def get_bond_lenght(self, bond):
rA = CachedCml.getMolecule(bond.atomA.elementType).property["Radius"]
rB = CachedCml.getMolecule(bond.atomB.elementType).property["Radius"]
bond_lenght = (rA + rB) * SPRITE_RADIUS * SCALE_FACTOR
if bond.bonds != 0:
bond_lenght *= BOND_LENGTH_FACTOR
return bond_lenght
def get_bond_lenght(self, bond):
rA = CachedCml.getMolecule(bond.atomA.elementType).property["Radius"]
rB = CachedCml.getMolecule(bond.atomB.elementType).property["Radius"]
bond_lenght = (rA + rB) * SPRITE_RADIUS * SCALE_FACTOR
if bond.bonds != 0:
bond_lenght *= BOND_LENGTH_FACTOR
return bond_lenght
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 create_info_frame(self, formula):
cml = CachedCml.getMolecule(formula)
info_text = pyglet.text.decode_html("<b>%s</b><br> %s" %
( cml.property.get("Name", "Undefined"),
cml.property.get("Description", "No Description Available")
))
info_doc = Document(info_text, height=self.height, width=self.width/2,
is_fixed_size = True)
info_frame = Frame(info_doc)
return info_frame
def addState(self, stateless):
default_order = ["Aqueous","Gas", "Liquid", "Solid"]
statefull = list()
for s in stateless:
m = CachedCml.getMolecule(s)
for k in default_order:
if k in m.states:
state = m.states[k].short
break
statefull.append(s+"(%s)"%state)
return statefull
def addState(self, stateless):
default_order = ["Aqueous", "Gas", "Liquid", "Solid"]
statefull = list()
for s in stateless:
m = CachedCml.getMolecule(s)
for k in default_order:
if k in m.states:
state = m.states[k].short
break
statefull.append(s + "(%s)" % state)
return statefull
def create_info_frame(self, formula):
cml = CachedCml.getMolecule(formula)
info_text = pyglet.text.decode_html(
"<b>%s</b><br> %s" %
(cml.property.get("Name", "Undefined"),
cml.property.get("Description", "No Description Available")))
info_doc = Document(info_text,
height=self.height,
width=self.width / 2,
is_fixed_size=True)
info_frame = Frame(info_doc)
return info_frame
def __init__(self, symbol, charge, space, batch, molecule, pos):
img = pyglet_util.load_image("atom-" + symbol.lower() + ".png")
group = RenderingOrder.elements
pyglet.sprite.Sprite.__init__(self, img, batch=batch, group=group, subpixel=True)
self.cml = CachedCml.getMolecule(symbol)
self.scale = self.cml.property["Radius"] * SCALE_FACTOR
self.create_electric_charge_sprite(charge, batch)
self.molecule = molecule
self.symbol = symbol
self.charge = charge
self.space = space
self.active = False
self.init_chipmunk()
self.move(pos)
def __init__(self, symbol, charge, space, batch, molecule, pos):
img = pyglet_util.load_image("atom-" + symbol.lower() + ".png")
group = RenderingOrder.elements
pyglet.sprite.Sprite.__init__(self,
img,
batch=batch,
group=group,
subpixel=True)
self.cml = CachedCml.getMolecule(symbol)
self.scale = self.cml.property["Radius"] * SCALE_FACTOR
self.create_electric_charge_sprite(charge, batch)
self.molecule = molecule
self.symbol = symbol
self.charge = charge
self.space = space
self.active = False
self.init_chipmunk()
self.move(pos)
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 __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 getMolecule(self,formula):
return CachedCml.getMolecule(formula)
def getMolecule(self, formula):
return CachedCml.getMolecule(formula)
