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 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()