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(
74 new StructureCommand("color", "0xffff00", "1//A/3-5+8/"));
75 assertEquals(commands.get(
77 new StructureCommand("color", "0xff0000", "0//A/3-9/"));
80 @Test(groups = "Functional")
81 public void testGetAtomSpec()
83 AtomSpecModel model = new AtomSpecModel();
84 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "");
85 model.addRange("1", 2, 4, "A");
86 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-4/");
87 model.addRange("1", 8, 8, "A");
88 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-4+8/");
89 model.addRange("1", 5, 7, "B");
90 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-4+8/ 1//B/5-7/");
91 model.addRange("1", 3, 5, "A");
92 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY), "1//A/2-5+8/ 1//B/5-7/");
93 model.addRange("0", 1, 4, "B");
94 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
95 "0//B/1-4/ 1//A/2-5+8/ 1//B/5-7/");
96 model.addRange("0", 5, 9, "C");
97 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
98 "0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-7/");
99 model.addRange("1", 8, 10, "B");
100 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
101 "0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-10/");
102 model.addRange("1", 8, 9, "B");
103 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
104 "0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-10/");
105 model.addRange("0", 3, 10, "C"); // subsumes 5-9
106 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
107 "0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/");
108 model.addRange("5", 25, 35, " ");
109 assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
110 "0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/ 5///25-35/");
114 @Test(groups = { "Functional" })
115 public void testSuperposeStructures()
117 AtomSpecModel ref = new AtomSpecModel();
118 ref.addRange("1", 12, 14, "A");
119 ref.addRange("1", 18, 18, "B");
120 ref.addRange("1", 22, 23, "B");
121 AtomSpecModel toAlign = new AtomSpecModel();
122 toAlign.addRange("2", 15, 17, "B");
123 toAlign.addRange("2", 20, 21, "B");
124 toAlign.addRange("2", 22, 22, "C");
125 List<StructureCommandI> commands = testee.superposeStructures(ref,
126 toAlign, AtomSpecType.ALPHA);
127 assertEquals(commands.size(), 2);
128 String refSpecCA = "(1//A/12-14/CA 1//B/18+22-23/CA";
129 String toAlignSpecCA = "(2//B/15-17+20-21/CA 2//C/22/CA";
130 String refSpec = "1//A/12-14/ 1//B/18+22-23/";
131 String toAlignSpec = "2//B/15-17+20-21/ 2//C/22/";
132 String altLoc = " and (altloc '' or altloc 'a'))";
133 // super command: separate arguments for regions to align
134 assertEquals(commands.get(0),
135 new StructureCommand("pair_fit", toAlignSpecCA+altLoc, refSpecCA+altLoc));
136 // show aligned regions: one argument for combined atom specs
137 assertEquals(commands.get(1), new StructureCommand("show", "cartoon",
138 refSpec + " " + toAlignSpec));
141 @Test(groups = "Functional")
142 public void testGetAtomSpec_alphaOnly()
144 AtomSpecModel model = new AtomSpecModel();
145 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
146 model.addRange("1", 2, 4, "A");
147 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "1//A/2-4/CA");
148 model.addRange("1", 8, 8, "A");
149 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "1//A/2-4+8/CA");
150 model.addRange("1", 5, 7, "B");
151 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
152 "1//A/2-4+8/CA 1//B/5-7/CA");
153 model.addRange("1", 3, 5, "A");
154 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
155 "1//A/2-5+8/CA 1//B/5-7/CA");
156 model.addRange("0", 1, 4, "B");
157 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
158 "0//B/1-4/CA 1//A/2-5+8/CA 1//B/5-7/CA");
159 model.addRange("0", 5, 9, "C");
160 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
161 "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-7/CA");
162 model.addRange("1", 8, 10, "B");
163 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
164 "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
165 model.addRange("1", 8, 9, "B");
166 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
167 "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
168 model.addRange("0", 3, 10, "C"); // subsumes 5-9
169 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
170 "0//B/1-4/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA");
171 model.addRange("5", 25, 35, " ");
172 assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
173 "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");
176 @Test(groups = "Functional")
177 public void testGetModelStartNo()
179 assertEquals(testee.getModelStartNo(), 0);
182 @Test(groups = "Functional")
183 public void testGetResidueSpec()
185 assertEquals(testee.getResidueSpec("ALA"), "resn ALA");
188 @Test(groups = "Functional")
189 public void testShowBackbone()
191 List<StructureCommandI> cmds = testee.showBackbone();
192 assertEquals(cmds.size(), 2);
193 assertEquals(cmds.get(0), new StructureCommand("hide", "everything"));
194 assertEquals(cmds.get(1), new StructureCommand("show", "ribbon"));
197 @Test(groups = "Functional")
198 public void testColourByCharge()
200 List<StructureCommandI> cmds = testee.colourByCharge();
201 assertEquals(cmds.size(), 4);
202 assertEquals(cmds.get(0), new StructureCommand("color", "white", "*"));
203 assertEquals(cmds.get(1),
204 new StructureCommand("color", "red", "resn ASP resn GLU"));
205 assertEquals(cmds.get(2),
206 new StructureCommand("color", "blue", "resn LYS resn ARG"));
207 assertEquals(cmds.get(3),
208 new StructureCommand("color", "yellow", "resn CYS"));
211 @Test(groups = "Functional")
212 public void testOpenCommandFile()
214 assertEquals(testee.openCommandFile("commands.pml"),
215 new StructureCommand("run", "commands.pml"));
218 @Test(groups = "Functional")
219 public void testSaveSession()
221 assertEquals(testee.saveSession("somewhere.pse"),
222 new StructureCommand("save", "somewhere.pse"));
225 @Test(groups = "Functional")
226 public void testOpenSession()
228 assertEquals(testee.openSession("/some/path"),
229 new StructureCommand("load", "/some/path", "", "0", "pse"));
232 @Test(groups = "Functional")
233 public void testColourByChain()
235 assertEquals(testee.colourByChain(),
236 new StructureCommand("spectrum", "chain"));
239 @Test(groups = "Functional")
240 public void testColourResidues()
242 assertEquals(testee.colourResidues("something",
244 new StructureCommand("color", "0xff00ff", "something"));
247 @Test(groups = "Functional")
248 public void testLoadFile()
250 assertEquals(testee.loadFile("/some/path"),
251 new StructureCommand("load", "/some/path"));
254 @Test(groups = "Functional")
255 public void testSetBackgroundColour()
257 assertEquals(testee.setBackgroundColour(
259 new StructureCommand("bg_color", "0xffafaf"));
262 @Test(groups = "Functional")
263 public void testSetAttribute()
265 AtomSpecModel model = new AtomSpecModel();
266 model.addRange("1", 89, 92, "A");
267 model.addRange("2", 12, 20, "B");
268 model.addRange("2", 8, 9, "B");
269 assertEquals(testee.setAttribute("jv_kd", "27.3", model),
270 new StructureCommand("iterate", "1//A/89-92/ 2//B/8-9+12-20/",
274 @Test(groups = { "Functional" })
275 public void testSetAttributes()
278 * make a map of { featureType, {featureValue, {residue range specification } } }
280 Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
281 Map<Object, AtomSpecModel> featureValues = new HashMap<>();
284 * start with just one feature/value...
286 featuresMap.put("chain", featureValues);
287 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A");
289 List<StructureCommandI> commands = testee.setAttributes(featuresMap);
290 assertEquals(commands.size(), 1);
293 * feature name gets a jv_ namespace prefix
295 assertEquals(commands.get(0), new StructureCommand("iterate",
296 "0//A/8-20/", "p.jv_chain='X'"));
298 // add same feature value, overlapping range
299 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 3, 9, "A");
300 // same feature value, contiguous range
301 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "A");
302 commands = testee.setAttributes(featuresMap);
303 assertEquals(commands.size(), 1);
304 assertEquals(commands.get(0), new StructureCommand("iterate",
305 "0//A/3-25/", "p.jv_chain='X'"));
307 // same feature value and model, different chain
308 ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "B");
309 // same feature value and chain, different model
310 ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A");
311 commands = testee.setAttributes(featuresMap);
312 assertEquals(commands.size(), 1);
313 StructureCommand expected1 = new StructureCommand("iterate",
314 "0//A/3-25/ 0//B/21-25/ 1//A/26-30/", "p.jv_chain='X'");
315 assertEquals(commands.get(0), expected1);
317 // same feature, different value
318 ChimeraCommands.addAtomSpecRange(featureValues, "Y", "0", 40, 50, "A");
319 commands = testee.setAttributes(featuresMap);
320 assertEquals(2, commands.size());
321 // commands are ordered by feature type but not by value
322 // so test for the expected command in either order
323 StructureCommandI cmd1 = commands.get(0);
324 StructureCommandI cmd2 = commands.get(1);
325 StructureCommand expected2 = new StructureCommand("iterate",
326 "0//A/40-50/", "p.jv_chain='Y'");
327 assertTrue(cmd1.equals(expected1) || cmd2.equals(expected1));
328 // String expected2 = "setattr #0/A:40-50 res jv_chain 'Y' create true";
329 assertTrue(cmd1.equals(expected2) || cmd2.equals(expected2));
332 featureValues.clear();
333 featuresMap.put("side-chain binding!", featureValues);
334 ChimeraCommands.addAtomSpecRange(featureValues,
335 "<html>metal <a href=\"http:a.b.c/x\"> 'ion!", "0", 7, 15, "A");
336 // feature names are sanitised to change non-alphanumeric to underscore
337 // feature values are sanitised to encode single quote characters
338 commands = testee.setAttributes(featuresMap);
339 assertEquals(commands.size(), 1);
340 StructureCommandI expected3 = new StructureCommand("iterate",
342 "p.jv_side_chain_binding_='<html>metal <a href=\"http:a.b.c/x\"> 'ion!'");
343 assertEquals(commands.get(0), expected3);
346 @Test(groups = "Functional")
347 public void testCloseViewer()
349 assertEquals(testee.closeViewer(), new StructureCommand("quit"));