fix to enable to vary or keep constant the reactant species specified…

… as boundary species in the original SBML file
flowersteam · Feb 26, 2024 · dc19c4a · dc19c4a
1 parent 40f766b
commit dc19c4a
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Showing 2 changed files with 10 additions and 4 deletions.
diff --git a/sbmltoodejax/modulegeneration.py b/sbmltoodejax/modulegeneration.py
@@ -9,6 +9,7 @@ def GenerateModel(modelData, outputFilePath,
                   ModelStepName: str='ModelStep',
                   ModelRolloutName: str='ModelRollout',
                   vary_constant_reactants: bool=False,
+                  vary_boundary_reactants: bool=False,
                   deltaT: float =0.1,
                   atol: float=1e-6,
                   rtol: float = 1e-12,
@@ -398,8 +399,9 @@ def ParseRHS(rawRateLaw, extended_param_names=[], reaction_name=None, yvar="y",
         reactionCounter += 1
         reaction = reactions[rxnId]
         for reactant in reaction.reactants:
-            if (reactant[1] in y_indexes) and (not species[reactant[1]].isBoundarySpecies):
-                stoichCoeffMat = stoichCoeffMat.at[y_indexes[reactant[1]], reactionIndex[rxnId]].add(reactant[0])
+            if (reactant[1] in y_indexes):
+                if (not species[reactant[1]].isBoundarySpecies) or vary_boundary_reactants:
+                    stoichCoeffMat = stoichCoeffMat.at[y_indexes[reactant[1]], reactionIndex[rxnId]].add(reactant[0])
 
     rateArray = ['0.0'] * len(y_indexes)
     for rule_name, rule in rateRules.items():

diff --git a/sbmltoodejax/utils.py b/sbmltoodejax/utils.py
@@ -3,7 +3,9 @@
 from sbmltoodejax.modulegeneration import GenerateModel
 from sbmltoodejax.parse import ParseSBMLFile
 
-def generate_biomodel(model_idx, model_fp="jax_model.py", deltaT=0.1, atol=1e-6, rtol=1e-12, mxstep=5000000):
+def generate_biomodel(model_idx, model_fp="jax_model.py",
+                      vary_constant_reactants=False, vary_boundary_reactants=False,
+                      deltaT=0.1, atol=1e-6, rtol=1e-12, mxstep=5000000):
     """Calls the `sbmltoodejax.modulegeneration.GenerateModel` for a SBML model hosted on the BioModel website and indexed by the provided `model_idx`.
 
     Args:
@@ -19,7 +21,9 @@ def generate_biomodel(model_idx, model_fp="jax_model.py", deltaT=0.1, atol=1e-6,
     """
     model_xml_body = get_content_for_model(model_idx)
     model_data = ParseSBMLFile(model_xml_body)
-    GenerateModel(model_data, model_fp, deltaT=deltaT, atol=atol, rtol=rtol, mxstep=mxstep)
+    GenerateModel(model_data, model_fp,
+                  vary_constant_reactants=vary_constant_reactants, vary_boundary_reactants=vary_boundary_reactants,
+                  deltaT=deltaT, atol=atol, rtol=rtol, mxstep=mxstep)
 
     return model_fp