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.util.Locale;
25 import java.awt.Color;
26 import java.util.ArrayList;
27 import java.util.Arrays;
28 import java.util.List;
31 import jalview.structure.AtomSpecModel;
32 import jalview.structure.StructureCommand;
33 import jalview.structure.StructureCommandI;
34 import jalview.structure.StructureCommandsBase;
35 import jalview.structure.StructureCommandsI.AtomSpecType;
36 import jalview.util.ColorUtils;
39 * Routines for generating Chimera commands for Jalview/Chimera binding
44 public class ChimeraCommands extends StructureCommandsBase
46 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/focus.html
47 private static final StructureCommand FOCUS_VIEW = new StructureCommand(
50 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listresattr
51 private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand(
54 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/stop.html
55 private static final StructureCommand CLOSE_CHIMERA = new StructureCommand(
58 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
59 private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand(
60 "listen stop selection");
62 private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand(
63 "listen stop models");
65 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listselection
66 private static final StructureCommand GET_SELECTION = new StructureCommand(
67 "list selection level residue");
69 private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
70 "~display all;~ribbon;chain @CA|P");
72 private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand(
73 "color white;color red ::ASP,GLU;color blue ::LYS,ARG;color yellow ::CYS");
75 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/rainbow.html
76 private static final StructureCommandI COLOUR_BY_CHAIN = new StructureCommand(
79 // Chimera clause to exclude alternate locations in atom selection
80 private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
83 public StructureCommandI colourResidues(String atomSpec, Color colour)
85 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/color.html
86 String colourCode = getColourString(colour);
87 return new StructureCommand("color " + colourCode + " " + atomSpec);
91 * Returns a colour formatted suitable for use in viewer command syntax
96 protected String getColourString(Color colour)
98 return ColorUtils.toTkCode(colour);
102 * Traverse the map of features/values/models/chains/positions to construct a
103 * list of 'setattr' commands (one per distinct feature type and value).
105 * The format of each command is
108 * <blockquote> setattr r <featureName> " " #modelnumber:range.chain
109 * e.g. setattr r jv_chain <value> #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
117 public List<StructureCommandI> setAttributes(
118 Map<String, Map<Object, AtomSpecModel>> featureMap)
120 List<StructureCommandI> commands = new ArrayList<>();
121 for (String featureType : featureMap.keySet())
123 String attributeName = makeAttributeName(featureType);
126 * clear down existing attributes for this feature
128 // 'problem' - sets attribute to None on all residues - overkill?
129 // commands.add("~setattr r " + attributeName + " :*");
131 Map<Object, AtomSpecModel> values = featureMap.get(featureType);
132 for (Object value : values.keySet())
135 * for each distinct value recorded for this feature type,
136 * add a command to set the attribute on the mapped residues
137 * Put values in single quotes, encoding any embedded single quotes
139 AtomSpecModel atomSpecModel = values.get(value);
140 String featureValue = value.toString();
141 featureValue = featureValue.replaceAll("\\'", "'");
142 StructureCommandI cmd = setAttribute(attributeName, featureValue,
152 * Returns a viewer command to set the given residue attribute value on
153 * residues specified by the AtomSpecModel, for example
156 * setatr res jv_chain 'primary' #1:12-34,48-55.B
159 * @param attributeName
160 * @param attributeValue
161 * @param atomSpecModel
164 protected StructureCommandI setAttribute(String attributeName,
165 String attributeValue, AtomSpecModel atomSpecModel)
167 StringBuilder sb = new StringBuilder(128);
168 sb.append("setattr res ").append(attributeName).append(" '")
169 .append(attributeValue).append("' ");
170 sb.append(getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY));
171 return new StructureCommand(sb.toString());
175 * Makes a prefixed and valid Chimera attribute name. A jv_ prefix is applied
176 * for a 'Jalview' namespace, and any non-alphanumeric character is converted
181 * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
184 protected String makeAttributeName(String featureType)
186 String attName = super.makeAttributeName(featureType);
189 * Chimera treats an attribute name ending in 'color' as colour-valued;
190 * Jalview doesn't, so prevent this by appending an underscore
192 if (attName.toUpperCase(Locale.ROOT).endsWith("COLOR"))
201 public StructureCommandI colourByChain()
203 return COLOUR_BY_CHAIN;
207 public List<StructureCommandI> colourByCharge()
209 return Arrays.asList(COLOUR_BY_CHARGE);
213 public String getResidueSpec(String residue)
215 return "::" + residue;
219 public StructureCommandI setBackgroundColour(Color col)
221 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/set.html#bgcolor
222 return new StructureCommand("set bgColor " + ColorUtils.toTkCode(col));
226 public StructureCommandI focusView()
232 public List<StructureCommandI> showChains(List<String> toShow)
235 * Construct a chimera command like
237 * ~display #*;~ribbon #*;ribbon :.A,:.B
239 StringBuilder cmd = new StringBuilder(64);
240 boolean first = true;
241 for (String chain : toShow)
243 String[] tokens = chain.split(":");
244 if (tokens.length == 2)
246 String showChainCmd = tokens[0] + ":." + tokens[1];
251 cmd.append(showChainCmd);
257 * could append ";focus" to this command to resize the display to fill the
258 * window, but it looks more helpful not to (easier to relate chains to the
261 final String command = "~display #*; ~ribbon #*; ribbon :"
263 return Arrays.asList(new StructureCommand(command));
267 public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
268 AtomSpecModel spec, AtomSpecType backbone)
271 * Form Chimera match command to match spec to ref
272 * (the first set of atoms are moved on to the second)
274 * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA
276 * @see https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
278 StringBuilder cmd = new StringBuilder();
279 String atomSpecAlphaOnly = getAtomSpec(spec, backbone);
280 String refSpecAlphaOnly = getAtomSpec(ref, backbone);
281 cmd.append("match ").append(atomSpecAlphaOnly).append(" ")
282 .append(refSpecAlphaOnly);
285 * show superposed residues as ribbon
287 String atomSpec = getAtomSpec(spec, AtomSpecType.RESIDUE_ONLY);
288 String refSpec = getAtomSpec(ref, AtomSpecType.RESIDUE_ONLY);
289 cmd.append("; ribbon ");
290 cmd.append(atomSpec).append("|").append(refSpec).append("; focus");
292 return Arrays.asList(new StructureCommand(cmd.toString()));
296 public StructureCommandI openCommandFile(String path)
298 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html
299 return new StructureCommand("open cmd:" + path);
303 public StructureCommandI saveSession(String filepath)
305 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/save.html
306 return new StructureCommand("save " + filepath);
310 * Returns the range(s) modelled by {@code atomSpec} formatted as a Chimera
311 * atomspec string, e.g.
314 * #0:15.A,28.A,54.A,70-72.A|#1:2.A,6.A,11.A,13-14.A
319 * <li>#0 is a model number</li>
320 * <li>15 or 70-72 is a residue number, or range of residue numbers</li>
321 * <li>.A is a chain identifier</li>
322 * <li>residue ranges are separated by comma</li>
323 * <li>atomspecs for distinct models are separated by | (or)</li>
331 * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
334 public String getAtomSpec(AtomSpecModel atomSpec, AtomSpecType specType)
336 StringBuilder sb = new StringBuilder(128);
337 boolean firstModel = true;
338 for (String model : atomSpec.getModels())
345 appendModel(sb, model, atomSpec, specType);
347 return sb.toString();
351 * A helper method to append an atomSpec string for atoms in the given model
358 protected void appendModel(StringBuilder sb, String model,
359 AtomSpecModel atomSpec, AtomSpecType specType)
361 sb.append("#").append(model).append(":");
363 boolean firstPositionForModel = true;
365 for (String chain : atomSpec.getChains(model))
367 chain = " ".equals(chain) ? chain : chain.trim();
369 List<int[]> rangeList = atomSpec.getRanges(model, chain);
370 for (int[] range : rangeList)
372 appendRange(sb, range[0], range[1], chain, firstPositionForModel,
374 firstPositionForModel = false;
377 if (specType == AtomSpecType.ALPHA)
380 * restrict to alpha carbon, no alternative locations
381 * (needed to ensuring matching atom counts for superposition)
383 sb.append("@CA").append(NO_ALTLOCS);
385 if (specType == AtomSpecType.PHOSPHATE)
387 sb.append("@P").append(NO_ALTLOCS);
392 public List<StructureCommandI> showBackbone()
394 return Arrays.asList(SHOW_BACKBONE);
398 public StructureCommandI loadFile(String file)
400 return new StructureCommand("open " + file);
404 public StructureCommandI openSession(String filepath)
406 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html
407 // this version of the command has no dependency on file extension
408 return new StructureCommand("open chimera:" + filepath);
412 public StructureCommandI closeViewer()
414 return CLOSE_CHIMERA;
418 public List<StructureCommandI> startNotifications(String uri)
420 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
421 List<StructureCommandI> cmds = new ArrayList<>();
422 cmds.add(new StructureCommand("listen start models url " + uri));
423 cmds.add(new StructureCommand(
424 "listen start select prefix SelectionChanged url " + uri));
429 public List<StructureCommandI> stopNotifications()
431 List<StructureCommandI> cmds = new ArrayList<>();
432 cmds.add(STOP_NOTIFY_MODELS);
433 cmds.add(STOP_NOTIFY_SELECTION);
438 public StructureCommandI getSelectedResidues()
440 return GET_SELECTION;
444 public StructureCommandI listResidueAttributes()
446 return LIST_RESIDUE_ATTRIBUTES;
450 public StructureCommandI getResidueAttributes(String attName)
452 // this alternative command
453 // list residues spec ':*/attName' attr attName
454 // doesn't report 'None' values (which is good), but
455 // fails for 'average.bfactor' (which is bad):
456 return new StructureCommand("list residues attr '" + attName + "'");