diff --git a/modelseedpy/fbapkg/fullthermopkg.py b/modelseedpy/fbapkg/fullthermopkg.py index 2842b1fb..397e9bd8 100644 --- a/modelseedpy/fbapkg/fullthermopkg.py +++ b/modelseedpy/fbapkg/fullthermopkg.py @@ -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): @@ -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, [], @@ -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