def test_simple_activator(self):
model = wc_lang.Model()
init_volume = wc_lang.core.InitVolume(
distribution=wc_ontology['WC:normal_distribution'],
mean=0.5,
std=0)
c = wc_lang.Compartment(id='c', init_volume=init_volume)
c.init_density = wc_lang.Parameter(id='density_' + c.id, value=1.)
volume = wc_lang.Function(id='volume_' + c.id)
volume.expression, error = wc_lang.FunctionExpression.deserialize(
f'{c.id} / {c.init_density.id}', {
wc_lang.Compartment: {
c.id: c
},
wc_lang.Parameter: {
c.init_density.id: c.init_density
},
})
assert error is None, str(error)
tf_species_type = wc_lang.SpeciesType(id='Activator')
tf_species = wc_lang.Species(species_type=tf_species_type,
compartment=c)
tf_species.id = tf_species.gen_id()
wc_lang.DistributionInitConcentration(species=tf_species, mean=0.5)
F_act, species, parameters, functions = utils.simple_activator(
model, 'transcription_rna1', tf_species)
self.assertEqual(
F_act,
'((1 + Activator[c] / (Ka_transcription_rna1_Activator * Avogadro * volume_c) * f_transcription_rna1_Activator) / '
'(1 + Activator[c] / (Ka_transcription_rna1_Activator * Avogadro * volume_c)))'
)
self.assertEqual(species, {'Activator[c]': tf_species})
self.assertEqual(functions, {'volume_c': volume})
self.assertEqual(set(model.parameters), set(parameters.values()))
self.assertEqual(
sorted(list(parameters.keys())),
sorted([
'Avogadro', 'f_transcription_rna1_Activator',
'Ka_transcription_rna1_Activator'
]))
self.assertEqual(
model.parameters.get_one(
id='Ka_transcription_rna1_Activator').type, None)
self.assertEqual(
model.parameters.get_one(
id='Ka_transcription_rna1_Activator').units,
unit_registry.parse_units('M'))
def test_unbounded_paths(self):
num_rxn = 8
# irrreversible reactions
# unbounded network
self.create_reaction_network(self.dfba_submodel, 'ring', **{'num_rxn': num_rxn, 'reversible': False,
'flux_max': float('inf')})
path_len = 2*num_rxn-1
g = self.model_analysis.get_digraph(self.dfba_submodel)
paths = self.model_analysis.unbounded_paths(g, self.species[0], [self.species[num_rxn-1]])
self.assertEqual(len(paths), 1)
self.assertEqual(len(paths[0]), path_len)
# bounded network
self.create_reaction_network(self.dfba_submodel, 'ring', **{'num_rxn': num_rxn, 'reversible': False})
g = self.model_analysis.get_digraph(self.dfba_submodel)
paths = self.model_analysis.unbounded_paths(g, self.species[0],
[self.species[num_rxn-1]], min_non_finite_ub=self.default_flux_max+1)
self.assertEqual(len(paths), 0)
# reversible reactions, paths on both sides of ring
# unbounded network
self.create_reaction_network(self.dfba_submodel, 'ring', **{'num_rxn': num_rxn, 'reversible': True,
'flux_max': float('inf')})
g = self.model_analysis.get_digraph(self.dfba_submodel)
paths = self.model_analysis.unbounded_paths(g, self.species[0], [self.species[num_rxn//2]])
self.assertEqual(len(paths), 2)
for p in paths:
self.assertEqual(len(p), num_rxn+1)
# bounded network
self.create_reaction_network(self.dfba_submodel, 'ring', **{'num_rxn': num_rxn, 'reversible': True})
g = self.model_analysis.get_digraph(self.dfba_submodel)
paths = self.model_analysis.unbounded_paths(g, self.species[0], [self.species[num_rxn//2]],
min_non_finite_ub=self.default_flux_max+1)
self.assertEqual(len(paths), 0)
# test exceptions
with self.assertRaisesRegex(ValueError, "'ex_species' should be a wc_lang.Species instance, but "):
self.model_analysis.unbounded_paths(None, 'species', None)
with self.assertRaisesRegex(ValueError, "elements of 'obj_fn_species' should be wc_lang.Species instances, but "):
self.model_analysis.unbounded_paths(None, wc_lang.Species(), ['species'])
def setUp(self):
# make model
self.model = wc_lang.Model(id='model')
comp = self.model.compartments.create(id='comp')
self.species = []
self.num_species = 20
for i in range(1, self.num_species+1):
spec_type = self.model.species_types.create(id=self.sp_id(i),
type=onto['WC:metabolite']) # metabolite
species = wc_lang.Species(
species_type=spec_type,
compartment=comp)
species.id = species.gen_id()
self.species.append(species)
self.dfba_submodel = self.model.submodels.create(
id='metabolism',
framework=onto['WC:dynamic_flux_balance_analysis'])
self.id_idx = 0
self.model_analysis = wc_analysis.model.fba.FbaModelAnalysis(self.model)
def main(examples_dir=os.path.join(os.path.dirname(__file__), 'examples')):
################################################################
# This code is used by literalinclude commands in wc_lang_tutorial.rst
# It contains many separate examples, each prefixed by a comment that delineates the
# start of the example and is used by a start-after option in a literalinclude.
# The line before each of these comments is:
# Don't change the next comment - it's used by a literalinclude
# Changes to these comments should be synchronized with changes to wc_lang_tutorial.rst
################################################################
# save the results of example commands so this function can be unit-tested
results = []
################################################
# Reading and writing models to/from files
################################################
model_filename = os.path.join(examples_dir, 'example_model.xlsx')
# Don't change the next comment - it's used by a literalinclude
# This example illustrates how to read a model from an Excel file
# 'model_filename' is the name of an Excel file storing a model
model = wc_lang.io.Reader().run(model_filename)[wc_lang.Model][0]
results.append("read model: '{}'".format(model.name))
if not os.path.isdir(examples_dir):
os.makedirs(examples_dir)
# Don't change the next comment - it's used by a literalinclude
# This example illustrates how to write a model to a set of .tsv files
# 'examples_dir' is a directory
model_filename_pattern = os.path.join(examples_dir, 'example_model-*.tsv')
wc_lang.io.Writer().run(model_filename_pattern, model, data_repo_metadata=False)
results.append("write a model to a set of .tsv files: '{}'".format(model_filename_pattern))
# Don't change the next comment - it's used by a literalinclude
# This example illustrates how to read a model from a set of .tsv files
model_from_tsv = wc_lang.io.Reader().run(model_filename_pattern)[wc_lang.Model][0]
results.append("read a model from a set of .tsv files: '{}'".format(model_from_tsv.name))
################################################
# Accessing model properties
################################################
# Don't change the next comment - it's used by a literalinclude
# ``wc_lang`` models have many attributes
model.id # the model's unique identifier
model.name # its human readable name
model.version # its version number
model.taxon # the taxon of the organism being modeled
model.submodels # a list of the model's submodels
model.compartments # " " " the model's compartments
model.species_types # " " " its species types
model.parameters # " " " its parameters
model.references # " " " publication sources for the model instance
model.identifiers # " " " identifiers in external namespaces for the model instance
results.append("referenced model attributes")
# Don't change the next comment - it's used by a literalinclude
# ``wc_lang`` also provides many convenience methods
model.get_compartments()
model.get_species_types()
model.get_submodels()
model.get_species()
model.get_distribution_init_concentrations()
model.get_reactions()
model.get_dfba_obj_reactions()
model.get_rate_laws()
model.get_parameters()
model.get_references()
results.append("referenced model convenience methods")
# Don't change the next comment - it's used by a literalinclude
# ``get_reactions()`` returns a list of all of the reactions in a model's submodels
reaction_identification = []
for reaction in model.get_reactions():
reaction_identification.append('submodel name: {}, reaction id: {}'.format(
reaction.submodel.name, reaction.id))
results.append("get_reactions entry 0: '{}'".format(reaction_identification[0]))
#################################################
# Building models and editing model properties
#################################################
# Don't change the next comment - it's used by a literalinclude
# The following illustrates how to program a trivial model
# create a model with one submodel and one compartment
prog_model = wc_lang.Model(id='programmatic_model', name='Programmatic model')
submodel = wc_lang.Submodel(id='submodel_1', model=prog_model)
cytosol = wc_lang.Compartment(id='c', name='Cytosol')
# create 5 species types
atp = wc_lang.SpeciesType(id='atp', name='ATP', model=prog_model)
adp = wc_lang.SpeciesType(id='adp', name='ADP', model=prog_model)
pi = wc_lang.SpeciesType(id='pi', name='Pi', model=prog_model)
h2o = wc_lang.SpeciesType(id='h2o', name='H2O', model=prog_model)
h = wc_lang.SpeciesType(id='h', name='H+', model=prog_model)
# create an 'ATP hydrolysis' reaction that uses these species types
atp_hydrolysis = wc_lang.Reaction(id='atp_hydrolysis', name='ATP hydrolysis')
# add two reactants, which have negative stoichiometric coefficients
atp_hydrolysis.participants.create(
species=wc_lang.Species(id='atp[c]', species_type=atp, compartment=cytosol), coefficient=-1)
atp_hydrolysis.participants.create(
species=wc_lang.Species(id='h2o[c]', species_type=h2o, compartment=cytosol), coefficient=-1)
# add three products, with positive stoichiometric coefficients
atp_hydrolysis.participants.create(
species=wc_lang.Species(id='adp[c]', species_type=adp, compartment=cytosol), coefficient=1)
atp_hydrolysis.participants.create(
species=wc_lang.Species(id='pi[c]', species_type=pi, compartment=cytosol), coefficient=1)
atp_hydrolysis.participants.create(
species=wc_lang.Species(id='h[c]', species_type=h, compartment=cytosol), coefficient=1)
# The previous illustrates how to program a trivial model
# Don't change the previous comment - it's used by a literalinclude
results.append("created model: '{}'".format(prog_model.name))
# Don't change the next comment - it's used by a literalinclude
# so that this assertion holds
assert(atp in prog_model.get_species_types())
# Don't change the next comment - it's used by a literalinclude
# these assertions hold
# 5 participants were added to the reaction
assert(len(atp_hydrolysis.participants) == 5)
first_reaction_participant = atp_hydrolysis.participants[0]
assert(first_reaction_participant.reactions[0] is atp_hydrolysis)
# Don't change the next comment - it's used by a literalinclude
# The attribues that can be initialized when a ``wc_lang.BaseModel`` class is instantiated
wc_lang.Model.Meta.attributes.keys()
wc_lang.Submodel.Meta.attributes.keys()
wc_lang.SpeciesType.Meta.attributes.keys()
wc_lang.Compartment.Meta.attributes.keys()
# Don't change the next comment - it's used by a literalinclude
# The following illustrates how to edit a model programmatically
atp_hydrolysis.comments = 'example comments'
atp_hydrolysis.reversible = False
#################################################
# Viewing Models and their attributes
#################################################
# pprint example
atp_hydrolysis.participants[0].pprint(max_depth=1)
#################################################
# Finding model components
#################################################
#################################################
# Completing and validating models
#################################################
# Don't change the next comment - it's used by a literalinclude
# This example illustrates how to validate ``prog_model``
prog_model.validate()
rv = prog_model.validate()
results.append("validate model: '{}'".format(rv))
# TODO: make this work: print(atp_hydrolysis.participants[0].reaction)
# TODO: make this work: print('len(atp_hydrolysis.participants)', len(atp_hydrolysis.participants))
#################################################
# Comparing and differencing models
#################################################
# Don't change the next comment - it's used by a literalinclude
# compare the semantic equality of ``model`` and ``model_from_tsv``
assert(model.is_equal(model_from_tsv) == True)
# Don't change the next comment - it's used by a literalinclude
# produces a textual description of the differences between two models
assert(model.difference(model_from_tsv) == '')
#################################################
# Normalizing models into a reproducible order
#################################################
# Don't change the next comment - it's used by a literalinclude
# The following code excerpt will normalize ``model`` into a reproducible order
model.normalize()
rv = model.normalize()
results.append("normalize model: '{}'".format(rv))
return results
def test_gen_mass_action_rate_law(self):
model = wc_lang.Model()
c = wc_lang.Compartment(id='c',
init_volume=wc_lang.InitVolume(mean=0.5))
c.init_density = wc_lang.Parameter(id='density_' + c.id, value=1.)
kinetic_parameter = wc_lang.Parameter(id='this_parameter', value=1.)
volume = wc_lang.Function(id='volume_' + c.id)
volume.expression, error = wc_lang.FunctionExpression.deserialize(
f'{c.id} / {c.init_density.id}', {
wc_lang.Compartment: {
c.id: c
},
wc_lang.Parameter: {
c.init_density.id: c.init_density
},
})
assert error is None, str(error)
species_types = {}
species = {}
for i in range(1, 7):
Id = 's' + str(i)
species_types[Id] = wc_lang.SpeciesType(id=Id)
species[Id + '_c'] = wc_lang.Species(
species_type=species_types[Id], compartment=c)
wc_lang.DistributionInitConcentration(species=species[Id + '_c'],
mean=0.5)
Id = 'e'
species_types[Id] = wc_lang.SpeciesType(id=Id)
species[Id + '_c'] = wc_lang.Species(species_type=species_types[Id],
compartment=c)
wc_lang.DistributionInitConcentration(species=species[Id + '_c'],
mean=0.5)
# ob_exp1, error = wc_lang.ObservableExpression.deserialize('s4[c] + s5[c]', {
# wc_lang.Species:{species['s4_c'].gen_id(): species['s4_c'],
# species['s5_c'].gen_id(): species['s5_c']}})
# assert error is None, str(error)
# modifier1 = wc_lang.Observable(id='e1', expression=ob_exp1)
# ob_exp2, error = wc_lang.ObservableExpression.deserialize('2 * s6[c]', {
# wc_lang.Species:{species['s6_c'].gen_id(): species['s6_c']}})
# assert error is None, str(error)
# modifier2 = wc_lang.Observable(id='e2', expression=ob_exp2)
participant1 = wc_lang.SpeciesCoefficient(species=species['s1_c'],
coefficient=-1)
participant2 = wc_lang.SpeciesCoefficient(species=species['s2_c'],
coefficient=-1)
participant3 = wc_lang.SpeciesCoefficient(species=species['s3_c'],
coefficient=1)
participant4 = wc_lang.SpeciesCoefficient(species=species['s4_c'],
coefficient=1)
enzyme_lhs = wc_lang.SpeciesCoefficient(species=species['e_c'],
coefficient=-1)
enzyme_rhs = wc_lang.SpeciesCoefficient(species=species['e_c'],
coefficient=1)
reaction = wc_lang.Reaction(
id='Assosication',
participants=[participant1, participant2, participant3])
rate_law, parameters = utils.gen_mass_action_rate_law(
model, reaction, kinetic_parameter)
self.assertTrue(
rate_law.expression == 'this_parameter * s1[c] * s2[c]'
or rate_law.expression == 'this_parameter * s2[c] * s1[c]')
self.assertEqual(set([i.gen_id() for i in rate_law.species]),
set(['s1[c]', 's2[c]']))
# self.assertEqual(set(rate_law.observables), set([modifier1, modifier2]))
self.assertEqual(set(rate_law.parameters), set(parameters))
# self.assertEqual(rate_law.parameters.get_one(id='k_r1').type, wc_ontology['WC:k_cat'])
self.assertEqual(
rate_law.parameters.get_one(id='this_parameter').units,
unit_registry.parse_units('s^-1 * molecule^-1'))
# self.assertEqual(rate_law.parameters.get_one(id='K_m_r1_s2').type, wc_ontology['WC:K_m'])
# self.assertEqual(rate_law.parameters.get_one(id='K_m_r1_s2').units, unit_registry.parse_units('M'))
reaction = wc_lang.Reaction(
id='Dissociation',
participants=[participant1, participant3, participant4])
rate_law, parameters = utils.gen_mass_action_rate_law(
model, reaction, kinetic_parameter)
self.assertEqual(rate_law.expression, 'this_parameter * s1[c]')
self.assertEqual(set([i.gen_id() for i in rate_law.species]),
set(['s1[c]']))
self.assertEqual(
rate_law.parameters.get_one(id='this_parameter').units,
unit_registry.parse_units('s^-1'))
reaction = wc_lang.Reaction(id='Degradation1',
participants=[participant1])
rate_law, parameters = utils.gen_mass_action_rate_law(
model, reaction, kinetic_parameter)
self.assertEqual(rate_law.expression, 'this_parameter * s1[c]')
self.assertEqual(set([i.gen_id() for i in rate_law.species]),
set(['s1[c]']))
self.assertEqual(
rate_law.parameters.get_one(id='this_parameter').units,
unit_registry.parse_units('s^-1'))
reaction = wc_lang.Reaction(
id='Degradation2',
participants=[participant1, enzyme_lhs, enzyme_rhs])
rate_law, parameters = utils.gen_mass_action_rate_law(
model, reaction, kinetic_parameter)
self.assertTrue(
rate_law.expression, 'this_parameter * s1[c] * e[c]'
or 'this_parameter * e[c] * s1[c]')
self.assertEqual(set([i.gen_id() for i in rate_law.species]),
set(['s1[c]', 'e[c]']))
self.assertEqual(
rate_law.parameters.get_one(id='this_parameter').units,
unit_registry.parse_units('s^-1 * molecule^-1'))
reaction = wc_lang.Reaction(id='Synthesis1',
participants=[participant3])
rate_law, parameters = utils.gen_mass_action_rate_law(
model, reaction, kinetic_parameter)
self.assertEqual(rate_law.expression, 'this_parameter')
self.assertEqual(set([i.gen_id() for i in rate_law.species]), set([]))
self.assertEqual(
rate_law.parameters.get_one(id='this_parameter').units,
unit_registry.parse_units('s^-1 * molecule'))
reaction = wc_lang.Reaction(
id='Synthesis2',
participants=[enzyme_lhs, enzyme_rhs, participant3])
rate_law, parameters = utils.gen_mass_action_rate_law(
model, reaction, kinetic_parameter)
self.assertEqual(rate_law.expression, 'this_parameter * e[c]')
self.assertEqual(set([i.gen_id() for i in rate_law.species]),
set(['e[c]']))
self.assertEqual(
rate_law.parameters.get_one(id='this_parameter').units,
unit_registry.parse_units('s^-1'))
reaction = wc_lang.Reaction(
id='Conversion',
participants=[participant1, enzyme_lhs, enzyme_rhs, participant3]
) # Ask Yin Hoon why I can add as many copies of participant2 as I want.
rate_law, parameters = utils.gen_mass_action_rate_law(
model, reaction, kinetic_parameter)
self.assertTrue(
rate_law.expression == 'this_parameter * s1[c] * e[c]'
or rate_law.expression == 'this_parameter * e[c] * s1[c]')
self.assertEqual(set([i.gen_id() for i in rate_law.species]),
set(['s1[c]', 'e[c]']))
self.assertEqual(
rate_law.parameters.get_one(id='this_parameter').units,
unit_registry.parse_units('s^-1 * molecule^-1'))
def test_gen_response_functions(self):
model = wc_lang.Model()
beta = 2
init_volume = wc_lang.core.InitVolume(
distribution=wc_ontology['WC:normal_distribution'],
mean=0.5,
std=0)
c = wc_lang.Compartment(id='c',
name='cytosol',
init_volume=init_volume)
c.init_density = wc_lang.Parameter(id='density_' + c.id, value=1.)
volume = wc_lang.Function(id='volume_' + c.id)
volume.expression, error = wc_lang.FunctionExpression.deserialize(
f'{c.id} / {c.init_density.id}', {
wc_lang.Compartment: {
c.id: c
},
wc_lang.Parameter: {
c.init_density.id: c.init_density
},
})
assert error is None, str(error)
reaction = wc_lang.Reaction()
species_types = {}
species = {}
for i in range(1, 5):
Id = 's' + str(i)
species_types[Id] = wc_lang.SpeciesType(
model=model, id=Id, name='species_type_{}'.format(i))
model_species = wc_lang.Species(model=model,
species_type=species_types[Id],
compartment=c)
model_species.id = model_species.gen_id()
species[Id + '_c'] = model_species
wc_lang.DistributionInitConcentration(species=species[Id + '_c'],
mean=0.5)
factors = [['s1', 'species_type_2'], ['s3'], ['species_type_4']]
factor_exp, all_species, all_parameters, all_volumes, all_observables = utils.gen_response_functions(
model, beta, 'reaction_id', 'reaction_class', c, factors)
self.assertEqual(factor_exp, [
'(reaction_class_factors_c_1 / (reaction_class_factors_c_1 + K_m_reaction_class_reaction_class_factors_c_1 * Avogadro * volume_c))',
'(s3[c] / (s3[c] + K_m_reaction_id_s3 * Avogadro * volume_c))',
'(s4[c] / (s4[c] + K_m_reaction_id_s4 * Avogadro * volume_c))'
])
self.assertEqual(
all_species, {
's1[c]': species['s1_c'],
's2[c]': species['s2_c'],
's3[c]': species['s3_c'],
's4[c]': species['s4_c']
})
self.assertEqual(len(all_parameters), 4)
self.assertEqual(all_parameters['Avogadro'].value,
scipy.constants.Avogadro)
self.assertEqual(all_parameters['Avogadro'].units,
unit_registry.parse_units('molecule mol^-1'))
self.assertEqual(
all_parameters['K_m_reaction_class_reaction_class_factors_c_1'].
value, beta * 1. / scipy.constants.Avogadro / c.init_volume.mean)
self.assertEqual(
all_parameters['K_m_reaction_class_reaction_class_factors_c_1'].
comments,
'The value was assumed to be 2 times the value of reaction_class_factors_c_1'
)
self.assertEqual(
all_parameters['K_m_reaction_id_s3'].value,
beta * 0.5 / scipy.constants.Avogadro / c.init_volume.mean)
self.assertEqual(all_parameters['K_m_reaction_id_s4'].type,
wc_ontology['WC:K_m'])
self.assertEqual(all_parameters['K_m_reaction_id_s4'].units,
unit_registry.parse_units('M'))
self.assertEqual(
all_parameters['K_m_reaction_id_s4'].comments,
'The value was assumed to be 2 times the concentration of s4 in cytosol'
)
self.assertEqual(all_volumes, {'volume_c': volume})
self.assertEqual(len(all_observables), 1)
self.assertEqual(len(model.observables), 1)
self.assertEqual(all_observables['reaction_class_factors_c_1'].name,
'factor for reaction_class in cytosol')
self.assertEqual(all_observables['reaction_class_factors_c_1'].units,
unit_registry.parse_units('molecule'))
self.assertEqual(
all_observables['reaction_class_factors_c_1'].expression.
expression, 's1[c] + s2[c]')
for i in range(5, 9):
Id = 's' + str(i)
species_types[Id] = wc_lang.SpeciesType(
model=model, id=Id, name='species_type_{}'.format(i))
model_species = wc_lang.Species(model=model,
species_type=species_types[Id],
compartment=c)
model_species.id = model_species.gen_id()
species[Id + '_c'] = model_species
wc_lang.DistributionInitConcentration(species=species[Id + '_c'],
mean=0.)
factors = [['s5', 'species_type_6'], ['s7'], ['species_type_8']]
factor_exp, all_species, all_parameters, all_volumes, all_observables = utils.gen_response_functions(
model, beta, 'reaction_id', 'reaction_class', c, factors)
self.assertEqual(len(model.observables), 2)
self.assertEqual(
all_parameters['K_m_reaction_class_reaction_class_factors_c_2'].
value, 1e-05)
self.assertEqual(
all_parameters['K_m_reaction_class_reaction_class_factors_c_2'].
comments,
'The value was assigned to 1e-05 because the value of reaction_class_factors_c_2 was zero'
)
self.assertEqual(all_parameters['K_m_reaction_id_s7'].value, 1e-05)
self.assertEqual(
all_parameters['K_m_reaction_id_s8'].comments,
'The value was assigned to 1e-05 because the concentration of s8 in cytosol was zero'
)
factors = [['s5', 'species_type_6']]
factor_exp, all_species, all_parameters, all_volumes, all_observables = utils.gen_response_functions(
model, beta, 'reaction_id2', 'reaction_class2', c, factors)
self.assertEqual(len(model.observables), 2)
self.assertEqual(
all_parameters['K_m_reaction_class2_reaction_class_factors_c_2'].
value, 1e-05)
def test_gen_michaelis_menten_like_propensity_function(self):
model = wc_lang.Model()
init_volume = wc_lang.core.InitVolume(
distribution=wc_ontology['WC:normal_distribution'],
mean=0.5,
std=0)
c = wc_lang.Compartment(id='c', init_volume=init_volume)
c.init_density = wc_lang.Parameter(id='density_' + c.id, value=1.)
volume = wc_lang.Function(id='volume_' + c.id)
volume.expression, error = wc_lang.FunctionExpression.deserialize(
f'{c.id} / {c.init_density.id}', {
wc_lang.Compartment: {
c.id: c
},
wc_lang.Parameter: {
c.init_density.id: c.init_density
},
})
assert error is None, str(error)
species_types = {}
species = {}
for i in range(1, 7):
Id = 's' + str(i)
species_types[Id] = wc_lang.SpeciesType(id=Id)
model_species = wc_lang.Species(species_type=species_types[Id],
compartment=c)
model_species.id = model_species.gen_id()
species[Id + '_c'] = model_species
wc_lang.DistributionInitConcentration(species=species[Id + '_c'],
mean=0.5)
participant1 = wc_lang.SpeciesCoefficient(species=species['s1_c'],
coefficient=-1)
participant2 = wc_lang.SpeciesCoefficient(species=species['s2_c'],
coefficient=-1)
participant3 = wc_lang.SpeciesCoefficient(species=species['s3_c'],
coefficient=-1)
participant4 = wc_lang.SpeciesCoefficient(species=species['s4_c'],
coefficient=-1)
participant5 = wc_lang.SpeciesCoefficient(species=species['s5_c'],
coefficient=1)
participant6 = wc_lang.SpeciesCoefficient(species=species['s6_c'],
coefficient=1)
reaction = wc_lang.Reaction(id='r1',
participants=[
participant1, participant2,
participant3, participant4,
participant5, participant6
])
with self.assertRaises(ValueError):
rate_law1, parameters = utils.gen_michaelis_menten_like_propensity_function(
model, reaction)
rate_law2, parameters = utils.gen_michaelis_menten_like_propensity_function(
model, reaction, substrates_as_modifiers=[species['s3_c']])
self.assertEqual(
rate_law2.expression, 'k_cat_r1 * s3[c] * '
'(s1[c] / (s1[c] + K_m_r1_s1 * Avogadro * volume_c)) * '
'(s2[c] / (s2[c] + K_m_r1_s2 * Avogadro * volume_c)) * '
'(s4[c] / (s4[c] + K_m_r1_s4 * Avogadro * volume_c))')
self.assertEqual(set([i.gen_id() for i in rate_law2.species]),
set(['s1[c]', 's2[c]', 's3[c]', 's4[c]']))
self.assertEqual(set(rate_law2.parameters), set(parameters))
self.assertEqual(
rate_law2.parameters.get_one(id='k_cat_r1').type,
wc_ontology['WC:k_cat'])
self.assertEqual(
rate_law2.parameters.get_one(id='k_cat_r1').units,
unit_registry.parse_units('s^-1 molecule^-1'))
self.assertEqual(
rate_law2.parameters.get_one(id='K_m_r1_s2').type,
wc_ontology['WC:K_m'])
self.assertEqual(
rate_law2.parameters.get_one(id='K_m_r1_s2').units,
unit_registry.parse_units('M'))
rate_law3, parameters = utils.gen_michaelis_menten_like_propensity_function(
model,
reaction,
substrates_as_modifiers=[species['s3_c']],
exclude_substrates=[species['s1_c']])
self.assertEqual(
rate_law3.expression, 'k_cat_r1 * s3[c] * '
'(s2[c] / (s2[c] + K_m_r1_s2 * Avogadro * volume_c)) * '
'(s4[c] / (s4[c] + K_m_r1_s4 * Avogadro * volume_c))')
self.assertEqual(set([i.gen_id() for i in rate_law3.species]),
set(['s2[c]', 's3[c]', 's4[c]']))
self.assertEqual(set(rate_law3.parameters), set(parameters))
def test_gen_michaelis_menten_like_rate_law(self):
model = wc_lang.Model()
init_volume = wc_lang.core.InitVolume(
distribution=wc_ontology['WC:normal_distribution'],
mean=0.5,
std=0)
c = wc_lang.Compartment(id='c', init_volume=init_volume)
c.init_density = wc_lang.Parameter(id='density_' + c.id, value=1.)
volume = wc_lang.Function(id='volume_' + c.id)
volume.expression, error = wc_lang.FunctionExpression.deserialize(
f'{c.id} / {c.init_density.id}', {
wc_lang.Compartment: {
c.id: c
},
wc_lang.Parameter: {
c.init_density.id: c.init_density
},
})
assert error is None, str(error)
species_types = {}
species = {}
for i in range(1, 7):
Id = 's' + str(i)
species_types[Id] = wc_lang.SpeciesType(id=Id)
species[Id + '_c'] = wc_lang.Species(
species_type=species_types[Id], compartment=c)
wc_lang.DistributionInitConcentration(species=species[Id + '_c'],
mean=0.5)
ob_exp1, error = wc_lang.ObservableExpression.deserialize(
's4[c] + s5[c]', {
wc_lang.Species: {
species['s4_c'].gen_id(): species['s4_c'],
species['s5_c'].gen_id(): species['s5_c']
}
})
assert error is None, str(error)
modifier1 = wc_lang.Observable(id='e1', expression=ob_exp1)
ob_exp2, error = wc_lang.ObservableExpression.deserialize(
'2 * s6[c]',
{wc_lang.Species: {
species['s6_c'].gen_id(): species['s6_c']
}})
assert error is None, str(error)
modifier2 = wc_lang.Observable(id='e2', expression=ob_exp2)
participant1 = wc_lang.SpeciesCoefficient(species=species['s1_c'],
coefficient=-1)
participant2 = wc_lang.SpeciesCoefficient(species=species['s2_c'],
coefficient=-1)
participant3 = wc_lang.SpeciesCoefficient(species=species['s3_c'],
coefficient=1)
participant4 = wc_lang.SpeciesCoefficient(species=species['s4_c'],
coefficient=-1)
participant5 = wc_lang.SpeciesCoefficient(species=species['s4_c'],
coefficient=1)
participant6 = wc_lang.SpeciesCoefficient(species=species['s6_c'],
coefficient=-1)
participant7 = wc_lang.SpeciesCoefficient(species=species['s6_c'],
coefficient=-1)
participant8 = wc_lang.SpeciesCoefficient(species=species['s6_c'],
coefficient=1)
reaction = wc_lang.Reaction(id='r1',
participants=[
participant1, participant2,
participant3, participant4,
participant5, participant6,
participant7, participant8
])
rate_law, parameters = utils.gen_michaelis_menten_like_rate_law(
model,
reaction,
modifiers=[modifier1, modifier2],
modifier_reactants=[species['s6_c']])
self.assertEqual(
rate_law.expression, 'k_cat_r1 * e1 * e2 * '
'(s1[c] / (s1[c] + K_m_r1_s1 * Avogadro * volume_c)) * '
'(s2[c] / (s2[c] + K_m_r1_s2 * Avogadro * volume_c)) * '
'(s6[c] / (s6[c] + K_m_r1_s6 * Avogadro * volume_c))')
self.assertEqual(set([i.gen_id() for i in rate_law.species]),
set(['s1[c]', 's2[c]', 's6[c]']))
self.assertEqual(set(rate_law.observables), set([modifier1,
modifier2]))
self.assertEqual(set(rate_law.parameters), set(parameters))
self.assertEqual(
rate_law.parameters.get_one(id='k_cat_r1').type,
wc_ontology['WC:k_cat'])
self.assertEqual(
rate_law.parameters.get_one(id='k_cat_r1').units,
unit_registry.parse_units('s^-1 molecule^-2'))
self.assertEqual(
rate_law.parameters.get_one(id='K_m_r1_s2').type,
wc_ontology['WC:K_m'])
self.assertEqual(
rate_law.parameters.get_one(id='K_m_r1_s2').units,
unit_registry.parse_units('M'))
reaction = wc_lang.Reaction(id='r1',
participants=[
participant1, participant2,
participant4, participant8
])
rate_law, parameters = utils.gen_michaelis_menten_like_rate_law(
model, reaction)
self.assertEqual(
rate_law.expression, 'k_cat_r1 * '
'(s1[c] / (s1[c] + K_m_r1_s1 * Avogadro * volume_c)) * '
'(s2[c] / (s2[c] + K_m_r1_s2 * Avogadro * volume_c)) * '
'(s4[c] / (s4[c] + K_m_r1_s4 * Avogadro * volume_c))')
reaction = wc_lang.Reaction(id='r1', participants=[participant3])
rate_law, parameters = utils.gen_michaelis_menten_like_rate_law(
model, reaction)
self.assertEqual(rate_law.expression, 'k_cat_r1')
reaction = wc_lang.Reaction(id='r1',
participants=[participant3, participant6])
rate_law, parameters = utils.gen_michaelis_menten_like_rate_law(
model, reaction, modifiers=[modifier1, species['s6_c']])
self.assertEqual(rate_law.expression, 'k_cat_r1 * e1 * s6[c]')
reaction = wc_lang.Reaction(id='r1',
participants=[
participant1, participant2,
participant4, participant8
])
rate_law, parameters = utils.gen_michaelis_menten_like_rate_law(
model, reaction, exclude_substrates=[species['s1_c']])
self.assertEqual(
rate_law.expression, 'k_cat_r1 * '
'(s2[c] / (s2[c] + K_m_r1_s2 * Avogadro * volume_c)) * '
'(s4[c] / (s4[c] + K_m_r1_s4 * Avogadro * volume_c))')
with self.assertRaises(TypeError) as ctx:
rate_law, parameters = utils.gen_michaelis_menten_like_rate_law(
model, reaction, modifiers=['s6_c'])
self.assertEqual(
'The modifiers contain element(s) that is not an observable or a species',
str(ctx.exception))
def test_sample_copy_num_from_concentration(self):
model = wc_lang.Model()
submodel = model.submodels.create(
id='submodel',
framework=onto['WC:stochastic_simulation_algorithm'])
compartment_c = model.compartments.create(
id='c', init_volume=wc_lang.InitVolume(mean=1.))
structure = wc_lang.ChemicalStructure(molecular_weight=10.)
species_types = {}
cus_species_types = {}
for cu in wc_lang.DistributionInitConcentration.units.choices:
id = str(cu).replace(' ', '_')
species_types[id] = model.species_types.create(id=id,
structure=structure)
cus_species_types[id] = cu
for other in ['no_units', 'no_concentration', 'no_std']:
species_types[other] = model.species_types.create(
id=other, structure=structure)
species = {}
for key, species_type in species_types.items():
species[key] = wc_lang.Species(species_type=species_type,
compartment=compartment_c)
species[key].id = species[key].gen_id()
conc_value = 2_000.
std_value = 0.
for key, sp in species.items():
if key in cus_species_types:
wc_lang.DistributionInitConcentration(
species=sp,
mean=conc_value,
std=std_value,
units=cus_species_types[key])
elif key == 'no_units':
wc_lang.DistributionInitConcentration(species=sp,
mean=conc_value,
std=std_value)
elif key == 'no_std':
wc_lang.DistributionInitConcentration(
species=sp,
mean=conc_value,
std=float('NaN'),
units=cus_species_types['molecule'])
elif key == 'no_concentration':
continue
conc_to_molecules = ModelUtilities.sample_copy_num_from_concentration
random_state = numpy.random.RandomState()
copy_number = conc_to_molecules(
species['molecule'],
species['molecule'].compartment.init_volume.mean, random_state)
self.assertEqual(copy_number, conc_value)
copy_number = conc_to_molecules(
species['molar'], species['molar'].compartment.init_volume.mean,
random_state)
self.assertEqual(copy_number, conc_value * Avogadro)
copy_number = conc_to_molecules(
species['no_units'],
species['no_units'].compartment.init_volume.mean, random_state)
self.assertEqual(copy_number, conc_value * Avogadro)
copy_number = conc_to_molecules(
species['millimolar'],
species['millimolar'].compartment.init_volume.mean, random_state)
self.assertEqual(copy_number, 10**-3 * conc_value * Avogadro)
copy_number = conc_to_molecules(
species['micromolar'],
species['micromolar'].compartment.init_volume.mean, random_state)
self.assertEqual(copy_number, 10**-6 * conc_value * Avogadro)
copy_number = conc_to_molecules(
species['nanomolar'],
species['nanomolar'].compartment.init_volume.mean, random_state)
self.assertEqual(copy_number, 10**-9 * conc_value * Avogadro)
copy_number = conc_to_molecules(
species['picomolar'],
species['picomolar'].compartment.init_volume.mean, random_state)
self.assertEqual(copy_number, 10**-12 * conc_value * Avogadro)
copy_number = conc_to_molecules(
species['femtomolar'],
species['femtomolar'].compartment.init_volume.mean, random_state)
self.assertAlmostEqual(copy_number,
10**-15 * conc_value * Avogadro,
delta=1)
copy_number = conc_to_molecules(
species['attomolar'],
species['attomolar'].compartment.init_volume.mean, random_state)
self.assertAlmostEqual(copy_number,
10**-18 * conc_value * Avogadro,
delta=1)
copy_number = conc_to_molecules(
species['no_concentration'],
species['no_concentration'].compartment.init_volume.mean,
random_state)
self.assertEqual(copy_number, 0)
conc = species['no_std'].distribution_init_concentration
copy_number = conc_to_molecules(
species['no_std'], species['no_std'].compartment.init_volume.mean,
random_state)
self.assertNotEqual(copy_number, conc_value)
with self.assertRaises(KeyError):
conc_to_molecules(
species['mol dm^-2'],
species['no_concentration'].compartment.init_volume.mean,
random_state)
species_tmp = wc_lang.Species(species_type=species_type,
compartment=compartment_c)
species_tmp.id = species_tmp.gen_id()
wc_lang.DistributionInitConcentration(
species=species_tmp,
mean=conc_value,
std=std_value,
units='not type(unit_registry.Unit)')
with self.assertRaisesRegex(ValueError, 'Unsupported unit type'):
conc_to_molecules(species_tmp,
species_tmp.compartment.init_volume.mean,
random_state)
species_tmp2 = wc_lang.Species(species_type=species_type,
compartment=compartment_c)
species_tmp2.id = species_tmp2.gen_id()
wc_lang.DistributionInitConcentration(
species=species_tmp2,
mean=conc_value,
std=std_value,
units=wc_lang.InitVolume.units.choices[0])
with self.assertRaisesRegex(ValueError, 'Unsupported unit'):
conc_to_molecules(species_tmp2,
species_tmp2.compartment.init_volume.mean,
random_state)