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Fixed bug where added cofactor reactions would get deleted #38

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Fixed bug where added cofactor reactions would get deleted #38

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4 changes: 3 additions & 1 deletion minedatabase/pickaxe.py
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Original file line number Diff line number Diff line change
Expand Up @@ -807,12 +807,13 @@ def _remove_cofactor_redundancy(self) -> None:
# Loop through identified compounds and update
# reactions/compounds accordingly
rxns_to_del = set()
cofactor_rxn_ids = set()
for cpd_id in cofactors_as_cpds:
rxn_ids = set(
self.compounds[cpd_id]["Product_of"]
+ self.compounds[cpd_id]["Reactant_in"]
)
rxns_to_del = rxns_to_del.union(rxn_ids)
rxns_to_del = rxns_to_del.union(rxn_ids).difference(cofactor_rxn_ids)
# Check and fix reactions as needed
for rxn_id in rxn_ids:
rxn = self.reactions[rxn_id]
Expand All @@ -832,6 +833,7 @@ def _remove_cofactor_redundancy(self) -> None:
products.append((s, self.compounds[product]))

cofactor_rxn_id, rxn_text = utils.get_reaction_hash(reactants, products)
cofactor_rxn_ids.add(cofactor_rxn_id)

# Check to see if reaction makes changes
# Reactions such as
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