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;
39 import jalview.structure.StructureCommandsI.AtomSpecType;
41 public class PymolCommandsTest
43 private PymolCommands testee;
45 @BeforeClass(alwaysRun = true)
48 testee = new PymolCommands();
51 @Test(groups = { "Functional" })
52 public void testColourBySequence()
55 Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
56 PymolCommands.addAtomSpecRange(map, Color.blue, "0", 2, 5, "A");
57 PymolCommands.addAtomSpecRange(map, Color.blue, "0", 7, 7, "B");
58 PymolCommands.addAtomSpecRange(map, Color.blue, "0", 9, 23, "A");
59 PymolCommands.addAtomSpecRange(map, Color.blue, "1", 1, 1, "A");
60 PymolCommands.addAtomSpecRange(map, Color.blue, "1", 4, 7, "B");
61 PymolCommands.addAtomSpecRange(map, Color.yellow, "1", 8, 8, "A");
62 PymolCommands.addAtomSpecRange(map, Color.yellow, "1", 3, 5, "A");
63 PymolCommands.addAtomSpecRange(map, Color.red, "0", 3, 5, "A");
64 PymolCommands.addAtomSpecRange(map, Color.red, "0", 6, 9, "A");
66 // Colours should appear in the Pymol command in the order in which
67 // they were added; within colour, by model, by chain, ranges in start order
68 List<StructureCommandI> commands = testee.colourBySequence(map);
69 assertEquals(commands.size(), 3);
70 assertEquals(commands.get(0), new StructureCommand("color", "0x0000ff",
71 "0//A/2-5+9-23/ 0//B/7/ 1//A/1/ 1//B/4-7/"));
72 assertEquals(commands.get(1),
73 new StructureCommand("color", "0xffff00", "1//A/3-5+8/"));
74 assertEquals(commands.get(2),
75 new StructureCommand("color", "0xff0000", "0//A/3-9/"));
78 @Test(groups = "Functional")
79 public void testGetAtomSpec()
81 AtomSpecModel model = new AtomSpecModel();
82 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
83 model.addRange("1", 2, 4, "A");
84 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
86 model.addRange("1", 8, 8, "A");
87 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
89 model.addRange("1", 5, 7, "B");
90 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
91 "1//A/2-4+8/ 1//B/5-7/");
92 model.addRange("1", 3, 5, "A");
93 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
94 "1//A/2-5+8/ 1//B/5-7/");
95 model.addRange("0", 1, 4, "B");
96 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
97 "0//B/1-4/ 1//A/2-5+8/ 1//B/5-7/");
98 model.addRange("0", 5, 9, "C");
99 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
100 "0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-7/");
101 model.addRange("1", 8, 10, "B");
102 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
103 "0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-10/");
104 model.addRange("1", 8, 9, "B");
105 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
106 "0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-10/");
107 model.addRange("0", 3, 10, "C"); // subsumes 5-9
108 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
109 "0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/");
110 model.addRange("5", 25, 35, " ");
111 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
112 "0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/ 5///25-35/");
116 @Test(groups = { "Functional" })
117 public void testSuperposeStructures()
119 AtomSpecModel ref = new AtomSpecModel();
120 ref.addRange("1", 12, 14, "A");
121 ref.addRange("1", 18, 18, "B");
122 ref.addRange("1", 22, 23, "B");
123 AtomSpecModel toAlign = new AtomSpecModel();
124 toAlign.addRange("2", 15, 17, "B");
125 toAlign.addRange("2", 20, 21, "B");
126 toAlign.addRange("2", 22, 22, "C");
127 List<StructureCommandI> commands = testee.superposeStructures(ref,
128 toAlign, AtomSpecType.ALPHA);
129 assertEquals(commands.size(), 4);
130 String refSpecCA = "(1//A/12-14/CA 1//B/18+22-23/CA";
131 String toAlignSpecCA = "(2//B/15-17+20-21/CA 2//C/22/CA";
132 String refSpec = "1//A/12-14/ 1//B/18+22-23/";
133 String toAlignSpec = "2//B/15-17+20-21/ 2//C/22/";
134 String altLoc = " and (altloc '' or altloc 'a'))";
135 // super command: separate arguments for regions to align
136 assertEquals(commands.get(1), new StructureCommand("pair_fit",
137 toAlignSpecCA + altLoc, refSpecCA + altLoc));
138 // show aligned regions: one argument for combined atom specs
139 assertEquals(commands.get(3), new StructureCommand("show", "cartoon",
140 refSpec + " " + toAlignSpec));
143 @Test(groups = "Functional")
144 public void testGetAtomSpec_alphaOnly()
146 AtomSpecModel model = new AtomSpecModel();
147 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
148 model.addRange("1", 2, 4, "A");
149 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
151 model.addRange("1", 8, 8, "A");
152 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
154 model.addRange("1", 5, 7, "B");
155 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
156 "1//A/2-4+8/CA 1//B/5-7/CA");
157 model.addRange("1", 3, 5, "A");
158 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
159 "1//A/2-5+8/CA 1//B/5-7/CA");
160 model.addRange("0", 1, 4, "B");
161 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
162 "0//B/1-4/CA 1//A/2-5+8/CA 1//B/5-7/CA");
163 model.addRange("0", 5, 9, "C");
164 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
165 "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-7/CA");
166 model.addRange("1", 8, 10, "B");
167 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
168 "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
169 model.addRange("1", 8, 9, "B");
170 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
171 "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
172 model.addRange("0", 3, 10, "C"); // subsumes 5-9
173 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
174 "0//B/1-4/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA");
175 model.addRange("5", 25, 35, " ");
176 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
177 "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");
180 @Test(groups = "Functional")
181 public void testGetModelStartNo()
183 assertEquals(testee.getModelStartNo(), 0);
186 @Test(groups = "Functional")
187 public void testGetResidueSpec()
189 assertEquals(testee.getResidueSpec("ALA"), "resn ALA");
192 @Test(groups = "Functional")
193 public void testShowBackbone()
195 List<StructureCommandI> cmds = testee.showBackbone();
196 assertEquals(cmds.size(), 2);
197 assertEquals(cmds.get(0), new StructureCommand("hide", "everything"));
198 assertEquals(cmds.get(1), new StructureCommand("show", "ribbon"));
201 @Test(groups = "Functional")
202 public void testColourByCharge()
204 List<StructureCommandI> cmds = testee.colourByCharge();
205 assertEquals(cmds.size(), 4);
206 assertEquals(cmds.get(0), new StructureCommand("color", "white", "*"));
207 assertEquals(cmds.get(1),
208 new StructureCommand("color", "red", "resn ASP resn GLU"));
209 assertEquals(cmds.get(2),
210 new StructureCommand("color", "blue", "resn LYS resn ARG"));
211 assertEquals(cmds.get(3),
212 new StructureCommand("color", "yellow", "resn CYS"));
215 @Test(groups = "Functional")
216 public void testOpenCommandFile()
218 assertEquals(testee.openCommandFile("commands.pml"),
219 new StructureCommand("run", "commands.pml"));
222 @Test(groups = "Functional")
223 public void testSaveSession()
225 assertEquals(testee.saveSession("somewhere.pse"),
226 new StructureCommand("save", "somewhere.pse"));
229 @Test(groups = "Functional")
230 public void testOpenSession()
232 assertEquals(testee.openSession("/some/path"),
233 new StructureCommand("load", "/some/path", "", "0", "pse"));
236 @Test(groups = "Functional")
237 public void testColourByChain()
239 assertEquals(testee.colourByChain(),
240 new StructureCommand("spectrum", "chain"));
243 @Test(groups = "Functional")
244 public void testColourResidues()
246 assertEquals(testee.colourResidues("something", Color.MAGENTA),
247 new StructureCommand("color", "0xff00ff", "something"));
250 @Test(groups = "Functional")
251 public void testLoadFile()
253 assertEquals(testee.loadFile("/some/path"),
254 new StructureCommand("load", "/some/path"));
257 @Test(groups = "Functional")
258 public void testSetBackgroundColour()
260 assertEquals(testee.setBackgroundColour(Color.PINK),
261 new StructureCommand("bg_color", "0xffafaf"));
264 @Test(groups = "Functional")
265 public void testSetAttribute()
267 AtomSpecModel model = new AtomSpecModel();
268 model.addRange("1", 89, 92, "A");
269 model.addRange("2", 12, 20, "B");
270 model.addRange("2", 8, 9, "B");
271 assertEquals(testee.setAttribute("jv_kd", "27.3", model),
272 new StructureCommand("iterate", "1//A/89-92/ 2//B/8-9+12-20/",
276 @Test(groups = { "Functional" })
277 public void testSetAttributes()
280 * make a map of { featureType, {featureValue, {residue range specification } } }
282 Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
283 Map<Object, AtomSpecModel> featureValues = new HashMap<>();
286 * start with just one feature/value...
288 featuresMap.put("chain", featureValues);
289 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A");
291 List<StructureCommandI> commands = testee.setAttributes(featuresMap);
292 assertEquals(commands.size(), 1);
295 * feature name gets a jv_ namespace prefix
297 assertEquals(commands.get(0), new StructureCommand("iterate",
298 "0//A/8-20/", "p.jv_chain='X'"));
300 // add same feature value, overlapping range
301 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 3, 9, "A");
302 // same feature value, contiguous range
303 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "A");
304 commands = testee.setAttributes(featuresMap);
305 assertEquals(commands.size(), 1);
306 assertEquals(commands.get(0), new StructureCommand("iterate",
307 "0//A/3-25/", "p.jv_chain='X'"));
309 // same feature value and model, different chain
310 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "B");
311 // same feature value and chain, different model
312 ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A");
313 commands = testee.setAttributes(featuresMap);
314 assertEquals(commands.size(), 1);
315 StructureCommand expected1 = new StructureCommand("iterate",
316 "0//A/3-25/ 0//B/21-25/ 1//A/26-30/", "p.jv_chain='X'");
317 assertEquals(commands.get(0), expected1);
319 // same feature, different value
320 ChimeraCommands.addAtomSpecRange(featureValues, "Y", "0", 40, 50, "A");
321 commands = testee.setAttributes(featuresMap);
322 assertEquals(2, commands.size());
323 // commands are ordered by feature type but not by value
324 // so test for the expected command in either order
325 StructureCommandI cmd1 = commands.get(0);
326 StructureCommandI cmd2 = commands.get(1);
327 StructureCommand expected2 = new StructureCommand("iterate",
328 "0//A/40-50/", "p.jv_chain='Y'");
329 assertTrue(cmd1.equals(expected1) || cmd2.equals(expected1));
330 // String expected2 = "setattr #0/A:40-50 res jv_chain 'Y' create true";
331 assertTrue(cmd1.equals(expected2) || cmd2.equals(expected2));
334 featureValues.clear();
335 featuresMap.put("side-chain binding!", featureValues);
336 ChimeraCommands.addAtomSpecRange(featureValues,
337 "<html>metal <a href=\"http:a.b.c/x\"> 'ion!", "0", 7, 15, "A");
338 // feature names are sanitised to change non-alphanumeric to underscore
339 // feature values are sanitised to encode single quote characters
340 commands = testee.setAttributes(featuresMap);
341 assertEquals(commands.size(), 1);
342 StructureCommandI expected3 = new StructureCommand("iterate",
344 "p.jv_side_chain_binding_='<html>metal <a href=\"http:a.b.c/x\"> 'ion!'");
345 assertEquals(commands.get(0), expected3);
348 @Test(groups = "Functional")
349 public void testCloseViewer()
351 assertEquals(testee.closeViewer(), new StructureCommand("quit"));