# -*- coding: utf-8 -*-
# Copyright 2018 Novo Nordisk Foundation Center for Biosustainability,
# Technical University of Denmark.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
"""Supporting functions for checks requiring the eQuilibrator API."""
from __future__ import absolute_import
import logging
from collections import Iterable, defaultdict
from sys import version_info
from six import iteritems, string_types
if version_info[:2] >= (3, 5):
from equilibrator_api import CompoundMatcher, Reaction
[docs] compound_matcher = CompoundMatcher()
[docs]logger = logging.getLogger(__name__)
[docs]def get_smallest_compound_id(compounds_identifiers):
"""
Return the smallest KEGG compound identifier from a list.
KEGG identifiers may map to compounds, drugs or glycans prefixed
respectively with "C", "D", and "G" followed by at least 5 digits. We
choose the lowest KEGG identifier with the assumption that several
identifiers are due to chirality and that the lower one represents the
more common form.
Parameters
----------
compounds_identifiers : list
A list of mixed KEGG identifiers.
Returns
-------
str
The KEGG compound identifier with the smallest number.
Raises
------
ValueError
When compound_identifiers contains no KEGG compound identifiers.
"""
return min(
(c for c in compounds_identifiers if c.startswith("C")),
key=lambda c: int(c[1:]),
)
[docs]def translate_reaction(reaction, metabolite_mapping):
"""
Return a mapping from KEGG compound identifiers to coefficients.
Parameters
----------
reaction : cobra.Reaction
The reaction whose metabolites are to be translated.
metabolite_mapping : dict
An existing mapping from cobra.Metabolite to KEGG compound identifier
that may already contain the metabolites in question or will have to be
extended.
Returns
-------
dict
The stoichiometry of the reaction given as a mapping from metabolite
KEGG identifier to coefficient.
"""
# Transport reactions where the same metabolite occurs in different
# compartments should have been filtered out but just to be sure, we add
# coefficients in the mapping.
stoichiometry = defaultdict(float)
for met, coef in iteritems(reaction.metabolites):
kegg_id = metabolite_mapping.setdefault(met, map_metabolite2kegg(met))
if kegg_id is None:
continue
stoichiometry[kegg_id] += coef
return dict(stoichiometry)
[docs]def find_thermodynamic_reversibility_index(reactions):
"""
Return the reversibility index of the given reactions.
To determine the reversibility index, we calculate
the reversibility index ln_gamma (see [1]_ section 3.5) of each reaction
using the eQuilibrator API [2]_.
Parameters
----------
reactions: list of cobra.Reaction
A list of reactions for which to calculate the reversibility index.
Returns
-------
tuple
list of cobra.Reaction, index pairs
A list of pairs of reactions and their reversibility indexes.
list of cobra.Reaction
A list of reactions which contain at least one metabolite that
could not be mapped to KEGG on the basis of its annotation.
list of cobra.Reaction
A list of reactions for which it is not possible to calculate the
standard change in Gibbs free energy potential. Reasons of failure
include that participating metabolites cannot be broken down with
the group contribution method.
list of cobra.Reaction
A list of reactions that are not chemically or redox balanced.
References
----------
.. [1] Elad Noor, Arren Bar-Even, Avi Flamholz, Yaniv Lubling, Dan Davidi,
Ron Milo; An integrated open framework for thermodynamics of
reactions that combines accuracy and coverage, Bioinformatics,
Volume 28, Issue 15, 1 August 2012, Pages 2037–2044,
https://doi.org/10.1093/bioinformatics/bts317
.. [2] https://pypi.org/project/equilibrator-api/
"""
incomplete_mapping = []
problematic_calculation = []
reversibility_indexes = []
unbalanced = []
metabolite_mapping = {}
for rxn in reactions:
stoich = translate_reaction(rxn, metabolite_mapping)
if len(stoich) < len(rxn.metabolites):
incomplete_mapping.append(rxn)
continue
try:
# Remove protons from stoichiometry.
if "C00080" in stoich:
del stoich["C00080"]
eq_rxn = Reaction(stoich, rxn.id)
except KeyError:
incomplete_mapping.append(rxn)
continue
if eq_rxn.check_full_reaction_balancing():
try:
ln_rev_index = eq_rxn.reversibility_index()
# TODO (Moritz Beber): Which exceptions can we expect here?
except Exception:
problematic_calculation.append(rxn)
continue
reversibility_indexes.append((rxn, ln_rev_index))
else:
unbalanced.append(rxn)
reversibility_indexes.sort(key=lambda p: abs(p[1]), reverse=True)
return (
reversibility_indexes,
incomplete_mapping,
problematic_calculation,
unbalanced,
)
