def test_lipo_sites_builder_abbrev():
model_dict = {'builder': 'lipo_sites',
'activation': 1,
'baxtranslocation': 1}
bd = Builder()
bd.build_model_from_dict(model_dict)
eq_(bd.model.name, 'ls_Baxtr1Activ1')
def test_one_cpt_builder_abbrev():
model_dict = {'builder': 'one_cpt',
'activation': 1,
'baxtranslocation': 1}
bd = Builder()
bd.build_model_from_dict(model_dict)
eq_(bd.model.name, '1c_Baxtr1Activ1')
def test_translocation_1():
"""Check translocation by checking for Bax_mono_translocates_sol_to_ves."""
model_dict = {'baxtranslocation': 1,
'bidtranslocation': 1}
bd = Builder()
bd.build_model_from_dict(model_dict)
print bd.model.rules
ok_(bd.model.rules['tBid_translocates_sol_to_ves'])
ok_(bd.model.rules['Bax_mono_translocates_sol_to_ves'])
'tBid_0': 20.,
'tBid_transloc_kf': 10**-1.89187047,
'tBid_transloc_kr': 10**-4.22923156,
'Bax_transloc_kf': 10**-5.47509186,
'Bax_transloc_kr': 10**-4.50648375,
'tBid_Bax_mem_bh3_kf': 10**-5.07143377,
'tBid_Bax_mem_bh3_kr': 10**3.70925668,
'tBid_Bax_ins_bh3_kc': 10**-1.46660821,
'c1_scaling': 10**0.982916,
'c2_scaling': 10**0.32449226,
'bid_fret1': 10**1.92229914,
}
"""
bd = Builder(params_dict=params_dict)
bd.build_model_from_dict(model_dict)
print(bd.model.parameters)
t = time_36
s = Solver(bd.model, t)
s.run()
n_species = s.y.shape[1]
plt.ion()
for spec_ix in range(n_species):
plt.figure()
plt.title(bd.model.species[spec_ix])
plt.plot(t, s.y[:,spec_ix])
#plt.ion()
#plt.figure('NBD')
def test_error_on_bleach_without_nbd():
model_dict = {'baxtranslocation': 1,
'activation': 1,
'bleach': 1}
bd = Builder()
bd.build_model_from_dict(model_dict)
def test_key_error_on_unknown_feature():
model_dict = {'asdf': 1}
bd = Builder()
bd.build_model_from_dict(model_dict)
def test_error_on_unknown_implementation():
model_dict = {'baxtranslocation': 9}
bd = Builder()
bd.build_model_from_dict(model_dict)
def test_model_name_sort_order():
model_dict = {'activation': 1,
'baxtranslocation': 1}
bd = Builder()
bd.build_model_from_dict(model_dict)
eq_(bd.model.name, 'Baxtr1Activ1')
