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  1. Project Clover database Tue Nov 18 2025 10:51:49 GMT
  2. Package jalview.ext.rbvi.chimera

File JalviewChimeraBinding.java

 

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60% of files have more coverage

Code metrics

78
204
28
1
814
497
82
0.4
7.29
28
2.93

Classes

Class Line # Actions
JalviewChimeraBinding 55 204 82
0.00%
 

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.ext.rbvi.chimera;
22   
23    import java.io.File;
24    import java.io.FileOutputStream;
25    import java.io.IOException;
26    import java.io.PrintWriter;
27    import java.net.BindException;
28    import java.util.ArrayList;
29    import java.util.Collections;
30    import java.util.LinkedHashMap;
31    import java.util.List;
32    import java.util.Map;
33   
34    import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
35    import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
36    import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
37    import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
38    import jalview.api.AlignmentViewPanel;
39    import jalview.bin.Console;
40    import jalview.datamodel.PDBEntry;
41    import jalview.datamodel.SearchResultMatchI;
42    import jalview.datamodel.SearchResultsI;
43    import jalview.datamodel.SequenceFeature;
44    import jalview.datamodel.SequenceI;
45    import jalview.gui.StructureViewer.ViewerType;
46    import jalview.httpserver.AbstractRequestHandler;
47    import jalview.io.DataSourceType;
48    import jalview.structure.AtomSpec;
49    import jalview.structure.AtomSpecModel;
50    import jalview.structure.StructureCommand;
51    import jalview.structure.StructureCommandI;
52    import jalview.structure.StructureSelectionManager;
53    import jalview.structures.models.AAStructureBindingModel;
54   
 
55    public abstract class JalviewChimeraBinding extends AAStructureBindingModel
56    {
57    public static final String CHIMERA_SESSION_EXTENSION = ".py";
58   
59    public static final String CHIMERA_FEATURE_GROUP = "Chimera";
60   
61    /*
62    * Object through which we talk to Chimera
63    */
64    private ChimeraManager chimeraManager;
65   
66    /*
67    * Object which listens to Chimera notifications
68    */
69    private AbstractRequestHandler chimeraListener;
70   
71    /*
72    * Map of ChimeraModel objects keyed by PDB full local file name
73    */
74    protected Map<String, List<ChimeraModel>> chimeraMaps = new LinkedHashMap<>();
75   
76    String lastHighlightCommand;
77   
78    /**
79    * Returns a model of the structure positions described by the Chimera format
80    * atomspec
81    *
82    * @param atomSpec
83    * @return
84    */
 
85  0 toggle protected AtomSpec parseAtomSpec(String atomSpec)
86    {
87  0 return AtomSpec.fromChimeraAtomspec(atomSpec);
88    }
89   
90    /**
91    * Open a PDB structure file in Chimera and set up mappings from Jalview.
92    *
93    * We check if the PDB model id is already loaded in Chimera, if so don't
94    * reopen it. This is the case if Chimera has opened a saved session file.
95    *
96    * @param pe
97    * @return
98    */
 
99  0 toggle public boolean openFile(PDBEntry pe)
100    {
101  0 String file = pe.getFile();
102  0 try
103    {
104  0 List<ChimeraModel> modelsToMap = new ArrayList<>();
105  0 List<ChimeraModel> oldList = chimeraManager.getModelList();
106  0 boolean alreadyOpen = false;
107   
108    /*
109    * If Chimera already has this model, don't reopen it, but do remap it.
110    */
111  0 for (ChimeraModel open : oldList)
112    {
113  0 if (open.getModelName().equals(pe.getId()))
114    {
115  0 alreadyOpen = true;
116  0 modelsToMap.add(open);
117    }
118    }
119   
120    /*
121    * If Chimera doesn't yet have this model, ask it to open it, and retrieve
122    * the model name(s) added by Chimera.
123    */
124  0 if (!alreadyOpen)
125    {
126  0 chimeraManager.openModel(file, pe.getId(), ModelType.PDB_MODEL);
127  0 addChimeraModel(pe, modelsToMap);
128    }
129   
130  0 chimeraMaps.put(file, modelsToMap);
131   
132  0 if (getSsm() != null)
133    {
134  0 getSsm().addStructureViewerListener(this);
135    }
136  0 return true;
137    } catch (Exception q)
138    {
139  0 log("Exception when trying to open model " + file + "\n"
140    + q.toString());
141  0 q.printStackTrace();
142    }
143  0 return false;
144    }
145   
146    /**
147    * Adds the ChimeraModel corresponding to the given PDBEntry, based on model
148    * name matching PDB id
149    *
150    * @param pe
151    * @param modelsToMap
152    */
 
153  0 toggle protected void addChimeraModel(PDBEntry pe,
154    List<ChimeraModel> modelsToMap)
155    {
156    /*
157    * Chimera: query for actual models and find the one with
158    * matching model name - already set in viewer.openModel()
159    */
160  0 List<ChimeraModel> newList = chimeraManager.getModelList();
161    // JAL-1728 newList.removeAll(oldList) does not work
162  0 for (ChimeraModel cm : newList)
163    {
164  0 if (cm.getModelName().equals(pe.getId()))
165    {
166  0 modelsToMap.add(cm);
167    }
168    }
169    }
170   
171    /**
172    * Constructor
173    *
174    * @param ssm
175    * @param pdbentry
176    * @param sequenceIs
177    * @param protocol
178    */
 
179  0 toggle public JalviewChimeraBinding(StructureSelectionManager ssm,
180    PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
181    DataSourceType protocol)
182    {
183  0 super(ssm, pdbentry, sequenceIs, protocol);
184  0 boolean chimeraX = ViewerType.CHIMERAX.equals(getViewerType());
185  0 chimeraManager = chimeraX
186    ? new ChimeraXManager(new StructureManager(true))
187    : new ChimeraManager(new StructureManager(true));
188  0 setStructureCommands(
189  0 chimeraX ? new ChimeraXCommands() : new ChimeraCommands());
190    }
191   
 
192  0 toggle @Override
193    protected ViewerType getViewerType()
194    {
195  0 return ViewerType.CHIMERA;
196    }
197   
198    /**
199    * Start a dedicated HttpServer to listen for Chimera notifications, and tell
200    * it to start listening
201    */
 
202  0 toggle public void startChimeraListener()
203    {
204  0 try
205    {
206  0 chimeraListener = new ChimeraListener(this);
207  0 startListening(chimeraListener.getUri());
208    } catch (BindException e)
209    {
210  0 jalview.bin.Console.errPrintln(
211    "Failed to start Chimera listener: " + e.getMessage());
212    }
213    }
214   
215    /**
216    * Close down the Jalview viewer and listener, and (optionally) the associated
217    * Chimera window.
218    */
 
219  0 toggle @Override
220    public void closeViewer(boolean closeChimera)
221    {
222  0 super.closeViewer(closeChimera);
223  0 if (this.chimeraListener != null)
224    {
225  0 chimeraListener.shutdown();
226  0 chimeraListener = null;
227    }
228   
229    /*
230    * the following call is added to avoid a stack trace error in Chimera
231    * after "stop really" is sent; Chimera > 1.14 will not need it; see also
232    * http://plato.cgl.ucsf.edu/trac/chimera/ticket/17597
233    */
234  0 if (closeChimera && (getViewerType() == ViewerType.CHIMERA))
235    {
236  0 chimeraManager.getChimeraProcess().destroy();
237    }
238   
239  0 chimeraManager.clearOnChimeraExit();
240  0 chimeraManager = null;
241    }
242   
243    /**
244    * Helper method to construct model spec in Chimera format:
245    * <ul>
246    * <li>#0 (#1 etc) for a PDB file with no sub-models</li>
247    * <li>#0.1 (#1.1 etc) for a PDB file with sub-models</li>
248    * <ul>
249    * Note for now we only ever choose the first of multiple models. This
250    * corresponds to the hard-coded Jmol equivalent (compare {1.1}). Refactor in
251    * future if there is a need to select specific sub-models.
252    *
253    * @param pdbfnum
254    * @return
255    */
 
256  0 toggle protected String getModelSpec(int pdbfnum)
257    {
258  0 if (pdbfnum < 0 || pdbfnum >= getPdbCount())
259    {
260  0 return "#" + pdbfnum; // temp hack for ChimeraX
261    }
262   
263    /*
264    * For now, the test for having sub-models is whether multiple Chimera
265    * models are mapped for the PDB file; the models are returned as a response
266    * to the Chimera command 'list models type molecule', see
267    * ChimeraManager.getModelList().
268    */
269  0 List<ChimeraModel> maps = chimeraMaps.get(getStructureFiles()[pdbfnum]);
270  0 boolean hasSubModels = maps != null && maps.size() > 1;
271  0 return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
272    }
273   
274    /**
275    * Launch Chimera, unless an instance linked to this object is already
276    * running. Returns true if Chimera is successfully launched, or already
277    * running, else false.
278    *
279    * @return
280    */
 
281  0 toggle public boolean launchChimera()
282    {
283  0 if (chimeraManager.isChimeraLaunched())
284    {
285  0 return true;
286    }
287   
288  0 boolean launched = chimeraManager.launchChimera(getChimeraPaths());
289  0 if (launched)
290    {
291  0 startExternalViewerMonitor(chimeraManager.getChimeraProcess());
292    }
293    else
294    {
295  0 log("Failed to launch Chimera!");
296    }
297  0 return launched;
298    }
299   
300    /**
301    * Returns a list of candidate paths to the Chimera program executable
302    *
303    * @return
304    */
 
305  0 toggle protected List<String> getChimeraPaths()
306    {
307  0 return StructureManager.getChimeraPaths(false);
308    }
309   
310    /**
311    * Answers true if the Chimera process is still running, false if ended or not
312    * started.
313    *
314    * @return
315    */
 
316  0 toggle @Override
317    public boolean isViewerRunning()
318    {
319  0 return chimeraManager != null && chimeraManager.isChimeraLaunched();
320    }
321   
322    /**
323    * Send a command to Chimera, and optionally log and return any responses.
324    *
325    * @param command
326    * @param getResponse
327    */
 
328  0 toggle @Override
329    public List<String> executeCommand(final StructureCommandI command,
330    boolean getResponse)
331    {
332  0 if (chimeraManager == null || command == null)
333    {
334    // ? thread running after viewer shut down
335  0 return null;
336    }
337  0 List<String> reply = null;
338    // trim command or it may never find a match in the replyLog!!
339  0 String cmd = command.getCommand().trim();
340  0 List<String> lastReply = chimeraManager.sendChimeraCommand(cmd,
341    getResponse);
342  0 if (getResponse)
343    {
344  0 reply = lastReply;
345  0 if (Console.isDebugEnabled())
346    {
347  0 Console.debug(
348    "Response from command ('" + cmd + "') was:\n" + lastReply);
349    }
350    }
351    else
352    {
353  0 if (Console.isDebugEnabled())
354    {
355  0 Console.debug("Command executed: " + cmd);
356    }
357    }
358   
359  0 return reply;
360    }
361   
 
362  0 toggle @Override
363    public synchronized String[] getStructureFiles()
364    {
365  0 if (chimeraManager == null)
366    {
367  0 return new String[0];
368    }
369   
370  0 return chimeraMaps.keySet()
371    .toArray(modelFileNames = new String[chimeraMaps.size()]);
372    }
373   
374    /**
375    * Construct and send a command to highlight zero, one or more atoms. We do
376    * this by sending an "rlabel" command to show the residue label at that
377    * position.
378    */
 
379  0 toggle @Override
380    public void highlightAtoms(List<AtomSpec> atoms)
381    {
382  0 if (atoms == null || atoms.size() == 0)
383    {
384  0 return;
385    }
386   
387  0 boolean forChimeraX = chimeraManager.isChimeraX();
388  0 StringBuilder cmd = new StringBuilder(128);
389  0 boolean first = true;
390  0 boolean found = false;
391   
392  0 for (AtomSpec atom : atoms)
393    {
394  0 int pdbResNum = atom.getPdbResNum();
395  0 String chain = atom.getChain();
396  0 String pdbfile = atom.getPdbFile();
397  0 List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
398  0 if (cms != null && !cms.isEmpty())
399    {
400  0 if (first)
401    {
402  0 cmd.append(forChimeraX ? "label #" : "rlabel #");
403    }
404    else
405    {
406  0 cmd.append(",");
407    }
408  0 first = false;
409  0 if (forChimeraX)
410    {
411  0 cmd.append(cms.get(0).getModelNumber()).append("/").append(chain)
412    .append(":").append(pdbResNum);
413    }
414    else
415    {
416  0 cmd.append(cms.get(0).getModelNumber()).append(":")
417    .append(pdbResNum);
418  0 if (!chain.equals(" ") && !forChimeraX)
419    {
420  0 cmd.append(".").append(chain);
421    }
422    }
423  0 found = true;
424    }
425    }
426  0 String command = cmd.toString();
427   
428    /*
429    * avoid repeated commands for the same residue
430    */
431  0 if (command.equals(lastHighlightCommand))
432    {
433  0 return;
434    }
435  0 if (!found)
436    {
437    // not a valid residue label command, so clear
438  0 cmd.setLength(0);
439    }
440    /*
441    * prepend with command
442    * to unshow the label for the previous residue
443    */
444  0 if (lastHighlightCommand != null)
445    {
446  0 cmd.insert(0, ";");
447  0 cmd.insert(0, lastHighlightCommand);
448  0 cmd.insert(0, "~");
449   
450    }
451  0 if (cmd.length() > 0)
452    {
453  0 executeCommand(true, null, new StructureCommand(cmd.toString()));
454    }
455   
456  0 if (found)
457    {
458  0 this.lastHighlightCommand = command;
459    }
460    }
461   
462    /**
463    * Query Chimera for its current selection, and highlight it on the alignment
464    */
 
465  0 toggle public void highlightChimeraSelection()
466    {
467    /*
468    * Ask Chimera for its current selection
469    */
470  0 StructureCommandI command = getCommandGenerator().getSelectedResidues();
471   
472  0 Runnable action = new Runnable()
473    {
 
474  0 toggle @Override
475    public void run()
476    {
477  0 List<String> chimeraReply = executeCommand(command, true);
478   
479  0 List<String> selectedResidues = new ArrayList<>();
480  0 if (chimeraReply != null)
481    {
482    /*
483    * expect 0, 1 or more lines of the format either
484    * Chimera:
485    * residue id #0:43.A type GLY
486    * ChimeraX:
487    * residue id /A:89 name THR index 88
488    * We are only interested in the atomspec (third token of the reply)
489    */
490  0 for (String inputLine : chimeraReply)
491    {
492  0 String[] inputLineParts = inputLine.split("\\s+");
493  0 if (inputLineParts.length >= 5)
494    {
495  0 selectedResidues.add(inputLineParts[2]);
496    }
497    }
498    }
499   
500    /*
501    * Parse model number, residue and chain for each selected position,
502    * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
503    */
504  0 List<AtomSpec> atomSpecs = convertStructureResiduesToAlignment(
505    selectedResidues);
506   
507    /*
508    * Broadcast the selection (which may be empty, if the user just cleared all
509    * selections)
510    */
511  0 getSsm().mouseOverStructure(atomSpecs);
512   
513    }
514    };
515  0 new Thread(action).start();
516    }
517   
518    /**
519    * Converts a list of Chimera(X) atomspecs to a list of AtomSpec representing
520    * the corresponding residues (if any) in Jalview
521    *
522    * @param structureSelection
523    * @return
524    */
 
525  0 toggle protected List<AtomSpec> convertStructureResiduesToAlignment(
526    List<String> structureSelection)
527    {
528  0 List<AtomSpec> atomSpecs = new ArrayList<>();
529  0 for (String atomSpec : structureSelection)
530    {
531  0 try
532    {
533  0 AtomSpec spec = parseAtomSpec(atomSpec);
534  0 String pdbfilename = getPdbFileForModel(spec.getModelNumber());
535  0 spec.setPdbFile(pdbfilename);
536  0 atomSpecs.add(spec);
537    } catch (IllegalArgumentException e)
538    {
539  0 Console.error("Failed to parse atomspec: " + atomSpec);
540    }
541    }
542  0 return atomSpecs;
543    }
544   
545    /**
546    * @param modelId
547    * @return
548    */
 
549  0 toggle protected String getPdbFileForModel(int modelId)
550    {
551    /*
552    * Work out the pdbfilename from the model number
553    */
554  0 String pdbfilename = modelFileNames[0];
555  0 findfileloop: for (String pdbfile : this.chimeraMaps.keySet())
556    {
557  0 for (ChimeraModel cm : chimeraMaps.get(pdbfile))
558    {
559  0 if (cm.getModelNumber() == modelId)
560    {
561  0 pdbfilename = pdbfile;
562  0 break findfileloop;
563    }
564    }
565    }
566  0 return pdbfilename;
567    }
568   
 
569  0 toggle private void log(String message)
570    {
571  0 jalview.bin.Console.errPrintln("## Chimera log: " + message);
572    }
573   
574    /**
575    * Constructs and send commands to Chimera to set attributes on residues for
576    * features visible in Jalview.
577    * <p>
578    * The syntax is: setattr r &lt;attName&gt; &lt;attValue&gt; &lt;atomSpec&gt;
579    * <p>
580    * For example: setattr r jv_chain "Ferredoxin-1, Chloroplastic" #0:94.A
581    *
582    * @param avp
583    * @return
584    */
 
585  0 toggle public int sendFeaturesToViewer(AlignmentViewPanel avp)
586    {
587    // TODO refactor as required to pull up to an interface
588   
589  0 Map<String, Map<Object, AtomSpecModel>> featureValues = buildFeaturesMap(
590    avp);
591  0 List<StructureCommandI> commands = getCommandGenerator()
592    .setAttributes(featureValues);
593  0 if (commands.size() > 10)
594    {
595  0 sendCommandsByFile(commands);
596    }
597    else
598    {
599  0 executeCommands(commands, false, null);
600    }
601  0 return commands.size();
602    }
603   
604    /**
605    * Write commands to a temporary file, and send a command to Chimera to open
606    * the file as a commands script. For use when sending a large number of
607    * separate commands would overload the REST interface mechanism.
608    *
609    * @param commands
610    */
 
611  0 toggle protected void sendCommandsByFile(List<StructureCommandI> commands)
612    {
613  0 try
614    {
615  0 File tmp = File.createTempFile("chim", getCommandFileExtension());
616  0 tmp.deleteOnExit();
617  0 PrintWriter out = new PrintWriter(new FileOutputStream(tmp));
618  0 for (StructureCommandI command : commands)
619    {
620  0 out.println(command.getCommand());
621    }
622  0 out.flush();
623  0 out.close();
624  0 String path = tmp.getAbsolutePath();
625  0 StructureCommandI command = getCommandGenerator()
626    .openCommandFile(path);
627  0 executeCommand(false, null, command);
628    } catch (IOException e)
629    {
630  0 jalview.bin.Console.errPrintln(
631    "Sending commands to Chimera via file failed with "
632    + e.getMessage());
633    }
634    }
635   
636    /**
637    * Returns the file extension required for a file of commands to be read by
638    * the structure viewer
639    *
640    * @return
641    */
 
642  0 toggle protected String getCommandFileExtension()
643    {
644  0 return ".com";
645    }
646   
647    /**
648    * Create features in Jalview for the given attribute name and structure
649    * residues.
650    *
651    * <pre>
652    * The residue list should be 0, 1 or more reply lines of the format:
653    * residue id #0:5.A isHelix -155.000836316 index 5
654    * or
655    * residue id #0:6.A isHelix None
656    * </pre>
657    *
658    * @param attName
659    * @param residues
660    * @return the number of features added
661    */
 
662  0 toggle protected int createFeaturesForAttributes(String attName,
663    List<String> residues)
664    {
665  0 int featuresAdded = 0;
666  0 String featureGroup = getViewerFeatureGroup();
667   
668  0 for (String residue : residues)
669    {
670  0 AtomSpec spec = null;
671  0 String[] tokens = residue.split(" ");
672  0 if (tokens.length < 5)
673    {
674  0 continue;
675    }
676  0 String atomSpec = tokens[2];
677  0 String attValue = tokens[4];
678   
679    /*
680    * ignore 'None' (e.g. for phi) or 'False' (e.g. for isHelix)
681    */
682  0 if ("None".equalsIgnoreCase(attValue)
683    || "False".equalsIgnoreCase(attValue))
684    {
685  0 continue;
686    }
687   
688  0 try
689    {
690  0 spec = parseAtomSpec(atomSpec);
691    } catch (IllegalArgumentException e)
692    {
693  0 Console.error("Problem parsing atomspec " + atomSpec);
694  0 continue;
695    }
696   
697  0 String chainId = spec.getChain();
698  0 String description = attValue;
699  0 float score = Float.NaN;
700  0 try
701    {
702  0 score = Float.valueOf(attValue);
703  0 description = chainId;
704    } catch (NumberFormatException e)
705    {
706    // was not a float value
707    }
708   
709  0 String pdbFile = getPdbFileForModel(spec.getModelNumber());
710  0 spec.setPdbFile(pdbFile);
711   
712  0 List<AtomSpec> atoms = Collections.singletonList(spec);
713   
714    /*
715    * locate the mapped position in the alignment (if any)
716    */
717  0 SearchResultsI sr = getSsm()
718    .findAlignmentPositionsForStructurePositions(atoms);
719   
720    /*
721    * expect one matched alignment position, or none
722    * (if the structure position is not mapped)
723    */
724  0 for (SearchResultMatchI m : sr.getResults())
725    {
726  0 SequenceI seq = m.getSequence();
727  0 int start = m.getStart();
728  0 int end = m.getEnd();
729  0 SequenceFeature sf = new SequenceFeature(attName, description,
730    start, end, score, featureGroup);
731    // todo: should SequenceFeature have an explicit property for chain?
732    // note: repeating the action shouldn't duplicate features
733  0 if (seq.addSequenceFeature(sf))
734    {
735  0 featuresAdded++;
736    }
737    }
738    }
739  0 return featuresAdded;
740    }
741   
742    /**
743    * Answers the feature group name to apply to features created in Jalview from
744    * Chimera attributes
745    *
746    * @return
747    */
 
748  0 toggle protected String getViewerFeatureGroup()
749    {
750    // todo pull up to interface
751  0 return CHIMERA_FEATURE_GROUP;
752    }
753   
 
754  0 toggle @Override
755    public String getModelIdForFile(String pdbFile)
756    {
757  0 List<ChimeraModel> foundModels = chimeraMaps.get(pdbFile);
758  0 if (foundModels != null && !foundModels.isEmpty())
759    {
760  0 return String.valueOf(foundModels.get(0).getModelNumber());
761    }
762  0 return "";
763    }
764   
765    /**
766    * Answers a (possibly empty) list of attribute names in Chimera[X], excluding
767    * any which were added from Jalview
768    *
769    * @return
770    */
 
771  0 toggle public List<String> getChimeraAttributes()
772    {
773  0 List<String> attributes = new ArrayList<>();
774  0 StructureCommandI command = getCommandGenerator()
775    .listResidueAttributes();
776  0 final List<String> reply = executeCommand(command, true);
777  0 if (reply != null)
778    {
779  0 for (String inputLine : reply)
780    {
781  0 String[] lineParts = inputLine.split("\\s");
782  0 if (lineParts.length == 2 && lineParts[0].equals("resattr"))
783    {
784  0 String attName = lineParts[1];
785    /*
786    * exclude attributes added from Jalview
787    */
788  0 if (!attName.startsWith(ChimeraCommands.NAMESPACE_PREFIX))
789    {
790  0 attributes.add(attName);
791    }
792    }
793    }
794    }
795  0 return attributes;
796    }
797   
798    /**
799    * Returns the file extension to use for a saved viewer session file (.py)
800    *
801    * @return
802    */
 
803  0 toggle @Override
804    public String getSessionFileExtension()
805    {
806  0 return CHIMERA_SESSION_EXTENSION;
807    }
808   
 
809  0 toggle @Override
810    public String getHelpURL()
811    {
812  0 return "https://www.cgl.ucsf.edu/chimera/docs/UsersGuide";
813    }
814    }
  • Report generated by OpenClover v 4.4.1 on Tue Nov 18 2025 11:02:12 GMT using coverage data from Tue Nov 18 2025 11:01:58 GMT.
  • OpenClover is free and open-source software.