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;
public class PymolCommandsTest
{
+ private PymolCommands testee;
+
+ @BeforeClass
+ public void setUp()
+ {
+ testee = new PymolCommands();
+ }
@Test(groups = { "Functional" })
public void testColourBySequence()
// 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);
+ List<StructureCommandI> commands = testee.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/)");
+ 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()
{
- StructureCommandsI testee = new PymolCommands();
AtomSpecModel model = new AtomSpecModel();
assertEquals(testee.getAtomSpec(model, false), "");
model.addRange("1", 2, 4, "A");
@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");
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);
+
+ // 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()
{
- StructureCommandsI testee = new PymolCommands();
AtomSpecModel model = new AtomSpecModel();
assertEquals(testee.getAtomSpec(model, true), "");
model.addRange("1", 2, 4, "A");
@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)");
+ assertEquals(cmds.get(0), new StructureCommand("hide", "everything"));
+ assertEquals(cmds.get(1), new StructureCommand("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)");
+ 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()
{
- PymolCommands testee = new PymolCommands();
- assertEquals(testee.openCommandFile("commands.pml").toString(),
- "run(commands.pml)");
+ assertEquals(testee.openCommandFile("commands.pml"),
+ new StructureCommand("run", "commands.pml"));
}
@Test(groups = "Functional")
public void testSaveSession()
{
- PymolCommands testee = new PymolCommands();
- assertEquals(testee.saveSession("somewhere.pse").toString(),
- "save(somewhere.pse)");
+ 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()
{
- PymolCommands testee = new PymolCommands();
- assertEquals(testee.colourByChain().toString(), "spectrum(chain)");
+ 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 testGetColourCommand()
+ public void testSetBackgroundColour()
{
- PymolCommands testee = new PymolCommands();
- assertEquals(
- testee.colourResidues("something", Color.MAGENTA).toString(),
- "color(0xff00ff,something)");
+ 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);
}
}
git://source.jalview.org / jalview.git / blobdiff