From 5495772e6566c5fe60e4764dd12ccd6e9f6ca53e Mon Sep 17 00:00:00 2001
From: AlberteSloth <158040192+AlberteSloth@users.noreply.github.com>
Date: Fri, 13 Dec 2024 14:21:13 +0100
Subject: [PATCH] Updated sbml_demo

---
 scripts/sbml_demo.py | 77 +++++++++++++++++++++++---------------------
 1 file changed, 40 insertions(+), 37 deletions(-)

diff --git a/scripts/sbml_demo.py b/scripts/sbml_demo.py
index 8307423..1bbe8af 100644
--- a/scripts/sbml_demo.py
+++ b/scripts/sbml_demo.py
@@ -11,54 +11,57 @@
 reactions_sympy = sbml.sbml_to_sympy(model_sbml)
 sym_module = sbml.sympy_to_enzax(reactions_sympy)
 
-parameters_all = [
-    ({p.getId(): p.getValue() for p in r.getKineticLaw().getListOfParameters()})
-    for r in model_sbml.getListOfReactions()
+species = [s.getId() for s in model_sbml.getListOfSpecies()]
+
+balanced_species = [
+    b.getId() 
+    for b in model_sbml.getListOfSpecies() 
+    if not b.boundary_condition
 ]
-parameters = {}
-for i in parameters_all:
-    parameters.update(i)
 
-compartments = {c.getId(): c.volume for c in model_sbml.getListOfCompartments()}
+reactions = [reaction.getId() 
+    for reaction in model_sbml.getListOfReactions()
+]
 
-species = [s.getId() for s in model_sbml.getListOfSpecies()]
+stoichiometry = {reaction.getId(): {r.getSpecies(): -r.getStoichiometry(), p.getSpecies(): p.getStoichiometry()} 
+    for reaction in model_sbml.getListOfReactions() 
+    for r in reaction.getListOfReactants()
+    for p in reaction.getListOfProducts()
+}
+
+structure = KineticModelStructure(
+    stoichiometry=stoichiometry,
+    species=species,
+    reactions=reactions,
+    balanced_species=balanced_species
+)
 
-balanced_species_dict = {}
-unbalanced_species_dict = {}
-for i in model_sbml.getListOfSpecies():
-    if not i.boundary_condition:
-        balanced_species_dict.update({i.getId(): i.getInitialConcentration()})
-    else:
-        unbalanced_species_dict.update({i.getId(): i.getInitialConcentration()})
+parameters_local = {
+    p.getId(): p.getValue()
+    for r in model_sbml.getListOfReactions()
+    for p in r.getKineticLaw().getListOfParameters()
+}
 
-balanced_ix = jnp.array([species.index(b) for b in balanced_species_dict])
-unbalanced_ix = jnp.array([species.index(u) for u in unbalanced_species_dict])
+parameters_global = {
+    p.getId(): p.getValue()
+    for p in model_sbml.getListOfParameters()
+    if p.constant
+}
 
-para = {**parameters, **compartments, **unbalanced_species_dict}
+compartments = {c.getId(): c.volume 
+    for c in model_sbml.getListOfCompartments()
+}
 
-stoichmatrix = jnp.zeros(
-    (model_sbml.getNumSpecies(), model_sbml.getNumReactions()),
-    dtype=jnp.float64,
-)
-i = 0
-for reaction in model_sbml.getListOfReactions():
-    for r in reaction.getListOfReactants():
-        stoichmatrix = stoichmatrix.at[species.index(r.getSpecies()), i].set(
-            -int(r.getStoichiometry())
-        )
-    for p in reaction.getListOfProducts():
-        stoichmatrix = stoichmatrix.at[species.index(p.getSpecies()), i].set(
-            int(p.getStoichiometry())
-        )
-    i += 1
+unbalanced_species = {
+    u.getId(): u.getInitialConcentration() 
+    for u in model_sbml.getListOfSpecies() 
+    if u.boundary_condition
+}
 
-structure = KineticModelStructure(
-    stoichmatrix, jnp.array(balanced_ix), jnp.array(unbalanced_ix)
-)
+para = {**parameters_local, **parameters_global, **compartments, **unbalanced_species}
 
 kinmodel_sbml = KineticModelSbml(
     parameters=para,
-    balanced_ids=balanced_species_dict,
     structure=structure,
     sym_module=sym_module,
 )