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
41 public class ChimeraCommands extends StructureCommandsBase
43 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/focus.html
44 private static final StructureCommand FOCUS_VIEW = new StructureCommand("focus");
46 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listresattr
47 private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand("list resattr");
49 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/stop.html
50 private static final StructureCommand CLOSE_CHIMERA = new StructureCommand("stop really");
52 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
53 private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand("listen stop selection");
55 private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand("listen stop models");
57 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listselection
58 private static final StructureCommand GET_SELECTION = new StructureCommand("list selection level residue");
60 private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
61 "~display all;~ribbon;chain @CA|P");
63 private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand(
64 "color white;color red ::ASP,GLU;color blue ::LYS,ARG;color yellow ::CYS");
66 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/rainbow.html
67 private static final StructureCommandI COLOUR_BY_CHAIN = new StructureCommand(
70 // Chimera clause to exclude alternate locations in atom selection
71 private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
74 public StructureCommandI colourResidues(String atomSpec, Color colour)
76 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/color.html
77 String colourCode = getColourString(colour);
78 return new StructureCommand("color " + colourCode + " " + atomSpec);
82 * Returns a colour formatted suitable for use in viewer command syntax
87 protected String getColourString(Color colour)
89 return ColorUtils.toTkCode(colour);
93 * Traverse the map of features/values/models/chains/positions to construct a
94 * list of 'setattr' commands (one per distinct feature type and value).
96 * The format of each command is
99 * <blockquote> setattr r <featureName> " " #modelnumber:range.chain
100 * e.g. setattr r jv_chain <value> #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
108 public List<StructureCommandI> setAttributes(
109 Map<String, Map<Object, AtomSpecModel>> featureMap)
111 List<StructureCommandI> commands = new ArrayList<>();
112 for (String featureType : featureMap.keySet())
114 String attributeName = makeAttributeName(featureType);
117 * clear down existing attributes for this feature
119 // 'problem' - sets attribute to None on all residues - overkill?
120 // commands.add("~setattr r " + attributeName + " :*");
122 Map<Object, AtomSpecModel> values = featureMap.get(featureType);
123 for (Object value : values.keySet())
126 * for each distinct value recorded for this feature type,
127 * add a command to set the attribute on the mapped residues
128 * Put values in single quotes, encoding any embedded single quotes
130 AtomSpecModel atomSpecModel = values.get(value);
131 String featureValue = value.toString();
132 featureValue = featureValue.replaceAll("\\'", "'");
133 StructureCommandI cmd = setAttribute(attributeName, featureValue,
143 * Returns a viewer command to set the given residue attribute value on
144 * residues specified by the AtomSpecModel, for example
147 * setatr res jv_chain 'primary' #1:12-34,48-55.B
150 * @param attributeName
151 * @param attributeValue
152 * @param atomSpecModel
155 protected StructureCommandI setAttribute(String attributeName,
156 String attributeValue,
157 AtomSpecModel atomSpecModel)
159 StringBuilder sb = new StringBuilder(128);
160 sb.append("setattr res ").append(attributeName).append(" '")
161 .append(attributeValue).append("' ");
162 sb.append(getAtomSpec(atomSpecModel, false));
163 return new StructureCommand(sb.toString());
167 * Makes a prefixed and valid Chimera attribute name. A jv_ prefix is applied
168 * for a 'Jalview' namespace, and any non-alphanumeric character is converted
173 * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
176 protected String makeAttributeName(String featureType)
178 String attName = super.makeAttributeName(featureType);
181 * Chimera treats an attribute name ending in 'color' as colour-valued;
182 * Jalview doesn't, so prevent this by appending an underscore
184 if (attName.toUpperCase().endsWith("COLOR"))
193 public StructureCommandI colourByChain()
195 return COLOUR_BY_CHAIN;
199 public List<StructureCommandI> colourByCharge()
201 return Arrays.asList(COLOUR_BY_CHARGE);
205 public String getResidueSpec(String residue)
207 return "::" + residue;
211 public StructureCommandI setBackgroundColour(Color col)
213 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/set.html#bgcolor
214 return new StructureCommand("set bgColor " + ColorUtils.toTkCode(col));
218 public StructureCommandI focusView()
224 public List<StructureCommandI> showChains(List<String> toShow)
227 * Construct a chimera command like
229 * ~display #*;~ribbon #*;ribbon :.A,:.B
231 StringBuilder cmd = new StringBuilder(64);
232 boolean first = true;
233 for (String chain : toShow)
235 String[] tokens = chain.split(":");
236 if (tokens.length == 2)
238 String showChainCmd = tokens[0] + ":." + tokens[1];
243 cmd.append(showChainCmd);
249 * could append ";focus" to this command to resize the display to fill the
250 * window, but it looks more helpful not to (easier to relate chains to the
253 final String command = "~display #*; ~ribbon #*; ribbon :"
255 return Arrays.asList(new StructureCommand(command));
259 public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
263 * Form Chimera match command to match spec to ref
264 * (the first set of atoms are moved on to the second)
266 * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA
268 * @see https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
270 StringBuilder cmd = new StringBuilder();
271 String atomSpecAlphaOnly = getAtomSpec(spec, true);
272 String refSpecAlphaOnly = getAtomSpec(ref, true);
273 cmd.append("match ").append(atomSpecAlphaOnly).append(" ").append(refSpecAlphaOnly);
276 * show superposed residues as ribbon
278 String atomSpec = getAtomSpec(spec, false);
279 String refSpec = getAtomSpec(ref, false);
280 cmd.append("; ribbon ");
281 cmd.append(atomSpec).append("|").append(refSpec).append("; focus");
283 return Arrays.asList(new StructureCommand(cmd.toString()));
287 public StructureCommandI openCommandFile(String path)
289 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html
290 return new StructureCommand("open cmd:" + path);
294 public StructureCommandI saveSession(String filepath)
296 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/save.html
297 return new StructureCommand("save " + filepath);
301 * Returns the range(s) modelled by {@code atomSpec} formatted as a Chimera
302 * atomspec string, e.g.
305 * #0:15.A,28.A,54.A,70-72.A|#1:2.A,6.A,11.A,13-14.A
310 * <li>#0 is a model number</li>
311 * <li>15 or 70-72 is a residue number, or range of residue numbers</li>
312 * <li>.A is a chain identifier</li>
313 * <li>residue ranges are separated by comma</li>
314 * <li>atomspecs for distinct models are separated by | (or)</li>
322 * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
325 public String getAtomSpec(AtomSpecModel atomSpec, boolean alphaOnly)
327 StringBuilder sb = new StringBuilder(128);
328 boolean firstModel = true;
329 for (String model : atomSpec.getModels())
336 appendModel(sb, model, atomSpec, alphaOnly);
338 return sb.toString();
342 * A helper method to append an atomSpec string for atoms in the given model
349 protected void appendModel(StringBuilder sb, String model,
350 AtomSpecModel atomSpec, boolean alphaOnly)
352 sb.append("#").append(model).append(":");
354 boolean firstPositionForModel = true;
356 for (String chain : atomSpec.getChains(model))
358 chain = " ".equals(chain) ? chain : chain.trim();
360 List<int[]> rangeList = atomSpec.getRanges(model, chain);
361 for (int[] range : rangeList)
363 appendRange(sb, range[0], range[1], chain, firstPositionForModel,
365 firstPositionForModel = false;
371 * restrict to alpha carbon, no alternative locations
372 * (needed to ensuring matching atom counts for superposition)
374 // TODO @P instead if RNA - add nucleotide flag to AtomSpecModel?
375 sb.append("@CA").append(NO_ALTLOCS);
380 public List<StructureCommandI> showBackbone()
382 return Arrays.asList(SHOW_BACKBONE);
386 public StructureCommandI loadFile(String file)
388 return new StructureCommand("open " + file);
392 public StructureCommandI openSession(String filepath)
394 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html
395 // this version of the command has no dependency on file extension
396 return new StructureCommand("open chimera:" + filepath);
400 public StructureCommandI closeViewer()
402 return CLOSE_CHIMERA;
406 public List<StructureCommandI> startNotifications(String uri)
408 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
409 List<StructureCommandI> cmds = new ArrayList<>();
410 cmds.add(new StructureCommand("listen start models url " + uri));
411 cmds.add(new StructureCommand("listen start select prefix SelectionChanged url " + uri));
416 public List<StructureCommandI> stopNotifications()
418 List<StructureCommandI> cmds = new ArrayList<>();
419 cmds.add(STOP_NOTIFY_MODELS);
420 cmds.add(STOP_NOTIFY_SELECTION);
425 public StructureCommandI getSelectedResidues()
427 return GET_SELECTION;
431 public StructureCommandI listResidueAttributes()
433 return LIST_RESIDUE_ATTRIBUTES;
437 public StructureCommandI getResidueAttributes(String attName)
439 // this alternative command
440 // list residues spec ':*/attName' attr attName
441 // doesn't report 'None' values (which is good), but
442 // fails for 'average.bfactor' (which is bad):
443 return new StructureCommand("list residues attr '" + attName + "'");