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Coverage Report

  1. Project Clover database Tue Nov 18 2025 10:51:49 GMT
  2. Package jalview.ext.rbvi.chimera

File ChimeraXCommands.java

 

Coverage histogram

../../../../img/srcFileCovDistChart10.png
0% of files have more coverage

Code metrics

8
57
18
1
294
182
22
0.39
3.17
18
1.22

Classes

Class Line # Actions
ChimeraXCommands 36 57 22
0.9759036397.6%
 

Contributing tests

This file is covered by 20 tests. .

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1    /*
2    * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
3    * Copyright (C) $$Year-Rel$$ The Jalview Authors
4    *
5    * This file is part of Jalview.
6    *
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.
11    *
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.
16    *
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.
20    */
21    package jalview.ext.rbvi.chimera;
22   
23    import java.awt.Color;
24    import java.util.ArrayList;
25    import java.util.Arrays;
26    import java.util.List;
27   
28    import jalview.structure.AtomSpecModel;
29    import jalview.structure.StructureCommand;
30    import jalview.structure.StructureCommandI;
31    import jalview.structure.StructureCommandsI.AtomSpecType;
32   
33    /**
34    * Routines for generating ChimeraX commands for Jalview/ChimeraX binding
35    */
 
36    public class ChimeraXCommands extends ChimeraCommands
37    {
38    // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#resattr
39    private static final StructureCommand LIST_RESIDUE_ATTRIBUTES = new StructureCommand(
40    "info resattr");
41   
42    // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/exit.html
43    private static final StructureCommand CLOSE_CHIMERAX = new StructureCommand(
44    "exit");
45   
46    // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#notify
47    private static final StructureCommand STOP_NOTIFY_SELECTION = new StructureCommand(
48    "info notify stop selection jalview");
49   
50    private static final StructureCommand STOP_NOTIFY_MODELS = new StructureCommand(
51    "info notify stop models jalview");
52   
53    // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/info.html#selection
54    private static final StructureCommand GET_SELECTION = new StructureCommand(
55    "info selection level residue");
56   
57    private static final StructureCommand SHOW_BACKBONE = new StructureCommand(
58    "~display all;~ribbon;show @CA|P atoms");
59   
60    // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/view.html
61    private static final StructureCommand FOCUS_VIEW = new StructureCommand(
62    "view");
63   
64    private static final StructureCommandI COLOUR_BY_CHARGE = new StructureCommand(
65    "color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow");
66   
 
67  1 toggle @Override
68    public List<StructureCommandI> colourByCharge()
69    {
70  1 return Arrays.asList(COLOUR_BY_CHARGE);
71    }
72   
 
73  1 toggle @Override
74    public String getResidueSpec(String residue)
75    {
76  1 return ":" + residue;
77    }
78   
 
79  4 toggle @Override
80    public StructureCommandI colourResidues(String atomSpec, Color colour)
81    {
82    // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/color.html
83  4 String colourCode = getColourString(colour);
84   
85  4 return new StructureCommand("color " + atomSpec + " " + colourCode);
86    }
87   
 
88  1 toggle @Override
89    public StructureCommandI focusView()
90    {
91  1 return FOCUS_VIEW;
92    }
93   
94    /**
95    * {@inheritDoc}
96    *
97    * @return
98    */
 
99  1 toggle @Override
100    public int getModelStartNo()
101    {
102  1 return 1;
103    }
104   
105    /**
106    * Returns a viewer command to set the given residue attribute value on
107    * residues specified by the AtomSpecModel, for example
108    *
109    * <pre>
110    * setattr #0/A:3-9,14-20,39-43 res jv_strand 'strand' create true
111    * </pre>
112    *
113    * @param attributeName
114    * @param attributeValue
115    * @param atomSpecModel
116    * @return
117    */
 
118  7 toggle @Override
119    protected StructureCommandI setAttribute(String attributeName,
120    String attributeValue, AtomSpecModel atomSpecModel)
121    {
122  7 StringBuilder sb = new StringBuilder(128);
123  7 sb.append("setattr ")
124    .append(getAtomSpec(atomSpecModel, AtomSpecType.RESIDUE_ONLY));
125  7 sb.append(" res ").append(attributeName).append(" '")
126    .append(attributeValue).append("'");
127  7 sb.append(" create true");
128  7 return new StructureCommand(sb.toString());
129    }
130   
 
131  1 toggle @Override
132    public StructureCommandI openCommandFile(String path)
133    {
134    // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html
135  1 return new StructureCommand("open " + path);
136    }
137   
 
138  1 toggle @Override
139    public StructureCommandI saveSession(String filepath)
140    {
141    // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html
142    // note ChimeraX will append ".cxs" to the filepath!
143  1 return new StructureCommand("save " + filepath + " format session");
144    }
145   
146    /**
147    * Returns the range(s) formatted as a ChimeraX atomspec, for example
148    * <p>
149    * #1/A:2-20,30-40/B:10-20|#2/A:12-30
150    * <p>
151    * Note there is no need to explicitly exclude ALTLOC atoms when
152    * {@code alphaOnly == true}, as this is the default behaviour of ChimeraX (a
153    * change from Chimera)
154    *
155    * @return
156    */
 
157  36 toggle @Override
158    public String getAtomSpec(AtomSpecModel atomSpec, AtomSpecType specType)
159    {
160  36 StringBuilder sb = new StringBuilder(128);
161  36 boolean firstModel = true;
162  36 for (String model : atomSpec.getModels())
163    {
164  52 if (!firstModel)
165    {
166  18 sb.append("|");
167    }
168  52 firstModel = false;
169  52 appendModel(sb, model, atomSpec);
170  52 if (specType == AtomSpecType.ALPHA)
171    {
172  19 sb.append("@CA");
173    }
174  52 if (specType == AtomSpecType.PHOSPHATE)
175    {
176  0 sb.append("@P");
177    }
178    }
179  36 return sb.toString();
180    }
181   
182    /**
183    * A helper method to append an atomSpec string for atoms in the given model
184    *
185    * @param sb
186    * @param model
187    * @param atomSpec
188    */
 
189  52 toggle protected void appendModel(StringBuilder sb, String model,
190    AtomSpecModel atomSpec)
191    {
192  52 sb.append("#").append(model);
193   
194  52 for (String chain : atomSpec.getChains(model))
195    {
196  86 boolean firstPositionForChain = true;
197  86 sb.append("/").append(chain.trim()).append(":");
198  86 List<int[]> rangeList = atomSpec.getRanges(model, chain);
199  86 boolean first = true;
200  86 for (int[] range : rangeList)
201    {
202  111 if (!first)
203    {
204  25 sb.append(",");
205    }
206  111 first = false;
207  111 appendRange(sb, range[0], range[1], chain, firstPositionForChain,
208    true);
209    }
210    }
211    }
212   
 
213  1 toggle @Override
214    public List<StructureCommandI> showBackbone()
215    {
216  1 return Arrays.asList(SHOW_BACKBONE);
217    }
218   
 
219  1 toggle @Override
220    public List<StructureCommandI> superposeStructures(AtomSpecModel ref,
221    AtomSpecModel spec, AtomSpecType backbone)
222    {
223    /*
224    * Form ChimeraX match command to match spec to ref
225    *
226    * match #1/A:2-94 toAtoms #2/A:1-93
227    *
228    * @see https://www.cgl.ucsf.edu/chimerax/docs/user/commands/align.html
229    */
230  1 StringBuilder cmd = new StringBuilder();
231  1 String atomSpec = getAtomSpec(spec, backbone);
232  1 String refSpec = getAtomSpec(ref, backbone);
233  1 cmd.append("align ").append(atomSpec).append(" toAtoms ")
234    .append(refSpec);
235   
236    /*
237    * show superposed residues as ribbon, others as chain
238    */
239  1 cmd.append("; ribbon ");
240  1 cmd.append(getAtomSpec(spec, AtomSpecType.RESIDUE_ONLY)).append("|");
241  1 cmd.append(getAtomSpec(ref, AtomSpecType.RESIDUE_ONLY))
242    .append("; view");
243   
244  1 return Arrays.asList(new StructureCommand(cmd.toString()));
245    }
246   
 
247  1 toggle @Override
248    public StructureCommandI openSession(String filepath)
249    {
250    // https://www.cgl.ucsf.edu/chimerax/docs/user/commands/open.html#composite
251    // this version of the command has no dependency on file extension
252  1 return new StructureCommand("open " + filepath + " format session");
253    }
254   
 
255  1 toggle @Override
256    public StructureCommandI closeViewer()
257    {
258  1 return CLOSE_CHIMERAX;
259    }
260   
 
261  1 toggle @Override
262    public List<StructureCommandI> startNotifications(String uri)
263    {
264  1 List<StructureCommandI> cmds = new ArrayList<>();
265  1 cmds.add(new StructureCommand(
266    "info notify start models jalview prefix ModelChanged url "
267    + uri));
268  1 cmds.add(new StructureCommand(
269    "info notify start selection jalview prefix SelectionChanged url "
270    + uri));
271  1 return cmds;
272    }
273   
 
274  1 toggle @Override
275    public List<StructureCommandI> stopNotifications()
276    {
277  1 List<StructureCommandI> cmds = new ArrayList<>();
278  1 cmds.add(STOP_NOTIFY_MODELS);
279  1 cmds.add(STOP_NOTIFY_SELECTION);
280  1 return cmds;
281    }
282   
 
283  1 toggle @Override
284    public StructureCommandI getSelectedResidues()
285    {
286  1 return GET_SELECTION;
287    }
288   
 
289  1 toggle @Override
290    public StructureCommandI listResidueAttributes()
291    {
292  1 return LIST_RESIDUE_ATTRIBUTES;
293    }
294    }
  • Report generated by OpenClover v 4.4.1 on Tue Nov 18 2025 11:02:12 GMT using coverage data from Tue Nov 18 2025 11:01:58 GMT.
  • OpenClover is free and open-source software.