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  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.ext.rbvi.chimera

File JalviewChimeraBinding.java

 

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56% of files have more coverage

Code metrics

72
197
28
1
785
475
79
0.4
7.04
28
2.82

Classes

Class Line # Actions
JalviewChimeraBinding 55 197 79
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.Cache;
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 atomspec
80    * @param atomSpec
81    * @return
82    */
 
83  0 toggle protected AtomSpec parseAtomSpec(String atomSpec)
84    {
85  0 return AtomSpec.fromChimeraAtomspec(atomSpec);
86    }
87   
88    /**
89    * Open a PDB structure file in Chimera and set up mappings from Jalview.
90    *
91    * We check if the PDB model id is already loaded in Chimera, if so don't reopen
92    * it. This is the case if Chimera has opened a saved session file.
93    *
94    * @param pe
95    * @return
96    */
 
97  0 toggle public boolean openFile(PDBEntry pe)
98    {
99  0 String file = pe.getFile();
100  0 try
101    {
102  0 List<ChimeraModel> modelsToMap = new ArrayList<>();
103  0 List<ChimeraModel> oldList = chimeraManager.getModelList();
104  0 boolean alreadyOpen = false;
105   
106    /*
107    * If Chimera already has this model, don't reopen it, but do remap it.
108    */
109  0 for (ChimeraModel open : oldList)
110    {
111  0 if (open.getModelName().equals(pe.getId()))
112    {
113  0 alreadyOpen = true;
114  0 modelsToMap.add(open);
115    }
116    }
117   
118    /*
119    * If Chimera doesn't yet have this model, ask it to open it, and retrieve
120    * the model name(s) added by Chimera.
121    */
122  0 if (!alreadyOpen)
123    {
124  0 chimeraManager.openModel(file, pe.getId(), ModelType.PDB_MODEL);
125  0 addChimeraModel(pe, modelsToMap);
126    }
127   
128  0 chimeraMaps.put(file, modelsToMap);
129   
130  0 if (getSsm() != null)
131    {
132  0 getSsm().addStructureViewerListener(this);
133    }
134  0 return true;
135    } catch (Exception q)
136    {
137  0 log("Exception when trying to open model " + file + "\n"
138    + q.toString());
139  0 q.printStackTrace();
140    }
141  0 return false;
142    }
143   
144    /**
145    * Adds the ChimeraModel corresponding to the given PDBEntry, based on model
146    * name matching PDB id
147    *
148    * @param pe
149    * @param modelsToMap
150    */
 
151  0 toggle protected void addChimeraModel(PDBEntry pe,
152    List<ChimeraModel> modelsToMap)
153    {
154    /*
155    * Chimera: query for actual models and find the one with
156    * matching model name - already set in viewer.openModel()
157    */
158  0 List<ChimeraModel> newList = chimeraManager.getModelList();
159    // JAL-1728 newList.removeAll(oldList) does not work
160  0 for (ChimeraModel cm : newList)
161    {
162  0 if (cm.getModelName().equals(pe.getId()))
163    {
164  0 modelsToMap.add(cm);
165    }
166    }
167    }
168   
169    /**
170    * Constructor
171    *
172    * @param ssm
173    * @param pdbentry
174    * @param sequenceIs
175    * @param protocol
176    */
 
177  0 toggle public JalviewChimeraBinding(StructureSelectionManager ssm,
178    PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
179    DataSourceType protocol)
180    {
181  0 super(ssm, pdbentry, sequenceIs, protocol);
182  0 boolean chimeraX = ViewerType.CHIMERAX.equals(getViewerType());
183  0 chimeraManager = chimeraX ? new ChimeraXManager(new StructureManager(true)) : new ChimeraManager(new StructureManager(true));
184  0 setStructureCommands(chimeraX ? new ChimeraXCommands() : new ChimeraCommands());
185    }
186   
 
187  0 toggle @Override
188    protected ViewerType getViewerType()
189    {
190  0 return ViewerType.CHIMERA;
191    }
192   
193    /**
194    * Start a dedicated HttpServer to listen for Chimera notifications, and tell it
195    * to start listening
196    */
 
197  0 toggle public void startChimeraListener()
198    {
199  0 try
200    {
201  0 chimeraListener = new ChimeraListener(this);
202  0 startListening(chimeraListener.getUri());
203    } catch (BindException e)
204    {
205  0 System.err.println(
206    "Failed to start Chimera listener: " + e.getMessage());
207    }
208    }
209   
210    /**
211    * Close down the Jalview viewer and listener, and (optionally) the associated
212    * Chimera window.
213    */
 
214  0 toggle @Override
215    public void closeViewer(boolean closeChimera)
216    {
217  0 super.closeViewer(closeChimera);
218  0 if (this.chimeraListener != null)
219    {
220  0 chimeraListener.shutdown();
221  0 chimeraListener = null;
222    }
223   
224    /*
225    * the following call is added to avoid a stack trace error in Chimera
226    * after "stop really" is sent; Chimera > 1.14 will not need it; see also
227    * http://plato.cgl.ucsf.edu/trac/chimera/ticket/17597
228    */
229  0 if (closeChimera && (getViewerType() == ViewerType.CHIMERA))
230    {
231  0 chimeraManager.getChimeraProcess().destroy();
232    }
233   
234  0 chimeraManager.clearOnChimeraExit();
235  0 chimeraManager = null;
236    }
237   
238    /**
239    * Helper method to construct model spec in Chimera format:
240    * <ul>
241    * <li>#0 (#1 etc) for a PDB file with no sub-models</li>
242    * <li>#0.1 (#1.1 etc) for a PDB file with sub-models</li>
243    * <ul>
244    * Note for now we only ever choose the first of multiple models. This
245    * corresponds to the hard-coded Jmol equivalent (compare {1.1}). Refactor in
246    * future if there is a need to select specific sub-models.
247    *
248    * @param pdbfnum
249    * @return
250    */
 
251  0 toggle protected String getModelSpec(int pdbfnum)
252    {
253  0 if (pdbfnum < 0 || pdbfnum >= getPdbCount())
254    {
255  0 return "#" + pdbfnum; // temp hack for ChimeraX
256    }
257   
258    /*
259    * For now, the test for having sub-models is whether multiple Chimera
260    * models are mapped for the PDB file; the models are returned as a response
261    * to the Chimera command 'list models type molecule', see
262    * ChimeraManager.getModelList().
263    */
264  0 List<ChimeraModel> maps = chimeraMaps.get(getStructureFiles()[pdbfnum]);
265  0 boolean hasSubModels = maps != null && maps.size() > 1;
266  0 return "#" + String.valueOf(pdbfnum) + (hasSubModels ? ".1" : "");
267    }
268   
269    /**
270    * Launch Chimera, unless an instance linked to this object is already
271    * running. Returns true if Chimera is successfully launched, or already
272    * running, else false.
273    *
274    * @return
275    */
 
276  0 toggle public boolean launchChimera()
277    {
278  0 if (chimeraManager.isChimeraLaunched())
279    {
280  0 return true;
281    }
282   
283  0 boolean launched = chimeraManager.launchChimera(getChimeraPaths());
284  0 if (launched)
285    {
286  0 startExternalViewerMonitor(chimeraManager.getChimeraProcess());
287    }
288    else
289    {
290  0 log("Failed to launch Chimera!");
291    }
292  0 return launched;
293    }
294   
295    /**
296    * Returns a list of candidate paths to the Chimera program executable
297    *
298    * @return
299    */
 
300  0 toggle protected List<String> getChimeraPaths()
301    {
302  0 return StructureManager.getChimeraPaths(false);
303    }
304   
305    /**
306    * Answers true if the Chimera process is still running, false if ended or not
307    * started.
308    *
309    * @return
310    */
 
311  0 toggle @Override
312    public boolean isViewerRunning()
313    {
314  0 return chimeraManager.isChimeraLaunched();
315    }
316   
317    /**
318    * Send a command to Chimera, and optionally log and return any responses.
319    *
320    * @param command
321    * @param getResponse
322    */
 
323  0 toggle @Override
324    public List<String> executeCommand(final StructureCommandI command,
325    boolean getResponse)
326    {
327  0 if (chimeraManager == null || command == null)
328    {
329    // ? thread running after viewer shut down
330  0 return null;
331    }
332  0 List<String> reply = null;
333    // trim command or it may never find a match in the replyLog!!
334  0 String cmd = command.getCommand().trim();
335  0 List<String> lastReply = chimeraManager
336    .sendChimeraCommand(cmd, getResponse);
337  0 if (getResponse)
338    {
339  0 reply = lastReply;
340  0 if (Cache.log.isDebugEnabled()) {
341  0 Cache.log.debug(
342    "Response from command ('" + cmd + "') was:\n" + lastReply);
343    }
344    }
345   
346  0 return reply;
347    }
348   
 
349  0 toggle @Override
350    public synchronized String[] getStructureFiles()
351    {
352  0 if (chimeraManager == null)
353    {
354  0 return new String[0];
355    }
356   
357  0 return chimeraMaps.keySet()
358    .toArray(modelFileNames = new String[chimeraMaps.size()]);
359    }
360   
361    /**
362    * Construct and send a command to highlight zero, one or more atoms. We do this
363    * by sending an "rlabel" command to show the residue label at that position.
364    */
 
365  0 toggle @Override
366    public void highlightAtoms(List<AtomSpec> atoms)
367    {
368  0 if (atoms == null || atoms.size() == 0)
369    {
370  0 return;
371    }
372   
373  0 boolean forChimeraX = chimeraManager.isChimeraX();
374  0 StringBuilder cmd = new StringBuilder(128);
375  0 boolean first = true;
376  0 boolean found = false;
377   
378  0 for (AtomSpec atom : atoms)
379    {
380  0 int pdbResNum = atom.getPdbResNum();
381  0 String chain = atom.getChain();
382  0 String pdbfile = atom.getPdbFile();
383  0 List<ChimeraModel> cms = chimeraMaps.get(pdbfile);
384  0 if (cms != null && !cms.isEmpty())
385    {
386  0 if (first)
387    {
388  0 cmd.append(forChimeraX ? "label #" : "rlabel #");
389    }
390    else
391    {
392  0 cmd.append(",");
393    }
394  0 first = false;
395  0 if (forChimeraX)
396    {
397  0 cmd.append(cms.get(0).getModelNumber())
398    .append("/").append(chain).append(":").append(pdbResNum);
399    }
400    else
401    {
402  0 cmd.append(cms.get(0).getModelNumber())
403    .append(":").append(pdbResNum);
404  0 if (!chain.equals(" ") && !forChimeraX)
405    {
406  0 cmd.append(".").append(chain);
407    }
408    }
409  0 found = true;
410    }
411    }
412  0 String command = cmd.toString();
413   
414    /*
415    * avoid repeated commands for the same residue
416    */
417  0 if (command.equals(lastHighlightCommand))
418    {
419  0 return;
420    }
421   
422    /*
423    * unshow the label for the previous residue
424    */
425  0 if (lastHighlightCommand != null)
426    {
427  0 executeCommand(false, null, new StructureCommand("~" + lastHighlightCommand));
428    }
429  0 if (found)
430    {
431  0 executeCommand(false, null, new StructureCommand(command));
432    }
433  0 this.lastHighlightCommand = command;
434    }
435   
436    /**
437    * Query Chimera for its current selection, and highlight it on the alignment
438    */
 
439  0 toggle public void highlightChimeraSelection()
440    {
441    /*
442    * Ask Chimera for its current selection
443    */
444  0 StructureCommandI command = getCommandGenerator().getSelectedResidues();
445   
446  0 Runnable action = new Runnable()
447    {
 
448  0 toggle @Override
449    public void run()
450    {
451  0 List<String> chimeraReply = executeCommand(command, true);
452   
453  0 List<String> selectedResidues = new ArrayList<>();
454  0 if (chimeraReply != null)
455    {
456    /*
457    * expect 0, 1 or more lines of the format either
458    * Chimera:
459    * residue id #0:43.A type GLY
460    * ChimeraX:
461    * residue id /A:89 name THR index 88
462    * We are only interested in the atomspec (third token of the reply)
463    */
464  0 for (String inputLine : chimeraReply)
465    {
466  0 String[] inputLineParts = inputLine.split("\\s+");
467  0 if (inputLineParts.length >= 5)
468    {
469  0 selectedResidues.add(inputLineParts[2]);
470    }
471    }
472    }
473   
474    /*
475    * Parse model number, residue and chain for each selected position,
476    * formatted as #0:123.A or #1.2:87.B (#model.submodel:residue.chain)
477    */
478  0 List<AtomSpec> atomSpecs = convertStructureResiduesToAlignment(
479    selectedResidues);
480   
481    /*
482    * Broadcast the selection (which may be empty, if the user just cleared all
483    * selections)
484    */
485  0 getSsm().mouseOverStructure(atomSpecs);
486   
487    }
488    };
489  0 new Thread(action).start();
490    }
491   
492    /**
493    * Converts a list of Chimera(X) atomspecs to a list of AtomSpec representing the
494    * corresponding residues (if any) in Jalview
495    *
496    * @param structureSelection
497    * @return
498    */
 
499  0 toggle protected List<AtomSpec> convertStructureResiduesToAlignment(
500    List<String> structureSelection)
501    {
502  0 List<AtomSpec> atomSpecs = new ArrayList<>();
503  0 for (String atomSpec : structureSelection)
504    {
505  0 try
506    {
507  0 AtomSpec spec = parseAtomSpec(atomSpec);
508  0 String pdbfilename = getPdbFileForModel(spec.getModelNumber());
509  0 spec.setPdbFile(pdbfilename);
510  0 atomSpecs.add(spec);
511    } catch (IllegalArgumentException e)
512    {
513  0 Cache.log.error("Failed to parse atomspec: " + atomSpec);
514    }
515    }
516  0 return atomSpecs;
517    }
518   
519    /**
520    * @param modelId
521    * @return
522    */
 
523  0 toggle protected String getPdbFileForModel(int modelId)
524    {
525    /*
526    * Work out the pdbfilename from the model number
527    */
528  0 String pdbfilename = modelFileNames[0];
529  0 findfileloop: for (String pdbfile : this.chimeraMaps.keySet())
530    {
531  0 for (ChimeraModel cm : chimeraMaps.get(pdbfile))
532    {
533  0 if (cm.getModelNumber() == modelId)
534    {
535  0 pdbfilename = pdbfile;
536  0 break findfileloop;
537    }
538    }
539    }
540  0 return pdbfilename;
541    }
542   
 
543  0 toggle private void log(String message)
544    {
545  0 System.err.println("## Chimera log: " + message);
546    }
547   
548    /**
549    * Constructs and send commands to Chimera to set attributes on residues for
550    * features visible in Jalview.
551    * <p>
552    * The syntax is: setattr r &lt;attName&gt; &lt;attValue&gt; &lt;atomSpec&gt;
553    * <p>
554    * For example: setattr r jv_chain "Ferredoxin-1, Chloroplastic" #0:94.A
555    *
556    * @param avp
557    * @return
558    */
 
559  0 toggle public int sendFeaturesToViewer(AlignmentViewPanel avp)
560    {
561    // TODO refactor as required to pull up to an interface
562   
563  0 Map<String, Map<Object, AtomSpecModel>> featureValues = buildFeaturesMap(
564    avp);
565  0 List<StructureCommandI> commands = getCommandGenerator()
566    .setAttributes(featureValues);
567  0 if (commands.size() > 10)
568    {
569  0 sendCommandsByFile(commands);
570    }
571    else
572    {
573  0 executeCommands(commands, false, null);
574    }
575  0 return commands.size();
576    }
577   
578    /**
579    * Write commands to a temporary file, and send a command to Chimera to open the
580    * file as a commands script. For use when sending a large number of separate
581    * commands would overload the REST interface mechanism.
582    *
583    * @param commands
584    */
 
585  0 toggle protected void sendCommandsByFile(List<StructureCommandI> commands)
586    {
587  0 try
588    {
589  0 File tmp = File.createTempFile("chim", getCommandFileExtension());
590  0 tmp.deleteOnExit();
591  0 PrintWriter out = new PrintWriter(new FileOutputStream(tmp));
592  0 for (StructureCommandI command : commands)
593    {
594  0 out.println(command.getCommand());
595    }
596  0 out.flush();
597  0 out.close();
598  0 String path = tmp.getAbsolutePath();
599  0 StructureCommandI command = getCommandGenerator()
600    .openCommandFile(path);
601  0 executeCommand(false, null, command);
602    } catch (IOException e)
603    {
604  0 System.err.println("Sending commands to Chimera via file failed with "
605    + e.getMessage());
606    }
607    }
608   
609    /**
610    * Returns the file extension required for a file of commands to be read by
611    * the structure viewer
612    * @return
613    */
 
614  0 toggle protected String getCommandFileExtension()
615    {
616  0 return ".com";
617    }
618   
619    /**
620    * Create features in Jalview for the given attribute name and structure
621    * residues.
622    *
623    * <pre>
624    * The residue list should be 0, 1 or more reply lines of the format:
625    * residue id #0:5.A isHelix -155.000836316 index 5
626    * or
627    * residue id #0:6.A isHelix None
628    * </pre>
629    *
630    * @param attName
631    * @param residues
632    * @return the number of features added
633    */
 
634  0 toggle protected int createFeaturesForAttributes(String attName,
635    List<String> residues)
636    {
637  0 int featuresAdded = 0;
638  0 String featureGroup = getViewerFeatureGroup();
639   
640  0 for (String residue : residues)
641    {
642  0 AtomSpec spec = null;
643  0 String[] tokens = residue.split(" ");
644  0 if (tokens.length < 5)
645    {
646  0 continue;
647    }
648  0 String atomSpec = tokens[2];
649  0 String attValue = tokens[4];
650   
651    /*
652    * ignore 'None' (e.g. for phi) or 'False' (e.g. for isHelix)
653    */
654  0 if ("None".equalsIgnoreCase(attValue)
655    || "False".equalsIgnoreCase(attValue))
656    {
657  0 continue;
658    }
659   
660  0 try
661    {
662  0 spec = parseAtomSpec(atomSpec);
663    } catch (IllegalArgumentException e)
664    {
665  0 Cache.log.error("Problem parsing atomspec " + atomSpec);
666  0 continue;
667    }
668   
669  0 String chainId = spec.getChain();
670  0 String description = attValue;
671  0 float score = Float.NaN;
672  0 try
673    {
674  0 score = Float.valueOf(attValue);
675  0 description = chainId;
676    } catch (NumberFormatException e)
677    {
678    // was not a float value
679    }
680   
681  0 String pdbFile = getPdbFileForModel(spec.getModelNumber());
682  0 spec.setPdbFile(pdbFile);
683   
684  0 List<AtomSpec> atoms = Collections.singletonList(spec);
685   
686    /*
687    * locate the mapped position in the alignment (if any)
688    */
689  0 SearchResultsI sr = getSsm()
690    .findAlignmentPositionsForStructurePositions(atoms);
691   
692    /*
693    * expect one matched alignment position, or none
694    * (if the structure position is not mapped)
695    */
696  0 for (SearchResultMatchI m : sr.getResults())
697    {
698  0 SequenceI seq = m.getSequence();
699  0 int start = m.getStart();
700  0 int end = m.getEnd();
701  0 SequenceFeature sf = new SequenceFeature(attName, description,
702    start, end, score, featureGroup);
703    // todo: should SequenceFeature have an explicit property for chain?
704    // note: repeating the action shouldn't duplicate features
705  0 if (seq.addSequenceFeature(sf))
706    {
707  0 featuresAdded++;
708    }
709    }
710    }
711  0 return featuresAdded;
712    }
713   
714    /**
715    * Answers the feature group name to apply to features created in Jalview from
716    * Chimera attributes
717    *
718    * @return
719    */
 
720  0 toggle protected String getViewerFeatureGroup()
721    {
722    // todo pull up to interface
723  0 return CHIMERA_FEATURE_GROUP;
724    }
725   
 
726  0 toggle @Override
727    public String getModelIdForFile(String pdbFile)
728    {
729  0 List<ChimeraModel> foundModels = chimeraMaps.get(pdbFile);
730  0 if (foundModels != null && !foundModels.isEmpty())
731    {
732  0 return String.valueOf(foundModels.get(0).getModelNumber());
733    }
734  0 return "";
735    }
736   
737    /**
738    * Answers a (possibly empty) list of attribute names in Chimera[X], excluding
739    * any which were added from Jalview
740    *
741    * @return
742    */
 
743  0 toggle public List<String> getChimeraAttributes()
744    {
745  0 List<String> attributes = new ArrayList<>();
746  0 StructureCommandI command = getCommandGenerator().listResidueAttributes();
747  0 final List<String> reply = executeCommand(command, true);
748  0 if (reply != null)
749    {
750  0 for (String inputLine : reply)
751    {
752  0 String[] lineParts = inputLine.split("\\s");
753  0 if (lineParts.length == 2 && lineParts[0].equals("resattr"))
754    {
755  0 String attName = lineParts[1];
756    /*
757    * exclude attributes added from Jalview
758    */
759  0 if (!attName.startsWith(ChimeraCommands.NAMESPACE_PREFIX))
760    {
761  0 attributes.add(attName);
762    }
763    }
764    }
765    }
766  0 return attributes;
767    }
768   
769    /**
770    * Returns the file extension to use for a saved viewer session file (.py)
771    *
772    * @return
773    */
 
774  0 toggle @Override
775    public String getSessionFileExtension()
776    {
777  0 return CHIMERA_SESSION_EXTENSION;
778    }
779   
 
780  0 toggle @Override
781    public String getHelpURL()
782    {
783  0 return "https://www.cgl.ucsf.edu/chimera/docs/UsersGuide";
784    }
785    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.