def test_production_envelope_with_constraints(self): r_target = 'R_EX_ac_e' r_biomass = ec_core_model.detect_biomass_reaction() xvals0, ymins0, ymaxs0 = production_envelope(ec_core_model, r_target, steps=5, constraints={'R_EX_o2_e': (0, 0)}) ec_core_model.bounds['R_EX_o2_e'] = (0, 0) xvals1, ymins1, ymaxs1 = production_envelope(ec_core_model, r_target, steps=5) self.assertEqual(xvals0, xvals1) self.assertEqual(ymins0, ymins1) self.assertEqual(ymaxs0, ymaxs1)
def test_production_envelope(self): r_target = 'R_EX_ac_e' r_biomass = ec_core_model.detect_biomass_reaction() xvals0, ymins0, ymaxs0 = production_envelope(ec_core_model, r_target, steps=5) xvals1, ymins1, ymaxs1 = flux_envelope(ec_core_model, r_x=r_biomass, r_y=r_target, steps=5) self.assertEqual(xvals0, xvals1) self.assertEqual(ymins0, ymins1) self.assertEqual(ymaxs0, ymaxs1)
Example: Flux Envelope Analysis @Author: Kai Zhuang """ __author__ = 'kaizhuang' from framed.analysis.variability import production_envelope, flux_envelope from framed.io_utils.sbml import load_sbml_model, CONSTRAINT_BASED from framed.core.fixes import fix_bigg_model import matplotlib.pyplot as plt ### Basic Setup SMALL_TEST_MODEL = 'models/ecoli_core_model.xml' ec_core_model = load_sbml_model(SMALL_TEST_MODEL, kind=CONSTRAINT_BASED) fix_bigg_model(ec_core_model) ### Make the production envelope, and plot it biomass, target_mins2, target_maxs2 = production_envelope(ec_core_model, 'R_EX_ac_e', steps=10, constraints={'R_EX_o2_e': (0, 0)}) print target_maxs2 plt.figure(1) plt.hold(True) plt.plot(biomass, target_maxs2) plt.plot(biomass, target_mins2) plt.ylim(ymin=-0.1) plt.show()