Integer, ChimeraModel> currentModelsMap;
77 private Logger logger = LoggerFactory
78 .getLogger(ext.edu.ucsf.rbvi.strucviz2.ChimeraManager.class);
80 private StructureManager structureManager;
82 public ChimeraManager(StructureManager structureManager)
84 this.structureManager = structureManager;
86 chimeraListenerThread = null;
87 currentModelsMap = new HashMap<>();
91 public List<ChimeraModel> getChimeraModels(String modelName)
93 List<ChimeraModel> models = getChimeraModels(modelName,
95 models.addAll(getChimeraModels(modelName, ModelType.SMILES));
99 public List<ChimeraModel> getChimeraModels(String modelName,
102 List<ChimeraModel> models = new ArrayList<>();
103 for (ChimeraModel model : currentModelsMap.values())
105 if (modelName.equals(model.getModelName())
106 && modelType.equals(model.getModelType()))
114 public Map<String, List<ChimeraModel>> getChimeraModelsMap()
116 Map<String, List<ChimeraModel>> models = new HashMap<>();
117 for (ChimeraModel model : currentModelsMap.values())
119 String modelName = model.getModelName();
120 if (!models.containsKey(modelName))
122 models.put(modelName, new ArrayList<ChimeraModel>());
124 if (!models.get(modelName).contains(model))
126 models.get(modelName).add(model);
132 public ChimeraModel getChimeraModel(Integer modelNumber,
133 Integer subModelNumber)
135 Integer key = ChimUtils.makeModelKey(modelNumber, subModelNumber);
136 if (currentModelsMap.containsKey(key))
138 return currentModelsMap.get(key);
143 public ChimeraModel getChimeraModel()
145 return currentModelsMap.values().iterator().next();
148 public Collection<ChimeraModel> getChimeraModels()
150 // this method is invoked by the model navigator dialog
151 return currentModelsMap.values();
154 public int getChimeraModelsCount(boolean smiles)
156 // this method is invokes by the model navigator dialog
157 int counter = currentModelsMap.size();
163 for (ChimeraModel model : currentModelsMap.values())
165 if (model.getModelType() == ModelType.SMILES)
173 public boolean hasChimeraModel(Integer modelNubmer)
175 return hasChimeraModel(modelNubmer, 0);
178 public boolean hasChimeraModel(Integer modelNubmer, Integer subModelNumber)
180 return currentModelsMap.containsKey(ChimUtils.makeModelKey(modelNubmer,
184 public void addChimeraModel(Integer modelNumber, Integer subModelNumber,
187 currentModelsMap.put(
188 ChimUtils.makeModelKey(modelNumber, subModelNumber), model);
191 public void removeChimeraModel(Integer modelNumber, Integer subModelNumber)
193 int modelKey = ChimUtils.makeModelKey(modelNumber, subModelNumber);
194 if (currentModelsMap.containsKey(modelKey))
196 currentModelsMap.remove(modelKey);
200 public List<ChimeraModel> openModel(String modelPath, ModelType type)
202 return openModel(modelPath, getFileNameFromPath(modelPath), type);
206 * Overloaded method to allow Jalview to pass in a model name.
213 public List<ChimeraModel> openModel(String modelPath, String modelName,
216 logger.info("chimera open " + modelPath);
218 List<ChimeraModel> modelList = getModelList();
219 List<String> response = null;
220 // TODO: [Optional] Handle modbase models
221 if (type == ModelType.MODBASE_MODEL)
223 response = sendChimeraCommand("open modbase:" + modelPath, true);
224 // } else if (type == ModelType.SMILES) {
225 // response = sendChimeraCommand("open smiles:" + modelName, true);
226 // modelName = "smiles:" + modelName;
230 response = sendChimeraCommand("open " + modelPath, true);
232 if (response == null)
234 // something went wrong
235 logger.warn("Could not open " + modelPath);
239 // patch for Jalview - set model name in Chimera
240 // TODO: find a variant that works for sub-models
241 for (ChimeraModel newModel : getModelList())
243 if (!modelList.contains(newModel))
245 newModel.setModelName(modelName);
247 "setattr M name " + modelName + " #"
248 + newModel.getModelNumber(), false);
249 modelList.add(newModel);
253 // assign color and residues to open models
254 for (ChimeraModel chimeraModel : modelList)
257 Color modelColor = isChimeraX() ? null : getModelColor(chimeraModel);
258 if (modelColor != null)
260 chimeraModel.setModelColor(modelColor);
263 // Get our properties (default color scheme, etc.)
264 // Make the molecule look decent
265 // chimeraSend("repr stick "+newModel.toSpec());
267 // Create the information we need for the navigator
268 if (type != ModelType.SMILES && !isChimeraX())
270 addResidues(chimeraModel);
274 sendChimeraCommand("focus", false);
275 // startListening(); // see ChimeraListener
280 * Refactored method to extract the last (or only) element delimited by file
286 private String getFileNameFromPath(String modelPath)
288 String modelName = modelPath;
289 if (modelPath == null)
293 // TODO: [Optional] Convert path to name in a better way
294 if (modelPath.lastIndexOf(File.separator) > 0)
296 modelName = modelPath
297 .substring(modelPath.lastIndexOf(File.separator) + 1);
299 else if (modelPath.lastIndexOf("/") > 0)
301 modelName = modelPath.substring(modelPath.lastIndexOf("/") + 1);
306 public void closeModel(ChimeraModel model)
308 // int model = structure.modelNumber();
309 // int subModel = structure.subModelNumber();
310 // Integer modelKey = makeModelKey(model, subModel);
312 logger.info("chimera close model " + model.getModelName());
313 if (currentModelsMap.containsKey(ChimUtils.makeModelKey(
314 model.getModelNumber(), model.getSubModelNumber())))
316 sendChimeraCommand("close " + model.toSpec(), false);
317 // currentModelNamesMap.remove(model.getModelName());
318 currentModelsMap.remove(ChimUtils.makeModelKey(
319 model.getModelNumber(), model.getSubModelNumber()));
320 // selectionList.remove(chimeraModel);
324 logger.warn("Could not find model " + model.getModelName()
330 public void startListening()
332 sendChimeraCommand("listen start models; listen start selection", false);
335 public void stopListening()
337 // TODO send this command when viewer connection is closed in Jalview
338 String command = isChimeraX
339 ? "info notify stop models jalview; info notify stop selection jalview"
340 : "listen stop models ; listen stop selection ";
341 sendChimeraCommand(command, false);
345 * Tell Chimera we are listening on the given URI
349 public void startListening(String uri)
351 String command = isChimeraX
352 ? ("info notify start models prefix ModelChanged jalview url "
354 + "; info notify start selection jalview prefix SelectionChanged url "
356 : ("listen start models url " + uri
357 + ";listen start select prefix SelectionChanged url "
359 sendChimeraCommand(command, false);
363 * Select something in Chimera
366 * the selection command to pass to Chimera
368 public void select(String command)
370 sendChimeraCommand("listen stop selection; " + command
371 + "; listen start selection", false);
376 sendChimeraCommand("focus", false);
379 public void clearOnChimeraExit()
382 currentModelsMap.clear();
383 this.chimeraRestPort = 0;
384 structureManager.clearOnChimeraExit();
387 public void exitChimera()
389 if (isChimeraLaunched() && chimera != null)
391 sendChimeraCommand("stop really", false);
394 // TODO is this too violent? could it force close the process
395 // before it has done an orderly shutdown?
397 } catch (Exception ex)
402 clearOnChimeraExit();
405 public Map<Integer, ChimeraModel> getSelectedModels()
407 Map<Integer, ChimeraModel> selectedModelsMap = new HashMap<>();
408 List<String> chimeraReply = sendChimeraCommand(
409 "list selection level molecule", true);
410 if (chimeraReply != null)
412 for (String modelLine : chimeraReply)
414 ChimeraModel chimeraModel = new ChimeraModel(modelLine);
415 Integer modelKey = ChimUtils.makeModelKey(
416 chimeraModel.getModelNumber(),
417 chimeraModel.getSubModelNumber());
418 selectedModelsMap.put(modelKey, chimeraModel);
421 return selectedModelsMap;
425 * Sends a 'list selection level residue' command to Chimera and returns the
426 * list of selected atomspecs
430 public List<String> getSelectedResidueSpecs()
432 List<String> selectedResidues = new ArrayList<>();
435 * skip for now if ChimeraX - request times out
439 return selectedResidues;
442 // in fact 'listinfo' (undocumented) works in ChimeraX
443 String command = (isChimeraX ? "info" : "list")
444 + " 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 modelList.add(new ChimeraModel("4zhp", ModelType.PDB_MODEL, 1, 0));
501 return modelList; // ChimeraX doesn't have 'list models' command
502 // List<String> list = sendChimeraCommand("list models type molecule",
506 // for (String modelLine : list)
508 // ChimeraModel chimeraModel = new ChimeraModel(modelLine);
509 // modelList.add(chimeraModel);
516 * Return the list of depiction presets available from within Chimera. Chimera
517 * will return the list as a series of lines with the format: Preset type
518 * number "description"
520 * @return list of presets
522 public List<String> getPresets()
524 ArrayList<String> presetList = new ArrayList<>();
525 List<String> output = sendChimeraCommand("preset list", true);
528 for (String preset : output)
530 preset = preset.substring(7); // Skip over the "Preset"
531 preset = preset.replaceFirst("\"", "(");
532 preset = preset.replaceFirst("\"", ")");
533 // string now looks like: type number (description)
534 presetList.add(preset);
540 public boolean isChimeraLaunched()
542 boolean launched = false;
548 // if we get here, process has ended
549 } catch (IllegalThreadStateException e)
551 // ok - not yet terminated
559 * Launch Chimera, unless an instance linked to this object is already
560 * running. Returns true if chimera is successfully launched, or already
561 * running, else false.
563 * @param chimeraPaths
566 public boolean launchChimera(List<String> chimeraPaths)
568 // Do nothing if Chimera is already launched
569 if (isChimeraLaunched())
574 // Try to launch Chimera (eventually using one of the possible paths)
575 String error = "Error message: ";
576 String workingPath = "";
577 // iterate over possible paths for starting Chimera
578 for (String chimeraPath : chimeraPaths)
582 // ensure symbolic links are resolved
583 chimeraPath = Paths.get(chimeraPath).toRealPath().toString();
584 isChimeraX = chimeraPath.toLowerCase().contains("chimerax");
585 File path = new File(chimeraPath);
586 // uncomment the next line to simulate Chimera not installed
587 // path = new File(chimeraPath + "x");
588 if (!path.canExecute())
590 error += "File '" + path + "' does not exist.\n";
593 List<String> args = new ArrayList<>();
594 args.add(chimeraPath);
595 // shows Chimera output window but suppresses REST responses:
596 // args.add("--debug");
600 args.add("remote rest start");
605 args.add("RESTServer");
607 ProcessBuilder pb = new ProcessBuilder(args);
608 chimera = pb.start();
610 workingPath = chimeraPath;
612 } catch (Exception e)
614 // Chimera could not be started using this path
615 error += e.getMessage();
618 // If no error, then Chimera was launched successfully
619 if (error.length() == 0)
621 this.chimeraRestPort = getPortNumber();
622 System.out.println("Chimera REST API started on port "
624 // structureManager.initChimTable();
625 structureManager.setChimeraPathProperty(workingPath);
626 // TODO: [Optional] Check Chimera version and show a warning if below 1.8
627 // Ask Chimera to give us updates
628 // startListening(); // later - see ChimeraListener
629 return (chimeraRestPort > 0);
632 // Tell the user that Chimera could not be started because of an error
638 * Read and return the port number returned in the reply to --start RESTServer
640 private int getPortNumber()
643 InputStream readChan = chimera.getInputStream();
644 BufferedReader lineReader = new BufferedReader(new InputStreamReader(
646 StringBuilder responses = new StringBuilder();
649 String response = lineReader.readLine();
650 while (response != null)
652 responses.append("\n" + response);
653 // expect: REST server on host 127.0.0.1 port port_number
654 // ChimeraX is the same except "REST server started on host..."
655 if (response.startsWith("REST server"))
657 String[] tokens = response.split(" ");
658 for (int i = 0; i < tokens.length - 1; i++)
660 if ("port".equals(tokens[i]))
662 port = Integer.parseInt(tokens[i + 1]);
669 break; // hack for hanging readLine()
671 response = lineReader.readLine();
673 } catch (Exception e)
675 logger.error("Failed to get REST port number from " + responses
676 + ": " + e.getMessage());
682 } catch (IOException e2)
689 .println("Failed to start Chimera with REST service, response was: "
692 logger.info("Chimera REST service listening on port " + chimeraRestPort);
697 * Determine the color that Chimera is using for this model.
700 * the ChimeraModel we want to get the Color for
701 * @return the default model Color for this model in Chimera
703 public Color getModelColor(ChimeraModel model)
705 List<String> colorLines = sendChimeraCommand(
706 "list model spec " + model.toSpec() + " attribute color", true);
707 if (colorLines == null || colorLines.size() == 0)
711 return ChimUtils.parseModelColor(colorLines.get(0));
716 * Get information about the residues associated with a model. This uses the
717 * Chimera listr command. We don't return the resulting residues, but we add
718 * the residues to the model.
721 * the ChimeraModel to get residue information for
724 public void addResidues(ChimeraModel model)
726 int modelNumber = model.getModelNumber();
727 int subModelNumber = model.getSubModelNumber();
728 // Get the list -- it will be in the reply log
729 List<String> reply = sendChimeraCommand(
730 "list residues spec " + model.toSpec(), true);
735 for (String inputLine : reply)
737 ChimeraResidue r = new ChimeraResidue(inputLine);
738 if (r.getModelNumber() == modelNumber
739 || r.getSubModelNumber() == subModelNumber)
746 public List<String> getAttrList()
748 List<String> attributes = new ArrayList<>();
749 String command = (isChimeraX ? "info " : "list") + "resattr";
750 final List<String> reply = sendChimeraCommand(command, true);
753 for (String inputLine : reply)
755 String[] lineParts = inputLine.split("\\s");
756 if (lineParts.length == 2 && lineParts[0].equals("resattr"))
758 attributes.add(lineParts[1]);
765 public Map<ChimeraResidue, Object> getAttrValues(String aCommand,
768 Map<ChimeraResidue, Object> values = new HashMap<>();
769 final List<String> reply = sendChimeraCommand("list residue spec "
770 + model.toSpec() + " attribute " + aCommand, true);
773 for (String inputLine : reply)
775 String[] lineParts = inputLine.split("\\s");
776 if (lineParts.length == 5)
778 ChimeraResidue residue = ChimUtils
779 .getResidue(lineParts[2], model);
780 String value = lineParts[4];
783 if (value.equals("None"))
787 if (value.equals("True") || value.equals("False"))
789 values.put(residue, Boolean.valueOf(value));
794 Double doubleValue = Double.valueOf(value);
795 values.put(residue, doubleValue);
796 } catch (NumberFormatException ex)
798 values.put(residue, value);
807 private volatile boolean busy = false;
809 private boolean isChimeraX;
812 * Send a command to Chimera.
815 * Command string to be send.
817 * Flag indicating whether the method should return the reply from
819 * @return List of Strings corresponding to the lines in the Chimera reply or
822 public List<String> sendChimeraCommand(String command, boolean reply)
824 System.out.println("chimeradebug>> " + command);
825 if (!isChimeraLaunched() || command == null
826 || "".equals(command.trim()))
830 // TODO do we need a maximum wait time before aborting?
836 } catch (InterruptedException q)
841 long startTime = System.currentTimeMillis();
844 return sendRestCommand(command);
848 * Make sure busy flag is reset come what may!
853 System.out.println("Chimera command took "
854 + (System.currentTimeMillis() - startTime) + "ms: "
862 * Sends the command to Chimera's REST API, and returns any response lines.
867 protected List<String> sendRestCommand(String command)
869 String restUrl = "http://127.0.0.1:" + this.chimeraRestPort + "/run";
870 List<NameValuePair> commands = new ArrayList<>(1);
871 String encoded = command.replace(" ", "+").replace("#", "%23")
872 .replace("|", "%7C").replace(";", "%3B");
873 commands.add(new BasicNameValuePair("command", encoded));
875 List<String> reply = new ArrayList<>();
876 BufferedReader response = null;
881 response = HttpClientUtils.doHttpGet(restUrl, commands,
882 CONNECTION_TIMEOUT_MS, REST_REPLY_TIMEOUT_MS);
886 response = HttpClientUtils.doHttpUrlPost(restUrl, commands,
887 CONNECTION_TIMEOUT_MS, REST_REPLY_TIMEOUT_MS);
890 while ((line = response.readLine()) != null)
894 } catch (Exception e)
896 logger.error("REST call '" + command + "' failed: " + e.getMessage());
899 if (response != null)
904 } catch (IOException e)
913 * Send a command to stdin of Chimera process, and optionally read any
920 protected List<String> sendStdinCommand(String command, boolean readReply)
922 chimeraListenerThread.clearResponse(command);
923 String text = command.concat("\n");
927 chimera.getOutputStream().write(text.getBytes());
928 chimera.getOutputStream().flush();
929 } catch (IOException e)
931 // logger.info("Unable to execute command: " + text);
932 // logger.info("Exiting...");
933 logger.warn("Unable to execute command: " + text);
934 logger.warn("Exiting...");
935 clearOnChimeraExit();
942 List<String> rsp = chimeraListenerThread.getResponse(command);
946 public StructureManager getStructureManager()
948 return structureManager;
951 public boolean isBusy()
956 public Process getChimeraProcess()
961 public boolean isChimeraX()
966 public void setChimeraX(boolean b)