def test_get_parameter(self):
params = basico.get_parameters()
self.assertEqual(params.shape[0], 3)
params = basico.get_parameters('epsilon')
self.assertEqual(params.shape[0], 1)
value = params.iloc[0].initial_value
self.assertEqual(value, 0.78)
def test_amount(self):
params = basico.get_parameters(type='assignment')
self.assertIsNone(params)
basico.add_amount_expressions()
params2 = basico.get_parameters(type='assignment')
self.assertIsNotNone(params2)
basico.remove_amount_expressions()
param3 = basico.get_parameters(type='assignment')
self.assertIsNone(param3)
def test_global_parameters(self):
basico.add_parameter('p', initial_value=3)
v = basico.get_parameters('p', exact=True)
self.assertIsNotNone(v)
basico.set_parameters('p',
exact=True,
initial_expression=' 1 / {Time}',
expression='{Time}',
status='assignment')
v = basico.as_dict(basico.get_parameters('p'))
self.assertEqual(v['type'], 'assignment')
self.assertEqual(v['expression'], 'Time')
self.assertEqual(v['initial_expression'], '')
basico.remove_parameter('p')
self.assertIsNone(basico.get_parameters('v', exact=True))
def test_set_parameter(self):
params = basico.get_parameters('epsilon')
self.assertEqual(params.shape[0], 1)
value = params.iloc[0].initial_value
self.assertEqual(value, 0.78)
basico.set_parameters('epsilon', initial_value=2.0)
params = basico.get_parameters('epsilon')
self.assertEqual(params.shape[0], 1)
value = params.iloc[0].initial_value
self.assertEqual(value, 2.0)
basico.set_parameters('Values[epsilon]', initial_value=3.0)
params = basico.get_parameters('Values[epsilon]')
self.assertEqual(params.shape[0], 1)
value = params.iloc[0].initial_value
self.assertEqual(value, 3.0)
def test_parameter_mapping(self):
m = 'Test_global_param'
dm = basico.new_model(name=m)
r = 'R'
basico.add_parameter('k_global', 1, unit='1/s')
basico.add_reaction(r, 'A -> B', function='Mass action (irreversible)')
params = basico.get_parameters()
self.assertTrue(len(params) == 1)
params2 = basico.get_reaction_parameters(r)
self.assertTrue(len(params2) == 1)
self.assertTrue(params2.type[0] == 'local')
basico.set_reaction(r, mapping={'k1': 'k_global'})
params2 = basico.get_reaction_parameters(r)
self.assertTrue(len(params2) == 1)
self.assertTrue(params2.type[0] == 'global')
basico.set_reaction(r, mapping={'k1': 1.0})
params2 = basico.get_reaction_parameters(r)
self.assertTrue(len(params2) == 1)
self.assertTrue(params2.type[0] == 'local')
basico.set_reaction_parameters('(R).k1', mapped_to='k_global')
params2 = basico.get_reaction_parameters(r)
self.assertTrue(len(params2) == 1)
self.assertTrue(params2.type[0] == 'global')
def test_get_parameters(self):
params = basico.get_parameters()
signal = params.loc['signal']
expression = signal.expression
self.assertTrue(expression != '')
conversion = basico.model_info._replace_names_with_cns(expression)
self.assertTrue(conversion != '')
expression = basico.model_info._replace_cns_with_names(conversion)
self.assertTrue(expression != '')
def test_add_ode(self):
basico.add_equation('d[PG]/dt=([E]/((k_4 [7-ADCA])/K_n +(k_5 [7-ADCA])/K_n +(k_6 [PGME])/K_si +k3))((k_2 [PGME])/K_s +(k_4b [CEX])/K_p )(k_3+(k_5 [7-ADCA])/K_n +(k_6 [PGME])/K_si )')
basico.add_equation(
'd[CEX]/dt=(k_2 [E][PGME])/K_s -([E]/((k_4 [7-ADCA])/K_n +(k_5 [7-ADCA])/K_n +(k_6 [PGME])/K_si +k3))((k_2 [PGME])/K_s +(k_4b [CEX])/K_p )(k_3+(k_5 [7-ADCA])/K_n )')
basico.add_equation(
'[E]=([EA]_0 exp(-k_d t))/(1+([PGME])/K_s + ((k_2 [PGME])/(K_s ((k_4 [7-ADCA])/K_n +(k_5 [7-ADCA])/K_n +(k_6 [PGME])/K_si +k3) ))(1+([7-ADCA])/K_n +([PGME])/K_si )+([CEX])/K_p +([PG])/K_p2i )')
species = basico.get_species()
self.assertEqual(species.loc['PG'].type, 'ode')
self.assertEqual(species.loc['PG'].expression, '[E] / ( Values[k_4] * [7-ADCA] / Values[K_n] + Values[k_5] * [7-ADCA] / Values[K_n] + Values[k_6] * [PGME] / Values[K_si] + Values[k3] ) * ( Values[k_2] * [PGME] / Values[K_s] + Values[k_4b] * [CEX] / Values[K_p] ) * ( Values[k_3] + Values[k_5] * [7-ADCA] / Values[K_n] + Values[k_6] * [PGME] / Values[K_si] )')
self.assertEqual(species.loc['E'].type, 'assignment')
self.assertEqual(species.loc['E'].expression, '[EA]_0 * exp ( - Values[k_d] * Time ) / ( 1 + [PGME] / Values[K_s] + Values[k_2] * [PGME] / ( Values[K_s] * ( Values[k_4] * [7-ADCA] / Values[K_n] + Values[k_5] * [7-ADCA] / Values[K_n] + Values[k_6] * [PGME] / Values[K_si] + Values[k3] ) ) * ( 1 + [7-ADCA] / Values[K_n] + [PGME] / Values[K_si] ) + [CEX] / Values[K_p] + [PG] / Values[K_p2i] )')
basico.add_equation('obs=sin(t)')
self.assertEqual(basico.get_parameters().loc['obs'].type, 'assignment')
self.assertEqual(basico.get_parameters().loc['obs'].expression, 'sin ( Time )')
# encountered an odd issue when pasting in equations with unicode characters
tokens = basico.model_info._tokenize_eqn(u'[E]=([E]_0 exp(-k_d t))/(1+[PGME]/K_s +[PGME]^2/(K_s K_si )+[7-ADCA]/K_n +((k_2 [PGME])/(K_s ((k_4 [7-ADCA])/K_n +(k_5 [7-ADCA])/K_n +k3) ))((k_2 [PGME])/K_s +(k_7 [PGME]^2)/(K_s K_si )+(k_4b [CEX])/K_p )(1+[7-ADCA]/K_n +[PGME]/K_si )+[CEX]/K_p +[PG]/K_p2i )')
self.assertTrue(tokens is not None)
self.assertEqual(tokens['tokens'][3], 'exp')
def test_load_biomodel(self):
dm = basico.load_biomodel(10)
self.assertTrue(dm is not None)
self.assertTrue(isinstance(dm, COPASI.CDataModel))
self.assertTrue('Kholodenko2000' in basico.model_io.overview())
basico.remove_datamodel(dm)
dm = basico.load_biomodel("MODEL1006230012")
self.assertTrue(dm is not None)
self.assertTrue(isinstance(dm, COPASI.CDataModel))
self.assertTrue('Stewart2009' in basico.model_io.overview())
params = basico.get_parameters()
self.assertEqual(params.shape[0], 176)
basico.remove_datamodel(dm)
def test_add_parameter(self):
basico.add_parameter('sin_time', type='assignment', expression='sin({Time})')
p = basico.get_parameters('sin_time')
self.assertEqual('assignment', str(p.iloc[0]['type']))
self.assertEqual('sin ( Time )', str(p.iloc[0]['expression']))
basico.remove_parameter('sin_time')