/*
* 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 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;
import jalview.structure.StructureCommandsI.AtomSpecType;
public class PymolCommandsTest
{
private PymolCommands testee;
@BeforeClass(alwaysRun = true)
public void setUp()
{
testee = new PymolCommands();
}
@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 = 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, AtomSpecType.RESIDUE_ONLY), "");
model.addRange("1", 2, 4, "A");
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"1//A/2-4/");
model.addRange("1", 8, 8, "A");
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"1//A/2-4+8/");
model.addRange("1", 5, 7, "B");
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"1//A/2-4+8/ 1//B/5-7/");
model.addRange("1", 3, 5, "A");
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"1//A/2-5+8/ 1//B/5-7/");
model.addRange("0", 1, 4, "B");
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"0//B/1-4/ 1//A/2-5+8/ 1//B/5-7/");
model.addRange("0", 5, 9, "C");
assertEquals(testee.getAtomSpec(model, AtomSpecType.RESIDUE_ONLY),
"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, AtomSpecType.RESIDUE_ONLY),
"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, AtomSpecType.RESIDUE_ONLY),
"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, AtomSpecType.RESIDUE_ONLY),
"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, AtomSpecType.RESIDUE_ONLY),
"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 commands = testee.superposeStructures(ref,
toAlign, AtomSpecType.ALPHA);
assertEquals(commands.size(), 4);
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 altLoc = " and (altloc '' or altloc 'a'))";
// super command: separate arguments for regions to align
assertEquals(commands.get(1), new StructureCommand("pair_fit",
toAlignSpecCA + altLoc, refSpecCA + altLoc));
// show aligned regions: one argument for combined atom specs
assertEquals(commands.get(3), new StructureCommand("show", "cartoon",
refSpec + " " + toAlignSpec));
}
@Test(groups = "Functional")
public void testGetAtomSpec_alphaOnly()
{
AtomSpecModel model = new AtomSpecModel();
assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA), "");
model.addRange("1", 2, 4, "A");
assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"1//A/2-4/CA");
model.addRange("1", 8, 8, "A");
assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"1//A/2-4+8/CA");
model.addRange("1", 5, 7, "B");
assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"1//A/2-4+8/CA 1//B/5-7/CA");
model.addRange("1", 3, 5, "A");
assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"1//A/2-5+8/CA 1//B/5-7/CA");
model.addRange("0", 1, 4, "B");
assertEquals(testee.getAtomSpec(model, AtomSpecType.ALPHA),
"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, AtomSpecType.ALPHA),
"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, AtomSpecType.ALPHA),
"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, AtomSpecType.ALPHA),
"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, AtomSpecType.ALPHA),
"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, AtomSpecType.ALPHA),
"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 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 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> featuresMap = new LinkedHashMap<>();
Map featureValues = new HashMap<>();
/*
* start with just one feature/value...
*/
featuresMap.put("chain", featureValues);
ChimeraCommands.addAtomSpecRange(featureValues, "X", "0", 8, 20, "A");
List 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,
"metal '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_='metal 'ion!'");
assertEquals(commands.get(0), expected3);
}
@Test(groups = "Functional")
public void testCloseViewer()
{
assertEquals(testee.closeViewer(), new StructureCommand("quit"));
}
}