def test_metabolites_formula_presence(model):
"""
Expect all metabolites to have a formula.
To be able to ensure that reactions are mass-balanced, all model
metabolites ought to be provided with a chemical formula. Since it may be
difficult to obtain formulas for certain metabolites this test serves as a
mere report. Models can still be stoichiometrically consistent even
when chemical formulas are not defined for each metabolite.
Implementation:
Check if each cobra.Metabolite has a non-empty "formula"
attribute. This attribute is set by the parser if there is an
fbc:chemicalFormula attribute for the corresponding species in the
SBML.
"""
ann = test_metabolites_formula_presence.annotation
ann["data"] = get_ids(
basic.check_metabolites_formula_presence(model))
ann["metric"] = len(ann["data"]) / len(model.metabolites)
ann["message"] = wrapper.fill(
"""There are a total of {}
metabolites ({:.2%}) without a formula: {}""".format(
len(ann["data"]), ann["metric"], truncate(ann["data"])))
assert len(ann["data"]) == 0, ann["message"]
def test_metabolites_formula_presence(read_only_model, store):
"""Expect all metabolites to have a formula."""
missing = [
met.id
for met in basic.check_metabolites_formula_presence(read_only_model)
]
store["metabolites_no_formula"] = missing
assert len(missing) == 0, "No formula found for the following "\
"metabolites: {}".format(", ".join(missing))
def test_metabolites_formula_presence(read_only_model):
"""
Expect all metabolites to have a formula.
To be able to ensure that reactions are mass-balanced, all model
metabolites ought to be provided with a chemical formula.
"""
ann = test_metabolites_formula_presence.annotation
ann["data"] = get_ids(
basic.check_metabolites_formula_presence(read_only_model))
ann["metric"] = len(ann["data"]) / len(read_only_model.metabolites)
ann["message"] = wrapper.fill("""There are a total of {}
metabolites ({:.2%}) without a formula: {}""".format(
len(ann["data"]), ann["metric"], truncate(ann["data"])))
assert len(ann["data"]) == 0, ann["message"]
def test_metabolites_formula_presence(read_only_model):
"""
Expect all metabolites to have a formula.
To be able to ensure that reactions are mass-balanced, all model
metabolites ought to be provided with a chemical formula. Since it may be
difficult to obtain formulas for certain metabolites this test serves as a
mere report. Models can still be stoichiometrically consistent even
when chemical formulas are not defined for each metabolite.
"""
ann = test_metabolites_formula_presence.annotation
ann["data"] = get_ids(
basic.check_metabolites_formula_presence(read_only_model))
ann["metric"] = len(ann["data"]) / len(read_only_model.metabolites)
ann["message"] = wrapper.fill(
"""There are a total of {}
metabolites ({:.2%}) without a formula: {}""".format(
len(ann["data"]), ann["metric"], truncate(ann["data"])))
assert len(ann["data"]) == 0, ann["message"]
def test_metabolites_formula_presence(model):
"""
Expect all metabolites to have a formula.
To be able to ensure that reactions are mass-balanced, all model
metabolites ought to be provided with a chemical formula. Since it may be
difficult to obtain formulas for certain metabolites this test serves as a
mere report. Models can still be stoichiometrically consistent even
when chemical formulas are not defined for each metabolite.
Implementation:
Check if each cobra.Metabolite has a non-empty "formula"
attribute. This attribute is set by the parser if there is an
fbc:chemicalFormula attribute for the corresponding species in the
SBML.
"""
ann = test_metabolites_formula_presence.annotation
ann["data"] = get_ids(basic.check_metabolites_formula_presence(model))
ann["metric"] = len(ann["data"]) / len(model.metabolites)
ann["message"] = wrapper.fill("""There are a total of {}
metabolites ({:.2%}) without a formula: {}""".format(
len(ann["data"]), ann["metric"], truncate(ann["data"])))
assert len(ann["data"]) == 0, ann["message"]
def test_metabolites_formula_presence(model, num):
"""Expect all metabolites to have a formula."""
assert len(basic.check_metabolites_formula_presence(model)) == num