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Sync fbapkg/kbasemediapkg.py from freiburgermsu fork #65

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Sync fbapkg/kbasemediapkg.py from freiburgermsu fork #65

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32 changes: 12 additions & 20 deletions modelseedpy/fbapkg/kbasemediapkg.py
100644 → 100755
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Original file line number Diff line number Diff line change
Expand Up @@ -2,18 +2,15 @@

from __future__ import absolute_import

import logging
from modelseedpy.fbapkg.basefbapkg import BaseFBAPkg
from modelseedpy.core.fbahelper import FBAHelper # !!! imported but not used
from modelseedpy.core.fbahelper import FBAHelper # !!! imported but not used
from numpy import log as ln
import logging

logger = logging.getLogger(__name__)


class KBaseMediaPkg(BaseFBAPkg):
"""
Base class for FBA packages
"""

def __init__(self, model):
BaseFBAPkg.__init__(self, model, "kbase media", {}, {})
self.current_media = None
Expand Down Expand Up @@ -46,30 +43,25 @@ def build_package(
self.parameters["media"] and self.parameters["media"].name == "Complete"
) and self.parameters["default_uptake"] == 0:
self.parameters["default_uptake"] = 100

# First initializing all exchanges to default uptake and excretion
exchange_list = self.modelutl.exchange_list()
for reaction in exchange_list:
if -1 * self.parameters["default_uptake"] > reaction.upper_bound:
reaction.upper_bound = self.parameters["default_excretion"]
reaction.lower_bound = -1 * self.parameters["default_uptake"]
else:
reaction.lower_bound = -1 * self.parameters["default_uptake"]
reaction.upper_bound = self.parameters["default_excretion"]

#First initializing all exchanges to default uptake and excretion
for reaction in self.modelutl.exchange_list():
reaction.lower_bound = -self.parameters["default_uptake"]
reaction.upper_bound = self.parameters["default_excretion"]

# Now constraining exchanges for specific compounds specified in the media
if self.parameters["media"]:
exchange_hash = self.modelutl.exchange_hash()
self.modelutl.build_metabolite_hash()
# self.modelutl.build_metabolite_hash()
for mediacpd in self.parameters["media"].mediacompounds:
mets = self.modelutl.find_met(mediacpd.id)
if len(mets) > 0:
for met in mets:
if met in exchange_hash:
exchange_hash[met].lower_bound = -1 * mediacpd.maxFlux
exchange_hash[met].upper_bound = -1 * mediacpd.minFlux
exchange_hash[met].lower_bound = -mediacpd.maxFlux
exchange_hash[met].upper_bound = -mediacpd.minFlux
if (
self.pkgmgr != None
self.pkgmgr is not None
and "FullThermoPkg" in self.pkgmgr.packages
):
logger.info("FullThermo constrained compound: ", met.id)
Expand Down
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