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Account for cases where forward rate law may not exist and fix impute…
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… kinetic constant for cases where the min and max fluxes are equivalent
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@YinHoon
YinHoon committed Mar 4, 2020
1 parent c381df0 commit a6c3f5f
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Showing 2 changed files with 51 additions and 24 deletions.
26 changes: 25 additions & 1 deletion tests/eukaryote/test_metabolism.py
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Original file line number Diff line number Diff line change
Expand Up @@ -752,11 +752,16 @@ def test_impute_kinetic_constant(self):

model = self.model
gen = self.gen
gen.clean_and_validate_options()
gen.clean_and_validate_options()

bound_values = {'ex_m1': (10, 10), 'ex_m2': (10, 10), 'ex_m3': (0, 0), 'r1': (0, 1), 'r2': (-2, 3), 'r3': (0, 3), 'r4': (0, None), 'biomass_reaction': (0, None)}
gen.impute_kinetic_constant(bound_values)

self.assertEqual(gen._law_bound_pairs[model.rate_laws.get_one(id='r1-forward')], 1)
self.assertEqual(gen._law_bound_pairs[model.rate_laws.get_one(id='r1-backward')], 0)
self.assertEqual(gen._law_bound_pairs[model.rate_laws.get_one(id='r2-forward')], 3)
self.assertEqual(gen._law_bound_pairs[model.rate_laws.get_one(id='r2-backward')], 2)
self.assertEqual(gen._law_bound_pairs[model.rate_laws.get_one(id='r3-forward')], 3)
self.assertEqual(model.parameters.get_one(id='k_cat_r1_forward_enzyme3').value, 150.)
self.assertEqual(model.parameters.get_one(id='k_cat_r1_forward_enzyme3').comments, 'Value imputed as the median of measured k_cat values')
self.assertEqual(model.parameters.get_one(id='k_cat_r1_backward_enzyme3').value, 150.)
Expand All @@ -771,3 +776,22 @@ def test_impute_kinetic_constant(self):
self.assertEqual(model.parameters.get_one(id='k_cat_r2_backward_enzyme2').comments, 'Value imputed based on FVA bound value')
self.assertEqual(model.parameters.get_one(id='k_cat_r3_forward_enzyme2').value, 300.)
self.assertEqual(model.parameters.get_one(id='k_cat_r3_forward_enzyme2').comments, 'Measured value adjusted to relax bound')

bound_values = {'ex_m1': (10, 10), 'ex_m2': (10, 10), 'ex_m3': (0, 0), 'r1': (1, 1), 'r2': (-2, -2), 'r3': (1, 3), 'r4': (0, None), 'biomass_reaction': (0, None)}
gen.impute_kinetic_constant(bound_values)

self.assertEqual(gen._law_bound_pairs[model.rate_laws.get_one(id='r1-forward')], 1)
self.assertEqual(gen._law_bound_pairs[model.rate_laws.get_one(id='r1-backward')], 0)
self.assertEqual(gen._law_bound_pairs[model.rate_laws.get_one(id='r2-forward')], 0)
self.assertEqual(gen._law_bound_pairs[model.rate_laws.get_one(id='r2-backward')], 2)
self.assertEqual(gen._law_bound_pairs[model.rate_laws.get_one(id='r3-forward')], 3)

bound_values = {'ex_m1': (10, 10), 'ex_m2': (10, 10), 'ex_m3': (0, 0), 'r1': (0, 0), 'r2': (-4, -2), 'r3': (3, 3), 'r4': (0, None), 'biomass_reaction': (0, None)}
gen.impute_kinetic_constant(bound_values)

self.assertEqual(gen._law_bound_pairs[model.rate_laws.get_one(id='r1-forward')], 0)
self.assertEqual(gen._law_bound_pairs[model.rate_laws.get_one(id='r1-backward')], 0)
self.assertEqual(gen._law_bound_pairs[model.rate_laws.get_one(id='r2-forward')], 0)
self.assertEqual(gen._law_bound_pairs[model.rate_laws.get_one(id='r2-backward')], 4)
self.assertEqual(gen._law_bound_pairs[model.rate_laws.get_one(id='r3-forward')], 3)

49 changes: 26 additions & 23 deletions wc_model_gen/eukaryote/metabolism.py
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Original file line number Diff line number Diff line change
Expand Up @@ -450,16 +450,19 @@ def calibrate_submodel(self):
elif reaction.rate_laws:

for_ratelaw = reaction.rate_laws.get_one(direction=wc_lang.RateLawDirection.forward)
if all(i.distribution_init_concentration.mean==0. for i in for_ratelaw.expression.species):
max_constr = 0.
elif not any(numpy.isnan(p.value) for p in for_ratelaw.expression.parameters):
max_constr = for_ratelaw.expression._parsed_expression.eval({
wc_lang.Species: {i.id: i.distribution_init_concentration.mean \
for i in for_ratelaw.expression.species}
}) * scale_factor
upper_bound_adjustable.append(reaction.id)
if for_ratelaw:
if all(i.distribution_init_concentration.mean==0. for i in for_ratelaw.expression.species):
max_constr = 0.
elif not any(numpy.isnan(p.value) for p in for_ratelaw.expression.parameters):
max_constr = for_ratelaw.expression._parsed_expression.eval({
wc_lang.Species: {i.id: i.distribution_init_concentration.mean \
for i in for_ratelaw.expression.species}
}) * scale_factor
upper_bound_adjustable.append(reaction.id)
else:
max_constr = None
else:
max_constr = None
max_constr = None

rev_ratelaw = reaction.rate_laws.get_one(direction=wc_lang.RateLawDirection.backward)
if rev_ratelaw:
Expand Down Expand Up @@ -785,24 +788,24 @@ def impute_kinetic_constant(self, bound_values):
median_kcat = numpy.median([k.value for i in submodel.reactions for j in i.rate_laws \
for k in j.expression.parameters if k.value and not numpy.isnan(k.value)])

law_bound_pairs = {}
for reaction in submodel.reactions:
self._law_bound_pairs = {}
for reaction in submodel.reactions:
if reaction.rate_laws:
bounds = bound_values[reaction.id]
if len(reaction.rate_laws)==1:
law_bound_pairs[reaction.rate_laws[0]] = bounds[1]
else:
if bounds[0]<=0 and bounds[1]>=0:
law_bound_pairs[reaction.rate_laws[0]] = bounds[1]
law_bound_pairs[reaction.rate_laws[1]] = -bounds[0]
elif bounds[0]>=0 and bounds[1]>=0:
law_bound_pairs[reaction.rate_laws[0]] = bounds[1]
law_bound_pairs[reaction.rate_laws[1]] = 0.
for_ratelaw = reaction.rate_laws.get_one(direction=wc_lang.RateLawDirection.forward)
rev_ratelaw = reaction.rate_laws.get_one(direction=wc_lang.RateLawDirection.backward)
if for_ratelaw:
if bounds[1] >= 0:
self._law_bound_pairs[for_ratelaw] = bounds[1]
else:
self._law_bound_pairs[for_ratelaw] = 0.
if rev_ratelaw:
if bounds[0] <= 0:
self._law_bound_pairs[rev_ratelaw] = -bounds[0]
else:
law_bound_pairs[reaction.rate_laws[0]] = 0.
law_bound_pairs[reaction.rate_laws[1]] = -bounds[0]
self._law_bound_pairs[rev_ratelaw] = 0.

for law, value in law_bound_pairs.items():
for law, value in self._law_bound_pairs.items():
complexes = law.expression.species
if value!=0.0:
if len(complexes) == 1:
Expand Down

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