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("focus");
49 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listresattr
50 private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand("list resattr");
52 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/stop.html
53 private static final StructureCommand CLOSE_CHIMERA = new StructureCommand("stop really");
55 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
56 private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand("listen stop selection");
58 private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand("listen stop models");
60 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html#listselection
61 private static final StructureCommand GET_SELECTION = new StructureCommand("list selection level residue");
63 private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
64 "~display all;~ribbon;chain @CA|P");
66 private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand(
67 "color white;color red ::ASP,GLU;color blue ::LYS,ARG;color yellow ::CYS");
69 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/rainbow.html
70 private static final StructureCommandI COLOUR_BY_CHAIN = new StructureCommand(
73 // Chimera clause to exclude alternate locations in atom selection
74 private static final String NO_ALTLOCS = "&~@.B-Z&~@.2-9";
77 public StructureCommandI colourResidues(String atomSpec, Color colour)
79 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/color.html
80 String colourCode = getColourString(colour);
81 return new StructureCommand("color " + colourCode + " " + atomSpec);
85 * Returns a colour formatted suitable for use in viewer command syntax
90 protected String getColourString(Color colour)
92 return ColorUtils.toTkCode(colour);
96 * Traverse the map of features/values/models/chains/positions to construct a
97 * list of 'setattr' commands (one per distinct feature type and value).
99 * The format of each command is
102 * <blockquote> setattr r <featureName> " " #modelnumber:range.chain
103 * e.g. setattr r jv_chain <value> #0:2.B,4.B,9-12.B|#1:1.A,2-6.A,...
111 public List<StructureCommandI> setAttributes(
112 Map<String, Map<Object, AtomSpecModel>> featureMap)
114 List<StructureCommandI> commands = new ArrayList<>();
115 for (String featureType : featureMap.keySet())
117 String attributeName = makeAttributeName(featureType);
120 * clear down existing attributes for this feature
122 // 'problem' - sets attribute to None on all residues - overkill?
123 // commands.add("~setattr r " + attributeName + " :*");
125 Map<Object, AtomSpecModel> values = featureMap.get(featureType);
126 for (Object value : values.keySet())
129 * for each distinct value recorded for this feature type,
130 * add a command to set the attribute on the mapped residues
131 * Put values in single quotes, encoding any embedded single quotes
133 AtomSpecModel atomSpecModel = values.get(value);
134 String featureValue = value.toString();
135 featureValue = featureValue.replaceAll("\\'", "'");
136 StructureCommandI cmd = setAttribute(attributeName, featureValue,
146 * Returns a viewer command to set the given residue attribute value on
147 * residues specified by the AtomSpecModel, for example
150 * setatr res jv_chain 'primary' #1:12-34,48-55.B
153 * @param attributeName
154 * @param attributeValue
155 * @param atomSpecModel
158 protected StructureCommandI setAttribute(String attributeName,
159 String attributeValue,
160 AtomSpecModel atomSpecModel)
162 StringBuilder sb = new StringBuilder(128);
163 sb.append("setattr res ").append(attributeName).append(" '")
164 .append(attributeValue).append("' ");
165 sb.append(getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY));
166 return new StructureCommand(sb.toString());
170 * Makes a prefixed and valid Chimera attribute name. A jv_ prefix is applied
171 * for a 'Jalview' namespace, and any non-alphanumeric character is converted
176 * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/setattr.html
179 protected String makeAttributeName(String featureType)
181 String attName = super.makeAttributeName(featureType);
184 * Chimera treats an attribute name ending in 'color' as colour-valued;
185 * Jalview doesn't, so prevent this by appending an underscore
187 if (attName.toUpperCase(Locale.ROOT).endsWith("COLOR"))
196 public StructureCommandI colourByChain()
198 return COLOUR_BY_CHAIN;
202 public List<StructureCommandI> colourByCharge()
204 return Arrays.asList(COLOUR_BY_CHARGE);
208 public String getResidueSpec(String residue)
210 return "::" + residue;
214 public StructureCommandI setBackgroundColour(Color col)
216 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/set.html#bgcolor
217 return new StructureCommand("set bgColor " + ColorUtils.toTkCode(col));
221 public StructureCommandI focusView()
227 public List<StructureCommandI> showChains(List<String> toShow)
230 * Construct a chimera command like
232 * ~display #*;~ribbon #*;ribbon :.A,:.B
234 StringBuilder cmd = new StringBuilder(64);
235 boolean first = true;
236 for (String chain : toShow)
238 String[] tokens = chain.split(":");
239 if (tokens.length == 2)
241 String showChainCmd = tokens[0] + ":." + tokens[1];
246 cmd.append(showChainCmd);
252 * could append ";focus" to this command to resize the display to fill the
253 * window, but it looks more helpful not to (easier to relate chains to the
256 final String command = "~display #*; ~ribbon #*; ribbon :"
258 return Arrays.asList(new StructureCommand(command));
262 public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
263 AtomSpecModel spec, AtomSpecType backbone)
266 * Form Chimera match command to match spec to ref
267 * (the first set of atoms are moved on to the second)
269 * match #1:1-30.B,81-100.B@CA #0:21-40.A,61-90.A@CA
271 * @see https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/match.html
273 StringBuilder cmd = new StringBuilder();
274 String atomSpecAlphaOnly = getAtomSpec(spec, backbone);
275 String refSpecAlphaOnly = getAtomSpec(ref, backbone);
276 cmd.append("match ").append(atomSpecAlphaOnly).append(" ").append(refSpecAlphaOnly);
279 * show superposed residues as ribbon
281 String atomSpec = getAtomSpec(spec, AtomSpecType.RESIDUE_ONLY);
282 String refSpec = getAtomSpec(ref, AtomSpecType.RESIDUE_ONLY);
283 cmd.append("; ribbon ");
284 cmd.append(atomSpec).append("|").append(refSpec).append("; focus");
286 return Arrays.asList(new StructureCommand(cmd.toString()));
290 public StructureCommandI openCommandFile(String path)
292 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html
293 return new StructureCommand("open cmd:" + path);
297 public StructureCommandI saveSession(String filepath)
299 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/save.html
300 return new StructureCommand("save " + filepath);
304 * Returns the range(s) modelled by {@code atomSpec} formatted as a Chimera
305 * atomspec string, e.g.
308 * #0:15.A,28.A,54.A,70-72.A|#1:2.A,6.A,11.A,13-14.A
313 * <li>#0 is a model number</li>
314 * <li>15 or 70-72 is a residue number, or range of residue numbers</li>
315 * <li>.A is a chain identifier</li>
316 * <li>residue ranges are separated by comma</li>
317 * <li>atomspecs for distinct models are separated by | (or)</li>
325 * @see https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/frameatom_spec.html
328 public String getAtomSpec(AtomSpecModel atomSpec, AtomSpecType specType)
330 StringBuilder sb = new StringBuilder(128);
331 boolean firstModel = true;
332 for (String model : atomSpec.getModels())
339 appendModel(sb, model, atomSpec, specType);
341 return sb.toString();
345 * A helper method to append an atomSpec string for atoms in the given model
352 protected void appendModel(StringBuilder sb, String model,
353 AtomSpecModel atomSpec, AtomSpecType specType)
355 sb.append("#").append(model).append(":");
357 boolean firstPositionForModel = true;
359 for (String chain : atomSpec.getChains(model))
361 chain = " ".equals(chain) ? chain : chain.trim();
363 List<int[]> rangeList = atomSpec.getRanges(model, chain);
364 for (int[] range : rangeList)
366 appendRange(sb, range[0], range[1], chain, firstPositionForModel,
368 firstPositionForModel = false;
371 if (specType == AtomSpecType.ALPHA)
374 * restrict to alpha carbon, no alternative locations
375 * (needed to ensuring matching atom counts for superposition)
377 sb.append("@CA").append(NO_ALTLOCS);
379 if (specType == AtomSpecType.PHOSPHATE)
381 sb.append("@P").append(NO_ALTLOCS);
386 public List<StructureCommandI> showBackbone()
388 return Arrays.asList(SHOW_BACKBONE);
392 public StructureCommandI loadFile(String file)
394 return new StructureCommand("open " + file);
398 public StructureCommandI openSession(String filepath)
400 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/filetypes.html
401 // this version of the command has no dependency on file extension
402 return new StructureCommand("open chimera:" + filepath);
406 public StructureCommandI closeViewer()
408 return CLOSE_CHIMERA;
412 public List<StructureCommandI> startNotifications(String uri)
414 // https://www.cgl.ucsf.edu/chimera/current/docs/UsersGuide/midas/listen.html
415 List<StructureCommandI> cmds = new ArrayList<>();
416 cmds.add(new StructureCommand("listen start models url " + uri));
417 cmds.add(new StructureCommand("listen start select prefix SelectionChanged url " + uri));
422 public List<StructureCommandI> stopNotifications()
424 List<StructureCommandI> cmds = new ArrayList<>();
425 cmds.add(STOP_NOTIFY_MODELS);
426 cmds.add(STOP_NOTIFY_SELECTION);
431 public StructureCommandI getSelectedResidues()
433 return GET_SELECTION;
437 public StructureCommandI listResidueAttributes()
439 return LIST_RESIDUE_ATTRIBUTES;
443 public StructureCommandI getResidueAttributes(String attName)
445 // this alternative command
446 // list residues spec ':*/attName' attr attName
447 // doesn't report 'None' values (which is good), but
448 // fails for 'average.bfactor' (which is bad):
449 return new StructureCommand("list residues attr '" + attName + "'");