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 testWriteAndParseReactions(self):
r = Cml.Reactions()
r1 = Cml.Reaction(["O", "O"], ["O2"])
r.reactions.append(r1)
r2 = Cml.Reaction(["H+", "H+"], ["H2"])
r.reactions.append(r2)
r.write("tests/writtenReactions.cml")
r = Cml.Reactions()
r.parse("tests/writtenReactions.cml")
self.assertEqual(r.reactions[0].reactants, ["O","O"])
self.assertEqual(r.reactions[0].products, ["O2"])
self.assertEqual(r.reactions[1].reactants, ['H+', 'H+'])
self.assertEqual(r.reactions[1].products, ["H2"])
os.remove("tests/writtenReactions.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 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 testParseReactions(self):
r = Cml.Reactions()
r.parse("tests/reactions.cml")
self.assertEqual(r.reactions[0].reactants, ["H2","O"])
self.assertEqual(r.reactions[0].products, ["H2O(s)"])
self.assertEqual(r.reactions[1].reactants, ['SO3', 'H2O'])
self.assertEqual(r.reactions[1].products, ["H2SO4(aq)"])
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 testParseLevel01(self):
m = Cml.Level()
m.parse("data/levels/01-Water.cml")
expected = ['H+(g)', 'O(g)', 'O(g)', 'H+(g)', 'P(g)', 'F(g)', 'Al(s)']
self.assertEqual(m.molecules, expected)
self.assertEqual(m.victory_condition, ["H2O"])
self.assertEqual(m.objective, "Create a water molecule")
self.assertEqual(m.hint, "H + H + O => H2O")
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 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 react(self, molecule):
ions = molecule.to_aqueous()
if ions != None and len(ions) > 0:
print(molecule.formula, "-(Water)>", ions)
cml = Cml.Reaction([molecule.formula],ions)
reaction = Reaction.Reaction(cml,[molecule.state_formula])
return reaction
elif Config.current.DEBUG:
print("Water beaker didnt react with:", molecule.formula)
def testParseLevel(self):
m = Cml.Level()
m.parse("tests/testlevel.cml")
expected = ['H+(g)', 'O(g)', 'O(g)', 'H+(g)', 'P(g)', 'F(g)', 'Al(s)']
self.assertEqual(m.molecules, expected)
self.assertEqual(m.victory_condition, ["H2O"])
self.assertEqual(m.objective, "Create a water molecule")
self.assertEqual(m.hint, "H + H + O => H2O")
self.assertEqual(m.effects[0].title, "Fire")
self.assertEqual(m.effects[0].value, 800)
self.assertEqual(m.effects[0].x2, 12)
self.assertEqual(m.effects[0].y2, 10)
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 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 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 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 on_btnSave_clicked(self, widget):
self.molecule.states = dict()
for col in self.modelStates:
name = col[0]
enthalpy = col[1] if col[1] != "" else None
entropy = col[2] if col[2] != "" else None
ions = col[3].split(',') if col[3] != "" else None
state = Cml.State(name, enthalpy, entropy, ions)
self.molecule.states[name] = state
self.molecule.property["Name"] = self.txtMoleculeName.get_text()
textbuffer = self.widget("textbufferDescription")
start_iter = textbuffer.get_start_iter()
end_iter = textbuffer.get_end_iter()
description = textbuffer.get_text(start_iter, end_iter, True)
self.molecule.property["Description"] = description
self.molecule.property["DescriptionAttribution"] = self.widget("txtAttribution").get_text()
self.molecule.property["DescriptionLicense"] = get_active_text(self.widget("cmbLicense"))
if self.molecule.is_atom:
self.molecule.property["Weight"] = float(self.txtAtomWeight.get_text())
self.molecule.property["Radius"] = float(self.txtAtomRadius.get_text())
self.molecule.write(self.filename)
def __init__(self,
formula_with_state,
space,
batch,
pos=None,
render_only=False):
self.space = space
self.batch = batch
self.creation_time = time.time()
formula, state = Reaction.split_state(formula_with_state)
self.formula = formula
self.cml = CachedCml.getMolecule(formula)
self.cml.normalize_pos()
self.current_state = self.cml.get_state(state)
if self.current_state is None and render_only:
self.current_state = Cml.State("Gas")
elif self.current_state is None:
raise Exception("Did not find state for:" + formula_with_state +
" existing states are:" +
str(self.cml.states.keys()))
if pos is None:
pos = (random.randint(10, 600), random.randint(200, 500))
self.pos = pos
self.create_atoms()
def testParseLevelWithMiningEffect(self):
m = Cml.Level()
m.parse("data/levels/12-Iron-1.cml")
self.assertEqual(m.effects[0].title, "Mining")
self.assertEqual(m.effects[0].molecules, ['Fe2O3(s)', 'Fe3O4(s)'])
def setupRealReactor(self):
cml = Cml.Reactions()
cml.parse("data/reactions.cml")
reactor = Reactor(cml.reactions)
return reactor
def setupSimpleReactor(self):
r1 = Cml.Reaction(["O", "H+"], ["OH-(aq)"])
r2 = Cml.Reaction(["O", "O"], ["O2(g)"])
return Reactor([r1, r2])
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)
def __init__(self):
self.moelcules = dict()
cml = Cml.Reactions()
cml.parse("data/reactions.cml")
self.reactor = Reactor(cml.reactions)
def setupSimpleReactor():
r1 = Cml.Reaction(["H2SO4(aq)", "NaCl(s)", "NaCl(s)"],
["HCl(g)", "HCl(g)", "Na2SO4(s)"])
r2 = Cml.Reaction(["OH-", "H+"], ["H2O(l)"])
return Reactor([r1, r2])
def get_current_level(self):
path = self.levels[self.current_level]
cml = Cml.Level()
cml.parse(path)
return Level(cml, self.window)
