GPR rules of split reactions are not selected properly

[voidsailor]

Hello again @Paulocracy :),

the problem from issue #12 is still present.

In create_smoment_model_reaction_wise, reactions are split if they have measured isoenzymes. The GPR rule of the original reaction is distributed accordingly among the new reactions and split GPR rules are stored in the dict "reaction_id_gene_rules_mapping". This dict uses the ids of the split reactions, e.g. "PCFLOPm_GPRSPLIT_1", as keys and a corresponding GPR rule as value.

Subsequently, in the main loop, pseudo metabolites should be added to every reaction. At the beginning of the loop, the reaction ids are split by "_GPRSPLIT_" yielding the id of the original reaction (i.e., "PCFLOPm") and overwriting the reaction name of the split reaction ("PCFLOPm_GPRSPLIT_1"):

autopacmen/autopacmen/submodules/create_smoment_model_reaction_wise.py

Lines 185 to 206 in 56474a5

	for model_reaction_id in model_reaction_ids:
	# Get the reaction and split the ID at the ID addition
	reaction = model.reactions.get_by_id(model_reaction_id)
	splitted_id = reaction.id.split(id_addition)
	# If the reaction has no name, ignore it
	if splitted_id[0] == "":
	continue
	# Take the reaction ID from the first part of the split
	reaction_id = splitted_id[0]
	# Remove GPRSPLIT name addition from reactions with measured protein concentrations
	if "_GPRSPLIT_" in reaction_id:
	reaction_id = reaction_id.split("_GPRSPLIT_")[0]
	# If the reaction has no associated enzyme stoichiometries, ignore it
	if reaction_id not in list(reaction_id_gene_rules_mapping.keys()):
	continue
	# If the reaction has no gene rule, ignore it
	gene_rule = reaction_id_gene_rules_mapping[reaction_id]
	if gene_rule == [""]:
	continue
	# If the reaction is manually excluded, ignore it

Later, the GPR rule of the split reaction is retrieved from the "reaction_id_gene_rules_mapping" dict but using the original reaction id instead of the id of the split reaction resulting in the same and incorrect pseudo metabolites being assigned to the split reactions.

I'll create a pull request later :)

(Sorry for spamming you with issues, I'm working my way through autoPACMEN for another project :D)