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Coverage Report

  1. Project Clover database Mon Dec 1 2025 15:35:32 GMT
  2. Package jalview.ext.jmol

File JmolCommands.java

 

Coverage histogram

../../../img/srcFileCovDistChart8.png
21% of files have more coverage

Code metrics

68
161
25
1
605
405
69
0.43
6.44
25
2.76

Classes

Class Line # Actions
JmolCommands 52 161 69
0.7913385679.1%
 

Contributing tests

This file is covered by 63 tests. .

Source view

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.jmol;
22   
23    import java.awt.Color;
24    import java.util.ArrayList;
25    import java.util.Arrays;
26    import java.util.List;
27    import java.util.Map;
28   
29    import jalview.api.AlignViewportI;
30    import jalview.api.AlignmentViewPanel;
31    import jalview.api.FeatureRenderer;
32    import jalview.api.SequenceRenderer;
33    import jalview.datamodel.AlignmentI;
34    import jalview.datamodel.HiddenColumns;
35    import jalview.datamodel.SequenceI;
36    import jalview.renderer.seqfeatures.FeatureColourFinder;
37    import jalview.structure.AtomSpecModel;
38    import jalview.structure.StructureCommand;
39    import jalview.structure.StructureCommandI;
40    import jalview.structure.StructureCommandsBase;
41    import jalview.structure.StructureMapping;
42    import jalview.structure.StructureSelectionManager;
43    import jalview.util.Comparison;
44    import jalview.util.Platform;
45   
46    /**
47    * Routines for generating Jmol commands for Jalview/Jmol binding
48    *
49    * @author JimP
50    *
51    */
 
52    public class JmolCommands extends StructureCommandsBase
53    {
54    private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
55    "select *; cartoons off; backbone");
56   
57    private static final StructureCommand FOCUS_VIEW = new StructureCommand(
58    "zoom 0");
59   
60    private static final StructureCommand COLOUR_ALL_WHITE = new StructureCommand(
61    "select *;color white;");
62   
63    private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand(
64    "select *;color white;select ASP,GLU;color red;"
65    + "select LYS,ARG;color blue;select CYS;color yellow");
66   
67    private static final StructureCommandI COLOUR_BY_CHAIN = new StructureCommand(
68    "select *;color chain");
69   
70    private static final String PIPE = "|";
71   
72    private static final String HYPHEN = "-";
73   
74    private static final String COLON = ":";
75   
76    private static final String SLASH = "/";
77   
78    /**
79    * {@inheritDoc}
80    *
81    * @return
82    */
 
83  1 toggle @Override
84    public int getModelStartNo()
85    {
86  1 return 1;
87    }
88   
89    /**
90    * Returns a string representation of the given colour suitable for inclusion
91    * in Jmol commands
92    *
93    * @param c
94    * @return
95    */
 
96  2174 toggle protected String getColourString(Color c)
97    {
98  2174 return c == null ? null
99    : String.format("[%d,%d,%d]", c.getRed(), c.getGreen(),
100    c.getBlue());
101    }
102   
 
103  1 toggle @Override
104    public StructureCommandI colourByChain()
105    {
106  1 return COLOUR_BY_CHAIN;
107    }
108   
 
109  1 toggle @Override
110    public List<StructureCommandI> colourByCharge()
111    {
112  1 return Arrays.asList(COLOUR_BY_CHARGE);
113    }
114   
 
115  0 toggle @Override
116    public List<StructureCommandI> colourByResidues(
117    Map<String, Color> colours)
118    {
119  0 List<StructureCommandI> cmds = super.colourByResidues(colours);
120  0 cmds.add(0, COLOUR_ALL_WHITE);
121  0 return cmds;
122    }
123   
 
124  1 toggle @Override
125    public StructureCommandI setBackgroundColour(Color col)
126    {
127  1 return new StructureCommand("background " + getColourString(col));
128    }
129   
 
130  1 toggle @Override
131    public StructureCommandI focusView()
132    {
133  1 return FOCUS_VIEW;
134    }
135   
 
136  10 toggle @Override
137    public List<StructureCommandI> showChains(List<String> toShow)
138    {
139  10 StringBuilder atomSpec = new StringBuilder(128);
140  10 boolean first = true;
141  10 for (String chain : toShow)
142    {
143  9 String[] tokens = chain.split(":");
144  9 if (tokens.length == 2)
145    {
146  9 if (!first)
147    {
148  4 atomSpec.append(" or ");
149    }
150  9 first = false;
151  9 atomSpec.append(":").append(tokens[1]).append(" /")
152    .append(tokens[0]);
153    }
154    }
155   
156  10 String spec = atomSpec.toString();
157  10 String command = "select *;restrict " + spec + ";cartoon;center "
158    + spec;
159  10 return Arrays.asList(new StructureCommand(command));
160    }
161   
162    /**
163    * Returns a command to superpose atoms in {@code atomSpec} to those in
164    * {@code refAtoms}, restricted to alpha carbons only (Phosphorous for rna).
165    * For example
166    *
167    * <pre>
168    * compare {2.1} {1.1} SUBSET {(*.CA | *.P) and conformation=1}
169    * ATOMS {1-87:A}{2-54:A|61-94:A} ROTATE TRANSLATE 1.0;
170    * </pre>
171    *
172    * where {@code conformation=1} excludes ALTLOC atom locations, and 1.0 is the
173    * time in seconds to animate the action. For this example, atoms in model 2
174    * are moved towards atoms in model 1.
175    * <p>
176    * The two atomspecs should each be for one model only, but may have more than
177    * one chain. The number of atoms specified should be the same for both
178    * models, though if not, Jmol may make a 'best effort' at superposition.
179    *
180    * @see https://chemapps.stolaf.edu/jmol/docs/#compare
181    */
 
182  6 toggle @Override
183    public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms,
184    AtomSpecModel atomSpec, AtomSpecType backbone)
185    {
186  6 StringBuilder sb = new StringBuilder(64);
187  6 String refModel = refAtoms.getModels().iterator().next();
188  6 String model2 = atomSpec.getModels().iterator().next();
189  6 sb.append(String.format("compare {%s.1} {%s.1}", model2, refModel));
190  6 sb.append(" SUBSET {(*.CA | *.P) and conformation=1} ATOMS {");
191   
192    /*
193    * command examples don't include modelspec with atoms, getAtomSpec does;
194    * it works, so leave it as it is for simplicity
195    */
196  6 sb.append(getAtomSpec(atomSpec, backbone)).append("}{");
197  6 sb.append(getAtomSpec(refAtoms, backbone)).append("}");
198  6 sb.append(" ROTATE TRANSLATE ");
199  6 sb.append(getCommandSeparator());
200   
201    /*
202    * show residues used for superposition as ribbon
203    */
204  6 sb.append("select ")
205    .append(getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY))
206    .append("|");
207  6 sb.append(getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY))
208    .append(getCommandSeparator()).append("cartoons");
209  6 return Arrays.asList(new StructureCommand(sb.toString()));
210    }
211   
 
212  3 toggle @Override
213    public List<StructureCommandI> centerViewOn(List<AtomSpecModel> residues)
214    {
215  3 StringBuilder sb = new StringBuilder(64);
216  3 sb.append("center ");
217  3 for (AtomSpecModel ranges : residues)
218    {
219  8 if (sb.length() > 9)
220    {
221  5 sb.append(" or ");
222    }
223  8 sb.append(getAtomSpec(ranges, AtomSpecType.RESIDUE_ONLY));
224    }
225  3 return Arrays.asList(new StructureCommand(sb.toString()));
226    }
227   
 
228  0 toggle @Override
229    public StructureCommandI openCommandFile(String path)
230    {
231    /*
232    * https://chemapps.stolaf.edu/jmol/docs/#script
233    * not currently used in Jalview
234    */
235  0 return new StructureCommand("script " + path);
236    }
237   
 
238  4 toggle @Override
239    public StructureCommandI saveSession(String filepath)
240    {
241    /*
242    * https://chemapps.stolaf.edu/jmol/docs/#writemodel
243    */
244  4 StructureCommand sc = new StructureCommand(
245    "write STATE \"" + Platform.escapeBackslashes(filepath) + "\"");
246  4 sc.setWaitNeeded(true);
247  4 return sc;
248    }
249   
 
250  2153 toggle @Override
251    protected StructureCommandI colourResidues(String atomSpec, Color colour)
252    {
253  2153 StringBuilder sb = new StringBuilder(atomSpec.length() + 20);
254  2153 sb.append("select ").append(atomSpec).append(getCommandSeparator())
255    .append("color").append(getColourString(colour));
256  2153 return new StructureCommand(sb.toString());
257    }
258   
 
259  0 toggle @Override
260    protected String getResidueSpec(String residue)
261    {
262  0 return residue;
263    }
264   
265    /**
266    * Generates a Jmol atomspec string like
267    *
268    * <pre>
269    * 2-5:A/1.1,8:A/1.1,5-10:B/2.1
270    * </pre>
271    *
272    * Parameter {@code alphaOnly} is not used here - this restriction is made by
273    * a separate clause in the {@code compare} (superposition) command.
274    */
 
275  2196 toggle @Override
276    public String getAtomSpec(AtomSpecModel model, AtomSpecType specType)
277    {
278  2196 StringBuilder sb = new StringBuilder(128);
279   
280  2196 boolean first = true;
281  2196 for (String modelNo : model.getModels())
282    {
283  2305 for (String chain : model.getChains(modelNo))
284    {
285  2324 for (int[] range : model.getRanges(modelNo, chain))
286    {
287  10878 if (!first)
288    {
289  8683 sb.append(PIPE);
290    }
291  10875 first = false;
292  10878 if (range[0] == range[1])
293    {
294  9170 sb.append(range[0]);
295    }
296    else
297    {
298  1707 sb.append(range[0]).append(HYPHEN).append(range[1]);
299    }
300  10875 sb.append(COLON).append(chain.trim()).append(SLASH);
301  10877 sb.append(String.valueOf(modelNo)).append(".1");
302    }
303    }
304    }
305   
306  2196 return sb.toString();
307    }
308   
 
309  4 toggle @Override
310    public List<StructureCommandI> showBackbone()
311    {
312  4 return Arrays.asList(SHOW_BACKBONE);
313    }
314   
 
315  13 toggle @Override
316    public StructureCommandI loadFile(String file)
317    {
318    // https://chemapps.stolaf.edu/jmol/docs/#loadfiles
319   
320  13 return new StructureCommand(
321    "load FILES \"" + escapeQuotedFilename(file) + "\"");
322    }
323   
324   
325    /**
326    * escape a filename coping with Jmol's quirks (Jmol 14.31.53 NOLOG4J) for
327    * resolving files on network drives
328    *
329    * @param file
330    * @return escaped file prepended with file: if necessary - needs to be
331    * wrapped in \\\"
332    */
 
333  87 toggle public static String escapeQuotedFilename(String file)
334    {
335  87 String prepend="";
336  87 if (file.startsWith("//") || file.startsWith("\\\\"))
337    {
338  4 prepend = "file:";
339    }
340  87 return prepend+Platform.escapeBackslashes(file);
341    }
342   
 
343  0 toggle @Override
344    public StructureCommandI restoreSession(String filePath)
345    {
346  0 return new StructureCommand("restore STATE \""
347    + escapeQuotedFilename(filePath) + "\"");
348    }
349   
 
350  0 toggle @Override
351    public List<StructureCommandI> showHetatms(List<String> toShow)
352    {
353    // always clear the current hetero cpk display
354   
355  0 StringBuilder sb = new StringBuilder();
356  0 sb.append("select hetero; cpk off;");
357   
358  0 if (toShow != null && !toShow.isEmpty())
359    {
360    // select what was requested
361  0 sb.append("select ");
362  0 boolean or = false;
363  0 for (String k : toShow)
364    {
365  0 sb.append(or ? " or " : " ");
366  0 sb.append(k);
367  0 or = true;
368    }
369    // and show as
370  0 sb.append("; cpk;");
371    }
372   
373  0 return Arrays.asList(new StructureCommand(sb.toString()));
374    }
375   
376    /**
377    * Obsolete method, only referenced from
378    * jalview.javascript.MouseOverStructureListener
379    *
380    * @param ssm
381    * @param files
382    * @param sequence
383    * @param sr
384    * @param viewPanel
385    * @return
386    */
 
387  1 toggle @Deprecated
388    public String[] colourBySequence(StructureSelectionManager ssm,
389    String[] files, SequenceI[][] sequence, SequenceRenderer sr,
390    AlignmentViewPanel viewPanel)
391    {
392    // TODO delete method
393   
394  1 FeatureRenderer fr = viewPanel.getFeatureRenderer();
395  1 FeatureColourFinder finder = new FeatureColourFinder(fr);
396  1 AlignViewportI viewport = viewPanel.getAlignViewport();
397  1 HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
398  1 AlignmentI al = viewport.getAlignment();
399  1 List<String> cset = new ArrayList<>();
400   
401  3 for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++)
402    {
403  2 StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]);
404  2 StringBuilder command = new StringBuilder(128);
405  2 List<String> str = new ArrayList<>();
406   
407  2 if (mapping == null || mapping.length < 1)
408    {
409  0 continue;
410    }
411   
412  4 for (int s = 0; s < sequence[pdbfnum].length; s++)
413    {
414  4 for (int sp, m = 0; m < mapping.length; m++)
415    {
416  ? if (mapping[m].getSequence() == sequence[pdbfnum][s]
417    && (sp = al.findIndex(sequence[pdbfnum][s])) > -1)
418    {
419  2 int lastPos = StructureMapping.UNASSIGNED_VALUE;
420  2 SequenceI asp = al.getSequenceAt(sp);
421  22 for (int r = 0; r < asp.getLength(); r++)
422    {
423    // no mapping to gaps in sequence
424  20 if (Comparison.isGap(asp.getCharAt(r)))
425    {
426  0 continue;
427    }
428  20 int pos = mapping[m].getPDBResNum(asp.findPosition(r));
429   
430  20 if (pos == lastPos)
431    {
432  0 continue;
433    }
434  20 if (pos == StructureMapping.UNASSIGNED_VALUE)
435    {
436    // terminate current colour op
437  0 if (command.length() > 0
438    && command.charAt(command.length() - 1) != ';')
439    {
440  0 command.append(";");
441    }
442    // reset lastPos
443  0 lastPos = StructureMapping.UNASSIGNED_VALUE;
444  0 continue;
445    }
446   
447  20 lastPos = pos;
448   
449  20 Color col = sr.getResidueColour(sequence[pdbfnum][s], r,
450    finder);
451   
452    /*
453    * shade hidden regions darker
454    */
455  20 if (!cs.isVisible(r))
456    {
457  6 col = Color.GRAY;
458    }
459   
460  20 String newSelcom = (mapping[m].getChain() != " "
461    ? ":" + mapping[m].getChain()
462    : "") + "/" + (pdbfnum + 1) + ".1" + ";color"
463    + getColourString(col);
464  20 if (command.length() > newSelcom.length() && command
465    .substring(command.length() - newSelcom.length())
466    .equals(newSelcom))
467    {
468  12 command = JmolCommands.condenseCommand(command, pos);
469  12 continue;
470    }
471    // TODO: deal with case when buffer is too large for Jmol to parse
472    // - execute command and flush
473   
474  8 if (command.length() > 0
475    && command.charAt(command.length() - 1) != ';')
476    {
477  6 command.append(";");
478    }
479   
480  8 if (command.length() > 51200)
481    {
482    // add another chunk
483  0 str.add(command.toString());
484  0 command.setLength(0);
485    }
486  8 command.append("select " + pos);
487  8 command.append(newSelcom);
488    }
489    // break;
490    }
491    }
492    }
493    {
494    // add final chunk
495  2 str.add(command.toString());
496  2 command.setLength(0);
497    }
498  2 cset.addAll(str);
499   
500    }
501  1 return cset.toArray(new String[cset.size()]);
502    }
503   
504    /**
505    * Helper method
506    *
507    * @param command
508    * @param pos
509    * @return
510    */
 
511  12 toggle @Deprecated
512    private static StringBuilder condenseCommand(StringBuilder command,
513    int pos)
514    {
515   
516    // work back to last 'select'
517  12 int p = command.length(), q = p;
518  12 do
519    {
520  74 p -= 6;
521  74 if (p < 1)
522    {
523  0 p = 0;
524    }
525  74 ;
526  ? } while ((q = command.indexOf("select", p)) == -1 && p > 0);
527   
528  12 StringBuilder sb = new StringBuilder(command.substring(0, q + 7));
529   
530  12 command = command.delete(0, q + 7);
531   
532  12 String start;
533   
534  12 if (command.indexOf("-") > -1)
535    {
536  8 start = command.substring(0, command.indexOf("-"));
537    }
538    else
539    {
540  4 start = command.substring(0, command.indexOf(":"));
541    }
542   
543  12 sb.append(start + "-" + pos + command.substring(command.indexOf(":")));
544   
545  12 return sb;
546    }
547   
 
548  2 toggle @Override
549    public StructureCommandI openSession(String filepath)
550    {
551  2 return loadFile(filepath);
552    }
553   
 
554  1 toggle @Override
555    public StructureCommandI closeViewer()
556    {
557  1 return null; // not an external viewer
558    }
559   
560    /**
561    * match up Jmol 14.31.53 NOLOG4J's idea of a filepath with Jalview's
562    * @param jmolFile
563    * @param jalviewFile
564    * @return true if strings resolve to the same resource
565    */
 
566  789 toggle public static boolean filePathMatch(String jmolFile,String jalviewFile)
567    {
568  789 if (jmolFile.equalsIgnoreCase(jalviewFile))
569    {
570  565 return true;
571    }
572  224 if (jmolFile.startsWith("file:") && (jalviewFile.startsWith("//") || jalviewFile.startsWith("\\\\")))
573    {
574  9 String jmolPath = jmolFile.substring(5);
575    // jmol needs file: at beginning for network mounts.
576  9 if (jmolPath.equalsIgnoreCase(jalviewFile))
577    {
578  3 return true;
579    }
580  6 if (jmolPath.startsWith("////"))
581    {
582    // faulty translation from backslash to forward slash - put it back the other way
583  2 jmolPath = jmolPath.replace("//", "/");
584    }
585  6 if (jmolPath.equalsIgnoreCase(jalviewFile))
586    {
587  0 return true;
588    }
589  6 if (jmolPath.startsWith("\\\\\\"))
590    {
591    // faulty translation from backslash to forward slash - put it back the other way
592  2 jmolPath = jmolPath.replace("\\\\", "//");
593    } // also normalises \\ to / for URLs
594  6 String jalviewPath = jalviewFile.replace("\\","/");
595  6 if (jmolPath.equalsIgnoreCase(jalviewPath))
596    {
597  4 return true;
598    }
599  2 jmolPath = jmolPath.replace("//", "/");
600  2 return jmolPath.equalsIgnoreCase(jalviewPath);
601   
602    }
603  215 return false;
604    }
605    }
  • Report generated by OpenClover v 4.4.1 on Mon Dec 1 2025 15:44:56 GMT using coverage data from Mon Dec 1 2025 15:44:42 GMT.
  • OpenClover is free and open-source software.