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.pymol;
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.BeforeClass;
33 import org.testng.annotations.Test;
35 import jalview.ext.rbvi.chimera.ChimeraCommands;
36 import jalview.structure.AtomSpecModel;
37 import jalview.structure.StructureCommand;
38 import jalview.structure.StructureCommandI;
40 public class PymolCommandsTest
42 private PymolCommands testee;
44 @BeforeClass(alwaysRun = true)
47 testee = new PymolCommands();
50 @Test(groups = { "Functional" })
51 public void testColourBySequence()
54 Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
55 PymolCommands.addAtomSpecRange(map, Color.blue, "0", 2, 5, "A");
56 PymolCommands.addAtomSpecRange(map, Color.blue, "0", 7, 7, "B");
57 PymolCommands.addAtomSpecRange(map, Color.blue, "0", 9, 23, "A");
58 PymolCommands.addAtomSpecRange(map, Color.blue, "1", 1, 1, "A");
59 PymolCommands.addAtomSpecRange(map, Color.blue, "1", 4, 7, "B");
60 PymolCommands.addAtomSpecRange(map, Color.yellow, "1", 8, 8, "A");
61 PymolCommands.addAtomSpecRange(map, Color.yellow, "1", 3, 5, "A");
62 PymolCommands.addAtomSpecRange(map, Color.red, "0", 3, 5, "A");
63 PymolCommands.addAtomSpecRange(map, Color.red, "0", 6, 9, "A");
65 // Colours should appear in the Pymol command in the order in which
66 // they were added; within colour, by model, by chain, ranges in start order
67 List<StructureCommandI> commands = testee.colourBySequence(map);
68 assertEquals(commands.size(), 3);
69 assertEquals(commands.get(0), new StructureCommand("color", "0x0000ff",
70 "0//A/2-5+9-23/ 0//B/7/ 1//A/1/ 1//B/4-7/"));
71 assertEquals(commands.get(
73 new StructureCommand("color", "0xffff00", "1//A/3-5+8/"));
74 assertEquals(commands.get(
76 new StructureCommand("color", "0xff0000", "0//A/3-9/"));
79 @Test(groups = "Functional")
80 public void testGetAtomSpec()
82 AtomSpecModel model = new AtomSpecModel();
83 assertEquals(testee.getAtomSpec(model, false), "");
84 model.addRange("1", 2, 4, "A");
85 assertEquals(testee.getAtomSpec(model, false), "1//A/2-4/");
86 model.addRange("1", 8, 8, "A");
87 assertEquals(testee.getAtomSpec(model, false), "1//A/2-4+8/");
88 model.addRange("1", 5, 7, "B");
89 assertEquals(testee.getAtomSpec(model, false), "1//A/2-4+8/ 1//B/5-7/");
90 model.addRange("1", 3, 5, "A");
91 assertEquals(testee.getAtomSpec(model, false), "1//A/2-5+8/ 1//B/5-7/");
92 model.addRange("0", 1, 4, "B");
93 assertEquals(testee.getAtomSpec(model, false),
94 "0//B/1-4/ 1//A/2-5+8/ 1//B/5-7/");
95 model.addRange("0", 5, 9, "C");
96 assertEquals(testee.getAtomSpec(model, false),
97 "0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-7/");
98 model.addRange("1", 8, 10, "B");
99 assertEquals(testee.getAtomSpec(model, false),
100 "0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-10/");
101 model.addRange("1", 8, 9, "B");
102 assertEquals(testee.getAtomSpec(model, false),
103 "0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-10/");
104 model.addRange("0", 3, 10, "C"); // subsumes 5-9
105 assertEquals(testee.getAtomSpec(model, false),
106 "0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/");
107 model.addRange("5", 25, 35, " ");
108 assertEquals(testee.getAtomSpec(model, false),
109 "0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/ 5///25-35/");
113 @Test(groups = { "Functional" })
114 public void testSuperposeStructures()
116 AtomSpecModel ref = new AtomSpecModel();
117 ref.addRange("1", 12, 14, "A");
118 ref.addRange("1", 18, 18, "B");
119 ref.addRange("1", 22, 23, "B");
120 AtomSpecModel toAlign = new AtomSpecModel();
121 toAlign.addRange("2", 15, 17, "B");
122 toAlign.addRange("2", 20, 21, "B");
123 toAlign.addRange("2", 22, 22, "C");
124 List<StructureCommandI> commands = testee.superposeStructures(ref,
126 assertEquals(commands.size(), 2);
127 String refSpecCA = "1//A/12-14/CA 1//B/18+22-23/CA";
128 String toAlignSpecCA = "2//B/15-17+20-21/CA 2//C/22/CA";
129 String refSpec = "1//A/12-14/ 1//B/18+22-23/";
130 String toAlignSpec = "2//B/15-17+20-21/ 2//C/22/";
132 // super command: separate arguments for regions to align
133 assertEquals(commands.get(0),
134 new StructureCommand("super", refSpecCA, toAlignSpecCA));
135 // show aligned regions: one argument for combined atom specs
136 assertEquals(commands.get(1), new StructureCommand("show", "cartoon",
137 refSpec + " " + toAlignSpec));
140 @Test(groups = "Functional")
141 public void testGetAtomSpec_alphaOnly()
143 AtomSpecModel model = new AtomSpecModel();
144 assertEquals(testee.getAtomSpec(model, true), "");
145 model.addRange("1", 2, 4, "A");
146 assertEquals(testee.getAtomSpec(model, true), "1//A/2-4/CA");
147 model.addRange("1", 8, 8, "A");
148 assertEquals(testee.getAtomSpec(model, true), "1//A/2-4+8/CA");
149 model.addRange("1", 5, 7, "B");
150 assertEquals(testee.getAtomSpec(model, true),
151 "1//A/2-4+8/CA 1//B/5-7/CA");
152 model.addRange("1", 3, 5, "A");
153 assertEquals(testee.getAtomSpec(model, true),
154 "1//A/2-5+8/CA 1//B/5-7/CA");
155 model.addRange("0", 1, 4, "B");
156 assertEquals(testee.getAtomSpec(model, true),
157 "0//B/1-4/CA 1//A/2-5+8/CA 1//B/5-7/CA");
158 model.addRange("0", 5, 9, "C");
159 assertEquals(testee.getAtomSpec(model, true),
160 "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-7/CA");
161 model.addRange("1", 8, 10, "B");
162 assertEquals(testee.getAtomSpec(model, true),
163 "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
164 model.addRange("1", 8, 9, "B");
165 assertEquals(testee.getAtomSpec(model, true),
166 "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
167 model.addRange("0", 3, 10, "C"); // subsumes 5-9
168 assertEquals(testee.getAtomSpec(model, true),
169 "0//B/1-4/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA");
170 model.addRange("5", 25, 35, " ");
171 assertEquals(testee.getAtomSpec(model, true),
172 "0//B/1-4/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA 5///25-35/CA");
175 @Test(groups = "Functional")
176 public void testGetModelStartNo()
178 assertEquals(testee.getModelStartNo(), 0);
181 @Test(groups = "Functional")
182 public void testGetResidueSpec()
184 assertEquals(testee.getResidueSpec("ALA"), "resn ALA");
187 @Test(groups = "Functional")
188 public void testShowBackbone()
190 List<StructureCommandI> cmds = testee.showBackbone();
191 assertEquals(cmds.size(), 2);
192 assertEquals(cmds.get(0), new StructureCommand("hide", "everything"));
193 assertEquals(cmds.get(1), new StructureCommand("show", "ribbon"));
196 @Test(groups = "Functional")
197 public void testColourByCharge()
199 List<StructureCommandI> cmds = testee.colourByCharge();
200 assertEquals(cmds.size(), 4);
201 assertEquals(cmds.get(0), new StructureCommand("color", "white", "*"));
202 assertEquals(cmds.get(1),
203 new StructureCommand("color", "red", "resn ASP resn GLU"));
204 assertEquals(cmds.get(2),
205 new StructureCommand("color", "blue", "resn LYS resn ARG"));
206 assertEquals(cmds.get(3),
207 new StructureCommand("color", "yellow", "resn CYS"));
210 @Test(groups = "Functional")
211 public void testOpenCommandFile()
213 assertEquals(testee.openCommandFile("commands.pml"),
214 new StructureCommand("run", "commands.pml"));
217 @Test(groups = "Functional")
218 public void testSaveSession()
220 assertEquals(testee.saveSession("somewhere.pse"),
221 new StructureCommand("save", "somewhere.pse"));
224 @Test(groups = "Functional")
225 public void testOpenSession()
227 assertEquals(testee.openSession("/some/path"),
228 new StructureCommand("load", "/some/path", "", "0", "pse"));
231 @Test(groups = "Functional")
232 public void testColourByChain()
234 assertEquals(testee.colourByChain(),
235 new StructureCommand("spectrum", "chain"));
238 @Test(groups = "Functional")
239 public void testColourResidues()
241 assertEquals(testee.colourResidues("something",
243 new StructureCommand("color", "0xff00ff", "something"));
246 @Test(groups = "Functional")
247 public void testLoadFile()
249 assertEquals(testee.loadFile("/some/path"),
250 new StructureCommand("load", "/some/path"));
253 @Test(groups = "Functional")
254 public void testSetBackgroundColour()
256 assertEquals(testee.setBackgroundColour(
258 new StructureCommand("bg_color", "0xffafaf"));
261 @Test(groups = "Functional")
262 public void testSetAttribute()
264 AtomSpecModel model = new AtomSpecModel();
265 model.addRange("1", 89, 92, "A");
266 model.addRange("2", 12, 20, "B");
267 model.addRange("2", 8, 9, "B");
268 assertEquals(testee.setAttribute("jv_kd", "27.3", model),
269 new StructureCommand("iterate", "1//A/89-92/ 2//B/8-9+12-20/",
273 @Test(groups = { "Functional" })
274 public void testSetAttributes()
277 * make a map of { featureType, {featureValue, {residue range specification } } }
279 Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
280 Map<Object, AtomSpecModel> featureValues = new HashMap<>();
283 * start with just one feature/value...
285 featuresMap.put("chain", featureValues);
286 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A");
288 List<StructureCommandI> commands = testee.setAttributes(featuresMap);
289 assertEquals(commands.size(), 1);
292 * feature name gets a jv_ namespace prefix
294 assertEquals(commands.get(0), new StructureCommand("iterate",
295 "0//A/8-20/", "p.jv_chain='X'"));
297 // add same feature value, overlapping range
298 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 3, 9, "A");
299 // same feature value, contiguous range
300 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "A");
301 commands = testee.setAttributes(featuresMap);
302 assertEquals(commands.size(), 1);
303 assertEquals(commands.get(0), new StructureCommand("iterate",
304 "0//A/3-25/", "p.jv_chain='X'"));
306 // same feature value and model, different chain
307 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "B");
308 // same feature value and chain, different model
309 ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A");
310 commands = testee.setAttributes(featuresMap);
311 assertEquals(commands.size(), 1);
312 StructureCommand expected1 = new StructureCommand("iterate",
313 "0//A/3-25/ 0//B/21-25/ 1//A/26-30/", "p.jv_chain='X'");
314 assertEquals(commands.get(0), expected1);
316 // same feature, different value
317 ChimeraCommands.addAtomSpecRange(featureValues, "Y", "0", 40, 50, "A");
318 commands = testee.setAttributes(featuresMap);
319 assertEquals(2, commands.size());
320 // commands are ordered by feature type but not by value
321 // so test for the expected command in either order
322 StructureCommandI cmd1 = commands.get(0);
323 StructureCommandI cmd2 = commands.get(1);
324 StructureCommand expected2 = new StructureCommand("iterate",
325 "0//A/40-50/", "p.jv_chain='Y'");
326 assertTrue(cmd1.equals(expected1) || cmd2.equals(expected1));
327 // String expected2 = "setattr #0/A:40-50 res jv_chain 'Y' create true";
328 assertTrue(cmd1.equals(expected2) || cmd2.equals(expected2));
331 featureValues.clear();
332 featuresMap.put("side-chain binding!", featureValues);
333 ChimeraCommands.addAtomSpecRange(featureValues,
334 "<html>metal <a href=\"http:a.b.c/x\"> 'ion!", "0", 7, 15, "A");
335 // feature names are sanitised to change non-alphanumeric to underscore
336 // feature values are sanitised to encode single quote characters
337 commands = testee.setAttributes(featuresMap);
338 assertEquals(commands.size(), 1);
339 StructureCommandI expected3 = new StructureCommand("iterate",
341 "p.jv_side_chain_binding_='<html>metal <a href=\"http:a.b.c/x\"> 'ion!'");
342 assertEquals(commands.get(0), expected3);
345 @Test(groups = "Functional")
346 public void testCloseViewer()
348 assertEquals(testee.closeViewer(), new StructureCommand("quit"));