2 * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3 * Copyright (C) $$Year-Rel$$ The Jalview Authors
5 * This file is part of Jalview.
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.
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.
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.
21 package jalview.ext.rbvi.chimera;
23 import java.awt.Color;
24 import java.util.ArrayList;
25 import java.util.Arrays;
26 import java.util.List;
29 import jalview.structure.AtomSpecModel;
30 import jalview.structure.StructureCommand;
31 import jalview.structure.StructureCommandI;
32 import jalview.structure.StructureCommandsBase;
33 import jalview.util.ColorUtils;
36 * Routines for generating Chimera commands for Jalview/Chimera binding
39 * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/framecommand.html
42 public class ChimeraCommands extends StructureCommandsBase
44 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/focus.html
45 private static final StructureCommand FOCUS_VIEW = new StructureCommand("focus");
47 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listresattr
48 private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand("list resattr");
50 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/stop.html
51 private static final StructureCommand CLOSE_CHIMERA = new StructureCommand("stop really");
53 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
54 private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand("listen stop selection");
56 private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand("listen stop models");
58 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listselection
59 private static final StructureCommand GET_SELECTION = new StructureCommand("list selection level residue");
61 private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
62 "~display all;~ribbon;chain @CA|P");
64 private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand(
65 "color white;color red ::ASP,GLU;color blue ::LYS,ARG;color yellow ::CYS");
67 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/rainbow.html
68 private static final StructureCommandI COLOUR_BY_CHAIN = new StructureCommand(
71 // Chimera clause to exclude alternate locations in atom selection
72 private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
75 public StructureCommandI colourResidues(String atomSpec, Color colour)
77 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/color.html
78 String colourCode = getColourString(colour);
79 return new StructureCommand("color " + colourCode + " " + atomSpec);
83 * Returns a colour formatted suitable for use in viewer command syntax
88 protected String getColourString(Color colour)
90 return ColorUtils.toTkCode(colour);
94 * Traverse the map of features/values/models/chains/positions to construct a
95 * list of 'setattr' commands (one per distinct feature type and value).
97 * The format of each command is
100 * <blockquote> setattr r <featureName> " " #modelnumber:range.chain
101 * e.g. setattr r jv_chain <value> #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
110 public List<StructureCommandI> setAttributes(
111 Map<String, Map<Object, AtomSpecModel>> featureMap)
113 List<StructureCommandI> commands = new ArrayList<>();
114 for (String featureType : featureMap.keySet())
116 String attributeName = makeAttributeName(featureType);
119 * clear down existing attributes for this feature
121 // 'problem' - sets attribute to None on all residues - overkill?
122 // commands.add("~setattr r " + attributeName + " :*");
124 Map<Object, AtomSpecModel> values = featureMap.get(featureType);
125 for (Object value : values.keySet())
128 * for each distinct value recorded for this feature type,
129 * add a command to set the attribute on the mapped residues
130 * Put values in single quotes, encoding any embedded single quotes
132 AtomSpecModel atomSpecModel = values.get(value);
133 String featureValue = value.toString();
134 featureValue = featureValue.replaceAll("\\'", "'");
135 StructureCommandI cmd = setAttribute(attributeName, featureValue,
145 * Returns a viewer command to set the given residue attribute value on
146 * residues specified by the AtomSpecModel, for example
149 * setatr res jv_chain 'primary' #1:12-34,48-55.B
152 * @param attributeName
153 * @param attributeValue
154 * @param atomSpecModel
157 protected StructureCommandI setAttribute(String attributeName,
158 String attributeValue,
159 AtomSpecModel atomSpecModel)
161 StringBuilder sb = new StringBuilder(128);
162 sb.append("setattr res ").append(attributeName).append(" '")
163 .append(attributeValue).append("' ");
164 sb.append(getAtomSpec(atomSpecModel, false));
165 return new StructureCommand(sb.toString());
169 * Makes a prefixed and valid Chimera attribute name. A jv_ prefix is applied
170 * for a 'Jalview' namespace, and any non-alphanumeric character is converted
175 * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
178 protected String makeAttributeName(String featureType)
180 String attName = super.makeAttributeName(featureType);
183 * Chimera treats an attribute name ending in 'color' as colour-valued;
184 * Jalview doesn't, so prevent this by appending an underscore
186 if (attName.toUpperCase().endsWith("COLOR"))
195 public StructureCommandI colourByChain()
197 return COLOUR_BY_CHAIN;
201 public List<StructureCommandI> colourByCharge()
203 return Arrays.asList(COLOUR_BY_CHARGE);
207 public String getResidueSpec(String residue)
209 return "::" + residue;
213 public StructureCommandI setBackgroundColour(Color col)
215 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/set.html#bgcolor
216 return new StructureCommand("set bgColor " + ColorUtils.toTkCode(col));
220 public StructureCommandI focusView()
226 public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
230 * Form Chimera match command to match spec to ref
231 * (the first set of atoms are moved on to the second)
233 * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA
235 * @see https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
237 StringBuilder cmd = new StringBuilder();
238 String atomSpecAlphaOnly = getAtomSpec(spec, true);
239 String refSpecAlphaOnly = getAtomSpec(ref, true);
240 cmd.append("match ").append(atomSpecAlphaOnly).append(" ").append(refSpecAlphaOnly);
243 * show superposed residues as ribbon
245 String atomSpec = getAtomSpec(spec, false);
246 String refSpec = getAtomSpec(ref, false);
247 cmd.append("; ribbon ");
248 cmd.append(atomSpec).append("|").append(refSpec).append("; focus");
250 return Arrays.asList(new StructureCommand(cmd.toString()));
254 public StructureCommandI openCommandFile(String path)
256 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html
257 return new StructureCommand("open cmd:" + path);
261 public StructureCommandI saveSession(String filepath)
263 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/save.html
264 return new StructureCommand("save " + filepath);
268 * Returns the range(s) modelled by {@code atomSpec} formatted as a Chimera
269 * atomspec string, e.g.
272 * #0:15.A,28.A,54.A,70-72.A|#1:2.A,6.A,11.A,13-14.A
277 * <li>#0 is a model number</li>
278 * <li>15 or 70-72 is a residue number, or range of residue numbers</li>
279 * <li>.A is a chain identifier</li>
280 * <li>residue ranges are separated by comma</li>
281 * <li>atomspecs for distinct models are separated by | (or)</li>
289 * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
292 public String getAtomSpec(AtomSpecModel atomSpec, boolean alphaOnly)
294 StringBuilder sb = new StringBuilder(128);
295 boolean firstModel = true;
296 for (String model : atomSpec.getModels())
303 appendModel(sb, model, atomSpec, alphaOnly);
305 return sb.toString();
309 * A helper method to append an atomSpec string for atoms in the given model
316 protected void appendModel(StringBuilder sb, String model,
317 AtomSpecModel atomSpec, boolean alphaOnly)
319 sb.append("#").append(model).append(":");
321 boolean firstPositionForModel = true;
323 for (String chain : atomSpec.getChains(model))
325 chain = " ".equals(chain) ? chain : chain.trim();
327 List<int[]> rangeList = atomSpec.getRanges(model, chain);
328 for (int[] range : rangeList)
330 appendRange(sb, range[0], range[1], chain, firstPositionForModel,
332 firstPositionForModel = false;
338 * restrict to alpha carbon, no alternative locations
339 * (needed to ensuring matching atom counts for superposition)
341 // TODO @P instead if RNA - add nucleotide flag to AtomSpecModel?
342 sb.append("@CA").append(NO_ALTLOCS);
347 public List<StructureCommandI> showBackbone()
349 return Arrays.asList(SHOW_BACKBONE);
353 public StructureCommandI loadFile(String file)
355 return new StructureCommand("open " + file);
359 public StructureCommandI openSession(String filepath)
361 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html
362 // this version of the command has no dependency on file extension
363 return new StructureCommand("open chimera:" + filepath);
367 public StructureCommandI showStructures(AtomSpecModel restrictTo)
369 if (restrictTo == null)
371 return new StructureCommand("ribbon");
374 String atomSpec = getAtomSpec(restrictTo, false);
375 String cmd = "ribbon " + atomSpec;
376 return new StructureCommand(cmd);
380 public StructureCommandI hideChain(String modelId, String chainId)
382 String what = "#" + modelId + ":." + chainId;
383 return new StructureCommand("~ribbon " + what + ";~display " + what);
387 public StructureCommandI hideAll()
389 return new StructureCommand("~display; ~ribbon");
391 public StructureCommandI closeViewer()
393 return CLOSE_CHIMERA;
397 public List<StructureCommandI> startNotifications(String uri)
399 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
400 List<StructureCommandI> cmds = new ArrayList<>();
401 cmds.add(new StructureCommand("listen start models url " + uri));
402 cmds.add(new StructureCommand("listen start select prefix SelectionChanged url " + uri));
407 public List<StructureCommandI> stopNotifications()
409 List<StructureCommandI> cmds = new ArrayList<>();
410 cmds.add(STOP_NOTIFY_MODELS);
411 cmds.add(STOP_NOTIFY_SELECTION);
416 public StructureCommandI getSelectedResidues()
418 return GET_SELECTION;
422 public StructureCommandI listResidueAttributes()
424 return LIST_RESIDUE_ATTRIBUTES;
428 public StructureCommandI getResidueAttributes(String attName)
430 // this alternative command
431 // list residues spec ':*/attName' attr attName
432 // doesn't report 'None' values (which is good), but
433 // fails for 'average.bfactor' (which is bad):
434 return new StructureCommand("list residues attr '" + attName + "'");