def test_modeh_replacement(self):
# prepare the cost model
g1 = mnm_repr.Gene('g1')
p1 = mnm_repr.Protein('p1')
met1 = mnm_repr.Metabolite('met1')
met2 = mnm_repr.Metabolite('met2')
cplx1 = mnm_repr.Complex('cplx1')
cytosol = mnm_repr.Cytosol()
cond1 = mnm_repr.PresentEntity(met1, cytosol)
cond2 = mnm_repr.PresentEntity(met2, cytosol)
cond3 = mnm_repr.PresentEntity(p1, cytosol)
cond4 = mnm_repr.PresentEntity(cplx1, cytosol)
growth = mnm_repr.Growth('growth', [cond2])
r1 = mnm_repr.Reaction('r1', [cond1], [cond2])
r2 = mnm_repr.Reaction('r2', [cond3], [cond4])
entities = [g1, p1, met1, met2, cplx1]
compartments = [cytosol]
activities = [growth, r1, r2]
setup_conds = [cond1, cond3]
model = CostModel(entities, compartments, activities, setup_conds)
model.set_all_basic_costs_to_1()
model.calculate_derived_costs(activities)
# test
out = exporter.modeh_replacement(model)
self.assertIsInstance(out, str)
def setUp(self):
self.con1 = mnm_repr.PresentEntity('ent1', 'comp1')
self.con2 = mnm_repr.PresentEntity('ent2', 'comp2')
self.con3 = mnm_repr.PresentEntity('ent3', 'comp3')
self.con4 = mnm_repr.PresentEntity('ent4', 'comp4')
self.act1 = mnm_repr.Activity('ID1', 'name1', [self.con1], [])
self.act2 = mnm_repr.Activity('ID2', 'name2', [self.con2], [])
def test_export_activity(self):
# one substrate, one catalyst, one transporter; one product
cond_subst = mnm_repr.PresentEntity(mnm_repr.Metabolite('met1'),
mnm_repr.Medium())
cond_cat = mnm_repr.PresentCatalyst(mnm_repr.Medium())
cond_trp = mnm_repr.PresentTransporter(mnm_repr.Medium())
prod = mnm_repr.PresentEntity(mnm_repr.Metabolite('met2'),
mnm_repr.Medium())
act = mnm_repr.Activity('a1', 'none', [cond_subst, cond_cat, cond_trp],
[prod])
act.reversibility = True
exported = exporter.export_activity(act)
# forward
self.assertIn('\nsubstrate(met1,none,c_01,a1).', exported)
self.assertIn('\nenz_required(a1).', exported)
self.assertIn('\nenz_compartment(c_01,a1).', exported)
self.assertIn('\ntransp_required(a1).', exported)
self.assertIn('\ntransp_compartment(c_01,a1).', exported)
self.assertIn('\nproduct(met2,none,c_01,a1).', exported)
# reversed
self.assertIn('\nproduct(met1,none,c_01,a1_rev).', exported)
self.assertIn('\nenz_required(a1_rev).', exported)
self.assertIn('\nenz_compartment(c_01,a1_rev).', exported)
self.assertIn('\ntransp_required(a1_rev).', exported)
self.assertIn('\ntransp_compartment(c_01,a1_rev).', exported)
self.assertIn('\nsubstrate(met2,none,c_01,a1_rev).', exported)
def test_cost_rules(self):
# prepare the cost model
g1 = mnm_repr.Gene('g1')
p1 = mnm_repr.Protein('p1')
met1 = mnm_repr.Metabolite('met1')
met2 = mnm_repr.Metabolite('met2')
cplx1 = mnm_repr.Complex('cplx1')
cytosol = mnm_repr.Cytosol()
cond1 = mnm_repr.PresentEntity(met1, cytosol)
cond2 = mnm_repr.PresentEntity(met2, cytosol)
cond3 = mnm_repr.PresentEntity(p1, cytosol)
cond4 = mnm_repr.PresentEntity(cplx1, cytosol)
growth = mnm_repr.Growth('growth', [cond2])
r1 = mnm_repr.Reaction('r1', [cond1], [cond2])
r2 = mnm_repr.Reaction('r2', [cond3], [cond4])
entities = [g1, p1, met1, met2, cplx1]
compartments = [cytosol]
activities = [growth, r1, r2]
setup_conds = [cond1, cond3]
model = CostModel(entities, compartments, activities, setup_conds)
model.set_all_basic_costs_to_1()
model.calculate_derived_costs(activities)
# test
out = exporter.cost_rules(model)
# self.assertIn('\ncost(1, 0) :- add(setup_present(met1, none, c_01)).', out)
self.assertEqual(len(out), 55)
def test_export_experiment_specification_elements(self):
# prepare the cost model
g1 = mnm_repr.Gene('g1')
p1 = mnm_repr.Protein('p1')
met1 = mnm_repr.Metabolite('met1')
met2 = mnm_repr.Metabolite('met2')
cplx1 = mnm_repr.Complex('cplx1')
cytosol = mnm_repr.Cytosol()
cond1 = mnm_repr.PresentEntity(met1, cytosol)
cond2 = mnm_repr.PresentEntity(met2, cytosol)
cond3 = mnm_repr.PresentEntity(p1, cytosol)
cond4 = mnm_repr.PresentEntity(cplx1, cytosol)
growth = mnm_repr.Growth('growth', [cond2])
r1 = mnm_repr.Reaction('r1', [cond1], [cond2])
r2 = mnm_repr.Reaction('r2', [cond3], [cond4])
entities = [g1, p1, met1, met2, cplx1]
compartments = [cytosol]
activities = [growth, r1, r2]
setup_conds = [cond1, cond3]
model = CostModel(entities, compartments, activities, setup_conds)
model.set_all_basic_costs_to_1()
model.calculate_derived_costs(activities)
# test
out = exporter.export_experiment_specification_elements(model)
self.assertEqual(len(out.keys()), 55)
self.assertNotIn(None, out.values())
def test_RevCIAddB_revise_ignoring(self):
met1 = mnm_repr.Metabolite('met1')
met2 = mnm_repr.Metabolite('met2')
comp1 = mnm_repr.Medium()
cond_subst_1 = mnm_repr.PresentEntity(met1, comp1)
cond_subst_2 = mnm_repr.PresentEntity(met2, comp1)
a1 = mnm_repr.Reaction('act1', [], [cond_subst_1, cond_subst_2])
a1.remove_cost = None
a1.reversibility = False
a2 = mnm_repr.Reaction('act1', [], [cond_subst_1])
a2.reversibility = False
# model to be revised
mod = mnm_repr.Model('m_0', [], [a1], [])
# results
des1 = exp_repr.ExperimentDescription(exp_repr.DetectionEntity('met1'),
[])
des2 = exp_repr.ExperimentDescription(exp_repr.DetectionEntity('met2'),
[])
res1 = exp_repr.Result('res_0', des1, 'false')
res2 = exp_repr.Result('res_1', des2, 'true')
exp1 = exp_repr.Experiment('exp_0', [res1])
exp2 = exp_repr.Experiment('exp_1', [res2])
# archive with results and parts for revision
arch = Archive()
arch.known_results = [exp1, exp2]
arch.mnm_activities = [a1, a2]
arch.mnm_entities = [met1, met2]
arch.mnm_compartments = [comp1]
rev = RevCIAddB(arch)
out = rev.revise(mod)
self.assertEqual(out[0], [])
self.assertEqual(out[1], True)
def test_make_derivative_models(self):
rev = RevisionModule('archive')
cond_subst_1 = mnm_repr.PresentEntity(mnm_repr.Metabolite('met1'),
mnm_repr.Medium())
cond_subst_2 = mnm_repr.PresentEntity(mnm_repr.Metabolite('met2'),
mnm_repr.Medium())
base_model = mnm_repr.Model(
'm1', [cond_subst_1], [],
[]) #model that is compatible with interventions
second_mod = mnm_repr.Model('deriv_m1_0', [cond_subst_1, cond_subst_2],
[], [])
third_mod = mnm_repr.Model('deriv_m1_1', [], [], [])
exd1 = exp_repr.ExperimentDescription(None,
[mnm_repr.Add(cond_subst_2)])
exd2 = exp_repr.ExperimentDescription(None,
[mnm_repr.Remove(cond_subst_1)])
res1 = exp_repr.Result('r1', exd1, True)
res2 = exp_repr.Result('r2', exd2, True)
extracted_results = [res1, res2] #need interventions in description
models_results = rev.make_derivative_models(base_model,
extracted_results)
self.assertEqual(models_results, {
base_model: [],
second_mod: [res1],
third_mod: [res2]
})
def test_export_termination_conds_consistency(self):
# one cond
cond_subst_1 = mnm_repr.PresentEntity(mnm_repr.Metabolite('met1'),
mnm_repr.Medium())
cond_subst_2 = mnm_repr.PresentEntity(mnm_repr.Metabolite('met2'),
mnm_repr.Medium())
m = mnm_repr.Model('m1', [], [], [cond_subst_1, cond_subst_2])
exported = exporter.export_termination_conds_consistency(m)
self.assertIn('\n:- not synthesizable(met1, none, c_01, m1).',
exported)
self.assertIn('\n:- not synthesizable(met2, none, c_01, m1).',
exported)
def test_ban_experiment(self):
comp = mnm_repr.Medium()
ent1 = mnm_repr.Metabolite('m1')
cond1 = mnm_repr.PresentEntity(ent1, comp)
inter1 = mnm_repr.Add(cond1)
ent2 = mnm_repr.Metabolite('m2')
cond2 = mnm_repr.PresentEntity(ent2, comp)
inter2 = mnm_repr.Remove(cond2)
exp_description = exp_repr.ExperimentDescription(
exp_repr.DetectionEntity('ent1'), [inter1, inter2])
out = exporter.ban_experiment(exp_description)
# print([out])
self.assertIn('\n:- designed(experiment(detection_entity_exp, ent1))',
out)
self.assertIn(',remove(setup_present(m2, none, c_01))', out)
self.assertIn(',add(setup_present(m1, none, c_01))', out)
def test_export_model_specification(self):
# 2 conds + 2 activ
cond_subst_1 = mnm_repr.PresentEntity(mnm_repr.Metabolite('met1'),
mnm_repr.Medium())
cond_subst_2 = mnm_repr.PresentEntity(mnm_repr.Metabolite('met2'),
mnm_repr.Medium())
act_1 = mnm_repr.Activity('a1', None, ['1'], [])
act_2 = mnm_repr.Activity('a2', None, ['2'], [])
m = mnm_repr.Model('m1', [cond_subst_1, cond_subst_2], [act_1, act_2],
[])
exported = exporter.export_model_specification(m)
self.assertIn('\nadded_to_model(setup_present(met1,none,c_01),m1).',
exported)
self.assertIn('\nadded_to_model(setup_present(met2,none,c_01),m1).',
exported)
self.assertIn('\nadded_to_model(a1,m1).', exported)
self.assertIn('\nadded_to_model(a2,m1).', exported)
def test_check_consistency_negative(self):
met1 = mnm_repr.Metabolite('met1')
met2 = mnm_repr.Metabolite('met2')
comp1 = mnm_repr.Medium()
cond_subst_1 = mnm_repr.PresentEntity(met1, comp1)
cond_subst_2 = mnm_repr.PresentEntity(met2, comp1)
base_model = mnm_repr.Model('m1', [cond_subst_1, cond_subst_2], [], [])
exd = exp_repr.ExperimentDescription(exp_repr.DetectionEntity('met1'),
[])
res = exp_repr.Result('r1', exd, 'false')
exp = exp_repr.Experiment('exp1', [res])
arch = Archive()
arch.mnm_entities = [met1, met2]
arch.mnm_compartments = [comp1]
ev1 = AdditionalModels([base_model])
ev2 = AcceptedResults(exp)
arch.record(ev1)
arch.record(ev2)
rev = RevisionModule(arch)
out = rev.check_consistency(base_model)
self.assertEqual(False, out)
def generate_all_possible(self, entities, compartments, activities,
setup_conds, import_activities):
# exp types:
self.types = {
DetectionEntity: None,
AdamTwoFactorExperiment: None,
ReconstructionActivity: None,
ReconstructionEnzReaction: None,
ReconstructionTransporterRequired: None,
LocalisationEntity: None,
DetectionActivity: None
}
# compartments for checking localisation:
self.design_compartment = {
'c_02': None,
'c_03': None,
'c_04': None,
'c_05': None,
'c_06': None,
'c_07': None,
'c_08': None,
'c_09': None,
'c_10': None,
'c_11': None,
'c_12': None,
'c_13': None,
'c_14': None,
'c_15': None,
'c_16': None,
'c_17': None,
'c_18': None,
'c_19': None,
'c_20': None,
'c_21': None,
'c_22': None,
'c_23': None,
'c_24': None,
'c_25': None,
'c_26': None,
'c_27': None,
'c_28': None,
'c_29': None,
'c_30': None,
'c_31': None,
'c_32': None,
'c_33': None,
'c_34': None
}
# rest of elements:
self.design_deletable = {}
self.design_available = {}
self.design_activity_rec = {}
self.design_activity_det = {}
self.design_entity_loc = {}
self.design_entity_det = {}
self.intervention_add = {}
self.intervention_remove = {}
#
for act in import_activities:
self.intervention_add[mnm_repr.Add(act)] = 1
#
for st in setup_conds:
# all genes can be removed; metabs can only be removed from medium
if (isinstance(st.entity, mnm_repr.Gene)
or isinstance(st.compartment, Medium)):
self.intervention_remove[mnm_repr.Remove(st)] = None
if isinstance(st.entity, mnm_repr.Gene):
self.design_deletable[st.entity] = None
#
for ent in entities:
if isinstance(ent, mnm_repr.Gene):
continue
else: # Met, Prot, Cplx
self.design_available[ent] = None
self.design_entity_det[ent] = None
if isinstance(ent, mnm_repr.Metabolite):
self.intervention_add[mnm_repr.Add(
mnm_repr.PresentEntity(ent, Medium()))] = None
else: # Prot, Cplx
self.design_entity_loc[ent] = None
#
for act in activities:
# don't test these additional import reactions: they're only to help with experiments
if act in import_activities:
continue
elif isinstance(act, mnm_repr.Growth):
self.design_activity_det[act] = None
else:
self.design_activity_rec[act] = None