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;
28 import jalview.structure.AtomSpecModel;
29 import jalview.structure.StructureCommand;
30 import jalview.structure.StructureCommandI;
33 * Routines for generating ChimeraX commands for Jalview/ChimeraX binding
35 public class ChimeraXCommands extends ChimeraCommands
37 // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#resattr
38 private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand(
41 // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/exit.html
42 private static final StructureCommand CLOSE_CHIMERAX = new StructureCommand(
45 // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#notify
46 private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand(
47 "info notify stop selection jalview");
49 private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand(
50 "info notify stop models jalview");
52 // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#selection
53 private static final StructureCommand GET_SELECTION = new StructureCommand(
54 "info selection level residue");
56 private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
57 "~display all;~ribbon;show @CA|P atoms");
59 // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/view.html
60 private static final StructureCommand FOCUS_VIEW = new StructureCommand(
63 private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand(
64 "color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow");
67 public List<StructureCommandI> colourByCharge()
69 return Arrays.asList(COLOUR_BY_CHARGE);
73 public String getResidueSpec(String residue)
79 public StructureCommandI colourResidues(String atomSpec, Color colour)
81 // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html
82 String colourCode = getColourString(colour);
84 return new StructureCommand("color " + atomSpec + " " + colourCode);
88 public StructureCommandI focusView()
99 public int getModelStartNo()
105 * Returns a viewer command to set the given residue attribute value on residues
106 * specified by the AtomSpecModel, for example
109 * setattr #0/A:3-9,14-20,39-43 res jv_strand 'strand' create true
112 * @param attributeName
113 * @param attributeValue
114 * @param atomSpecModel
118 protected StructureCommandI setAttribute(String attributeName,
119 String attributeValue, AtomSpecModel atomSpecModel)
121 StringBuilder sb = new StringBuilder(128);
122 sb.append("setattr ").append(getAtomSpec(atomSpecModel, false));
123 sb.append(" res ").append(attributeName).append(" '")
124 .append(attributeValue).append("'");
125 sb.append(" create true");
126 return new StructureCommand(sb.toString());
130 public StructureCommandI openCommandFile(String path)
132 // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html
133 return new StructureCommand("open " + path);
137 public StructureCommandI saveSession(String filepath)
139 // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html
140 // note ChimeraX will append ".cxs" to the filepath!
141 return new StructureCommand("save " + filepath + " format session");
145 * Returns the range(s) formatted as a ChimeraX atomspec, for example
147 * #1/A:2-20,30-40/B:10-20|#2/A:12-30
149 * Note there is no need to explicitly exclude ALTLOC atoms when
150 * {@code alphaOnly == true}, as this is the default behaviour of ChimeraX (a
151 * change from Chimera)
156 public String getAtomSpec(AtomSpecModel atomSpec, boolean alphaOnly)
158 StringBuilder sb = new StringBuilder(128);
159 boolean firstModel = true;
160 for (String model : atomSpec.getModels())
167 appendModel(sb, model, atomSpec);
170 // TODO @P if RNA - add nucleotide flag to AtomSpecModel?
174 return sb.toString();
178 * A helper method to append an atomSpec string for atoms in the given model
184 protected void appendModel(StringBuilder sb, String model,
185 AtomSpecModel atomSpec)
187 sb.append("#").append(model);
189 for (String chain : atomSpec.getChains(model))
191 boolean firstPositionForChain = true;
192 sb.append("/").append(chain.trim()).append(":");
193 List<int[]> rangeList = atomSpec.getRanges(model, chain);
194 boolean first = true;
195 for (int[] range : rangeList)
202 appendRange(sb, range[0], range[1], chain, firstPositionForChain,
209 public List<StructureCommandI> showBackbone()
211 return Arrays.asList(SHOW_BACKBONE);
215 public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
219 * Form ChimeraX match command to match spec to ref
221 * match #1/A:2-94 toAtoms #2/A:1-93
223 * @see https://www.cgl.ucsf.edu/chimerax/docs/user/commands/align.html
225 StringBuilder cmd = new StringBuilder();
226 String atomSpec = getAtomSpec(spec, true);
227 String refSpec = getAtomSpec(ref, true);
228 cmd.append("align ").append(atomSpec).append(" toAtoms ")
232 * show superposed residues as ribbon, others as chain
234 cmd.append("; ribbon ");
235 cmd.append(getAtomSpec(spec, false)).append("|");
236 cmd.append(getAtomSpec(ref, false)).append("; view");
238 return Arrays.asList(new StructureCommand(cmd.toString()));
242 public StructureCommandI openSession(String filepath)
244 // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html#composite
245 // this version of the command has no dependency on file extension
246 return new StructureCommand("open " + filepath + " format session");
250 public StructureCommandI closeViewer()
252 return CLOSE_CHIMERAX;
256 public List<StructureCommandI> startNotifications(String uri)
258 List<StructureCommandI> cmds = new ArrayList<>();
259 cmds.add(new StructureCommand(
260 "info notify start models jalview prefix ModelChanged url "
262 cmds.add(new StructureCommand(
263 "info notify start selection jalview prefix SelectionChanged url "
269 public List<StructureCommandI> stopNotifications()
271 List<StructureCommandI> cmds = new ArrayList<>();
272 cmds.add(STOP_NOTIFY_MODELS);
273 cmds.add(STOP_NOTIFY_SELECTION);
278 public StructureCommandI getSelectedResidues()
280 return GET_SELECTION;
284 public StructureCommandI listResidueAttributes()
286 return LIST_RESIDUE_ATTRIBUTES;