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 int REST_REPLY_TIMEOUT_MS = 15000;
32 private static final int CONNECTION_TIMEOUT_MS = 100;
34 private static final boolean debug = false;
36 private int chimeraRestPort;
38 private Process chimera;
40 private ListenerThreads chimeraListenerThread;
42 private Map<Integer, ChimeraModel> currentModelsMap;
44 private Logger logger = LoggerFactory
45 .getLogger(ext.edu.ucsf.rbvi.strucviz2.ChimeraManager.class);
47 private StructureManager structureManager;
49 public ChimeraManager(StructureManager structureManager)
51 this.structureManager = structureManager;
53 chimeraListenerThread = null;
54 currentModelsMap = new HashMap<Integer, ChimeraModel>();
58 public List<ChimeraModel> getChimeraModels(String modelName)
60 List<ChimeraModel> models = getChimeraModels(modelName,
62 models.addAll(getChimeraModels(modelName, ModelType.SMILES));
66 public List<ChimeraModel> getChimeraModels(String modelName,
69 List<ChimeraModel> models = new ArrayList<ChimeraModel>();
70 for (ChimeraModel model : currentModelsMap.values())
72 if (modelName.equals(model.getModelName())
73 && modelType.equals(model.getModelType()))
81 public Map<String, List<ChimeraModel>> getChimeraModelsMap()
83 Map<String, List<ChimeraModel>> models = new HashMap<String, List<ChimeraModel>>();
84 for (ChimeraModel model : currentModelsMap.values())
86 String modelName = model.getModelName();
87 if (!models.containsKey(modelName))
89 models.put(modelName, new ArrayList<ChimeraModel>());
91 if (!models.get(modelName).contains(model))
93 models.get(modelName).add(model);
99 public ChimeraModel getChimeraModel(Integer modelNumber,
100 Integer subModelNumber)
102 Integer key = ChimUtils.makeModelKey(modelNumber, subModelNumber);
103 if (currentModelsMap.containsKey(key))
105 return currentModelsMap.get(key);
110 public ChimeraModel getChimeraModel()
112 return currentModelsMap.values().iterator().next();
115 public Collection<ChimeraModel> getChimeraModels()
117 // this method is invoked by the model navigator dialog
118 return currentModelsMap.values();
121 public int getChimeraModelsCount(boolean smiles)
123 // this method is invokes by the model navigator dialog
124 int counter = currentModelsMap.size();
130 for (ChimeraModel model : currentModelsMap.values())
132 if (model.getModelType() == ModelType.SMILES)
140 public boolean hasChimeraModel(Integer modelNubmer)
142 return hasChimeraModel(modelNubmer, 0);
145 public boolean hasChimeraModel(Integer modelNubmer, Integer subModelNumber)
147 return currentModelsMap.containsKey(ChimUtils.makeModelKey(modelNubmer,
151 public void addChimeraModel(Integer modelNumber, Integer subModelNumber,
154 currentModelsMap.put(
155 ChimUtils.makeModelKey(modelNumber, subModelNumber), model);
158 public void removeChimeraModel(Integer modelNumber, Integer subModelNumber)
160 int modelKey = ChimUtils.makeModelKey(modelNumber, subModelNumber);
161 if (currentModelsMap.containsKey(modelKey))
163 currentModelsMap.remove(modelKey);
167 public List<ChimeraModel> openModel(String modelPath, ModelType type)
169 return openModel(modelPath, getFileNameFromPath(modelPath), type);
173 * Overloaded method to allow Jalview to pass in a model name.
180 public List<ChimeraModel> openModel(String modelPath, String modelName,
183 logger.info("chimera open " + modelPath);
185 List<ChimeraModel> modelList = getModelList();
186 List<String> response = null;
187 // TODO: [Optional] Handle modbase models
188 if (type == ModelType.MODBASE_MODEL)
190 response = sendChimeraCommand("open modbase:" + modelPath, true);
191 // } else if (type == ModelType.SMILES) {
192 // response = sendChimeraCommand("open smiles:" + modelName, true);
193 // modelName = "smiles:" + modelName;
197 response = sendChimeraCommand("open " + modelPath, true);
199 if (response == null)
201 // something went wrong
202 logger.warn("Could not open " + modelPath);
206 // patch for Jalview - set model name in Chimera
207 // TODO: find a variant that works for sub-models
208 for (ChimeraModel newModel : getModelList())
210 if (!modelList.contains(newModel))
212 newModel.setModelName(modelName);
214 "setattr M name " + modelName + " #"
215 + newModel.getModelNumber(), false);
216 modelList.add(newModel);
220 // assign color and residues to open models
221 for (ChimeraModel chimeraModel : modelList)
224 Color modelColor = getModelColor(chimeraModel);
225 if (modelColor != null)
227 chimeraModel.setModelColor(modelColor);
230 // Get our properties (default color scheme, etc.)
231 // Make the molecule look decent
232 // chimeraSend("repr stick "+newModel.toSpec());
234 // Create the information we need for the navigator
235 if (type != ModelType.SMILES)
237 addResidues(chimeraModel);
241 sendChimeraCommand("focus", false);
242 // startListening(); // see ChimeraListener
247 * Refactored method to extract the last (or only) element delimited by file
253 private String getFileNameFromPath(String modelPath)
255 String modelName = modelPath;
256 if (modelPath == null)
260 // TODO: [Optional] Convert path to name in a better way
261 if (modelPath.lastIndexOf(File.separator) > 0)
263 modelName = modelPath
264 .substring(modelPath.lastIndexOf(File.separator) + 1);
266 else if (modelPath.lastIndexOf("/") > 0)
268 modelName = modelPath.substring(modelPath.lastIndexOf("/") + 1);
273 public void closeModel(ChimeraModel model)
275 // int model = structure.modelNumber();
276 // int subModel = structure.subModelNumber();
277 // Integer modelKey = makeModelKey(model, subModel);
279 logger.info("chimera close model " + model.getModelName());
280 if (currentModelsMap.containsKey(ChimUtils.makeModelKey(
281 model.getModelNumber(), model.getSubModelNumber())))
283 sendChimeraCommand("close " + model.toSpec(), false);
284 // currentModelNamesMap.remove(model.getModelName());
285 currentModelsMap.remove(ChimUtils.makeModelKey(
286 model.getModelNumber(), model.getSubModelNumber()));
287 // selectionList.remove(chimeraModel);
291 logger.warn("Could not find model " + model.getModelName()
297 public void startListening()
299 sendChimeraCommand("listen start models; listen start selection", false);
302 public void stopListening()
304 sendChimeraCommand("listen stop models ; listen stop selection ", false);
308 * Tell Chimera we are listening on the given URI
312 public void startListening(String uri)
314 sendChimeraCommand("listen start models url " + uri
315 + ";listen start select prefix SelectionChanged url " + uri,
320 * Select something in Chimera
323 * the selection command to pass to Chimera
325 public void select(String command)
327 sendChimeraCommand("listen stop selection; " + command
328 + "; listen start selection", false);
333 sendChimeraCommand("focus", false);
336 public void clearOnChimeraExit()
339 currentModelsMap.clear();
340 this.chimeraRestPort = 0;
341 structureManager.clearOnChimeraExit();
344 public void exitChimera()
346 if (isChimeraLaunched() && chimera != null)
348 sendChimeraCommand("stop really", false);
352 } catch (Exception ex)
357 clearOnChimeraExit();
360 public Map<Integer, ChimeraModel> getSelectedModels()
362 Map<Integer, ChimeraModel> selectedModelsMap = new HashMap<Integer, ChimeraModel>();
363 List<String> chimeraReply = sendChimeraCommand(
364 "list selection level molecule", true);
365 if (chimeraReply != null)
367 for (String modelLine : chimeraReply)
369 ChimeraModel chimeraModel = new ChimeraModel(modelLine);
370 Integer modelKey = ChimUtils.makeModelKey(
371 chimeraModel.getModelNumber(),
372 chimeraModel.getSubModelNumber());
373 selectedModelsMap.put(modelKey, chimeraModel);
376 return selectedModelsMap;
380 * Sends a 'list selection level residue' command to Chimera and returns the
381 * list of selected atomspecs
385 public List<String> getSelectedResidueSpecs()
387 List<String> selectedResidues = new ArrayList<String>();
388 List<String> chimeraReply = sendChimeraCommand(
389 "list selection level residue", true);
390 if (chimeraReply != null)
392 for (String inputLine : chimeraReply)
394 String[] inputLineParts = inputLine.split("\\s+");
395 if (inputLineParts.length == 5)
397 selectedResidues.add(inputLineParts[2]);
401 return selectedResidues;
404 public void getSelectedResidues(
405 Map<Integer, ChimeraModel> selectedModelsMap)
407 List<String> chimeraReply = sendChimeraCommand(
408 "list selection level residue", true);
409 if (chimeraReply != null)
411 for (String inputLine : chimeraReply)
413 ChimeraResidue r = new ChimeraResidue(inputLine);
414 Integer modelKey = ChimUtils.makeModelKey(r.getModelNumber(),
415 r.getSubModelNumber());
416 if (selectedModelsMap.containsKey(modelKey))
418 ChimeraModel model = selectedModelsMap.get(modelKey);
426 * Return the list of ChimeraModels currently open. Warning: if smiles model
427 * name too long, only part of it with "..." is printed.
430 * @return List of ChimeraModel's
432 // TODO: [Optional] Handle smiles names in a better way in Chimera?
433 public List<ChimeraModel> getModelList()
435 List<ChimeraModel> modelList = new ArrayList<ChimeraModel>();
436 List<String> list = sendChimeraCommand("list models type molecule",
440 for (String modelLine : list)
442 ChimeraModel chimeraModel = new ChimeraModel(modelLine);
443 modelList.add(chimeraModel);
450 * Return the list of depiction presets available from within Chimera. Chimera
451 * will return the list as a series of lines with the format: Preset type
452 * number "description"
454 * @return list of presets
456 public List<String> getPresets()
458 ArrayList<String> presetList = new ArrayList<String>();
459 List<String> output = sendChimeraCommand("preset list", true);
462 for (String preset : output)
464 preset = preset.substring(7); // Skip over the "Preset"
465 preset = preset.replaceFirst("\"", "(");
466 preset = preset.replaceFirst("\"", ")");
467 // string now looks like: type number (description)
468 presetList.add(preset);
474 public boolean isChimeraLaunched()
476 boolean launched = false;
482 // if we get here, process has ended
483 } catch (IllegalThreadStateException e)
485 // ok - not yet terminated
493 * Launch Chimera, unless an instance linked to this object is already
494 * running. Returns true if chimera is successfully launched, or already
495 * running, else false.
497 * @param chimeraPaths
500 public boolean launchChimera(List<String> chimeraPaths)
502 // Do nothing if Chimera is already launched
503 if (isChimeraLaunched())
508 // Try to launch Chimera (eventually using one of the possible paths)
509 String error = "Error message: ";
510 String workingPath = "";
511 // iterate over possible paths for starting Chimera
512 for (String chimeraPath : chimeraPaths)
514 File path = new File(chimeraPath);
515 // uncomment the next line to simulate Chimera not installed
516 // path = new File(chimeraPath + "x");
517 if (!path.canExecute())
519 error += "File '" + path + "' does not exist.\n";
524 List<String> args = new ArrayList<String>();
525 args.add(chimeraPath);
526 // shows Chimera output window but suppresses REST responses:
527 // args.add("--debug");
529 args.add("RESTServer");
530 ProcessBuilder pb = new ProcessBuilder(args);
531 chimera = pb.start();
533 workingPath = chimeraPath;
535 } catch (Exception e)
537 // Chimera could not be started
538 error += e.getMessage();
541 // If no error, then Chimera was launched successfully
542 if (error.length() == 0)
544 this.chimeraRestPort = getPortNumber();
545 System.out.println("Chimera REST API started on port "
547 // structureManager.initChimTable();
548 structureManager.setChimeraPathProperty(workingPath);
549 // TODO: [Optional] Check Chimera version and show a warning if below 1.8
550 // Ask Chimera to give us updates
551 // startListening(); // later - see ChimeraListener
552 return (chimeraRestPort > 0);
555 // Tell the user that Chimera could not be started because of an error
561 * Read and return the port number returned in the reply to --start RESTServer
563 private int getPortNumber()
566 InputStream readChan = chimera.getInputStream();
567 BufferedReader lineReader = new BufferedReader(new InputStreamReader(
569 StringBuilder responses = new StringBuilder();
572 String response = lineReader.readLine();
573 while (response != null)
575 responses.append("\n" + response);
576 // expect: REST server on host 127.0.0.1 port port_number
577 if (response.startsWith("REST server"))
579 String[] tokens = response.split(" ");
580 if (tokens.length == 7 && "port".equals(tokens[5]))
582 port = Integer.parseInt(tokens[6]);
586 response = lineReader.readLine();
588 } catch (Exception e)
590 logger.error("Failed to get REST port number from " + responses
591 + ": " + e.getMessage());
597 } catch (IOException e2)
604 .println("Failed to start Chimera with REST service, response was: "
607 logger.info("Chimera REST service listening on port " + chimeraRestPort);
612 * Determine the color that Chimera is using for this model.
615 * the ChimeraModel we want to get the Color for
616 * @return the default model Color for this model in Chimera
618 public Color getModelColor(ChimeraModel model)
620 List<String> colorLines = sendChimeraCommand(
621 "list model spec " + model.toSpec() + " attribute color", true);
622 if (colorLines == null || colorLines.size() == 0)
626 return ChimUtils.parseModelColor(colorLines.get(0));
631 * Get information about the residues associated with a model. This uses the
632 * Chimera listr command. We don't return the resulting residues, but we add
633 * the residues to the model.
636 * the ChimeraModel to get residue information for
639 public void addResidues(ChimeraModel model)
641 int modelNumber = model.getModelNumber();
642 int subModelNumber = model.getSubModelNumber();
643 // Get the list -- it will be in the reply log
644 List<String> reply = sendChimeraCommand(
645 "list residues spec " + model.toSpec(), true);
650 for (String inputLine : reply)
652 ChimeraResidue r = new ChimeraResidue(inputLine);
653 if (r.getModelNumber() == modelNumber
654 || r.getSubModelNumber() == subModelNumber)
661 public List<String> getAttrList()
663 List<String> attributes = new ArrayList<String>();
664 final List<String> reply = sendChimeraCommand("list resattr", true);
667 for (String inputLine : reply)
669 String[] lineParts = inputLine.split("\\s");
670 if (lineParts.length == 2 && lineParts[0].equals("resattr"))
672 attributes.add(lineParts[1]);
679 public Map<ChimeraResidue, Object> getAttrValues(String aCommand,
682 Map<ChimeraResidue, Object> values = new HashMap<ChimeraResidue, Object>();
683 final List<String> reply = sendChimeraCommand("list residue spec "
684 + model.toSpec() + " attribute " + aCommand, true);
687 for (String inputLine : reply)
689 String[] lineParts = inputLine.split("\\s");
690 if (lineParts.length == 5)
692 ChimeraResidue residue = ChimUtils
693 .getResidue(lineParts[2], model);
694 String value = lineParts[4];
697 if (value.equals("None"))
701 if (value.equals("True") || value.equals("False"))
703 values.put(residue, Boolean.valueOf(value));
708 Double doubleValue = Double.valueOf(value);
709 values.put(residue, doubleValue);
710 } catch (NumberFormatException ex)
712 values.put(residue, value);
721 private volatile boolean busy = false;
724 * Send a command to Chimera.
727 * Command string to be send.
729 * Flag indicating whether the method should return the reply from
731 * @return List of Strings corresponding to the lines in the Chimera reply or
734 public List<String> sendChimeraCommand(String command, boolean reply)
736 // System.out.println("chimeradebug>> " + command);
737 if (!isChimeraLaunched() || command == null
738 || "".equals(command.trim()))
742 // TODO do we need a maximum wait time before aborting?
748 } catch (InterruptedException q)
753 long startTime = System.currentTimeMillis();
756 return sendRestCommand(command);
760 * Make sure busy flag is reset come what may!
765 System.out.println("Chimera command took "
766 + (System.currentTimeMillis() - startTime) + "ms: "
774 * Sends the command to Chimera's REST API, and returns any response lines.
779 protected List<String> sendRestCommand(String command)
781 String restUrl = "http://127.0.0.1:" + this.chimeraRestPort + "/run";
782 List<NameValuePair> commands = new ArrayList<NameValuePair>(1);
783 commands.add(new BasicNameValuePair("command", command));
785 List<String> reply = new ArrayList<String>();
786 BufferedReader response = null;
789 response = HttpClientUtils.doHttpUrlPost(restUrl, commands, CONNECTION_TIMEOUT_MS,
790 REST_REPLY_TIMEOUT_MS);
792 while ((line = response.readLine()) != null)
796 } catch (Exception e)
798 logger.error("REST call '" + command + "' failed: " + e.getMessage());
801 if (response != null)
806 } catch (IOException e)
815 * Send a command to stdin of Chimera process, and optionally read any
822 protected List<String> sendStdinCommand(String command, boolean readReply)
824 chimeraListenerThread.clearResponse(command);
825 String text = command.concat("\n");
829 chimera.getOutputStream().write(text.getBytes());
830 chimera.getOutputStream().flush();
831 } catch (IOException e)
833 // logger.info("Unable to execute command: " + text);
834 // logger.info("Exiting...");
835 logger.warn("Unable to execute command: " + text);
836 logger.warn("Exiting...");
837 clearOnChimeraExit();
844 List<String> rsp = chimeraListenerThread.getResponse(command);
848 public StructureManager getStructureManager()
850 return structureManager;
853 public boolean isBusy()