def create_fva_model(sbml, r_id2bounds, new_sbml):
def r_updater(r):
l_b, u_b = r_id2bounds[format_r_id(r.id)]
set_bounds(r, l_b, max(u_b, 0))
if l_b * u_b >= 0:
r.setReversible(False)
r_ids = set(r_id2bounds.keys()) | {format_r_id(r_id, False) for r_id in r_id2bounds.keys()}
r_ids2sbml(r_ids, sbml, new_sbml, 'FVA', r_updater)
return new_sbml
def visualize_model(sbml, vis_r_ids, id2mask, id2color, title, info, invisible_layers, layer2mask, res_dir, tab2html):
combined_sbml = os.path.join(res_dir, "Combined_model.xml")
r_ids2sbml(vis_r_ids, sbml, combined_sbml, "combined")
doc = libsbml.SBMLReader().readSBML(combined_sbml)
model = doc.getModel()
id2mask = get_full_id2mask(id2mask, model)
process_sbml(
combined_sbml,
verbose=True,
web_page_prefix="visualization",
generalize=False,
id2mask=id2mask,
layer2mask=layer2mask,
tab2html=tab2html,
title=title,
id2color=id2color,
tabs=None,
info=info,
invisible_layers=invisible_layers,
)