/*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.ext.pymol;
import static org.testng.Assert.assertEquals;
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsI;
import java.awt.Color;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import org.testng.annotations.Test;
public class PymolCommandsTest
{
@Test(groups = { "Functional" })
public void testColourBySequence()
{
Map 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 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 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 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 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(),
"@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.getColourCommand("something", Color.MAGENTA).toString(),
"color(0xff00ff,something)");
}
}