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JmolCommands | 52 | 139 | 56 |
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 | @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 | 1668 | protected String getColourString(Color c) |
97 | { | |
98 | 1668 | return c == null ? null |
99 | : String.format("[%d,%d,%d]", c.getRed(), c.getGreen(), | |
100 | c.getBlue()); | |
101 | } | |
102 | ||
103 | 1 | @Override |
104 | public StructureCommandI colourByChain() | |
105 | { | |
106 | 1 | return COLOUR_BY_CHAIN; |
107 | } | |
108 | ||
109 | 1 | @Override |
110 | public List<StructureCommandI> colourByCharge() | |
111 | { | |
112 | 1 | return Arrays.asList(COLOUR_BY_CHARGE); |
113 | } | |
114 | ||
115 | 0 | @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 | @Override |
125 | public StructureCommandI setBackgroundColour(Color col) | |
126 | { | |
127 | 1 | return new StructureCommand("background " + getColourString(col)); |
128 | } | |
129 | ||
130 | 1 | @Override |
131 | public StructureCommandI focusView() | |
132 | { | |
133 | 1 | return FOCUS_VIEW; |
134 | } | |
135 | ||
136 | 0 | @Override |
137 | public List<StructureCommandI> showChains(List<String> toShow) | |
138 | { | |
139 | 0 | StringBuilder atomSpec = new StringBuilder(128); |
140 | 0 | boolean first = true; |
141 | 0 | for (String chain : toShow) |
142 | { | |
143 | 0 | String[] tokens = chain.split(":"); |
144 | 0 | if (tokens.length == 2) |
145 | { | |
146 | 0 | if (!first) |
147 | { | |
148 | 0 | atomSpec.append(" or "); |
149 | } | |
150 | 0 | first = false; |
151 | 0 | atomSpec.append(":").append(tokens[1]).append(" /") |
152 | .append(tokens[0]); | |
153 | } | |
154 | } | |
155 | ||
156 | 0 | String spec = atomSpec.toString(); |
157 | 0 | String command = "select *;restrict " + spec + ";cartoon;center " |
158 | + spec; | |
159 | 0 | 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 | 2 | @Override |
183 | public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms, | |
184 | AtomSpecModel atomSpec, AtomSpecType backbone) | |
185 | { | |
186 | 2 | StringBuilder sb = new StringBuilder(64); |
187 | 2 | String refModel = refAtoms.getModels().iterator().next(); |
188 | 2 | String model2 = atomSpec.getModels().iterator().next(); |
189 | 2 | sb.append(String.format("compare {%s.1} {%s.1}", model2, refModel)); |
190 | 2 | 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 | 2 | sb.append(getAtomSpec(atomSpec, backbone)).append("}{"); |
197 | 2 | sb.append(getAtomSpec(refAtoms, backbone)).append("}"); |
198 | 2 | sb.append(" ROTATE TRANSLATE "); |
199 | 2 | sb.append(getCommandSeparator()); |
200 | ||
201 | /* | |
202 | * show residues used for superposition as ribbon | |
203 | */ | |
204 | 2 | sb.append("select ") |
205 | .append(getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY)) | |
206 | .append("|"); | |
207 | 2 | sb.append(getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY)) |
208 | .append(getCommandSeparator()).append("cartoons"); | |
209 | 2 | return Arrays.asList(new StructureCommand(sb.toString())); |
210 | } | |
211 | ||
212 | 1 | @Override |
213 | public List<StructureCommandI> centerViewOn(List<AtomSpecModel> residues) | |
214 | { | |
215 | 1 | StringBuilder sb = new StringBuilder(64); |
216 | 1 | sb.append("center "); |
217 | 1 | for (AtomSpecModel ranges : residues) |
218 | { | |
219 | 2 | if (sb.length() > 9) |
220 | { | |
221 | 1 | sb.append(" or "); |
222 | } | |
223 | 2 | sb.append(getAtomSpec(ranges, AtomSpecType.RESIDUE_ONLY)); |
224 | } | |
225 | 1 | return Arrays.asList(new StructureCommand(sb.toString())); |
226 | } | |
227 | ||
228 | 0 | @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 | 3 | @Override |
239 | public StructureCommandI saveSession(String filepath) | |
240 | { | |
241 | /* | |
242 | * https://chemapps.stolaf.edu/jmol/docs/#writemodel | |
243 | */ | |
244 | 3 | StructureCommand sc = new StructureCommand( |
245 | "write STATE \"" + filepath + "\""); | |
246 | 3 | sc.setWaitNeeded(true); |
247 | 3 | return sc; |
248 | } | |
249 | ||
250 | 1647 | @Override |
251 | protected StructureCommandI colourResidues(String atomSpec, Color colour) | |
252 | { | |
253 | 1647 | StringBuilder sb = new StringBuilder(atomSpec.length() + 20); |
254 | 1647 | sb.append("select ").append(atomSpec).append(getCommandSeparator()) |
255 | .append("color").append(getColourString(colour)); | |
256 | 1647 | return new StructureCommand(sb.toString()); |
257 | } | |
258 | ||
259 | 0 | @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 | 1668 | @Override |
276 | public String getAtomSpec(AtomSpecModel model, AtomSpecType specType) | |
277 | { | |
278 | 1668 | StringBuilder sb = new StringBuilder(128); |
279 | ||
280 | 1667 | boolean first = true; |
281 | 1667 | for (String modelNo : model.getModels()) |
282 | { | |
283 | 1676 | for (String chain : model.getChains(modelNo)) |
284 | { | |
285 | 1696 | for (int[] range : model.getRanges(modelNo, chain)) |
286 | { | |
287 | 7743 | if (!first) |
288 | { | |
289 | 6076 | sb.append(PIPE); |
290 | } | |
291 | 7742 | first = false; |
292 | 7743 | if (range[0] == range[1]) |
293 | { | |
294 | 6695 | sb.append(range[0]); |
295 | } | |
296 | else | |
297 | { | |
298 | 1048 | sb.append(range[0]).append(HYPHEN).append(range[1]); |
299 | } | |
300 | 7743 | sb.append(COLON).append(chain.trim()).append(SLASH); |
301 | 7743 | sb.append(String.valueOf(modelNo)).append(".1"); |
302 | } | |
303 | } | |
304 | } | |
305 | ||
306 | 1668 | return sb.toString(); |
307 | } | |
308 | ||
309 | 2 | @Override |
310 | public List<StructureCommandI> showBackbone() | |
311 | { | |
312 | 2 | return Arrays.asList(SHOW_BACKBONE); |
313 | } | |
314 | ||
315 | 4 | @Override |
316 | public StructureCommandI loadFile(String file) | |
317 | { | |
318 | // https://chemapps.stolaf.edu/jmol/docs/#loadfiles | |
319 | 4 | return new StructureCommand( |
320 | "load FILES \"" + Platform.escapeBackslashes(file) + "\""); | |
321 | } | |
322 | ||
323 | 0 | @Override |
324 | public StructureCommandI restoreSession(String filePath) | |
325 | { | |
326 | 0 | return new StructureCommand("restore STATE \"" |
327 | + Platform.escapeBackslashes(filePath) + "\""); | |
328 | } | |
329 | ||
330 | 0 | @Override |
331 | public List<StructureCommandI> showHetatms(List<String> toShow) | |
332 | { | |
333 | // always clear the current hetero cpk display | |
334 | ||
335 | 0 | StringBuilder sb = new StringBuilder(); |
336 | 0 | sb.append("select hetero; cpk off;"); |
337 | ||
338 | 0 | if (toShow != null && !toShow.isEmpty()) |
339 | { | |
340 | // select what was requested | |
341 | 0 | sb.append("select "); |
342 | 0 | boolean or = false; |
343 | 0 | for (String k : toShow) |
344 | { | |
345 | 0 | sb.append(or ? " or " : " "); |
346 | 0 | sb.append(k); |
347 | 0 | or = true; |
348 | } | |
349 | // and show as | |
350 | 0 | sb.append("; cpk;"); |
351 | } | |
352 | ||
353 | 0 | return Arrays.asList(new StructureCommand(sb.toString())); |
354 | } | |
355 | ||
356 | /** | |
357 | * Obsolete method, only referenced from | |
358 | * jalview.javascript.MouseOverStructureListener | |
359 | * | |
360 | * @param ssm | |
361 | * @param files | |
362 | * @param sequence | |
363 | * @param sr | |
364 | * @param viewPanel | |
365 | * @return | |
366 | */ | |
367 | 1 | @Deprecated |
368 | public String[] colourBySequence(StructureSelectionManager ssm, | |
369 | String[] files, SequenceI[][] sequence, SequenceRenderer sr, | |
370 | AlignmentViewPanel viewPanel) | |
371 | { | |
372 | // TODO delete method | |
373 | ||
374 | 1 | FeatureRenderer fr = viewPanel.getFeatureRenderer(); |
375 | 1 | FeatureColourFinder finder = new FeatureColourFinder(fr); |
376 | 1 | AlignViewportI viewport = viewPanel.getAlignViewport(); |
377 | 1 | HiddenColumns cs = viewport.getAlignment().getHiddenColumns(); |
378 | 1 | AlignmentI al = viewport.getAlignment(); |
379 | 1 | List<String> cset = new ArrayList<>(); |
380 | ||
381 | 3 | for (int pdbfnum = 0; pdbfnum < files.length; pdbfnum++) |
382 | { | |
383 | 2 | StructureMapping[] mapping = ssm.getMapping(files[pdbfnum]); |
384 | 2 | StringBuilder command = new StringBuilder(128); |
385 | 2 | List<String> str = new ArrayList<>(); |
386 | ||
387 | 2 | if (mapping == null || mapping.length < 1) |
388 | { | |
389 | 0 | continue; |
390 | } | |
391 | ||
392 | 4 | for (int s = 0; s < sequence[pdbfnum].length; s++) |
393 | { | |
394 | 4 | for (int sp, m = 0; m < mapping.length; m++) |
395 | { | |
396 | ? | if (mapping[m].getSequence() == sequence[pdbfnum][s] |
397 | && (sp = al.findIndex(sequence[pdbfnum][s])) > -1) | |
398 | { | |
399 | 2 | int lastPos = StructureMapping.UNASSIGNED_VALUE; |
400 | 2 | SequenceI asp = al.getSequenceAt(sp); |
401 | 22 | for (int r = 0; r < asp.getLength(); r++) |
402 | { | |
403 | // no mapping to gaps in sequence | |
404 | 20 | if (Comparison.isGap(asp.getCharAt(r))) |
405 | { | |
406 | 0 | continue; |
407 | } | |
408 | 20 | int pos = mapping[m].getPDBResNum(asp.findPosition(r)); |
409 | ||
410 | 20 | if (pos == lastPos) |
411 | { | |
412 | 0 | continue; |
413 | } | |
414 | 20 | if (pos == StructureMapping.UNASSIGNED_VALUE) |
415 | { | |
416 | // terminate current colour op | |
417 | 0 | if (command.length() > 0 |
418 | && command.charAt(command.length() - 1) != ';') | |
419 | { | |
420 | 0 | command.append(";"); |
421 | } | |
422 | // reset lastPos | |
423 | 0 | lastPos = StructureMapping.UNASSIGNED_VALUE; |
424 | 0 | continue; |
425 | } | |
426 | ||
427 | 20 | lastPos = pos; |
428 | ||
429 | 20 | Color col = sr.getResidueColour(sequence[pdbfnum][s], r, |
430 | finder); | |
431 | ||
432 | /* | |
433 | * shade hidden regions darker | |
434 | */ | |
435 | 20 | if (!cs.isVisible(r)) |
436 | { | |
437 | 6 | col = Color.GRAY; |
438 | } | |
439 | ||
440 | 20 | String newSelcom = (mapping[m].getChain() != " " |
441 | ? ":" + mapping[m].getChain() | |
442 | : "") + "/" + (pdbfnum + 1) + ".1" + ";color" | |
443 | + getColourString(col); | |
444 | 20 | if (command.length() > newSelcom.length() && command |
445 | .substring(command.length() - newSelcom.length()) | |
446 | .equals(newSelcom)) | |
447 | { | |
448 | 12 | command = JmolCommands.condenseCommand(command, pos); |
449 | 12 | continue; |
450 | } | |
451 | // TODO: deal with case when buffer is too large for Jmol to parse | |
452 | // - execute command and flush | |
453 | ||
454 | 8 | if (command.length() > 0 |
455 | && command.charAt(command.length() - 1) != ';') | |
456 | { | |
457 | 6 | command.append(";"); |
458 | } | |
459 | ||
460 | 8 | if (command.length() > 51200) |
461 | { | |
462 | // add another chunk | |
463 | 0 | str.add(command.toString()); |
464 | 0 | command.setLength(0); |
465 | } | |
466 | 8 | command.append("select " + pos); |
467 | 8 | command.append(newSelcom); |
468 | } | |
469 | // break; | |
470 | } | |
471 | } | |
472 | } | |
473 | { | |
474 | // add final chunk | |
475 | 2 | str.add(command.toString()); |
476 | 2 | command.setLength(0); |
477 | } | |
478 | 2 | cset.addAll(str); |
479 | ||
480 | } | |
481 | 1 | return cset.toArray(new String[cset.size()]); |
482 | } | |
483 | ||
484 | /** | |
485 | * Helper method | |
486 | * | |
487 | * @param command | |
488 | * @param pos | |
489 | * @return | |
490 | */ | |
491 | 12 | @Deprecated |
492 | private static StringBuilder condenseCommand(StringBuilder command, | |
493 | int pos) | |
494 | { | |
495 | ||
496 | // work back to last 'select' | |
497 | 12 | int p = command.length(), q = p; |
498 | 12 | do |
499 | { | |
500 | 74 | p -= 6; |
501 | 74 | if (p < 1) |
502 | { | |
503 | 0 | p = 0; |
504 | } | |
505 | 74 | ; |
506 | ? | } while ((q = command.indexOf("select", p)) == -1 && p > 0); |
507 | ||
508 | 12 | StringBuilder sb = new StringBuilder(command.substring(0, q + 7)); |
509 | ||
510 | 12 | command = command.delete(0, q + 7); |
511 | ||
512 | 12 | String start; |
513 | ||
514 | 12 | if (command.indexOf("-") > -1) |
515 | { | |
516 | 8 | start = command.substring(0, command.indexOf("-")); |
517 | } | |
518 | else | |
519 | { | |
520 | 4 | start = command.substring(0, command.indexOf(":")); |
521 | } | |
522 | ||
523 | 12 | sb.append(start + "-" + pos + command.substring(command.indexOf(":"))); |
524 | ||
525 | 12 | return sb; |
526 | } | |
527 | ||
528 | 2 | @Override |
529 | public StructureCommandI openSession(String filepath) | |
530 | { | |
531 | 2 | return loadFile(filepath); |
532 | } | |
533 | ||
534 | 1 | @Override |
535 | public StructureCommandI closeViewer() | |
536 | { | |
537 | 1 | return null; // not an external viewer |
538 | } | |
539 | } |