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PymolCommands | 44 | 77 | 25 |
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.pymol; | |
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.structure.AtomSpecModel; | |
30 | import jalview.structure.StructureCommand; | |
31 | import jalview.structure.StructureCommandI; | |
32 | import jalview.structure.StructureCommandsBase; | |
33 | ||
34 | /** | |
35 | * A class that generates commands to send to PyMol over its XML-RPC interface. | |
36 | * <p> | |
37 | * Note that because the xml-rpc interface can only accept one command at a | |
38 | * time, we can't concatenate commands, and must instead form and send them | |
39 | * individually. | |
40 | * | |
41 | * @see https://pymolwiki.org/index.php/Category:Commands | |
42 | * @see https://pymolwiki.org/index.php/RPC | |
43 | */ | |
44 | public class PymolCommands extends StructureCommandsBase | |
45 | { | |
46 | // https://pymol.org/dokuwiki/doku.php?id=command:zoom | |
47 | // not currently documented on | |
48 | // https://pymolwiki.org/index.php/Category:Commands | |
49 | private static final StructureCommand FOCUS_VIEW = new StructureCommand( | |
50 | "zoom"); | |
51 | ||
52 | // https://pymolwiki.org/index.php/Quit | |
53 | private static final StructureCommand CLOSE_PYMOL = new StructureCommand( | |
54 | "quit"); | |
55 | ||
56 | // not currently documented on | |
57 | // https://pymolwiki.org/index.php/Category:Commands | |
58 | private static final StructureCommand COLOUR_BY_CHAIN = new StructureCommand( | |
59 | "spectrum", "chain"); | |
60 | ||
61 | private static final List<StructureCommandI> COLOR_BY_CHARGE = Arrays | |
62 | .asList(new StructureCommand("color", "white", "*"), | |
63 | new StructureCommand("color", "red", "resn ASP resn GLU"), | |
64 | new StructureCommand("color", "blue", | |
65 | "resn LYS resn ARG"), | |
66 | new StructureCommand("color", "yellow", "resn CYS")); | |
67 | ||
68 | private static final List<StructureCommandI> SHOW_BACKBONE = Arrays | |
69 | .asList(new StructureCommand("hide", "everything"), | |
70 | new StructureCommand("show", "ribbon")); | |
71 | ||
72 | 1 | @Override |
73 | public StructureCommandI colourByChain() | |
74 | { | |
75 | 1 | return COLOUR_BY_CHAIN; |
76 | } | |
77 | ||
78 | 1 | @Override |
79 | public List<StructureCommandI> colourByCharge() | |
80 | { | |
81 | 1 | return COLOR_BY_CHARGE; |
82 | } | |
83 | ||
84 | 1 | @Override |
85 | public StructureCommandI setBackgroundColour(Color col) | |
86 | { | |
87 | // https://pymolwiki.org/index.php/Bg_Color | |
88 | 1 | return new StructureCommand("bg_color", getColourString(col)); |
89 | } | |
90 | ||
91 | /** | |
92 | * Returns a colour formatted suitable for use in viewer command syntax. For | |
93 | * example, red is {@code "0xff0000"}. | |
94 | * | |
95 | * @param c | |
96 | * @return | |
97 | */ | |
98 | 5 | protected String getColourString(Color c) |
99 | { | |
100 | 5 | return String.format("0x%02x%02x%02x", c.getRed(), c.getGreen(), |
101 | c.getBlue()); | |
102 | } | |
103 | ||
104 | 0 | @Override |
105 | public StructureCommandI focusView() | |
106 | { | |
107 | 0 | return FOCUS_VIEW; |
108 | } | |
109 | ||
110 | 0 | @Override |
111 | public List<StructureCommandI> showChains(List<String> toShow) | |
112 | { | |
113 | // https://pymolwiki.org/index.php/Show | |
114 | 0 | List<StructureCommandI> commands = new ArrayList<>(); |
115 | 0 | commands.add(new StructureCommand("hide", "everything")); |
116 | 0 | commands.add(new StructureCommand("show", "lines")); |
117 | 0 | StringBuilder chains = new StringBuilder(); |
118 | 0 | for (String chain : toShow) |
119 | { | |
120 | 0 | chains.append(" chain ").append(chain); |
121 | } | |
122 | 0 | commands.add( |
123 | new StructureCommand("show", "cartoon", chains.toString())); | |
124 | 0 | return commands; |
125 | } | |
126 | ||
127 | 1 | @Override |
128 | public List<StructureCommandI> superposeStructures(AtomSpecModel refAtoms, | |
129 | AtomSpecModel atomSpec, AtomSpecType specType) | |
130 | { | |
131 | ||
132 | // https://pymolwiki.org/index.php/Super | |
133 | 1 | List<StructureCommandI> commands = new ArrayList<>(); |
134 | 1 | String refAtomsAlphaOnly = "(" + getAtomSpec(refAtoms, specType) |
135 | + " and (altloc '' or altloc 'a'))"; | |
136 | 1 | String atomSpec2AlphaOnly = "(" + getAtomSpec(atomSpec, specType) |
137 | + " and (altloc '' or altloc 'a'))"; | |
138 | // pair_fit mobile -> reference | |
139 | // crashes when undo is enabled on 2.5.2 (incentive) | |
140 | 1 | commands.add(new StructureCommand("undo_disable")); |
141 | 1 | commands.add(new StructureCommand("pair_fit", atomSpec2AlphaOnly, |
142 | refAtomsAlphaOnly)); | |
143 | 1 | commands.add(new StructureCommand("undo_enable")); |
144 | ||
145 | /* | |
146 | * and show superposed residues as cartoon | |
147 | */ | |
148 | 1 | String refAtomsAll = getAtomSpec(refAtoms, AtomSpecType.RESIDUE_ONLY); |
149 | 1 | String atomSpec2All = getAtomSpec(atomSpec, AtomSpecType.RESIDUE_ONLY); |
150 | 1 | commands.add(new StructureCommand("show", "cartoon", |
151 | refAtomsAll + " " + atomSpec2All)); | |
152 | ||
153 | 1 | return commands; |
154 | } | |
155 | ||
156 | 1 | @Override |
157 | public StructureCommandI openCommandFile(String path) | |
158 | { | |
159 | // https://pymolwiki.org/index.php/Run | |
160 | 1 | return new StructureCommand("run", path); // should be .pml |
161 | } | |
162 | ||
163 | 1 | @Override |
164 | public StructureCommandI saveSession(String filepath) | |
165 | { | |
166 | // https://pymolwiki.org/index.php/Save#EXAMPLES | |
167 | 1 | return new StructureCommand("save", filepath); // should be .pse |
168 | } | |
169 | ||
170 | /** | |
171 | * Returns a selection string in PyMOL 'selection macro' format: | |
172 | * | |
173 | * <pre> | |
174 | * modelId// chain/residues/ | |
175 | * </pre> | |
176 | * | |
177 | * If more than one chain, makes a selection expression for each, and they are | |
178 | * separated by spaces. | |
179 | * | |
180 | * @see https://pymolwiki.org/index.php/Selection_Macros | |
181 | */ | |
182 | 36 | @Override |
183 | public String getAtomSpec(AtomSpecModel model, AtomSpecType specType) | |
184 | { | |
185 | 36 | StringBuilder sb = new StringBuilder(64); |
186 | 36 | boolean first = true; |
187 | 36 | for (String modelId : model.getModels()) |
188 | { | |
189 | 52 | for (String chain : model.getChains(modelId)) |
190 | { | |
191 | 86 | if (!first) |
192 | { | |
193 | 52 | sb.append(" "); |
194 | } | |
195 | 86 | first = false; |
196 | 86 | List<int[]> rangeList = model.getRanges(modelId, chain); |
197 | 86 | chain = chain.trim(); |
198 | 86 | sb.append(modelId).append("//").append(chain).append("/"); |
199 | 86 | boolean firstRange = true; |
200 | 86 | for (int[] range : rangeList) |
201 | { | |
202 | 111 | if (!firstRange) |
203 | { | |
204 | 25 | sb.append("+"); |
205 | } | |
206 | 111 | firstRange = false; |
207 | 111 | sb.append(String.valueOf(range[0])); |
208 | 111 | if (range[0] != range[1]) |
209 | { | |
210 | 86 | sb.append("-").append(String.valueOf(range[1])); |
211 | } | |
212 | } | |
213 | 86 | sb.append("/"); |
214 | 86 | if (specType == AtomSpecType.ALPHA) |
215 | { | |
216 | 34 | sb.append("CA"); |
217 | } | |
218 | 86 | if (specType == AtomSpecType.PHOSPHATE) |
219 | { | |
220 | 0 | sb.append("P"); |
221 | } | |
222 | } | |
223 | } | |
224 | 36 | return sb.toString(); |
225 | } | |
226 | ||
227 | 1 | @Override |
228 | public List<StructureCommandI> showBackbone() | |
229 | { | |
230 | 1 | return SHOW_BACKBONE; |
231 | } | |
232 | ||
233 | 4 | @Override |
234 | protected StructureCommandI colourResidues(String atomSpec, Color colour) | |
235 | { | |
236 | // https://pymolwiki.org/index.php/Color | |
237 | 4 | return new StructureCommand("color", getColourString(colour), atomSpec); |
238 | } | |
239 | ||
240 | 1 | @Override |
241 | protected String getResidueSpec(String residue) | |
242 | { | |
243 | // https://pymolwiki.org/index.php/Selection_Algebra | |
244 | 1 | return "resn " + residue; |
245 | } | |
246 | ||
247 | 1 | @Override |
248 | public StructureCommandI loadFile(String file) | |
249 | { | |
250 | 1 | return new StructureCommand("load", file); |
251 | } | |
252 | ||
253 | /** | |
254 | * Overrides the default implementation (which generates concatenated | |
255 | * commands) to generate one per colour (because the XML-RPC interface to | |
256 | * PyMOL only accepts one command at a time) | |
257 | * | |
258 | * @param colourMap | |
259 | * @return | |
260 | */ | |
261 | 1 | @Override |
262 | public List<StructureCommandI> colourBySequence( | |
263 | Map<Object, AtomSpecModel> colourMap) | |
264 | { | |
265 | 1 | List<StructureCommandI> commands = new ArrayList<>(); |
266 | 1 | for (Object key : colourMap.keySet()) |
267 | { | |
268 | 3 | Color colour = (Color) key; |
269 | 3 | final AtomSpecModel colourData = colourMap.get(colour); |
270 | 3 | commands.add(getColourCommand(colourData, colour)); |
271 | } | |
272 | ||
273 | 1 | return commands; |
274 | } | |
275 | ||
276 | /** | |
277 | * Returns a viewer command to set the given atom property value on atoms | |
278 | * specified by the AtomSpecModel, for example | |
279 | * | |
280 | * <pre> | |
281 | * iterate 4zho//B/12-34,48-55/CA,jv_chain='primary' | |
282 | * </pre> | |
283 | * | |
284 | * @param attributeName | |
285 | * @param attributeValue | |
286 | * @param atomSpecModel | |
287 | * @return | |
288 | */ | |
289 | 7 | protected StructureCommandI setAttribute(String attributeName, |
290 | String attributeValue, AtomSpecModel atomSpecModel) | |
291 | { | |
292 | 7 | StringBuilder sb = new StringBuilder(128); |
293 | 7 | sb.append("p.").append(attributeName).append("='") |
294 | .append(attributeValue).append("'"); | |
295 | 7 | String atomSpec = getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY); |
296 | 7 | return new StructureCommand("iterate", atomSpec, sb.toString()); |
297 | } | |
298 | ||
299 | /** | |
300 | * Traverse the map of features/values/models/chains/positions to construct a | |
301 | * list of 'set property' commands (one per distinct feature type and value). | |
302 | * The values are stored in the 'p' dictionary of user-defined properties of | |
303 | * each atom. | |
304 | * <p> | |
305 | * The format of each command is | |
306 | * | |
307 | * <pre> | |
308 | * <blockquote> iterate atomspec, p.featureName='value' | |
309 | * e.g. iterate 4zho//A/23,28-29/CA, p.jv_Metal='Fe' | |
310 | * </blockquote> | |
311 | * </pre> | |
312 | * | |
313 | * @param featureMap | |
314 | * @return | |
315 | */ | |
316 | 5 | @Override |
317 | public List<StructureCommandI> setAttributes( | |
318 | Map<String, Map<Object, AtomSpecModel>> featureMap) | |
319 | { | |
320 | 5 | List<StructureCommandI> commands = new ArrayList<>(); |
321 | 5 | for (String featureType : featureMap.keySet()) |
322 | { | |
323 | 5 | String attributeName = makeAttributeName(featureType); |
324 | ||
325 | /* | |
326 | * todo: clear down existing attributes for this feature? | |
327 | */ | |
328 | // commands.add(new StructureCommand("iterate", "all", | |
329 | // "p."+attributeName+"='None'"); //? | |
330 | ||
331 | 5 | Map<Object, AtomSpecModel> values = featureMap.get(featureType); |
332 | 5 | for (Object value : values.keySet()) |
333 | { | |
334 | /* | |
335 | * for each distinct value recorded for this feature type, | |
336 | * add a command to set the attribute on the mapped residues | |
337 | * Put values in single quotes, encoding any embedded single quotes | |
338 | */ | |
339 | 6 | AtomSpecModel atomSpecModel = values.get(value); |
340 | 6 | String featureValue = value.toString(); |
341 | 6 | featureValue = featureValue.replaceAll("\\'", "'"); |
342 | 6 | StructureCommandI cmd = setAttribute(attributeName, featureValue, |
343 | atomSpecModel); | |
344 | 6 | commands.add(cmd); |
345 | } | |
346 | } | |
347 | ||
348 | 5 | return commands; |
349 | } | |
350 | ||
351 | 1 | @Override |
352 | public StructureCommandI openSession(String filepath) | |
353 | { | |
354 | // https://pymolwiki.org/index.php/Load | |
355 | // this version of the command has no dependency on file extension | |
356 | 1 | return new StructureCommand("load", filepath, "", "0", "pse"); |
357 | } | |
358 | ||
359 | 1 | @Override |
360 | public StructureCommandI closeViewer() | |
361 | { | |
362 | // https://pymolwiki.org/index.php/Quit | |
363 | 1 | return CLOSE_PYMOL; |
364 | } | |
365 | ||
366 | 0 | @Override |
367 | public List<StructureCommandI> centerViewOn(List<AtomSpecModel> residues) | |
368 | { | |
369 | // TODO Auto-generated method stub | |
370 | 0 | return null; |
371 | } | |
372 | ||
373 | } |