def test_compile_crn_directives(self):
a = Species(name='a')
b = Species(name='b')
species_list = [a, b]
rxn = Reaction.from_massaction(inputs=[a], outputs=[b], k_forward=0.1)
CRN = ChemicalReactionNetwork(species_list, [rxn])
# create a component
component = Component("comp")
# creating a mock update function to decouple the update process from the rest of the code
def mock_update_reactions():
rxn = Reaction.from_massaction(inputs=[a], outputs=[b], k_forward=0.1)
return [rxn]
def mock_update_species():
return [a, b]
component.update_species = mock_update_species
component.update_reactions = mock_update_reactions
mixture = Mixture(components=[component])
#All the directives used below should not change the CRN.
#They just remove some checks and safegaurds, but compilation should work the same in this simple case.
#directives are best used in specific cases to compile very large models where speed is essential
crn_from_mixture1 = mixture.compile_crn(copy_objects = False)
# test that the mixture has the same species as the manually build CRN object
self.assertEqual(set(CRN.species), set(crn_from_mixture1.species))
# test that the mixture has the same reactions as the manually build CRN object
self.assertEqual(CRN.reactions, crn_from_mixture1.reactions)
crn_from_mixture2 = mixture.compile_crn(add_reaction_species = False)
# test that the mixture has the same species as the manually build CRN object
self.assertEqual(set(CRN.species), set(crn_from_mixture2.species))
# test that the mixture has the same reactions as the manually build CRN object
self.assertEqual(CRN.reactions, crn_from_mixture2.reactions)
crn_from_mixture3 = mixture.compile_crn(initial_concentrations_at_end = True)
# test that the mixture has the same species as the manually build CRN object
self.assertEqual(set(CRN.species), set(crn_from_mixture3.species))
# test that the mixture has the same reactions as the manually build CRN object
self.assertEqual(CRN.reactions, crn_from_mixture3.reactions)
def test_compile_crn(self):
a = Species(name='a')
b = Species(name='b')
species_list = [a, b]
rxn = Reaction.from_massaction(inputs=[a], outputs=[b], k_forward=0.1)
CRN = ChemicalReactionNetwork(species_list, [rxn])
# create a component
component = Component("comp")
# creating a mock update function to decouple the update process from the rest of the code
def mock_update_reactions():
rxn = Reaction.from_massaction(inputs=[a], outputs=[b], k_forward=0.1)
return [rxn]
def mock_update_species():
return [a, b]
component.update_species = mock_update_species
component.update_reactions = mock_update_reactions
mixture = Mixture(components=[component])
crn_from_mixture = mixture.compile_crn()
# test that the mixture has the same species as the manually build CRN object
self.assertEqual(set(CRN.species), set(crn_from_mixture.species))
# test that the mixture has the same reactions as the manually build CRN object
self.assertEqual(CRN.reactions, crn_from_mixture.reactions)
def test_compile_crn(self):
from biocrnpyler import ChemicalReactionNetwork
from biocrnpyler import Species
from biocrnpyler import Reaction
from biocrnpyler import Mixture
a = Species(name='a')
b = Species(name='b')
species_list = [a, b]
def mock_update_reactions():
rxn = Reaction(inputs=[a], outputs=[b], k=0.1)
return [rxn]
rxn = Reaction(inputs=[a], outputs=[b], k=0.1)
CRN = ChemicalReactionNetwork(species_list, [rxn])
mixture = Mixture(species=species_list)
mixture.update_reactions = mock_update_reactions
crn_from_mixture = mixture.compile_crn()
self.assertEqual(CRN.species, crn_from_mixture.species)
self.assertEqual(CRN.reactions, crn_from_mixture.reactions)
def test_compile_crn(self):
a = Species(name='a')
b = Species(name='b')
species_list = [a, b]
# creating a mock update function to decouple the update process from the rest of the code
def mock_update_reactions():
rxn = Reaction(inputs=[a], outputs=[b], k=0.1)
return [rxn]
rxn = Reaction(inputs=[a], outputs=[b], k=0.1)
CRN = ChemicalReactionNetwork(species_list, [rxn])
mixture = Mixture(species=species_list)
mixture.update_reactions = mock_update_reactions
crn_from_mixture = mixture.compile_crn()
# test that the mixture has the same species as the manually build CRN object
self.assertEqual(CRN.species, crn_from_mixture.species)
# test that the mixture has the same reactions as the manually build CRN object
self.assertEqual(CRN.reactions, crn_from_mixture.reactions)