def get_interventions(self, components):
interventions = []
add_setup = [st for st in components if st.startswith('add(setup_')]
add_activ = list(
set([st for st in components if st.startswith('add')]) -
set(add_setup))
remove = [st for st in components if st.startswith('remove(')]
for st in add_setup:
splitted = st.split('add(setup_present(')[1].split(')')[0].split(
',')
entity = self.archive.get_matching_element(splitted[0],
splitted[1])
compartment = self.archive.get_matching_element(splitted[2])
interventions.append(Add(PresentEntity(entity, compartment)))
for st in add_activ:
splitted = st.split('add(')[1].split(')')[0]
activity = self.archive.get_matching_element(splitted)
interventions.append(Add(activity))
for st in remove:
splitted = st.split('remove(setup_present(')[1].split(
')')[0].split(',')
entity = self.archive.get_matching_element(splitted[0],
splitted[1])
compartment = self.archive.get_matching_element(splitted[2])
interventions.append(Remove(PresentEntity(entity, compartment)))
# removing used stuff from components
[components.remove(st) for st in add_setup]
[components.remove(st) for st in add_activ]
[components.remove(st) for st in remove]
return interventions
def test_in_vitro_basic(self):
met1 = Metabolite('met1')
met2 = Metabolite('met2')
cytosol = Cytosol()
cond1 = PresentEntity(met1, cytosol)
cond2 = PresentEntity(met2, cytosol)
r1 = Reaction('r1', [cond1], [cond2])
self.oracle = Oracle(None, [], [r1], None, [], [], [])
expD = ExperimentDescription(ReconstructionActivity('r1'), [])
out = self.oracle.execute_in_vitro_exp(expD)
self.assertEqual(out.outcome, 'true')
def setUp(self):
# models:
self.g1 = Gene('g1')
self.p1 = Protein('p1')
self.met1 = Metabolite('met1')
self.met2 = Metabolite('met2')
self.cplx1 = Complex('cplx1')
self.cytosol = Cytosol()
self.cond1 = PresentEntity(self.met1, self.cytosol)
self.cond2 = PresentEntity(self.met2, self.cytosol)
self.cond3 = PresentEntity(self.p1, self.cytosol)
self.cond4 = PresentEntity(self.cplx1, self.cytosol)
self.growth = Growth('growth', [self.cond2])
self.growth.reversibility = False
self.r1 = Reaction('r1', [self.cond1], [self.cond2])
self.r2 = Reaction('r2', [self.cond3], [self.cond4])
self.r1.reversibility = False
self.r2.reversibility = False
self.entities = [self.g1, self.p1, self.met1, self.met2, self.cplx1]
self.compartments = [self.cytosol]
self.activities = [self.growth, self.r1, self.r2]
self.setup_conds = [self.cond1, self.cond3]
self.mod1 = Model('m0', self.setup_conds, [self.growth, self.r1], [])
self.mod2 = Model('m1', self.setup_conds, [self.growth, self.r2], [])
# cost_module:
self.cost_model = CostModel(self.entities, self.compartments,
self.activities, self.setup_conds)
self.cost_model.set_all_basic_costs_to_1()
self.cost_model.calculate_derived_costs(self.activities)
self.cost_model.remove_None_valued_elements()
# known results (one exp, both models consistent)
self.exd = exp_repr.ExperimentDescription(
exp_repr.DetectionEntity('met1'), [])
self.res = exp_repr.Result('res1', self.exd, 'true')
self.exp = exp_repr.Experiment('exp1', [self.res])
# archive
self.arch = Archive()
self.arch.working_models = [self.mod1, self.mod2]
self.arch.known_results = [self.exp]
self.arch.mnm_compartments = self.compartments
self.arch.mnm_entities = self.entities
self.arch.mnm_activities = self.activities
# exp module
self.exp_module = ExperimentModule(self.arch, self.cost_model, False)
def test_in_vitro_enz(self):
met1 = Metabolite('met1')
met2 = Metabolite('met2')
cytosol = Cytosol()
cond1 = PresentEntity(met1, cytosol)
cond2 = PresentEntity(met2, cytosol)
cond_enz = PresentCatalyst(cytosol)
r1 = Reaction('r1', [cond1, cond_enz], [cond2])
enz = Protein('p1', properties=[Catalyses(r1)])
self.oracle = Oracle(None, [enz], [r1], None, [], [], [])
expD = ExperimentDescription(ReconstructionEnzReaction('r1', 'p1'), [])
out = self.oracle.execute_in_vitro_exp(expD)
self.assertEqual(out.outcome, 'true')
def test_in_vitro_basic_SLOPPY_ORACLE_WITH_FLIP(self):
met1 = Metabolite('met1')
met2 = Metabolite('met2')
cytosol = Cytosol()
cond1 = PresentEntity(met1, cytosol)
cond2 = PresentEntity(met2, cytosol)
r1 = Reaction('r1', [cond1], [cond2])
self.oracle = SloppyOracle(None, [], [r1],
None, [], [], [],
error_parameter=1.00)
expD = ExperimentDescription(ReconstructionActivity('r1'), [])
out = self.oracle.execute_in_vitro_exp(expD)
self.assertEqual(out.outcome, 'false')
def test_in_vitro_transp(self):
met1 = Metabolite('met1')
met2 = Metabolite('met2')
cytosol = Cytosol()
cond1 = PresentEntity(met1, cytosol)
cond2 = PresentEntity(met2, cytosol)
cond_trp = PresentTransporter(cytosol)
r1 = Reaction('r1', [cond1, cond_trp], [cond2])
transp = Protein('p1', properties=[Transports(r1)])
self.oracle = Oracle(None, [transp], [r1], None, [], [], [])
expD = ExperimentDescription(
ReconstructionTransporterRequired('r1', 'p1'), [])
out = self.oracle.execute_in_vitro_exp(expD)
self.assertEqual(out.outcome, 'true')
def setUp(self):
self.g1 = Gene('g1')
self.p1 = Protein('p1')
self.met1 = Metabolite('met1')
self.met2 = Metabolite('met2')
self.cplx1 = Complex('cplx1')
self.cytosol = Cytosol()
self.cond1 = PresentEntity(self.met1, self.cytosol)
self.cond2 = PresentEntity(self.met2, self.cytosol)
self.cond3 = PresentEntity(self.p1, self.cytosol)
self.cond4 = PresentEntity(self.cplx1, self.cytosol)
self.growth = Growth('growth', [self.cond2])
self.r1 = Reaction('r1', [self.cond1], [self.cond2])
self.r2 = Reaction('r2', [self.cond3], [self.cond4])
self.entities = [self.g1, self.p1, self.met1, self.met2, self.cplx1]
self.compartments = [self.cytosol]
self.activities = [self.growth, self.r1, self.r2]
self.setup_conds = [self.cond1, self.cond3]
self.model = CostModel(self.entities, self.compartments,
self.activities, self.setup_conds)
def setUp(self):
self.g1 = Gene('g1')
self.p1 = Protein('p1')
self.met1 = Metabolite('met1')
self.met2 = Metabolite('met2')
self.cplx1 = Complex('cplx1')
self.cytosol = Cytosol()
self.cond1 = PresentEntity(self.met1, self.cytosol)
self.cond2 = PresentEntity(self.met2, self.cytosol)
self.cond3 = PresentEntity(self.p1, self.cytosol)
self.cond4 = PresentEntity(self.cplx1, self.cytosol)
self.growth = Growth('growth', [self.cond2])
self.growth.reversibility = False
self.r1 = Reaction('r1', [self.cond1], [self.cond2])
self.r2 = Reaction('r2', [self.cond3], [self.cond4])
self.r1.reversibility = False
self.r2.reversibility = False
self.entities = [self.g1, self.p1, self.met1, self.met2, self.cplx1]
self.compartments = [self.cytosol]
self.activities = [self.growth, self.r1, self.r2]
self.setup_conds = [self.cond1, self.cond3]
self.mod1 = Model('m0', self.setup_conds, [self.growth, self.r1], [])
self.mod2 = Model('m1', self.setup_conds, [self.growth, self.r2], [])
self.archive = Archive()
self.archive.working_models.update([self.mod1, self.mod2])
self.archive.mnm_compartments = list(self.compartments)
self.archive.mnm_entities = list(self.entities)
self.archive.mnm_activities = list(self.activities)
self.oracle = Oracle(self.archive, [], [], self.mod1, self.entities,
self.compartments, self.activities)