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 static org.testng.Assert.assertEquals;
24 import static org.testng.Assert.assertTrue;
26 import java.awt.Color;
27 import java.util.HashMap;
28 import java.util.LinkedHashMap;
29 import java.util.List;
32 import org.testng.annotations.Test;
34 import jalview.structure.AtomSpecModel;
35 import jalview.structure.StructureCommandI;
36 import jalview.structure.StructureCommandsI;
38 public class ChimeraXCommandsTest
40 @Test(groups = { "Functional" })
41 public void testColourByCharge()
43 List<StructureCommandI> cmd = new ChimeraXCommands().colourByCharge();
44 assertEquals(cmd.size(), 1);
45 assertEquals(cmd.get(0).getCommand(),
46 "color white;color :ASP,GLU red;color :LYS,ARG blue;color :CYS yellow");
49 @Test(groups = { "Functional" })
50 public void testColourByChain()
52 StructureCommandI cmd = new ChimeraXCommands().colourByChain();
53 assertEquals(cmd.getCommand(), "rainbow chain");
56 @Test(groups = { "Functional" })
57 public void testFocusView()
59 StructureCommandI cmd = new ChimeraXCommands().focusView();
60 assertEquals(cmd.getCommand(), "view");
63 @Test(groups = { "Functional" })
64 public void testColourBySequence()
66 Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
67 ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 2, 5, "A");
68 ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 7, 7, "B");
69 ChimeraCommands.addAtomSpecRange(map, Color.blue, "1", 9, 23, "A");
70 ChimeraCommands.addAtomSpecRange(map, Color.blue, "2", 1, 1, "A");
71 ChimeraCommands.addAtomSpecRange(map, Color.blue, "2", 4, 7, "B");
72 ChimeraCommands.addAtomSpecRange(map, Color.yellow, "2", 8, 8, "A");
73 ChimeraCommands.addAtomSpecRange(map, Color.yellow, "2", 3, 5, "A");
74 ChimeraCommands.addAtomSpecRange(map, Color.red, "1", 3, 5, "A");
75 ChimeraCommands.addAtomSpecRange(map, Color.red, "1", 6, 9, "A");
78 * Colours should appear in the Chimera command in the order in which
79 * they were added; within colour, by model, by chain, ranges in start order
81 List<StructureCommandI> commands = new ChimeraXCommands()
82 .colourBySequence(map);
83 assertEquals(commands.size(), 1);
84 assertEquals(commands.get(0).getCommand(),
85 "color #1/A:2-5,9-23/B:7|#2/A:1/B:4-7 #0000ff;color #2/A:3-5,8 #ffff00;color #1/A:3-9 #ff0000");
88 @Test(groups = { "Functional" })
89 public void testSetAttributes()
92 * make a map of { featureType, {featureValue, {residue range specification } } }
94 Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
95 Map<Object, AtomSpecModel> featureValues = new HashMap<>();
98 * start with just one feature/value...
100 featuresMap.put("chain", featureValues);
101 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A");
103 ChimeraXCommands commandGenerator = new ChimeraXCommands();
104 List<StructureCommandI> commands = commandGenerator
105 .setAttributes(featuresMap);
106 assertEquals(commands.size(), 1);
109 * feature name gets a jv_ namespace prefix
110 * feature value is quoted in case it contains spaces
112 assertEquals(commands.get(0).getCommand(),
113 "setattr #0/A:8-20 res jv_chain 'X' create true");
115 // add same feature value, overlapping range
116 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 3, 9, "A");
117 // same feature value, contiguous range
118 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "A");
119 commands = commandGenerator.setAttributes(featuresMap);
120 assertEquals(commands.size(), 1);
121 assertEquals(commands.get(0).getCommand(),
122 "setattr #0/A:3-25 res jv_chain 'X' create true");
124 // same feature value and model, different chain
125 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "B");
126 // same feature value and chain, different model
127 ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A");
128 commands = commandGenerator.setAttributes(featuresMap);
129 assertEquals(commands.size(), 1);
130 String expected1 = "setattr #0/A:3-25/B:21-25|#1/A:26-30 res jv_chain 'X' create true";
131 assertEquals(commands.get(0).getCommand(), expected1);
133 // same feature, different value
134 ChimeraCommands.addAtomSpecRange(featureValues, "Y", "0", 40, 50, "A");
135 commands = commandGenerator.setAttributes(featuresMap);
136 assertEquals(2, commands.size());
137 // commands are ordered by feature type but not by value
138 // so test for the expected command in either order
139 String cmd1 = commands.get(0).getCommand();
140 String cmd2 = commands.get(1).getCommand();
142 cmd1.equals(expected1) || cmd2.equals(expected1));
143 String expected2 = "setattr #0/A:40-50 res jv_chain 'Y' create true";
145 cmd1.equals(expected2) || cmd2.equals(expected2));
148 featureValues.clear();
149 featuresMap.put("side-chain binding!", featureValues);
150 ChimeraCommands.addAtomSpecRange(featureValues,
151 "<html>metal <a href=\"http:a.b.c/x\"> 'ion!", "0", 7, 15,
153 // feature names are sanitised to change non-alphanumeric to underscore
154 // feature values are sanitised to encode single quote characters
155 commands = commandGenerator.setAttributes(featuresMap);
156 assertEquals(commands.size(), 1);
157 String expected3 = "setattr #0/A:7-15 res jv_side_chain_binding_ '<html>metal <a href=\"http:a.b.c/x\"> 'ion!' create true";
158 assertTrue(commands.get(0).getCommand().equals(expected3));
161 @Test(groups = { "Functional" })
162 public void testSuperposeStructures()
164 StructureCommandsI testee = new ChimeraXCommands();
165 AtomSpecModel ref = new AtomSpecModel();
166 ref.addRange("1", 12, 14, "A");
167 ref.addRange("1", 18, 18, "B");
168 ref.addRange("1", 22, 23, "B");
169 AtomSpecModel toAlign = new AtomSpecModel();
170 toAlign.addRange("2", 15, 17, "B");
171 toAlign.addRange("2", 20, 21, "B");
172 toAlign.addRange("2", 22, 22, "C");
173 List<StructureCommandI> command = testee.superposeStructures(ref,
175 assertEquals(command.size(), 1);
176 String cmd = command.get(0).getCommand();
177 String refSpec = "#1/A:12-14/B:18,22-23";
178 String toAlignSpec = "#2/B:15-17,20-21/C:22";
181 * superposition arguments include AlphaCarbon restriction,
182 * ribbon command does not
184 String expected = String.format(
185 "align %s@CA toAtoms %s@CA; ribbon %s|%s; view",
186 toAlignSpec, refSpec, toAlignSpec, refSpec);
187 assertEquals(cmd, expected);
190 @Test(groups = "Functional")
191 public void testGetAtomSpec()
193 StructureCommandsI testee = new ChimeraXCommands();
194 AtomSpecModel model = new AtomSpecModel();
195 assertEquals(testee.getAtomSpec(model, false), "");
196 model.addRange("1", 2, 4, "A");
197 assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4");
198 model.addRange("1", 8, 8, "A");
199 assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8");
200 model.addRange("1", 5, 7, "B");
201 assertEquals(testee.getAtomSpec(model, false), "#1/A:2-4,8/B:5-7");
202 model.addRange("1", 3, 5, "A");
203 assertEquals(testee.getAtomSpec(model, false), "#1/A:2-5,8/B:5-7");
204 model.addRange("0", 1, 4, "B");
205 assertEquals(testee.getAtomSpec(model, false),
206 "#0/B:1-4|#1/A:2-5,8/B:5-7");
207 model.addRange("0", 5, 9, "C");
208 assertEquals(testee.getAtomSpec(model, false),
209 "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-7");
210 model.addRange("1", 8, 10, "B");
211 assertEquals(testee.getAtomSpec(model, false),
212 "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
213 model.addRange("1", 8, 9, "B");
214 assertEquals(testee.getAtomSpec(model, false),
215 "#0/B:1-4/C:5-9|#1/A:2-5,8/B:5-10");
216 model.addRange("0", 3, 10, "C"); // subsumes 5-9
217 assertEquals(testee.getAtomSpec(model, false),
218 "#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10");
219 model.addRange("5", 25, 35, " ");
220 assertEquals(testee.getAtomSpec(model, false),
221 "#0/B:1-4/C:3-10|#1/A:2-5,8/B:5-10|#5/:25-35");
224 @Test(groups = "Functional")
225 public void testGetAtomSpec_alphaOnly()
227 StructureCommandsI testee = new ChimeraXCommands();
228 AtomSpecModel model = new AtomSpecModel();
229 assertEquals(testee.getAtomSpec(model, true), "");
230 model.addRange("1", 2, 4, "A");
231 assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4@CA");
232 model.addRange("1", 8, 8, "A");
233 assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8@CA");
234 model.addRange("1", 5, 7, "B");
235 assertEquals(testee.getAtomSpec(model, true), "#1/A:2-4,8/B:5-7@CA");
236 model.addRange("1", 3, 5, "A");
237 assertEquals(testee.getAtomSpec(model, true), "#1/A:2-5,8/B:5-7@CA");
238 model.addRange("0", 1, 4, "B");
239 assertEquals(testee.getAtomSpec(model, true),
240 "#0/B:1-4@CA|#1/A:2-5,8/B:5-7@CA");
241 model.addRange("0", 5, 9, "C");
242 assertEquals(testee.getAtomSpec(model, true),
243 "#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-7@CA");
244 model.addRange("1", 8, 10, "B");
245 assertEquals(testee.getAtomSpec(model, true),
246 "#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-10@CA");
247 model.addRange("1", 8, 9, "B");
248 assertEquals(testee.getAtomSpec(model, true),
249 "#0/B:1-4/C:5-9@CA|#1/A:2-5,8/B:5-10@CA");
250 model.addRange("0", 3, 10, "C"); // subsumes 5-9
251 assertEquals(testee.getAtomSpec(model, true),
252 "#0/B:1-4/C:3-10@CA|#1/A:2-5,8/B:5-10@CA");
253 model.addRange("5", 25, 35, " "); // empty chain code
254 assertEquals(testee.getAtomSpec(model, true),
255 "#0/B:1-4/C:3-10@CA|#1/A:2-5,8/B:5-10@CA|#5/:25-35@CA");
258 @Test(groups = "Functional")
259 public void testGetModelStartNo()
261 StructureCommandsI testee = new ChimeraXCommands();
262 assertEquals(testee.getModelStartNo(), 1);
265 @Test(groups = "Functional")
266 public void testGetResidueSpec()
268 ChimeraCommands testee = new ChimeraXCommands();
269 assertEquals(testee.getResidueSpec("ALA"), ":ALA");
272 @Test(groups = "Functional")
273 public void testShowBackbone()
275 ChimeraCommands testee = new ChimeraXCommands();
276 List<StructureCommandI> showBackbone = testee.showBackbone();
277 assertEquals(showBackbone.size(), 1);
278 assertEquals(showBackbone.get(0).getCommand(),
279 "~display all;~ribbon;show @CA|P atoms");
282 @Test(groups = "Functional")
283 public void testOpenCommandFile()
285 ChimeraCommands testee = new ChimeraXCommands();
286 assertEquals(testee.openCommandFile("nowhere").getCommand(),
290 @Test(groups = "Functional")
291 public void testSaveSession()
293 ChimeraCommands testee = new ChimeraXCommands();
294 assertEquals(testee.saveSession("somewhere").getCommand(),
295 "save somewhere format session");
298 @Test(groups = "Functional")
299 public void testGetColourCommand()
301 ChimeraCommands testee = new ChimeraXCommands();
302 assertEquals(testee.colourResidues("something", Color.MAGENTA)
304 "color something #ff00ff");
307 @Test(groups = "Functional")
308 public void testSetAttribute()
310 ChimeraCommands testee = new ChimeraXCommands();
311 AtomSpecModel model = new AtomSpecModel();
312 model.addRange("1", 89, 92, "A");
313 model.addRange("2", 12, 20, "B");
314 model.addRange("2", 8, 9, "B");
315 assertEquals(testee.setAttribute("phi", "27.3", model).getCommand(),
316 "setattr #1/A:89-92|#2/B:8-9,12-20 res phi '27.3' create true");