--- /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 java.awt.Color;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.testng.annotations.Test;
+
+import jalview.structure.AtomSpecModel;
+import jalview.structure.StructureCommandI;
+import jalview.structure.StructureCommandsI;
+
+public class PymolCommandsTest
+{
+
+ @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 = new PymolCommands()
+ .colourBySequence(map);
+ assertEquals(commands.size(), 3);
+ assertEquals(commands.get(0).toString(),
+ "color(0x0000ff,0//A/2-5+9-23/ 0//B/7/ 1//A/1/ 1//B/4-7/)");
+ assertEquals(commands.get(1).toString(), "color(0xffff00,1//A/3-5+8/)");
+ assertEquals(
+ commands.get(2).toString(), "color(0xff0000,0//A/3-9/)");
+ }
+
+ @Test(groups = "Functional")
+ public void testGetAtomSpec()
+ {
+ StructureCommandsI testee = new PymolCommands();
+ 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()
+ {
+ StructureCommandsI testee = new PymolCommands();
+ 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/";
+ String expected1 = String.format("super(%s,%s)", refSpecCA,
+ toAlignSpecCA);
+ String expected2 = String.format("show(cartoon,%s %s)", refSpec,
+ toAlignSpec);
+ assertEquals(commands.get(0).toString(), expected1);
+ assertEquals(commands.get(1).toString(), expected2);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetAtomSpec_alphaOnly()
+ {
+ StructureCommandsI testee = new PymolCommands();
+ 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()
+ {
+ StructureCommandsI testee = new PymolCommands();
+ assertEquals(testee.getModelStartNo(), 0);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetResidueSpec()
+ {
+ PymolCommands testee = new PymolCommands();
+ assertEquals(testee.getResidueSpec("ALA"), "resn ALA");
+ }
+
+ @Test(groups = "Functional")
+ public void testShowBackbone()
+ {
+ PymolCommands testee = new PymolCommands();
+ List<StructureCommandI> cmds = testee.showBackbone();
+ assertEquals(cmds.size(), 2);
+ assertEquals(cmds.get(0).toString(), "hide(everything)");
+ assertEquals(cmds.get(1).toString(), "show(ribbon)");
+ }
+
+ @Test(groups = "Functional")
+ public void testColourByCharge()
+ {
+ PymolCommands testee = new PymolCommands();
+ List<StructureCommandI> cmds = testee.colourByCharge();
+ assertEquals(cmds.size(), 4);
+ assertEquals(cmds.get(0).toString(), "color(white,*)");
+ assertEquals(cmds.get(1).toString(), "color(red,resn ASP resn GLU)");
+ assertEquals(cmds.get(2).toString(), "color(blue,resn LYS resn ARG)");
+ assertEquals(cmds.get(3).toString(), "color(yellow,resn CYS)");
+ }
+
+ @Test(groups = "Functional")
+ public void testOpenCommandFile()
+ {
+ PymolCommands testee = new PymolCommands();
+ assertEquals(testee.openCommandFile("commands.pml").toString(),
+ "run(commands.pml)");
+ }
+
+ @Test(groups = "Functional")
+ public void testSaveSession()
+ {
+ PymolCommands testee = new PymolCommands();
+ assertEquals(testee.saveSession("somewhere.pse").toString(),
+ "save(somewhere.pse)");
+ }
+
+ @Test(groups = "Functional")
+ public void testColourByChain()
+ {
+ PymolCommands testee = new PymolCommands();
+ assertEquals(testee.colourByChain().toString(), "spectrum(chain)");
+ }
+
+ @Test(groups = "Functional")
+ public void testGetColourCommand()
+ {
+ PymolCommands testee = new PymolCommands();
+ assertEquals(
+ testee.colourResidues("something", Color.MAGENTA).toString(),
+ "color(0xff00ff,something)");
+ }
+}
git://source.jalview.org / jalview.git / blobdiff