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Fullthermo #9

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135 changes: 71 additions & 64 deletions modelseedpy/fbapkg/fullthermopkg.py
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Original file line number Diff line number Diff line change
Expand Up @@ -13,127 +13,134 @@ class FullThermoPkg(BaseFBAPkg):
@staticmethod
def default_concentration():
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-07,3.16228E-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-07,3.16228E-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
}

@staticmethod
def default_deltaG_error():
return {
"cpd00067":0#KJ/mol - H delta G is based on pH and so has no error
"cpd00067":0 #KJ/mol - H delta G is based on pH and so has no error
}

@staticmethod
def default_compartment_potential():
return {
"e0":0,#Extracellular MUST be the zero reference for compartment electrochemical potential (so community modeling works)
"c0":-160#mV = 0.33 (pHint - pHext) - 143.33 where pHint = 7 and pHext = 6.5
"e0":0, #Extracellular MUST be the zero reference for compartment electrochemical potential (so community modeling works)
"c0":-160 #mV = 0.33 (pHint - pHext) - 143.33 where pHint = 7 and pHext = 6.5
}

def __init__(self,model):
BaseFBAPkg.__init__(self,model,"full thermo",{"logconc":"metabolite","dgerr":"metabolite"},{"potc":"metabolite"})
self.pkgmgr.addpkgs(["SimpleThermoPkg"])

def build_package(self,parameters, verbose = True):
self.validate_parameters(parameters,["modelseed_path"],{
"default_max_conc":0.02,#M
"default_min_conc":0.000001,#M
"default_max_error":5,#KJ/mol
def build_package(self,
parameters: dict, # simulation parameters
verbose: bool = True
):
# amalgamate default and specified paramters
self.validate_parameters(parameters, # specified parameters
["modelseed_db_path"] # required parameter for uploading the ModelSEED Database
,{ # default parameters
"default_max_conc":0.02, #M
"default_min_conc":0.000001, #M
"default_max_error":5, #KJ/mol
"custom_concentrations":{},
"custom_deltaG_error":{},
"compartment_potential":{},
"temperature":298,#K
"custom_compartment_potential":{},
"temperature":298, #K
"filter":None,
"infeasible_model": False,
'dgbin':False
})
self.parameters["modelseed_api"] = FBAHelper.get_modelseed_db_api(self.parameters["modelseed_path"])
self.parameters["modelseed_api"] = FBAHelper.get_modelseed_db_api(self.parameters["modelseed_db_path"])
# implements an accommodating variable to encourage feasibility
simple_thermo_parameters = {
"filter":self.parameters["filter"],
"min_potential":-100000,#KJ/mol
"max_potential":100000,#KJ/mol
"min_potential":-100000, #KJ/mol
"max_potential":100000, #KJ/mol
'dgbin':self.parameters['dgbin']
}

if self.parameters['infeasible_model']:
simple_thermo_parameters['dgbin'] = True
self.pkgmgr.getpkg("SimpleThermoPkg").build_package(simple_thermo_parameters)
self.parameters["combined_custom_concentrations"] = FullThermoPkg.default_concentration()

self.parameters["concentrations"] = FullThermoPkg.default_concentration()
for cpd in self.parameters["custom_concentrations"]:
self.parameters["combined_custom_concentrations"][cpd] = self.parameters["custom_concentrations"][cpd]
self.parameters["combined_custom_deltaG_error"] = FullThermoPkg.default_deltaG_error()
self.parameters["concentrations"][cpd] = self.parameters["custom_concentrations"][cpd]
self.parameters["deltaG_error"] = FullThermoPkg.default_deltaG_error()
for cpd in self.parameters["custom_deltaG_error"]:
self.parameters["combined_custom_deltaG_error"][cpd] = self.parameters["custom_deltaG_error"][cpd]
self.parameters["combined_custom_comp_pot"] = FullThermoPkg.default_compartment_potential()
for cmp in self.parameters["compartment_potential"]:
self.parameters["combined_custom_comp_pot"][cmp] = self.parameters["compartment_potential"][cmp]
self.parameters["deltaG_error"][cpd] = self.parameters["custom_deltaG_error"][cpd]
self.parameters["compartment_potential"] = FullThermoPkg.default_compartment_potential()
for cmp in self.parameters["custom_compartment_potential"]:
self.parameters["compartment_potential"][cmp] = self.parameters["custom_compartment_potential"][cmp]

msid_hash = {}
for metabolite in self.model.metabolites:
msid = FBAHelper.modelseed_id_from_cobra_metabolite(metabolite)
if msid != None:
if msid not in msid_hash:
msid_hash[msid] = {}
msid_hash[msid][metabolite.id] = metabolite
#Build concentration variable
self.build_variable(metabolite,"logconc")
#Build error variable
self.build_variable(metabolite,"dgerr")
#Build the potential constraint
self.build_constraint(metabolite, verbose)

self._build_variable(metabolite,"logconc") #Build concentration variable
self._build_variable(metabolite,"dgerr") #Build error variable
self._build_constraint(metabolite, verbose) #Build the potential constraint

def build_variable(self,object,type):
msid = FBAHelper.modelseed_id_from_cobra_metabolite(object)
if type == "logconc" and msid != "cpd00001":#Do not make a concentration variable for water
def build_variable(self,cobra_obj,obj_type):
msid = FBAHelper.modelseed_id_from_cobra_metabolite(cobra_obj)
if obj_type == "logconc" and msid != "cpd00001": #Do not make a concentration variable for water
lb = ln(self.parameters["default_min_conc"])
ub = ln(self.parameters["default_max_conc"])
if object.id in self.parameters["combined_custom_concentrations"]:
lb = ln(self.parameters["combined_custom_concentrations"][object.id][0])
ub = ln(self.parameters["combined_custom_concentrations"][object.id][1])
return BaseFBAPkg.build_variable(self,"logconc",lb,ub,"continuous",object)
elif type == "dgerr":
if cobra_obj.id in self.parameters["concentrations"]:
lb = ln(self.parameters["concentrations"][cobra_obj.id][0])
ub = ln(self.parameters["concentrations"][cobra_obj.id][1])
return BaseFBAPkg.build_variable(self,"logconc",lb,ub,"continuous",cobra_obj)
elif obj_type == "dgerr":
ub = self.parameters["default_max_error"]
if object.id in self.parameters["combined_custom_deltaG_error"]:
ub = self.parameters["combined_custom_deltaG_error"][object.id]
return BaseFBAPkg.build_variable(self,"dgerr",-1*ub,ub,"continuous",object)
if cobra_obj.id in self.parameters["deltaG_error"]:
ub = self.parameters["deltaG_error"][cobra_obj.id]
return BaseFBAPkg.build_variable(self,"dgerr",-1*ub,ub,"continuous",cobra_obj)

def build_constraint(self,object, verbose):
def build_constraint(self, cobra_obj, verbose):
#potential(i) (KJ/mol) = deltaG(i) (KJ/mol) + R * T(K) * lnconc(i) + charge(i) * compartment_potential
if object.id not in self.pkgmgr.getpkg("SimpleThermoPkg").variables["potential"]:
if cobra_obj.id not in self.pkgmgr.getpkg("SimpleThermoPkg").variables["potential"]:
return None
msid = FBAHelper.modelseed_id_from_cobra_metabolite(object)
msid = FBAHelper.modelseed_id_from_cobra_metabolite(cobra_obj)
if msid == None:
if verbose:
print(object.id+" has no modelseed ID!")
print(cobra_obj.id+" has no modelseed ID!")
return None
mscpd = self.parameters["modelseed_api"].get_seed_compound(msid)
if mscpd is None:
if verbose:
print(object.id+" has modelseed ID "+msid+" but cannot be found in ModelSEED DB!")
print(cobra_obj.id+" has modelseed ID "+msid+" but cannot be found in ModelSEED DB!")
return None
if mscpd.deltag == 10000000:
if verbose:
print(object.id+" has modelseed ID "+msid+" but does not have a valid deltaG!")
print(cobra_obj.id+" has modelseed ID "+msid+" but does not have a valid deltaG!")
return None
Faraday = physical_constants['Faraday constant'][0]#C/mol
compartment_potential = 0
if object.compartment in self.parameters["combined_custom_comp_pot"]:
compartment_potential = self.parameters["combined_custom_comp_pot"][object.compartment]
constant = mscpd.deltag/calorie + object.charge*Faraday*compartment_potential/kilo/kilo
if cobra_obj.compartment in self.parameters["combined_custom_comp_pot"]:
compartment_potential = self.parameters["combined_custom_comp_pot"][cobra_obj.compartment]
constant = mscpd.deltag/calorie + cobra_obj.charge*Faraday*compartment_potential/kilo/kilo
coef = {
self.pkgmgr.getpkg("SimpleThermoPkg").variables["potential"][object.id]:1,
self.variables["dgerr"][object.id]:-1
self.pkgmgr.getpkg("SimpleThermoPkg").variables["potential"][cobra_obj.id]:1,
self.variables["dgerr"][cobra_obj.id]:-1
}
if msid != "cpd00001":#Water concentration should not contribute to potential
coef[self.variables["logconc"][object.id]] = -1*R/kilo*self.parameters["temperature"]
return BaseFBAPkg.build_constraint(self,"potc",constant,constant,coef,object)
coef[self.variables["logconc"][cobra_obj.id]] = -1*R/kilo*self.parameters["temperature"]
return BaseFBAPkg.build_constraint(self,"potc",constant,constant,coef,cobra_obj)