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Sync fbapkg/reactionusepkg.py from freiburgermsu fork #69

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261 changes: 131 additions & 130 deletions modelseedpy/fbapkg/reactionusepkg.py
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Original file line number Diff line number Diff line change
@@ -1,130 +1,131 @@
# -*- coding: utf-8 -*-

from __future__ import absolute_import
import logging

logger = logging.getLogger(__name__)
from optlang.symbolics import Zero, add # !!! add is never used
from modelseedpy.fbapkg.basefbapkg import BaseFBAPkg
from modelseedpy.core.fbahelper import FBAHelper

# Base class for FBA packages
class ReactionUsePkg(BaseFBAPkg):
def __init__(self, model):
BaseFBAPkg.__init__(
self,
model,
"reaction use",
{"fu": "reaction", "ru": "reaction"},
{
"fu": "reaction",
"ru": "reaction",
"exclusion": "none",
"urev": "reaction",
},
)

def build_package(self, rxn_filter=None, reversibility=False):
for rxn in self.model.reactions:
# Checking that reaction passes input filter if one is provided
if rxn_filter == None:
self.build_variable(rxn, "=")
self.build_constraint(rxn, reversibility)
elif rxn.id in rxn_filter:
self.build_variable(rxn, rxn_filter[rxn.id])
self.build_constraint(rxn, reversibility)

def build_variable(self, cobra_obj, direction):
variable = None
if (
(direction == ">" or direction == "=")
and cobra_obj.upper_bound > 0
and cobra_obj.id not in self.variables["fu"]
):
variable = BaseFBAPkg.build_variable(self, "fu", 0, 1, "binary", cobra_obj)
if (
(direction == "<" or direction == "=")
and cobra_obj.lower_bound < 0
and cobra_obj.id not in self.variables["ru"]
):
variable = BaseFBAPkg.build_variable(self, "ru", 0, 1, "binary", cobra_obj)
return variable

def build_constraint(self, cobra_obj, reversibility):
constraint = None
if (
cobra_obj.id not in self.constraints["fu"]
and cobra_obj.id in self.variables["fu"]
):
constraint = BaseFBAPkg.build_constraint(
self,
"fu",
0,
None,
{
self.variables["fu"][cobra_obj.id]: 1000,
cobra_obj.forward_variable: -1,
},
cobra_obj,
)
if (
cobra_obj.id not in self.constraints["ru"]
and cobra_obj.id in self.variables["ru"]
):
constraint = BaseFBAPkg.build_constraint(
self,
"ru",
0,
None,
{
self.variables["ru"][cobra_obj.id]: 1000,
cobra_obj.reverse_variable: -1,
},
cobra_obj,
)
if all(
[
reversibility,
cobra_obj.id in self.variables["ru"],
cobra_obj.id in self.variables["fu"],
]
):
constraint = BaseFBAPkg.build_constraint(
self,
"urev",
None,
1,
{
self.variables["ru"][cobra_obj.id]: 1,
self.variables["fu"][cobra_obj.id]: 1,
},
cobra_obj,
)
return constraint

def build_exclusion_constraint(self, flux_values=None):
flux_values = flux_values or FBAHelper.compute_flux_values_from_variables(
self.model
)
count = len(self.constraints["exclusion"])
solution_coef = {}
solution_size = 0
for rxnid, flux in flux_values.items():
if flux > Zero:
solution_size += 1
solution_coef[self.variables["fu"][rxnid]] = 1
elif flux < -1 * Zero:
solution_size += 1
solution_coef[self.variables["ru"][rxnid]] = 1
if len(solution_coef) > 0:
const_name = "exclusion." + str(count + 1)
self.constraints["exclusion"][const_name] = self.model.problem.Constraint(
Zero, lb=None, ub=(solution_size - 1), name=const_name
)
self.model.add_cons_vars(self.constraints["exclusion"][const_name])
self.model.solver.update()
self.constraints["exclusion"][const_name].set_linear_coefficients(
solution_coef
)
return self.constraints["exclusion"][const_name]
return None
# -*- coding: utf-8 -*-

from __future__ import absolute_import
import logging

logger = logging.getLogger(__name__)
from optlang.symbolics import Zero, add # !!! add is never used
from modelseedpy.fbapkg.basefbapkg import BaseFBAPkg

# Base class for FBA packages
class ReactionUsePkg(BaseFBAPkg):
def __init__(self, model):
BaseFBAPkg.__init__(
self,
model,
"reaction use",
{"fu": "reaction", "ru": "reaction"},
{
"fu": "reaction",
"ru": "reaction",
"exclusion": "none",
"urev": "reaction",
},
)

def build_package(self, rxn_filter=None, reversibility=False):
for rxn in self.model.reactions:
# Checking that reaction passes input filter if one is provided
if rxn_filter == None:
self.build_variable(rxn, "=")
self.build_constraint(rxn, reversibility)
elif rxn.id in rxn_filter:
self.build_variable(rxn, rxn_filter[rxn.id])
self.build_constraint(rxn, reversibility)

def build_variable(self, cobra_obj, direction):
variable = None
if (
(direction == ">" or direction == "=")
and cobra_obj.upper_bound > 0
and cobra_obj.id not in self.variables["fu"]
):
variable = BaseFBAPkg.build_variable(self, "fu", 0, 1, "binary", cobra_obj)
if (
(direction == "<" or direction == "=")
and cobra_obj.lower_bound < 0
and cobra_obj.id not in self.variables["ru"]
):
variable = BaseFBAPkg.build_variable(self, "ru", 0, 1, "binary", cobra_obj)
return variable

def build_constraint(self, cobra_obj, reversibility):
constraint = None
if (
cobra_obj.id not in self.constraints["fu"]
and cobra_obj.id in self.variables["fu"]
):
constraint = BaseFBAPkg.build_constraint(
self,
"fu",
0,
None,
{
self.variables["fu"][cobra_obj.id]: 1000,
cobra_obj.forward_variable: -1,
},
cobra_obj,
)
if (
cobra_obj.id not in self.constraints["ru"]
and cobra_obj.id in self.variables["ru"]
):
constraint = BaseFBAPkg.build_constraint(
self,
"ru",
0,
None,
{
self.variables["ru"][cobra_obj.id]: 1000,
cobra_obj.reverse_variable: -1,
},
cobra_obj,
)
if all(
[
reversibility,
cobra_obj.id in self.variables["ru"],
cobra_obj.id in self.variables["fu"],
]
):
constraint = BaseFBAPkg.build_constraint(
self,
"urev",
None,
1,
{
self.variables["ru"][cobra_obj.id]: 1,
self.variables["fu"][cobra_obj.id]: 1,
},
cobra_obj,
)
return constraint

def build_exclusion_constraint(self, flux_values=None):
# Deferred import to avoid circular dependency
from modelseedpy.core.fbahelper import FBAHelper
flux_values = flux_values or FBAHelper.compute_flux_values_from_variables(
self.model
)
count = len(self.constraints["exclusion"])
solution_coef = {}
solution_size = 0
for rxnid, flux in flux_values.items():
if flux > Zero:
solution_size += 1
solution_coef[self.variables["fu"][rxnid]] = 1
elif flux < -1 * Zero:
solution_size += 1
solution_coef[self.variables["ru"][rxnid]] = 1
if len(solution_coef) > 0:
const_name = "exclusion." + str(count + 1)
self.constraints["exclusion"][const_name] = self.model.problem.Constraint(
Zero, lb=None, ub=(solution_size - 1), name=const_name
)
self.model.add_cons_vars(self.constraints["exclusion"][const_name])
self.model.solver.update()
self.constraints["exclusion"][const_name].set_linear_coefficients(
solution_coef
)
return self.constraints["exclusion"][const_name]
return None
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