def testReadAndWriteDescription(self):
m = Cml.Molecule()
m.property["Description"] = "H20 is the base of all life."
m.property["Description-Attribution"] = "Wikipedia, CC-BY-SA"
m.write("tests/testWrite.cml")
m = Cml.Molecule()
m.parse("tests/testWrite.cml")
self.assertEqual(m.property["Description"], "H20 is the base of all life.")
self.assertEqual(m.property["Description-Attribution"], "Wikipedia, CC-BY-SA")
os.remove("tests/testWrite.cml")
def testWriteAndParsePropertys(self):
m = Cml.Molecule()
m.atoms["a1"] = Cml.Atom("a1", "H", 0, 0, 0)
m.property["Name"] = "Hydrogen"
m.property["Weight"] = 1.0
m.property["Radius"] = 25
m.write("tests/testHydrogen.cml")
m = Cml.Molecule()
m.parse("tests/testHydrogen.cml")
self.assertEqual(m.property["Name"], "Hydrogen")
self.assertEqual(m.property["Weight"], 1.0)
self.assertEqual(m.property["Radius"], 25)
self.assertEqual(m.is_atom, True)
os.remove("tests/testHydrogen.cml")
def testWriteAndParseStatePropertys(self):
m = Cml.Molecule()
gas = Cml.State("Gas", -426, 64)
aq = Cml.State("Aqueous", ions=["Na+", "OH-"])
m.states["Gas"] = gas
m.states["Aqueous"] = aq
m.write("tests/testSodiumhydroxide.cml")
m = Cml.Molecule()
m.parse("tests/testSodiumhydroxide.cml")
self.assertEqual(m.states["Gas"].enthalpy, -426)
self.assertEqual(m.states["Gas"].entropy, 64)
self.assertEqual(m.states["Aqueous"].ions, ["Na+", "OH-"])
self.assertEqual(m.states["Aqueous"].ions_str, "Na+,OH-")
os.remove("tests/testSodiumhydroxide.cml")
def testParsePropane(self):
m = Cml.Molecule()
m.parse("tests/testPropane.cml")
self.assertEqual(len(m.atoms), 12)
self.assertEqual(len(m.bonds), 11)
self.assertEqual(m.atoms["a1"].elementType, "H")
self.assertEqual(m.atoms["a1"].formalCharge, 0)
self.assertEqual(m.atoms["a1"].x, -4.719821)
self.assertEqual(m.atoms["a1"].y, 1.866564)
self.assertEqual(m.atoms["a1"].z, -1.096199)
self.assertEqual(m.atoms["a1"].pos, (-4.719821, 1.866564))
self.assertEqual(m.atoms["a2"].x, -4.299694)
self.assertEqual(m.atoms["a2"].y, 2.06041)
self.assertEqual(m.atoms["a2"].z, -2.091249)
self.assertEqual(m.atoms["a2"].pos, (-4.299694, 2.06041))
self.assertEqual(m.atoms["a2"].elementType, "C")
self.assertEqual(m.atoms["a2"].formalCharge, 0)
self.assertEqual(m.bonds[0].atomA.id, "a1")
self.assertEqual(m.bonds[0].atomB.id, "a2")
self.assertAlmostEqual(m.bonds[0].atomA.x, -4.719821)
self.assertAlmostEqual(m.bonds[0].atomA.y, 1.866564)
self.assertAlmostEqual(m.bonds[0].atomA.z, -1.096199)
self.assertAlmostEqual(m.bonds[0].atomB.x, -4.299694)
self.assertAlmostEqual(m.bonds[0].atomB.y, 2.06041)
self.assertAlmostEqual(m.bonds[0].atomB.z, -2.091249)
def testCachedMolecule(self):
m = Cml.Molecule()
m.parse("tests/testPropane.cml")
m.write("tests/testWrite.cml")
c = CachedCml.getMoleculeCml("tests/testWrite.cml")
self.assertEqual(len(m.atoms), 12)
self.assertEqual(len(m.bonds), 11)
self.assertEqual(m.atoms["a1"].elementType, "H")
self.assertAlmostEqual(m.atoms["a1"].x, -4.719821)
self.assertAlmostEqual(m.atoms["a1"].y, 1.866564)
self.assertAlmostEqual(m.atoms["a1"].z, -1.096199)
self.assertAlmostEqual(m.atoms["a2"].x, -4.299694)
self.assertAlmostEqual(m.atoms["a2"].y, 2.06041)
self.assertAlmostEqual(m.atoms["a2"].z, -2.091249)
self.assertEqual(m.atoms["a2"].elementType, "C")
self.assertEqual(m.bonds[0].atomA.id, "a1")
self.assertEqual(m.bonds[0].atomB.id, "a2")
os.remove("tests/testWrite.cml")
c = CachedCml.getMoleculeCml("tests/testWrite.cml")
self.assertEqual(len(m.atoms), 12)
self.assertEqual(len(m.bonds), 11)
self.assertEqual(m.atoms["a1"].elementType, "H")
self.assertAlmostEqual(m.atoms["a1"].x, -4.719821)
self.assertAlmostEqual(m.atoms["a1"].y, 1.866564)
self.assertAlmostEqual(m.atoms["a1"].z, -1.096199)
self.assertAlmostEqual(m.atoms["a2"].x, -4.299694)
self.assertAlmostEqual(m.atoms["a2"].y, 2.06041)
self.assertAlmostEqual(m.atoms["a2"].z, -2.091249)
self.assertEqual(m.atoms["a2"].elementType, "C")
self.assertEqual(m.bonds[0].atomA.id, "a1")
self.assertEqual(m.bonds[0].atomB.id, "a2")
def getMoleculeCml(filename):
global __cml_cache
if filename in __cml_cache:
return __cml_cache[filename]
m = Cml.Molecule()
m.parse(filename)
__cml_cache[filename] = m
return m
def testParseStatePropertys(self):
m = Cml.Molecule()
m.parse("tests/testProperty.cml")
self.assertEqual(m.states["Gas"].enthalpy, -426)
self.assertEqual(m.states["Gas"].entropy, 64)
self.assertEqual(m.states["Gas"].short, "g")
self.assertEqual(m.get_state("g").entropy, 64)
self.assertEqual(m.get_state("l"), None)
self.assertEqual(m.states["Aqueous"].ions, ["Na+", "OH-"])
def testParseMoleculeWithoutBonds(self):
m = Cml.Molecule()
m.parse("data/molecule/NaCl.cml")
self.assertEqual(len(m.atoms), 2)
self.assertEqual(len(m.bonds), 1)
self.assertEqual(m.atoms["a1"].elementType, "Na")
self.assertEqual(m.atoms["a1"].formalCharge, 1)
self.assertEqual(m.atoms["a1"].x, 1.0)
self.assertEqual(m.atoms["a1"].y, 0.0)
self.assertEqual(m.atoms["a2"].x, 0.0)
self.assertEqual(m.atoms["a2"].y, 0.0)
self.assertEqual(m.atoms["a2"].elementType, "Cl")
self.assertEqual(m.atoms["a2"].formalCharge, -1)
def testParseAmmonia(self):
m = Cml.Molecule()
m.parse("tests/testAmmonia.cml")
self.assertEqual(len(m.atoms), 4)
self.assertEqual(len(m.bonds), 3)
self.assertEqual(m.atoms["a1"].elementType, "N")
self.assertEqual(m.atoms["a1"].x, 1.0)
self.assertEqual(m.atoms["a1"].y, 0.0)
self.assertEqual(m.atoms["a2"].x, 2.02)
self.assertEqual(m.atoms["a2"].y, 0.0)
self.assertEqual(m.atoms["a2"].elementType, "H")
self.assertEqual(m.bonds[0].atomA.id, "a1")
self.assertEqual(m.bonds[0].atomB.id, "a2")
self.assertEqual(m.is_atom, False)
def testCreateMoleculeWithCharge(self):
m = Cml.Molecule()
a1 = Cml.Atom("a1", "C",-1, 0, 0)
a2 = Cml.Atom("a2", "O", 1, 1, 0)
m.atoms["a1"] = a1
m.atoms["a2"] = a2
b = Cml.Bond(a1, a2, 2)
m.bonds.append(b)
m.write("tests/testOxygen.cml")
m = Cml.Molecule()
m.parse("tests/testOxygen.cml")
self.assertAlmostEqual(m.atoms["a1"].x, 0.0)
self.assertAlmostEqual(m.atoms["a1"].y, 0.0)
self.assertEqual(m.atoms["a1"].elementType, "C")
self.assertEqual(m.atoms["a1"].formalCharge,-1)
self.assertAlmostEqual(m.atoms["a2"].x, 1.0)
self.assertAlmostEqual(m.atoms["a2"].y, 0.0)
self.assertEqual(m.atoms["a2"].elementType, "O")
self.assertEqual(m.atoms["a2"].formalCharge,1)
self.assertEqual(m.bonds[0].atomA.id, "a1")
self.assertEqual(m.bonds[0].atomB.id, "a2")
self.assertEqual(m.bonds[0].bonds, 2)
os.remove("tests/testOxygen.cml")
def testSortedAtoms(self):
m = Cml.Molecule()
m.parse("tests/testPropane.cml")
self.assertEqual(m.atoms_sorted[0].id, "a1")
self.assertEqual(m.atoms_sorted[1].id, "a2")
self.assertEqual(m.atoms_sorted[2].id, "a3")
self.assertEqual(m.atoms_sorted[3].id, "a4")
self.assertEqual(m.atoms_sorted[4].id, "a5")
self.assertEqual(m.atoms_sorted[5].id, "a6")
self.assertEqual(m.atoms_sorted[6].id, "a7")
self.assertEqual(m.atoms_sorted[7].id, "a8")
self.assertEqual(m.atoms_sorted[8].id, "a9")
self.assertEqual(m.atoms_sorted[9].id, "a10")
self.assertEqual(m.atoms_sorted[10].id, "a11")
self.assertEqual(m.atoms_sorted[11].id, "a12")
self.assertEqual(m.getDigits("asdas23434"), 23434)
def openFile(self, filename):
self.filename = filename
self.current_pos = self.folder_list.index(filename)
molecule = Cml.Molecule()
self.molecule = molecule
molecule.parse(filename)
formula = filename.split("/")[-1].split(".cml")[0]
state_formula = formula+"(g)"
cml2img.convert_cml2png(state_formula, "preview.png")
pixBuffPreview = Pixbuf.new_from_file("preview.png")
imgPreview = self.widget("imgPreview")
imgPreview.set_from_pixbuf(pixBuffPreview)
self.txtMoleculeName = self.widget("txtName")
self.txtAtomWeight = self.widget("txtWeight")
self.txtAtomRadius = self.widget("txtRadius")
self.txtMoleculeName.set_text(str(molecule.property.get("Name", "")))
self.widget("txtAttribution").set_text(
molecule.property.get("DescriptionAttribution", ""))
self.widget("textbufferDescription").set_text(
molecule.property.get("Description", ""))
if self.molecule.is_atom:
self.setAtomSettings()
else:
self.txtAtomWeight.set_text("")
self.txtAtomWeight.set_sensitive(False)
self.txtAtomRadius.set_text("")
self.txtAtomRadius.set_sensitive(False)
self.modelStates.clear()
for state in molecule.states.values():
stateList = [state.name, state.enthalpy, state.entropy, state.ions_str]
stateList = [str(x) if x is not None else "" for x in stateList]
self.modelStates.append(stateList)
self.widget("cmbLicense").set_active(-1)
index = 0
for license in self.widget("liststoreLicenses"):
if license[0] == molecule.property.get("DescriptionLicense", "N/A"):
self.widget("cmbLicense").set_active(index)
break
index += 1
def testNormalizePos(self):
m = Cml.Molecule()
m.parse("tests/testPropane.cml")
self.assertEqual(m.max_pos(), (-0.605318, 3.557669, -1.096199))
self.assertEqual(m.min_pos(), (-4.928943, 1.137126, -4.097433))
m.normalize_pos()
self.assertEqual(m.max_pos(), (4.323625, 2.4205430000000003, 3.0012339999999997))
self.assertEqual(m.min_pos(), (0.0, 0.0, 0.0))
self.assertEqual(len(m.atoms), 12)
self.assertEqual(len(m.bonds), 11)
self.assertEqual(m.atoms["a1"].elementType, "H")
self.assertAlmostEqual(m.atoms["a1"].x, 0.209122)
self.assertAlmostEqual(m.atoms["a1"].y, 0.729438)
self.assertAlmostEqual(m.atoms["a1"].z, 3.001234)
self.assertAlmostEqual(m.atoms["a2"].x, 0.629249)
self.assertAlmostEqual(m.atoms["a2"].y, 0.923284)
self.assertAlmostEqual(m.atoms["a2"].z, 2.006184)
self.assertEqual(m.atoms["a2"].elementType, "C")
self.assertEqual(m.bonds[0].atomA.id, "a1")
self.assertEqual(m.bonds[0].atomB.id, "a2")
def testAllMolecules(self):
for filename in glob.glob("data/molecule/*"):
m = Cml.Molecule()
m.parse(filename)
self.assertNotEqual(len(m.states), 0, msg="%s dont have any state info!" % filename)
