1 package ext.edu.ucsf.rbvi.strucviz2;
3 import jalview.ws.HttpClientUtils;
6 import java.io.BufferedReader;
8 import java.io.IOException;
9 import java.io.InputStream;
10 import java.io.InputStreamReader;
11 import java.util.ArrayList;
12 import java.util.Collection;
13 import java.util.HashMap;
14 import java.util.List;
17 import org.apache.http.NameValuePair;
18 import org.apache.http.message.BasicNameValuePair;
19 import org.slf4j.Logger;
20 import org.slf4j.LoggerFactory;
22 import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
23 import ext.edu.ucsf.rbvi.strucviz2.port.ListenerThreads;
26 * This object maintains the Chimera communication information.
28 public class ChimeraManager
30 private static final boolean debug = false;
32 private int chimeraRestPort;
34 private Process chimera;
36 private ListenerThreads chimeraListenerThread;
38 private Map<Integer, ChimeraModel> currentModelsMap;
40 private Logger logger = LoggerFactory
41 .getLogger(ext.edu.ucsf.rbvi.strucviz2.ChimeraManager.class);
43 private StructureManager structureManager;
45 public ChimeraManager(StructureManager structureManager)
47 this.structureManager = structureManager;
49 chimeraListenerThread = null;
50 currentModelsMap = new HashMap<Integer, ChimeraModel>();
54 public List<ChimeraModel> getChimeraModels(String modelName)
56 List<ChimeraModel> models = getChimeraModels(modelName,
58 models.addAll(getChimeraModels(modelName, ModelType.SMILES));
62 public List<ChimeraModel> getChimeraModels(String modelName,
65 List<ChimeraModel> models = new ArrayList<ChimeraModel>();
66 for (ChimeraModel model : currentModelsMap.values())
68 if (modelName.equals(model.getModelName())
69 && modelType.equals(model.getModelType()))
77 public Map<String, List<ChimeraModel>> getChimeraModelsMap()
79 Map<String, List<ChimeraModel>> models = new HashMap<String, List<ChimeraModel>>();
80 for (ChimeraModel model : currentModelsMap.values())
82 String modelName = model.getModelName();
83 if (!models.containsKey(modelName))
85 models.put(modelName, new ArrayList<ChimeraModel>());
87 if (!models.get(modelName).contains(model))
89 models.get(modelName).add(model);
95 public ChimeraModel getChimeraModel(Integer modelNumber,
96 Integer subModelNumber)
98 Integer key = ChimUtils.makeModelKey(modelNumber, subModelNumber);
99 if (currentModelsMap.containsKey(key))
101 return currentModelsMap.get(key);
106 public ChimeraModel getChimeraModel()
108 return currentModelsMap.values().iterator().next();
111 public Collection<ChimeraModel> getChimeraModels()
113 // this method is invoked by the model navigator dialog
114 return currentModelsMap.values();
117 public int getChimeraModelsCount(boolean smiles)
119 // this method is invokes by the model navigator dialog
120 int counter = currentModelsMap.size();
126 for (ChimeraModel model : currentModelsMap.values())
128 if (model.getModelType() == ModelType.SMILES)
136 public boolean hasChimeraModel(Integer modelNubmer)
138 return hasChimeraModel(modelNubmer, 0);
141 public boolean hasChimeraModel(Integer modelNubmer, Integer subModelNumber)
143 return currentModelsMap.containsKey(ChimUtils.makeModelKey(modelNubmer,
147 public void addChimeraModel(Integer modelNumber, Integer subModelNumber,
150 currentModelsMap.put(
151 ChimUtils.makeModelKey(modelNumber, subModelNumber), model);
154 public void removeChimeraModel(Integer modelNumber, Integer subModelNumber)
156 int modelKey = ChimUtils.makeModelKey(modelNumber, subModelNumber);
157 if (currentModelsMap.containsKey(modelKey))
159 currentModelsMap.remove(modelKey);
163 public List<ChimeraModel> openModel(String modelPath, ModelType type)
165 return openModel(modelPath, getFileNameFromPath(modelPath), type);
169 * Overloaded method to allow Jalview to pass in a model name.
176 public List<ChimeraModel> openModel(String modelPath, String modelName,
179 logger.info("chimera open " + modelPath);
181 List<ChimeraModel> modelList = getModelList();
182 List<String> response = null;
183 // TODO: [Optional] Handle modbase models
184 if (type == ModelType.MODBASE_MODEL)
186 response = sendChimeraCommand("open modbase:" + modelPath, true);
187 // } else if (type == ModelType.SMILES) {
188 // response = sendChimeraCommand("open smiles:" + modelName, true);
189 // modelName = "smiles:" + modelName;
193 response = sendChimeraCommand("open " + modelPath, true);
195 if (response == null)
197 // something went wrong
198 logger.warn("Could not open " + modelPath);
202 // patch for Jalview - set model name in Chimera
203 // TODO: find a variant that works for sub-models
204 for (ChimeraModel newModel : getModelList())
206 if (!modelList.contains(newModel))
208 newModel.setModelName(modelName);
210 "setattr M name " + modelName + " #"
211 + newModel.getModelNumber(), false);
212 modelList.add(newModel);
216 // assign color and residues to open models
217 for (ChimeraModel chimeraModel : modelList)
220 Color modelColor = getModelColor(chimeraModel);
221 if (modelColor != null)
223 chimeraModel.setModelColor(modelColor);
226 // Get our properties (default color scheme, etc.)
227 // Make the molecule look decent
228 // chimeraSend("repr stick "+newModel.toSpec());
230 // Create the information we need for the navigator
231 if (type != ModelType.SMILES)
233 addResidues(chimeraModel);
237 sendChimeraCommand("focus", false);
238 // startListening(); // see ChimeraListener
243 * Refactored method to extract the last (or only) element delimited by file
249 private String getFileNameFromPath(String modelPath)
251 String modelName = modelPath;
252 if (modelPath == null)
256 // TODO: [Optional] Convert path to name in a better way
257 if (modelPath.lastIndexOf(File.separator) > 0)
259 modelName = modelPath
260 .substring(modelPath.lastIndexOf(File.separator) + 1);
262 else if (modelPath.lastIndexOf("/") > 0)
264 modelName = modelPath.substring(modelPath.lastIndexOf("/") + 1);
269 public void closeModel(ChimeraModel model)
271 // int model = structure.modelNumber();
272 // int subModel = structure.subModelNumber();
273 // Integer modelKey = makeModelKey(model, subModel);
275 logger.info("chimera close model " + model.getModelName());
276 if (currentModelsMap.containsKey(ChimUtils.makeModelKey(
277 model.getModelNumber(), model.getSubModelNumber())))
279 sendChimeraCommand("close " + model.toSpec(), false);
280 // currentModelNamesMap.remove(model.getModelName());
281 currentModelsMap.remove(ChimUtils.makeModelKey(
282 model.getModelNumber(), model.getSubModelNumber()));
283 // selectionList.remove(chimeraModel);
287 logger.warn("Could not find model " + model.getModelName()
293 public void startListening()
295 sendChimeraCommand("listen start models; listen start selection", false);
298 public void stopListening()
300 sendChimeraCommand("listen stop models ; listen stop selection ", false);
304 * Tell Chimera we are listening on the given URI
308 public void startListening(String uri)
310 sendChimeraCommand("listen start models url " + uri
311 + ";listen start select prefix SelectionChanged url " + uri,
316 * Select something in Chimera
319 * the selection command to pass to Chimera
321 public void select(String command)
323 sendChimeraCommand("listen stop selection; " + command
324 + "; listen start selection", false);
329 sendChimeraCommand("focus", false);
332 public void clearOnChimeraExit()
335 currentModelsMap.clear();
336 this.chimeraRestPort = 0;
337 structureManager.clearOnChimeraExit();
340 public void exitChimera()
342 if (isChimeraLaunched() && chimera != null)
344 sendChimeraCommand("stop really", false);
348 } catch (Exception ex)
353 clearOnChimeraExit();
356 public Map<Integer, ChimeraModel> getSelectedModels()
358 Map<Integer, ChimeraModel> selectedModelsMap = new HashMap<Integer, ChimeraModel>();
359 List<String> chimeraReply = sendChimeraCommand(
360 "list selection level molecule", true);
361 if (chimeraReply != null)
363 for (String modelLine : chimeraReply)
365 ChimeraModel chimeraModel = new ChimeraModel(modelLine);
366 Integer modelKey = ChimUtils.makeModelKey(
367 chimeraModel.getModelNumber(),
368 chimeraModel.getSubModelNumber());
369 selectedModelsMap.put(modelKey, chimeraModel);
372 return selectedModelsMap;
376 * Sends a 'list selection level residue' command to Chimera and returns the
377 * list of selected atomspecs
381 public List<String> getSelectedResidueSpecs()
383 List<String> selectedResidues = new ArrayList<String>();
384 List<String> chimeraReply = sendChimeraCommand(
385 "list selection level residue", true);
386 if (chimeraReply != null)
388 for (String inputLine : chimeraReply)
390 String[] inputLineParts = inputLine.split("\\s+");
391 if (inputLineParts.length == 5)
393 selectedResidues.add(inputLineParts[2]);
397 return selectedResidues;
400 public void getSelectedResidues(
401 Map<Integer, ChimeraModel> selectedModelsMap)
403 List<String> chimeraReply = sendChimeraCommand(
404 "list selection level residue", true);
405 if (chimeraReply != null)
407 for (String inputLine : chimeraReply)
409 ChimeraResidue r = new ChimeraResidue(inputLine);
410 Integer modelKey = ChimUtils.makeModelKey(r.getModelNumber(),
411 r.getSubModelNumber());
412 if (selectedModelsMap.containsKey(modelKey))
414 ChimeraModel model = selectedModelsMap.get(modelKey);
422 * Return the list of ChimeraModels currently open. Warning: if smiles model
423 * name too long, only part of it with "..." is printed.
426 * @return List of ChimeraModel's
428 // TODO: [Optional] Handle smiles names in a better way in Chimera?
429 public List<ChimeraModel> getModelList()
431 List<ChimeraModel> modelList = new ArrayList<ChimeraModel>();
432 List<String> list = sendChimeraCommand("list models type molecule",
436 for (String modelLine : list)
438 ChimeraModel chimeraModel = new ChimeraModel(modelLine);
439 modelList.add(chimeraModel);
446 * Return the list of depiction presets available from within Chimera. Chimera
447 * will return the list as a series of lines with the format: Preset type
448 * number "description"
450 * @return list of presets
452 public List<String> getPresets()
454 ArrayList<String> presetList = new ArrayList<String>();
455 List<String> output = sendChimeraCommand("preset list", true);
458 for (String preset : output)
460 preset = preset.substring(7); // Skip over the "Preset"
461 preset = preset.replaceFirst("\"", "(");
462 preset = preset.replaceFirst("\"", ")");
463 // string now looks like: type number (description)
464 presetList.add(preset);
470 public boolean isChimeraLaunched()
472 boolean launched = false;
478 // if we get here, process has ended
479 } catch (IllegalThreadStateException e)
481 // ok - not yet terminated
489 * Launch Chimera, unless an instance linked to this object is already
490 * running. Returns true if chimera is successfully launched, or already
491 * running, else false.
493 * @param chimeraPaths
496 public boolean launchChimera(List<String> chimeraPaths)
498 // Do nothing if Chimera is already launched
499 if (isChimeraLaunched())
504 // Try to launch Chimera (eventually using one of the possible paths)
505 String error = "Error message: ";
506 String workingPath = "";
507 // iterate over possible paths for starting Chimera
508 for (String chimeraPath : chimeraPaths)
510 File path = new File(chimeraPath);
511 // uncomment the next line to simulate Chimera not installed
512 // path = new File(chimeraPath + "x");
513 if (!path.canExecute())
515 error += "File '" + path + "' does not exist.\n";
520 List<String> args = new ArrayList<String>();
521 args.add(chimeraPath);
522 // shows Chimera output window but suppresses REST responses:
523 // args.add("--debug");
525 args.add("RESTServer");
526 ProcessBuilder pb = new ProcessBuilder(args);
527 chimera = pb.start();
529 workingPath = chimeraPath;
531 } catch (Exception e)
533 // Chimera could not be started
534 error += e.getMessage();
537 // If no error, then Chimera was launched successfully
538 if (error.length() == 0)
540 this.chimeraRestPort = getPortNumber();
541 System.out.println("Chimera REST API started on port "
543 // structureManager.initChimTable();
544 structureManager.setChimeraPathProperty(workingPath);
545 // TODO: [Optional] Check Chimera version and show a warning if below 1.8
546 // Ask Chimera to give us updates
547 // startListening(); // later - see ChimeraListener
548 return (chimeraRestPort > 0);
551 // Tell the user that Chimera could not be started because of an error
557 * Read and return the port number returned in the reply to --start RESTServer
559 private int getPortNumber()
562 InputStream readChan = chimera.getInputStream();
563 BufferedReader lineReader = new BufferedReader(new InputStreamReader(
565 StringBuilder responses = new StringBuilder();
568 String response = lineReader.readLine();
569 while (response != null)
571 responses.append("\n" + response);
572 // expect: REST server on host 127.0.0.1 port port_number
573 if (response.startsWith("REST server"))
575 String[] tokens = response.split(" ");
576 if (tokens.length == 7 && "port".equals(tokens[5]))
578 port = Integer.parseInt(tokens[6]);
582 response = lineReader.readLine();
584 } catch (Exception e)
586 logger.error("Failed to get REST port number from " + responses
587 + ": " + e.getMessage());
593 } catch (IOException e2)
600 .println("Failed to start Chimera with REST service, response was: "
603 logger.info("Chimera REST service listening on port " + chimeraRestPort);
608 * Determine the color that Chimera is using for this model.
611 * the ChimeraModel we want to get the Color for
612 * @return the default model Color for this model in Chimera
614 public Color getModelColor(ChimeraModel model)
616 List<String> colorLines = sendChimeraCommand(
617 "list model spec " + model.toSpec() + " attribute color", true);
618 if (colorLines == null || colorLines.size() == 0)
622 return ChimUtils.parseModelColor(colorLines.get(0));
627 * Get information about the residues associated with a model. This uses the
628 * Chimera listr command. We don't return the resulting residues, but we add
629 * the residues to the model.
632 * the ChimeraModel to get residue information for
635 public void addResidues(ChimeraModel model)
637 int modelNumber = model.getModelNumber();
638 int subModelNumber = model.getSubModelNumber();
639 // Get the list -- it will be in the reply log
640 List<String> reply = sendChimeraCommand(
641 "list residues spec " + model.toSpec(), true);
646 for (String inputLine : reply)
648 ChimeraResidue r = new ChimeraResidue(inputLine);
649 if (r.getModelNumber() == modelNumber
650 || r.getSubModelNumber() == subModelNumber)
657 public List<String> getAttrList()
659 List<String> attributes = new ArrayList<String>();
660 final List<String> reply = sendChimeraCommand("list resattr", true);
663 for (String inputLine : reply)
665 String[] lineParts = inputLine.split("\\s");
666 if (lineParts.length == 2 && lineParts[0].equals("resattr"))
668 attributes.add(lineParts[1]);
675 public Map<ChimeraResidue, Object> getAttrValues(String aCommand,
678 Map<ChimeraResidue, Object> values = new HashMap<ChimeraResidue, Object>();
679 final List<String> reply = sendChimeraCommand("list residue spec "
680 + model.toSpec() + " attribute " + aCommand, true);
683 for (String inputLine : reply)
685 String[] lineParts = inputLine.split("\\s");
686 if (lineParts.length == 5)
688 ChimeraResidue residue = ChimUtils
689 .getResidue(lineParts[2], model);
690 String value = lineParts[4];
693 if (value.equals("None"))
697 if (value.equals("True") || value.equals("False"))
699 values.put(residue, Boolean.valueOf(value));
704 Double doubleValue = Double.valueOf(value);
705 values.put(residue, doubleValue);
706 } catch (NumberFormatException ex)
708 values.put(residue, value);
717 private volatile boolean busy = false;
720 * Send a command to Chimera.
723 * Command string to be send.
725 * Flag indicating whether the method should return the reply from
727 * @return List of Strings corresponding to the lines in the Chimera reply or
730 public List<String> sendChimeraCommand(String command, boolean reply)
732 // System.out.println("chimeradebug>> " + command);
733 if (!isChimeraLaunched() || command == null
734 || "".equals(command.trim()))
738 // TODO do we need a maximum wait time before aborting?
744 } catch (InterruptedException q)
749 long startTime = System.currentTimeMillis();
752 return sendRestCommand(command);
756 * Make sure busy flag is reset come what may!
761 System.out.println("Chimera command took "
762 + (System.currentTimeMillis() - startTime) + "ms: "
770 * Sends the command to Chimera's REST API, and returns any response lines.
775 protected List<String> sendRestCommand(String command)
777 String restUrl = "http://127.0.0.1:" + this.chimeraRestPort + "/run";
778 List<NameValuePair> commands = new ArrayList<NameValuePair>(1);
779 commands.add(new BasicNameValuePair("command", command));
781 List<String> reply = new ArrayList<String>();
782 BufferedReader response = null;
785 response = HttpClientUtils
786 .doHttpUrlPost(restUrl, commands, 100, 5000);
788 while ((line = response.readLine()) != null)
792 } catch (Exception e)
794 logger.error("REST call '" + command + "' failed: " + e.getMessage());
797 if (response != null)
802 } catch (IOException e)
811 * Send a command to stdin of Chimera process, and optionally read any
818 protected List<String> sendStdinCommand(String command, boolean readReply)
820 chimeraListenerThread.clearResponse(command);
821 String text = command.concat("\n");
825 chimera.getOutputStream().write(text.getBytes());
826 chimera.getOutputStream().flush();
827 } catch (IOException e)
829 // logger.info("Unable to execute command: " + text);
830 // logger.info("Exiting...");
831 logger.warn("Unable to execute command: " + text);
832 logger.warn("Exiting...");
833 clearOnChimeraExit();
840 List<String> rsp = chimeraListenerThread.getResponse(command);
844 public StructureManager getStructureManager()
846 return structureManager;
849 public boolean isBusy()