--- /dev/null
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.ext.pymol;
+
+import static org.testng.Assert.assertEquals;
+import static org.testng.Assert.assertTrue;
+
+import java.awt.Color;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+import jalview.ext.rbvi.chimera.ChimeraCommands;
+import jalview.structure.AtomSpecModel;
+import jalview.structure.StructureCommand;
+import jalview.structure.StructureCommandI;
+
+public class PymolCommandsTest
+{
+ private PymolCommands testee;
+
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ testee = new PymolCommands();
+ }
+
+ @Test(groups = { "Functional" })
+ public void testColourBySequence()
+ {
+
+ Map<Object, AtomSpecModel> map = new LinkedHashMap<>();
+ PymolCommands.addAtomSpecRange(map, Color.blue, "0", 2, 5, "A");
+ PymolCommands.addAtomSpecRange(map, Color.blue, "0", 7, 7, "B");
+ PymolCommands.addAtomSpecRange(map, Color.blue, "0", 9, 23, "A");
+ PymolCommands.addAtomSpecRange(map, Color.blue, "1", 1, 1, "A");
+ PymolCommands.addAtomSpecRange(map, Color.blue, "1", 4, 7, "B");
+ PymolCommands.addAtomSpecRange(map, Color.yellow, "1", 8, 8, "A");
+ PymolCommands.addAtomSpecRange(map, Color.yellow, "1", 3, 5, "A");
+ PymolCommands.addAtomSpecRange(map, Color.red, "0", 3, 5, "A");
+ PymolCommands.addAtomSpecRange(map, Color.red, "0", 6, 9, "A");
+
+ // Colours should appear in the Pymol command in the order in which
+ // they were added; within colour, by model, by chain, ranges in start order
+ List<StructureCommandI> commands = testee.colourBySequence(map);
+ assertEquals(commands.size(), 3);
+ assertEquals(commands.get(0), new StructureCommand("color", "0x0000ff",
+ "0//A/2-5+9-23/ 0//B/7/ 1//A/1/ 1//B/4-7/"));
+ assertEquals(commands.get(
+ 1),
+ new StructureCommand("color", "0xffff00", "1//A/3-5+8/"));
+ assertEquals(commands.get(
+ 2),
+ new StructureCommand("color", "0xff0000", "0//A/3-9/"));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetAtomSpec()
+ {
+ AtomSpecModel model = new AtomSpecModel();
+ assertEquals(testee.getAtomSpec(model, false), "");
+ model.addRange("1", 2, 4, "A");
+ assertEquals(testee.getAtomSpec(model, false), "1//A/2-4/");
+ model.addRange("1", 8, 8, "A");
+ assertEquals(testee.getAtomSpec(model, false), "1//A/2-4+8/");
+ model.addRange("1", 5, 7, "B");
+ assertEquals(testee.getAtomSpec(model, false), "1//A/2-4+8/ 1//B/5-7/");
+ model.addRange("1", 3, 5, "A");
+ assertEquals(testee.getAtomSpec(model, false), "1//A/2-5+8/ 1//B/5-7/");
+ model.addRange("0", 1, 4, "B");
+ assertEquals(testee.getAtomSpec(model, false),
+ "0//B/1-4/ 1//A/2-5+8/ 1//B/5-7/");
+ model.addRange("0", 5, 9, "C");
+ assertEquals(testee.getAtomSpec(model, false),
+ "0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-7/");
+ model.addRange("1", 8, 10, "B");
+ assertEquals(testee.getAtomSpec(model, false),
+ "0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-10/");
+ model.addRange("1", 8, 9, "B");
+ assertEquals(testee.getAtomSpec(model, false),
+ "0//B/1-4/ 0//C/5-9/ 1//A/2-5+8/ 1//B/5-10/");
+ model.addRange("0", 3, 10, "C"); // subsumes 5-9
+ assertEquals(testee.getAtomSpec(model, false),
+ "0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/");
+ model.addRange("5", 25, 35, " ");
+ assertEquals(testee.getAtomSpec(model, false),
+ "0//B/1-4/ 0//C/3-10/ 1//A/2-5+8/ 1//B/5-10/ 5///25-35/");
+
+ }
+
+ @Test(groups = { "Functional" })
+ public void testSuperposeStructures()
+ {
+ AtomSpecModel ref = new AtomSpecModel();
+ ref.addRange("1", 12, 14, "A");
+ ref.addRange("1", 18, 18, "B");
+ ref.addRange("1", 22, 23, "B");
+ AtomSpecModel toAlign = new AtomSpecModel();
+ toAlign.addRange("2", 15, 17, "B");
+ toAlign.addRange("2", 20, 21, "B");
+ toAlign.addRange("2", 22, 22, "C");
+ List<StructureCommandI> commands = testee.superposeStructures(ref,
+ toAlign);
+ assertEquals(commands.size(), 2);
+ String refSpecCA = "1//A/12-14/CA 1//B/18+22-23/CA";
+ String toAlignSpecCA = "2//B/15-17+20-21/CA 2//C/22/CA";
+ String refSpec = "1//A/12-14/ 1//B/18+22-23/";
+ String toAlignSpec = "2//B/15-17+20-21/ 2//C/22/";
+
+ // super command: separate arguments for regions to align
+ assertEquals(commands.get(0),
+ new StructureCommand("super", refSpecCA, toAlignSpecCA));
+ // show aligned regions: one argument for combined atom specs
+ assertEquals(commands.get(1), new StructureCommand("show", "cartoon",
+ refSpec + " " + toAlignSpec));
+ }
+
+ @Test(groups = "Functional")
+ public void testGetAtomSpec_alphaOnly()
+ {
+ AtomSpecModel model = new AtomSpecModel();
+ assertEquals(testee.getAtomSpec(model, true), "");
+ model.addRange("1", 2, 4, "A");
+ assertEquals(testee.getAtomSpec(model, true), "1//A/2-4/CA");
+ model.addRange("1", 8, 8, "A");
+ assertEquals(testee.getAtomSpec(model, true), "1//A/2-4+8/CA");
+ model.addRange("1", 5, 7, "B");
+ assertEquals(testee.getAtomSpec(model, true),
+ "1//A/2-4+8/CA 1//B/5-7/CA");
+ model.addRange("1", 3, 5, "A");
+ assertEquals(testee.getAtomSpec(model, true),
+ "1//A/2-5+8/CA 1//B/5-7/CA");
+ model.addRange("0", 1, 4, "B");
+ assertEquals(testee.getAtomSpec(model, true),
+ "0//B/1-4/CA 1//A/2-5+8/CA 1//B/5-7/CA");
+ model.addRange("0", 5, 9, "C");
+ assertEquals(testee.getAtomSpec(model, true),
+ "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-7/CA");
+ model.addRange("1", 8, 10, "B");
+ assertEquals(testee.getAtomSpec(model, true),
+ "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
+ model.addRange("1", 8, 9, "B");
+ assertEquals(testee.getAtomSpec(model, true),
+ "0//B/1-4/CA 0//C/5-9/CA 1//A/2-5+8/CA 1//B/5-10/CA");
+ model.addRange("0", 3, 10, "C"); // subsumes 5-9
+ assertEquals(testee.getAtomSpec(model, true),
+ "0//B/1-4/CA 0//C/3-10/CA 1//A/2-5+8/CA 1//B/5-10/CA");
+ model.addRange("5", 25, 35, " ");
+ assertEquals(testee.getAtomSpec(model, true),
+ "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");
+ }
+
+ @Test(groups = "Functional")
+ public void testGetModelStartNo()
+ {
+ assertEquals(testee.getModelStartNo(), 0);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetResidueSpec()
+ {
+ assertEquals(testee.getResidueSpec("ALA"), "resn ALA");
+ }
+
+ @Test(groups = "Functional")
+ public void testShowBackbone()
+ {
+ List<StructureCommandI> cmds = testee.showBackbone();
+ assertEquals(cmds.size(), 2);
+ assertEquals(cmds.get(0), new StructureCommand("hide", "everything"));
+ assertEquals(cmds.get(1), new StructureCommand("show", "ribbon"));
+ }
+
+ @Test(groups = "Functional")
+ public void testColourByCharge()
+ {
+ List<StructureCommandI> cmds = testee.colourByCharge();
+ assertEquals(cmds.size(), 4);
+ assertEquals(cmds.get(0), new StructureCommand("color", "white", "*"));
+ assertEquals(cmds.get(1),
+ new StructureCommand("color", "red", "resn ASP resn GLU"));
+ assertEquals(cmds.get(2),
+ new StructureCommand("color", "blue", "resn LYS resn ARG"));
+ assertEquals(cmds.get(3),
+ new StructureCommand("color", "yellow", "resn CYS"));
+ }
+
+ @Test(groups = "Functional")
+ public void testOpenCommandFile()
+ {
+ assertEquals(testee.openCommandFile("commands.pml"),
+ new StructureCommand("run", "commands.pml"));
+ }
+
+ @Test(groups = "Functional")
+ public void testSaveSession()
+ {
+ assertEquals(testee.saveSession("somewhere.pse"),
+ new StructureCommand("save", "somewhere.pse"));
+ }
+
+ @Test(groups = "Functional")
+ public void testOpenSession()
+ {
+ assertEquals(testee.openSession("/some/path"),
+ new StructureCommand("load", "/some/path", "", "0", "pse"));
+ }
+
+ @Test(groups = "Functional")
+ public void testColourByChain()
+ {
+ assertEquals(testee.colourByChain(),
+ new StructureCommand("spectrum", "chain"));
+ }
+
+ @Test(groups = "Functional")
+ public void testColourResidues()
+ {
+ assertEquals(testee.colourResidues("something",
+ Color.MAGENTA),
+ new StructureCommand("color", "0xff00ff", "something"));
+ }
+
+ @Test(groups = "Functional")
+ public void testLoadFile()
+ {
+ assertEquals(testee.loadFile("/some/path"),
+ new StructureCommand("load", "/some/path"));
+ }
+
+ @Test(groups = "Functional")
+ public void testSetBackgroundColour()
+ {
+ assertEquals(testee.setBackgroundColour(
+ Color.PINK),
+ new StructureCommand("bg_color", "0xffafaf"));
+ }
+
+ @Test(groups = "Functional")
+ public void testSetAttribute()
+ {
+ AtomSpecModel model = new AtomSpecModel();
+ model.addRange("1", 89, 92, "A");
+ model.addRange("2", 12, 20, "B");
+ model.addRange("2", 8, 9, "B");
+ assertEquals(testee.setAttribute("jv_kd", "27.3", model),
+ new StructureCommand("iterate", "1//A/89-92/ 2//B/8-9+12-20/",
+ "p.jv_kd='27.3'"));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testSetAttributes()
+ {
+ /*
+ * make a map of { featureType, {featureValue, {residue range specification } } }
+ */
+ Map<String, Map<Object, AtomSpecModel>> featuresMap = new LinkedHashMap<>();
+ Map<Object, AtomSpecModel> featureValues = new HashMap<>();
+
+ /*
+ * start with just one feature/value...
+ */
+ featuresMap.put("chain", featureValues);
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A");
+
+ List<StructureCommandI> commands = testee.setAttributes(featuresMap);
+ assertEquals(commands.size(), 1);
+
+ /*
+ * feature name gets a jv_ namespace prefix
+ */
+ assertEquals(commands.get(0), new StructureCommand("iterate",
+ "0//A/8-20/", "p.jv_chain='X'"));
+
+ // add same feature value, overlapping range
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 3, 9, "A");
+ // same feature value, contiguous range
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "A");
+ commands = testee.setAttributes(featuresMap);
+ assertEquals(commands.size(), 1);
+ assertEquals(commands.get(0), new StructureCommand("iterate",
+ "0//A/3-25/", "p.jv_chain='X'"));
+
+ // same feature value and model, different chain
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 21, 25, "B");
+ // same feature value and chain, different model
+ ChimeraCommands.addAtomSpecRange(featureValues, "X", "1", 26, 30, "A");
+ commands = testee.setAttributes(featuresMap);
+ assertEquals(commands.size(), 1);
+ StructureCommand expected1 = new StructureCommand("iterate",
+ "0//A/3-25/ 0//B/21-25/ 1//A/26-30/", "p.jv_chain='X'");
+ assertEquals(commands.get(0), expected1);
+
+ // same feature, different value
+ ChimeraCommands.addAtomSpecRange(featureValues, "Y", "0", 40, 50, "A");
+ commands = testee.setAttributes(featuresMap);
+ assertEquals(2, commands.size());
+ // commands are ordered by feature type but not by value
+ // so test for the expected command in either order
+ StructureCommandI cmd1 = commands.get(0);
+ StructureCommandI cmd2 = commands.get(1);
+ StructureCommand expected2 = new StructureCommand("iterate",
+ "0//A/40-50/", "p.jv_chain='Y'");
+ assertTrue(cmd1.equals(expected1) || cmd2.equals(expected1));
+ // String expected2 = "setattr #0/A:40-50 res jv_chain 'Y' create true";
+ assertTrue(cmd1.equals(expected2) || cmd2.equals(expected2));
+
+ featuresMap.clear();
+ featureValues.clear();
+ featuresMap.put("side-chain binding!", featureValues);
+ ChimeraCommands.addAtomSpecRange(featureValues,
+ "<html>metal <a href=\"http:a.b.c/x\"> 'ion!", "0", 7, 15, "A");
+ // feature names are sanitised to change non-alphanumeric to underscore
+ // feature values are sanitised to encode single quote characters
+ commands = testee.setAttributes(featuresMap);
+ assertEquals(commands.size(), 1);
+ StructureCommandI expected3 = new StructureCommand("iterate",
+ "0//A/7-15/",
+ "p.jv_side_chain_binding_='<html>metal <a href=\"http:a.b.c/x\"> 'ion!'");
+ assertEquals(commands.get(0), expected3);
+ }
+
+ @Test(groups = "Functional")
+ public void testCloseViewer()
+ {
+ assertEquals(testee.closeViewer(), new StructureCommand("quit"));
+ }
+}
git://source.jalview.org / jalview.git / blobdiff