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HOTFIX: Homo-Dimer Reaction Propensities #329

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Merged
briandrawert merged 1 commit into from
Oct 26, 2022
Merged

HOTFIX: Homo-Dimer Reaction Propensities #329

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28 changes: 18 additions & 10 deletions spatialpy/core/reaction.py
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Original file line number Diff line number Diff line change
Expand Up @@ -100,18 +100,20 @@ def __init__(self, name=None, reactants=None, products=None, propensity_function
if reactants is not None:
for r in reactants:
rtype = type(r).__name__
if rtype == 'Species':
self.reactants[r.name] = reactants[r]
name = r.name if rtype == 'Species' else r
if name in self.reactants:
self.reactants[name] += reactants[r]
else:
self.reactants[r] = reactants[r]

self.reactants[name] = reactants[r]
if products is not None:
for p in products:
rtype = type(p).__name__
if rtype == 'Species':
self.products[p.name] = products[p]
ptype = type(p).__name__
name = p.name if ptype == 'Species' else p
if name in self.products:
self.products[name] += products[p]
else:
self.products[p] = products[p]
self.products[name] = products[p]

if self.marate is not None:
rtype = type(self.marate).__name__
Expand Down Expand Up @@ -343,7 +345,10 @@ def add_product(self, species, stoichiometry):
except TypeError as err:
raise ReactionError(f"Failed to validate product. Reason given: {err}") from err

self.products[name] = stoichiometry
if name in self.products:
self.products[name] += stoichiometry
else:
self.products[name] = stoichiometry

def add_reactant(self, species, stoichiometry):
"""
Expand All @@ -362,7 +367,10 @@ def add_reactant(self, species, stoichiometry):
except TypeError as err:
raise ReactionError(f"Failed to validate reactant. Reason given: {err}") from err

self.reactants[name] = stoichiometry
if name in self.reactants:
self.reactants[name] += stoichiometry
else:
self.reactants[name] = stoichiometry
if self.massaction and self.type == "mass-action":
self._create_mass_action()

Expand Down