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Fix compartment removal in reaction rates for sbml2bngl #421

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Merged
akutuva21 merged 1 commit into from
Jun 2, 2026
Merged

Fix compartment removal in reaction rates for sbml2bngl #421

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20 changes: 4 additions & 16 deletions bionetgen/atomizer/sbml2bngl.py
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Original file line number Diff line number Diff line change
Expand Up @@ -734,24 +734,12 @@ def analyzeReactionRate(
# Remove compartments if we use them.
# if not self.noCompartment:
compartments_to_remove = [sympy.symbols(comp) for comp in compartmentList]
# TODO: This is not fully correct, we need to know what
# compartment is on what side which is not currently
# being provided to this function
for comp in compartments_to_remove:
if comp in sym.atoms():
# Further issue, I know that this should be
# a multiplication but for BMD2 this is actually a
# problem? In fact, it looks like this is the case
# for regular mass action in SBML?
# This doesn't look right and it is a current
# hack?
n, d = sym.as_numer_denom()
if comp in n.atoms():
sym = sym / comp
elif comp in d.atoms():
sym = sym * comp
else:
pass
# By substituting 1 for the compartment size, we simply
# remove it from the rate equation appropriately regardless of
# where it appears in the expression
sym = sym.subs(comp, 1)

# If we are splitting, we don't need to do much
if split_rxn:
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