djinnome / rxneqn

This is code to support the computation of stoichiometric equations for the Thermodynamic Electon Equivalents Model (TEEM) developed by Rittman and McCarty.

RxnEqn

This is code to support the computation of stoichiometric equations for the Thermodynamic Electon Equivalents Model (TEEM) developed by Rittman and McCarty.

Installation

To install:

git clone https://github.com/djinnome/rxneqn.git
cd rxneqn
pip install .

Usage

ChemicalFormula

>>> from rxneqn import ChemicalFormula
>>> chemical_formula = 'C6H12O5.5N'
>>> cf = ChemicalFormula(chemical_formula)
>>> cf.get_chemical_composition()

C            6
Charge       0
H           12
N            1
O         11/2
dtype: object

Mixture

>>> from rxneqn import Mixture
>>> mix = Mixture('3 C6H12O6 + 4 NO2-')
>>> mix.subtract_from_mixture(Mixture('5 NO2- + H+'))

3 C6H12O6

Reaction

>>> from rxneqn import Reaction
>>> rxn = Reaction('1/4 CO2 + 1/12NH3 + H+  ==> 1/12 CH3CHNH2COOH + 1/3 H2O + OH-')
>>> rxn -  Reaction('CO2 + H2O ==> 4 HCO3')

H+ + 4 HCO3 + 1/12 NH3 ==> 1/12 CH3CHNH2COOH + 3/4 CO2 + 4/3 H2O + OH-

rxn.normalize()

3 CO2 + 12 H+ + NH3 ==> CH3CHNH2COOH + 4 H2O + 12 OH-

HalfReactionBalancer

>>> from rxneqn import HalfReactionBalancer
>>> alanine = 'CH3CHNH2COOH'
>>> carbon_dioxide = 'CO2'
>>> nitrogen_source = 'NH3'
>>> half_rxn = HalfReactionBalancer() #carbon_dioxide, alanine, 'C', nitrogen_source)
>>> truth_eqn = """1/24 C6H12O6 + 1/4 H2O ==> 1/4 CO2 + E- + H+
E- + 6/5 H+ + 1/5 NO3- ==> 3/5 H2O + 1/10 N2
1/24 C6H12O6 + 1/5 H+ + 1/5 NO3- ==> 1/4 CO2 + 7/20 H2O + 1/10 N2
1/4 CO2 + E- + H+ + 1/12 NH3 ==> 1/12 CH3CHNH2COOH + 1/3 H2O
1/5 CO2 + E- + H+ + 1/20 HCO3- + 1/20 NH4+ ==> 1/20 C5H7O2N + 9/20 H2O
1/8 CO2 + E- + H+ ==> 1/8 CH4 + 1/4 H2O
1/6 CO2 + E- + H+ + 1/12 HCO3- + 1/12 NH4+ ==> 1/12 CH3CHNH2COOH + 5/12 H2O
1/12 CH3CHNH2COOH + 1/6 H2O ==> 1/8 CH4 + 1/24 CO2 + 1/12 HCO3- + 1/12 NH4+
1/5 CO2 + E- + H+ + 1/10 HCO3- ==> 1/10 CH3COCOO- + 2/5 H2O
1/4 CO2 + E- + H+ + 1/12 NH3 ==> 1/12 CH3CHNH2COOH + 1/3 H2O
1/6 CO2 + E- + H+ + 1/12 HCO3- + 1/12 NH4+ ==> 1/12 CH3CHNH2COOH + 5/12 H2O
1/12 CO2 + E- + H+ + 1/6 HCO3- + 1/12 NH4+ ==> 1/12 CH3CHNH2COO- + 1/2 H2O""".split('\n')
>>> eqn = {}
>>> eqn[13] = half_rxn.balance_half_reaction('C6H12O6', 'CO2')
>>> eqn[14] = half_rxn.balance_half_reaction('NO3-', 'N2',nitrogen_source='NO3-')
>>> eqn[15] = eqn[13] +  eqn[14] 
>>> eqn[16] = half_rxn.balance_half_reaction(carbon_dioxide, alanine, nitrogen_source)
>>> eqn[17] = half_rxn.balance_half_reaction('CO2', 'C5H7O2N','NH4+')
>>> table3 = {'O-12': '1/8 CO2 + H+ + E- ==> 1/8 CH4 + 1/4 H2O',
         'O-2': '1/6 CO2 + 1/12 NH4+ + 1/12 HCO3- + H+ + E- ==> 1/12 CH3CHNH2COOH + 5/12 H2O',
         'O-3': str(half_rxn.balance_half_reaction('CO2','C6H5COO-'))}

>>> eqn[18] = Reaction(table3['O-12'])
>>> eqn[19] = Reaction(table3['O-2'])
>>> eqn[20] = eqn[18] - eqn[19]
>>> eqn[21] = half_rxn.balance_half_reaction('CO2','CH3COCOO-')
>>> eqn[22] = half_rxn.balance_half_reaction('CO2','CH3CHNH2COOH','NH3')
>>> eqn[23] = half_rxn.balance_half_reaction('CO2','CH3CHNH2COOH','NH4+')
>>> eqn[24] = half_rxn.balance_half_reaction('CO2','CH3CHNH2COO-','NH4+')

>>> k = 0

>>> for i in eqn:
    	assert( str(eqn[i]) == truth_eqn[k] )
    	k += 1
>>> print("{} out of {} tests passed".format(k, len(eqn))

12 out of 12 tests passed