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Fixing correct use of inheritance for build_constraint() function #155

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Merged
Fxe merged 2 commits into from
Apr 18, 2025
Merged

Fixing correct use of inheritance for build_constraint() function #155

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264e753
Fixing correct use of inheritance for build_constraint() function
samseaver Apr 17, 2025
217edfd
Another fix for incorrect call
samseaver Apr 17, 2025
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58 changes: 27 additions & 31 deletions modelseedpy/fbapkg/flexiblebiomasspkg.py
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Original file line number Diff line number Diff line change
Expand Up @@ -77,11 +77,11 @@ def build_package(self, parameters):
newrxns = []
class_coef = {"rna": {}, "dna": {}, "protein": {}, "energy": {}}
refcpd = {
"cpd00001": None,
"cpd00009": None,
"cpd00012": None,
"cpd00067": None,
"cpd00002": None,
"cpd00001": None, # Water
"cpd00009": None, # Orthophosphate
"cpd00012": None, # Pyrophosphate
"cpd00067": None, # Proton
"cpd00002": None, # ATP
}
# Finding all reference compounds in the model
msid_hash = self.modelutl.msid_hash()
Expand All @@ -94,10 +94,10 @@ def build_package(self, parameters):
met_class[metabolite] = None
msid = MSModelUtil.metabolite_msid(metabolite)
if (
msid != "cpd11416"
and msid != "cpd11463"
and msid != "cpd11462"
and msid != "cpd11461"
msid != "cpd11416" # Biomass
and msid != "cpd11463" # Protein
and msid != "cpd11462" # RNA
and msid != "cpd11461" # DNA
and msid != None
):
if msid in refcpd:
Expand Down Expand Up @@ -209,7 +209,7 @@ def build_package(self, parameters):
self.build_constraint(
self.new_reactions[met_class + "_flex"], "flxcls"
)
if parameters["add_total_biomass_constraint"]:
if self.parameters["add_total_biomass_constraint"]:
self.build_constraint(self.parameters["bio_rxn"], "flxbio")

def build_variable(self, object, type): # !!! can the function be removed?
Expand Down Expand Up @@ -254,7 +254,7 @@ def build_constraint(self, cobra_obj, obj_type):
if abs(massdiff) > 0.00001:
coef[rxn.forward_variable] = massdiff
coef[rxn.reverse_variable] = -massdiff
return BaseFBAPkg.build_constraint(self, obj_type, 0, 0, coef, cobra_obj)
return super().build_constraint(obj_type, 0, 0, coef, cobra_obj)
elif obj_type == "flxcpd" or obj_type == "flxcls":
first_entry = None
second_entry = None
Expand Down Expand Up @@ -293,7 +293,7 @@ def build_constraint(self, cobra_obj, obj_type):
# If the value is positive, lock in the forward variable and set the reverse to zero
if first_entry > 0:
if product:
const = self.build_constraint(
const = super().build_constraint(
"f" + obj_type,
0,
0,
Expand All @@ -302,7 +302,7 @@ def build_constraint(self, cobra_obj, obj_type):
)
object.lower_bound = 0
else:
const = self.build_constraint(
const = super().build_constraint(
"f" + obj_type,
0,
0,
Expand All @@ -313,7 +313,7 @@ def build_constraint(self, cobra_obj, obj_type):
# If the value is negative, lock in the reverse variable and set the forward to zero
elif first_entry < 0:
if product:
const = self.build_constraint(
const = super().build_constraint(
"r" + obj_type,
0,
0,
Expand All @@ -322,7 +322,7 @@ def build_constraint(self, cobra_obj, obj_type):
)
object.upper_bound = 0
else:
const = self.build_constraint(
const = super().build_constraint(
"r" + obj_type,
0,
0,
Expand All @@ -337,8 +337,7 @@ def build_constraint(self, cobra_obj, obj_type):
elif second_entry >= 0:
if first_entry >= 0:
if product:
const = BaseFBAPkg.build_constraint(
self,
const = super().build_constraint(
"f" + obj_type,
0,
None,
Expand All @@ -347,17 +346,15 @@ def build_constraint(self, cobra_obj, obj_type):
)
object.lower_bound = 0
if first_entry > 0:
BaseFBAPkg.build_constraint(
self,
super().build_constraint(
"r" + obj_type,
0,
None,
{biovar: -first_entry, object.forward_variable: 1},
cobra_obj,
)
else:
const = BaseFBAPkg.build_constraint(
self,
const = super().build_constraint(
"f" + obj_type,
0,
None,
Expand All @@ -366,8 +363,7 @@ def build_constraint(self, cobra_obj, obj_type):
)
object.upper_bound = 0
if first_entry > 0:
BaseFBAPkg.build_constraint(
self,
super().build_constraint(
"r" + obj_type,
0,
None,
Expand All @@ -376,29 +372,29 @@ def build_constraint(self, cobra_obj, obj_type):
)
else:
if product:
const = self.build_constraint(
const = super().build_constraint(
"f" + obj_type,
0,
None,
{biovar: second_entry, object.forward_variable: -1},
cobra_obj,
)
self.build_constraint(
super().build_constraint(
"r" + obj_type,
0,
None,
{biovar: -first_entry, object.reverse_variable: -1},
cobra_obj,
)
else:
const = self.build_constraint(
const = super().build_constraint(
"f" + obj_type,
0,
None,
{biovar: second_entry, object.reverse_variable: -1},
cobra_obj,
)
self.build_constraint(
super().build_constraint(
"r" + obj_type,
0,
None,
Expand All @@ -408,23 +404,23 @@ def build_constraint(self, cobra_obj, obj_type):
else:
if second_entry < 0:
if product:
const = self.build_constraint(
const = super().build_constraint(
"f" + obj_type,
0,
None,
{biovar: second_entry, object.reverse_variable: 1},
cobra_obj,
)
else:
const = self.build_constraint(
const = super().build_constraint(
"f" + obj_type,
0,
None,
{biovar: second_entry, object.forward_variable: 1},
cobra_obj,
)
if product:
self.build_constraint(
super().build_constraint(
"r" + obj_type,
0,
None,
Expand All @@ -433,7 +429,7 @@ def build_constraint(self, cobra_obj, obj_type):
)
object.lower_bound = 0
else:
self.build_constraint(
super().build_constraint(
"r" + obj_type,
0,
None,
Expand Down
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