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Sync fbapkg/fullthermopkg.py from freiburgermsu fork #63

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70 changes: 25 additions & 45 deletions modelseedpy/fbapkg/fullthermopkg.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,51 +13,21 @@
# Base class for FBA packages
class FullThermoPkg(BaseFBAPkg):
@staticmethod
def default_concentration():
def default_concentrations():
return {
"cpd00067_c0": [0.0000001, 0.0000001], # M H+ - equivalent to pHint = 7
"cpd00007_c0": [1e-07, 8.2e-06], # M O2 instracellular
"cpd00011_c0": [1e-08, 0.0014], # M CO2 instracellular
"cpd00067_e0": [
3.16228e-08,
3.16228e-07,
], # M H+ - equivalent to pHext = 6.5
"cpd00009_e0": [
0.056,
0.056,
], # Extracellular phosphate - overridden by media when media concentration is given
"cpd00048_e0": [
0.0030,
0.0030,
], # Extracellular sulfate - overridden by media when media concentration is given
"cpd00013_e0": [
0.019,
0.019,
], # Extracellular ammonia - overridden by media when media concentration is given
"cpd00971_e0": [
0.16,
0.16,
], # Extracellular sodium - overridden by media when media concentration is given
"cpd00205_e0": [
0.022,
0.022,
], # Extracellular potassium - overridden by media when media concentration is given
"cpd10515_e0": [
0.062,
0.062,
], # Extracellular Fe2+ - overridden by media when media concentration is given
"cpd00011_e0": [
0.00010,
0.00010,
], # Extracellular CO2 - overridden by media when media concentration is given
"cpd00007_e0": [
8.2e-06,
8.2e-06,
], # Extracellular O2 - overridden by media when media concentration is given
"cpd00027_e0": [
0.020,
0.020,
], # Extracellular glucose - overridden by media when media concentration is given
"cpd00067_c0":[0.0000001,0.0000001], #M H+ - equivalent to pHint = 7
"cpd00007_c0":[1E-07,8.2E-06], #M O2 instracellular
"cpd00011_c0":[1E-08,0.0014], #M CO2 instracellular
"cpd00067_e0":[3.16228E-08,3.16228E-07], #M H+ - equivalent to pHext = 6.5
"cpd00009_e0":[0.056,0.056], #Extracellular phosphate - overridden by media when media concentration is given
"cpd00048_e0":[0.0030,0.0030], #Extracellular sulfate - overridden by media when media concentration is given
"cpd00013_e0":[0.019,0.019], #Extracellular ammonia - overridden by media when media concentration is given
"cpd00971_e0":[0.16,0.16], #Extracellular sodium - overridden by media when media concentration is given
"cpd00205_e0":[0.022,0.022], #Extracellular potassium - overridden by media when media concentration is given
"cpd10515_e0":[0.062,0.062], #Extracellular Fe2+ - overridden by media when media concentration is given
"cpd00011_e0":[0.00010,0.00010], #Extracellular CO2 - overridden by media when media concentration is given
"cpd00007_e0":[8.2E-06,8.2E-06], #Extracellular O2 - overridden by media when media concentration is given
"cpd00027_e0":[0.020,0.020] #Extracellular glucose - overridden by media when media concentration is given
}

def __init__(self, model):
Expand All @@ -70,7 +40,16 @@ def __init__(self, model):
)
self.pkgmgr.addpkgs(["SimpleThermoPkg"])

def build_package(self, parameters, verbose=True):
def build_package(self,
parameters: dict, # simulation parameters
verbose: bool = True
):
# define hard-coded defaults
self.parameters["deltaG_error"] = FullThermoPkg.default_deltaG_error()
self.parameters["compartment_potential"] = FullThermoPkg.default_compartment_potentials()
self.parameters["concentrations"] = FullThermoPkg.default_concentrations()

# amalgamate default and specified paramters
self.validate_parameters(
parameters,
[],
Expand Down Expand Up @@ -119,6 +98,7 @@ def build_package(self, parameters, verbose=True):
if msid not in msid_hash:
msid_hash[msid] = {}
msid_hash[msid][metabolite.id] = metabolite

# Build concentration variable
self.build_logconc_variable(metabolite)
# Build error variable
Expand Down
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