Coverage Report
File JmolCommands.java
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29% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| JmolCommands | 52 | 139 | 56 |
Contributing tests
This file is covered by 38 tests.
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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.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 | 1368 | protected String getColourString(Color c) |
| 97 | { | |
| 98 | 1369 | 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 | 1348 | @Override |
| 251 | protected StructureCommandI colourResidues(String atomSpec, Color colour) | |
| 252 | { | |
| 253 | 1348 | StringBuilder sb = new StringBuilder(atomSpec.length() + 20); |
| 254 | 1347 | sb.append("select ").append(atomSpec).append(getCommandSeparator()) |
| 255 | .append("color").append(getColourString(colour)); | |
| 256 | 1348 | 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 | 1369 | @Override |
| 276 | public String getAtomSpec(AtomSpecModel model, AtomSpecType specType) | |
| 277 | { | |
| 278 | 1369 | StringBuilder sb = new StringBuilder(128); |
| 279 | ||
| 280 | 1369 | boolean first = true; |
| 281 | 1369 | for (String modelNo : model.getModels()) |
| 282 | { | |
| 283 | 1378 | for (String chain : model.getChains(modelNo)) |
| 284 | { | |
| 285 | 1397 | for (int[] range : model.getRanges(modelNo, chain)) |
| 286 | { | |
| 287 | 6317 | if (!first) |
| 288 | { | |
| 289 | 4949 | sb.append(PIPE); |
| 290 | } | |
| 291 | 6317 | first = false; |
| 292 | 6317 | if (range[0] == range[1]) |
| 293 | { | |
| 294 | 5446 | sb.append(range[0]); |
| 295 | } | |
| 296 | else | |
| 297 | { | |
| 298 | 871 | sb.append(range[0]).append(HYPHEN).append(range[1]); |
| 299 | } | |
| 300 | 6316 | sb.append(COLON).append(chain.trim()).append(SLASH); |
| 301 | 6316 | sb.append(String.valueOf(modelNo)).append(".1"); |
| 302 | } | |
| 303 | } | |
| 304 | } | |
| 305 | ||
| 306 | 1369 | 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 | } |