Source code for memote.support.basic
# -*- coding: utf-8 -*-
# Copyright 2017 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 basic checks performed on the model object."""
from __future__ import absolute_import
import logging
from memote.support.helpers import find_atp_adp_converting_reactions
__all__ = ("check_metabolites_formula_presence",)
LOGGER = logging.getLogger(__name__)
def check_metabolites_charge_presence(model):
"""Return the list of model metabolites that have no associated charge."""
return [met for met in model.metabolites if met.charge is None]
def check_gene_protein_reaction_rule_presence(model):
"""Return the list of model reactions that have no associated gene rule."""
return [rxn for rxn in model.reactions if not rxn.gene_reaction_rule]
def find_nonzero_constrained_reactions(model):
"""Return list of reactions with non-zero, non-maximal bounds."""
return [rxn for rxn in model.reactions if
0 > rxn.lower_bound > -1000 or
0 < rxn.upper_bound < 1000]
def find_zero_constrained_reactions(model):
"""Return list of reactions that are constrained to zero flux."""
return [rxn for rxn in model.reactions if
rxn.lower_bound == 0 and
rxn.upper_bound == 0]
def find_irreversible_reactions(model):
"""Return list of reactions that are irreversible."""
return [rxn for rxn in model.reactions if rxn.reversibility is False]
def find_unconstrained_reactions(model):
"""Return list of reactions that are not constrained at all."""
return [rxn for rxn in model.reactions if
rxn.lower_bound <= -1000 and
rxn.upper_bound >= 1000]
def find_ngam(model):
"""
Return a the non growth-associated maintenance reaction.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
"""
atp_adp_conv_rxns = find_atp_adp_converting_reactions(model)
return [rxn for rxn in atp_adp_conv_rxns
if rxn.build_reaction_string() == 'atp_c + h2o_c --> '
'adp_c + h_c + pi_c' and not
rxn.lower_bound <= 0]
def calculate_metabolic_coverage(model):
"""
Return the ratio of reactions and genes included in the model.
According to [1] this is a good quality indicator expressing the degree of
metabolic coverage i.e. modeling detail of a given reconstruction. The
authors explain that models with a 'high level of modeling detail have
ratios >1, and [models] with low level of detail have ratios <1'. They
explain that 'this difference arises because [models] with basic or
intermediate levels of detail often include many reactions in which several
gene products and their enzymatic transformations are ‘lumped’'.
References
----------
[1] Monk, J., Nogales, J., & Palsson, B. O. (2014). Optimizing genome-scale
network reconstructions. Nature Biotechnology, 32(5), 447–452.
http://doi.org/10.1038/nbt.2870
"""
if len(model.reactions) == 0 or len(model.genes) == 0:
raise ValueError("The model contains no reactions or genes.")
return float(len(model.reactions)) / float(len(model.genes))
