def find_protein_complexes(model):
"""
Find tuples of gene identifiers that comprise functional enzyme complexes.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
Returns
-------
set
A set of tuples of genes that are connected via "AND" in
gene-protein-reaction rules (GPR) and thus constitute protein
complexes.
"""
protein_complexes = set()
for rxn in model.reactions:
if rxn.gene_reaction_rule:
for candidate in helpers.find_functional_units(
rxn.gene_reaction_rule):
if len(candidate) >= 2:
protein_complexes.add(tuple(candidate))
return protein_complexes
def find_protein_complexes(model):
"""
Find tuples of gene identifiers that constitute functional enzyme complexes.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
"""
protein_complexes = set()
for rxn in model.reactions:
if rxn.gene_reaction_rule:
for candidate in helpers.find_functional_units(
rxn.gene_reaction_rule):
if len(candidate) >= 2:
protein_complexes.add(tuple(candidate))
return protein_complexes
def test_find_functional_units(gpr_str, expected):
"""Expect type of enzyme complexes to be identified correctly."""
assert list(helpers.find_functional_units(gpr_str)) == expected