+ ChimeraCommands.makeAttributeName("!this is-a_very*{odd(name"),
+ "jv__this_is_a_very__odd_name");
+ // name ending in color gets underscore appended
+ assertEquals(ChimeraCommands.makeAttributeName("helixColor"),
+ "jv_helixColor_");
+ }
+
+ @Test(groups = "Functional")
+ public void testGetAtomSpec()
+ {
+ StructureCommandsI testee = new ChimeraCommands();
+ AtomSpecModel model = new AtomSpecModel();
+ assertEquals(testee.getAtomSpec(model, false), "");
+ model.addRange(1, 2, 4, "A");
+ assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A");
+ model.addRange(1, 8, 8, "A");
+ assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A,8.A");
+ model.addRange(1, 5, 7, "B");
+ assertEquals(testee.getAtomSpec(model, false), "#1:2-4.A,8.A,5-7.B");
+ model.addRange(1, 3, 5, "A");
+ assertEquals(testee.getAtomSpec(model, false), "#1:2-5.A,8.A,5-7.B");
+ model.addRange(0, 1, 4, "B");
+ assertEquals(testee.getAtomSpec(model, false),
+ "#0:1-4.B|#1:2-5.A,8.A,5-7.B");
+ model.addRange(0, 5, 9, "C");
+ assertEquals(testee.getAtomSpec(model, false),
+ "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-7.B");
+ model.addRange(1, 8, 10, "B");
+ assertEquals(testee.getAtomSpec(model, false),
+ "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
+ model.addRange(1, 8, 9, "B");
+ assertEquals(testee.getAtomSpec(model, false),
+ "#0:1-4.B,5-9.C|#1:2-5.A,8.A,5-10.B");
+ model.addRange(0, 3, 10, "C"); // subsumes 5-9
+ assertEquals(testee.getAtomSpec(model, false),
+ "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B");
+ model.addRange(5, 25, 35, " "); // empty chain code - e.g. from homology
+ // modelling
+ assertEquals(testee.getAtomSpec(model, false),
+ "#0:1-4.B,3-10.C|#1:2-5.A,8.A,5-10.B|#5:25-35.");
+
+ }
+
+ @Test(groups = { "Functional" })
+ public void testSuperposeStructures()
+ {
+ StructureCommandsI testee = new ChimeraCommands();
+ 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");
+ String command = testee.superposeStructures(ref, toAlign);
+ String refSpec = "#1:12-14.A,18.B,22-23.B@CA|P&~@.B-Z&~@.2-9";
+ String toAlignSpec = "#2:15-17.B,20-21.B,22.C@CA|P&~@.B-Z&~@.2-9";
+ String expected = String.format(
+ "match %s %s;~display all; chain @CA|P; ribbon %s|%s; focus",
+ refSpec, toAlignSpec, refSpec, toAlignSpec);
+ assertEquals(command, expected);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetAtomSpec_alphaOnly()
+ {
+ StructureCommandsI testee = new ChimeraCommands();
+ AtomSpecModel model = new AtomSpecModel();
+ assertEquals(testee.getAtomSpec(model, true), "");
+ model.addRange(1, 2, 4, "A");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#1:2-4.A@CA|P&~@.B-Z&~@.2-9");
+ model.addRange(1, 8, 8, "A");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#1:2-4.A,8.A@CA|P&~@.B-Z&~@.2-9");
+ model.addRange(1, 5, 7, "B");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#1:2-4.A,8.A,5-7.B@CA|P&~@.B-Z&~@.2-9");
+ model.addRange(1, 3, 5, "A");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#1:2-5.A,8.A,5-7.B@CA|P&~@.B-Z&~@.2-9");
+ model.addRange(0, 1, 4, "B");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0:1-4.B@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA|P&~@.B-Z&~@.2-9");
+ model.addRange(0, 5, 9, "C");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0:1-4.B,5-9.C@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-7.B@CA|P&~@.B-Z&~@.2-9");
+ model.addRange(1, 8, 10, "B");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0:1-4.B,5-9.C@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9");
+ model.addRange(1, 8, 9, "B");
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0:1-4.B,5-9.C@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9");
+ model.addRange(0, 3, 10, "C"); // subsumes 5-9
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0:1-4.B,3-10.C@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9");
+ model.addRange(5, 25, 35, " "); // empty chain code
+ assertEquals(testee.getAtomSpec(model, true),
+ "#0:1-4.B,3-10.C@CA|P&~@.B-Z&~@.2-9|#1:2-5.A,8.A,5-10.B@CA|P&~@.B-Z&~@.2-9|#5:25-35.@CA|P&~@.B-Z&~@.2-9");
+
+ }
+
+ @Test(groups = "Functional")
+ public void testGetModelStartNo()
+ {
+ StructureCommandsI testee = new ChimeraCommands();
+ assertEquals(testee.getModelStartNo(), 0);
+ }
+
+ @Test(groups = "Functional")
+ public void testGetResidueSpec()
+ {
+ ChimeraCommands testee = new ChimeraCommands();
+ assertEquals(testee.getResidueSpec("ALA"), "::ALA");
+ }
+
+ @Test(groups = "Functional")
+ public void testShowBackbone()
+ {
+ ChimeraCommands testee = new ChimeraCommands();
+ assertEquals(testee.showBackbone(), "~display all;chain @CA|P");
+ }
+
+ @Test(groups = "Functional")
+ public void testOpenCommandFile()
+ {
+ ChimeraCommands testee = new ChimeraCommands();
+ assertEquals(testee.openCommandFile("nowhere"), "open cmd:nowhere");
+ }
+
+ @Test(groups = "Functional")
+ public void testSaveSession()
+ {
+ ChimeraCommands testee = new ChimeraCommands();
+ assertEquals(testee.saveSession("somewhere"), "save somewhere");
+ }
+
+ @Test(groups = "Functional")
+ public void testGetColourCommand()
+ {
+ ChimeraCommands testee = new ChimeraCommands();
+ assertEquals(testee.getColourCommand("something", Color.MAGENTA),
+ "color #ff00ff something");
+ }
+
+ @Test(groups = "Functional")
+ public void testSetAttribute()
+ {
+ ChimeraCommands testee = new ChimeraCommands();
+ 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("phi", "27.3", model),
+ "setattr res phi '27.3' #1:89-92.A|#2:8-9.B,12-20.B");