Source code for memote.support.helpers
# -*- coding: utf-8 -*-
# Copyright 2016 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.
"""Helper functions that are used all over the memote package."""
from __future__ import absolute_import
import logging
import re
from builtins import dict
LOGGER = logging.getLogger(__name__)
[docs]def find_transport_reactions(model):
"""
Return a list of all transport reactions.
A transport reaction is defined as follows:
1. It contains metabolites from at least 2 compartments and
2. at least 1 metabolite undergoes no chemical reaction, i.e.,
the formula stays the same on both sides of the equation.
Will not identify transport via the PTS System.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
"""
compartment_spanning_rxns = \
[rxn for rxn in model.reactions if len(rxn.get_compartments()) >= 2]
transport_reactions = []
for rxn in compartment_spanning_rxns:
rxn_reactants = set([met.formula for met in rxn.reactants])
rxn_products = set([met.formula for met in rxn.products])
transported_mets = \
[formula for formula in rxn_reactants if formula in rxn_products]
# Excluding H-pumping reactions for now.
if set(transported_mets).issubset(set('H')):
pass
# Excluding redox-reactions which only transport electrons
elif set(transported_mets).issubset(set(['X', 'XH2'])):
pass
elif len(transported_mets) >= 1:
transport_reactions.append(rxn)
return transport_reactions
[docs]def find_atp_adp_converting_reactions(model):
"""
Find reactions which interact with ATP and ADP.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
"""
atp_all_comp_rxn_list = []
for met in model.metabolites:
if re.match('^atp_.*', met.id):
atp_all_comp_rxn_list.append(met.reactions)
adp_all_comp_rxn_list = []
for met in model.metabolites:
if re.match('^adp_.*', met.id):
adp_all_comp_rxn_list.append(met.reactions)
atp_union = set().union(*atp_all_comp_rxn_list)
adp_union = set().union(*adp_all_comp_rxn_list)
return atp_union.intersection(adp_union)
[docs]def find_biomass_reaction(model):
"""
Return a list of the biomass reaction(s) of the model.
Parameters
----------
model : cobra.Model
The metabolic model under investigation.
"""
return [rxn for rxn in model.reactions if "biomass" in rxn.id.lower()]
[docs]def df2dict(df):
"""Turn a `pandas.DataFrame` into a `dict` of lists."""
blob = dict((key, df[key].tolist()) for key in df.columns)
blob["index"] = df.index.tolist()
return blob
[docs]def find_demand_reactions(model):
"""
Return a list of demand reactions.
[1] defines demand reactions as:
-- 'unbalanced network reactions that allow the accumulation of a compound'
-- reactions that are chiefly added during the gap-filling process
-- as a means of dealing with 'compounds that are known to be produced by
the organism [..] (i) for which no information is available about their
fractional distribution to the biomass or (ii) which may only be produced
in some environmental conditions
-- reactions with a formula such as: 'met_c -> '
Demand reactions differ from exchange reactions in that the metabolites
are not removed from the extracellular environment, but from any of the
organism's compartments.
Parameters
----------
model : cobra.Model
A cobrapy metabolic model
References
----------
[1] Thiele, I., & Palsson, B. Ø. (2010, January). A protocol for generating
a high-quality genome-scale metabolic reconstruction. Nature protocols.
Nature Publishing Group. http://doi.org/10.1038/nprot.2009.203
"""
demand_and_exchange_rxns = set(model.exchanges)
return [rxn for rxn in demand_and_exchange_rxns
if not rxn.reversibility and not
any(c in rxn.get_compartments() for c in ['e'])]
[docs]def find_sink_reactions(model):
"""
Return a list of sink reactions.
[1] defines sink reactions as:
-- 'similar to demand reactions' but reversible, thus able to supply the
model with metabolites
-- reactions that are chiefly added during the gap-filling process
-- as a means of dealing with 'compounds that are produced by nonmetabolic
cellular processes but that need to be metabolized'
-- reactions with a formula such as: 'met_c <-> '
Sink reactions differ from exchange reactions in that the metabolites
are not removed from the extracellular environment, but from any of the
organism's compartments.
Parameters
----------
model : cobra.Model
A cobrapy metabolic model
References
----------
[1] Thiele, I., & Palsson, B. Ø. (2010, January). A protocol for generating
a high-quality genome-scale metabolic reconstruction. Nature protocols.
Nature Publishing Group. http://doi.org/10.1038/nprot.2009.203
"""
demand_and_exchange_rxns = set(model.exchanges)
return [rxn for rxn in demand_and_exchange_rxns
if rxn.reversibility and not
any(c in rxn.get_compartments() for c in ['e'])]
[docs]def find_exchange_rxns(model):
"""
Return a list of exchange reactions.
[1] defines exchange reactions as:
-- reactions that 'define the extracellular environment'
-- 'unbalanced, extra-organism reactions that represent the supply to or
removal of metabolites from the extra-organism "space"'
-- reactions with a formula such as: 'met_e -> ' or ' -> met_e' or
'met_e <=> '
Exchange reactions differ from demand reactions in that the metabolites
are removed from or added to the extracellular environment only. With this
the uptake or secretion of a metabolite is modeled, respectively.
Parameters
----------
model : cobra.Model
A cobrapy metabolic model
References
----------
[1] Thiele, I., & Palsson, B. Ø. (2010, January). A protocol for generating
a high-quality genome-scale metabolic reconstruction. Nature protocols.
Nature Publishing Group. http://doi.org/10.1038/nprot.2009.203
"""
demand_and_exchange_rxns = set(model.exchanges)
return [rxn for rxn in demand_and_exchange_rxns
if any(c in rxn.get_compartments() for c in ['e'])]
