6.1.1.6.1.2. pytfa.thermo.metabolite

Thermodynamic computations for metabolites

6.1.1.6.1.2.1. Module Contents

6.1.1.6.1.2.1.1. Classes

MetaboliteThermo

A class representing the thermodynamic values of a enzyme

6.1.1.6.1.2.1.2. Attributes

CPD_PROTON

DEFAULT_VAL

pytfa.CPD_PROTON = cpd00067
pytfa.DEFAULT_VAL
class pytfa.MetaboliteThermo(metData, pH, ionicStr, temperature=std.TEMPERATURE_0, min_ph=std.MIN_PH, max_ph=std.MAX_PH, debye_huckel_b=std.DEBYE_HUCKEL_B_0, thermo_unit='kJ/mol', debug=False)

A class representing the thermodynamic values of a enzyme

Parameters

  • metData (dict) – A dictionary containing the values for the enzyme, from the thermodynamic database

  • pH (float) – The pH of the enzyme’s compartment

  • ionicStr (float) – The ionic strength of the enzyme’s compartment

  • temperature –

  • min_ph –

  • max_ph –

  • debye_huckel_b –

  • thermo_unit (string) – The unit used in metData’s values

  • debug (bool) – Optional If set to True, some debugging values will be printed. This is only useful for development or debugging purposes.

Note

The values are automatically computed on class creation. Usually you don’t have to call any methods defined by this class, but only to access the attributes you need.

The available attributes are :

Since the reactions expose similar values through a dictionnary, it is better to access the attributes aforementionned of this class as if it was a dictionnary : enzyme.thermo['pH'].

__getitem__(self, key)
__repr__(self)

Return repr(self).

keys(self)
values(self)
items(self)
__cmp__(self, dict_)
__contains__(self, item)
__iter__(self)
__unicode__(self)
calcDGis(self)

Calculate the transformed Gibbs energy of formation of specie with given pH and ionic strength using formula given by Goldberg and Tewari, 1991

Equation 4.5-6 in Alberty’s book

Returns

DG_is for the enzyme

Return type

float

calcDGsp(self)

Calculate the transformed Gibbs energy of formation of specie with given pH and ionic strength using formula given by Goldberg and Tewari, 1991

Equation 4.4-10 in Alberty’s book

Returns

DG_sp for the enzyme

Return type

float

calc_potential(self)

Calculate the binding polynomial of a specie, with pK values

Returns

The potential of the enzyme

Return type

float

get_pka(self)

Get the pKas of the enzyme

Returns

The pKas of the enzyme

Return type

list(float)

_calc_pka(self, pka, sigmanusq)
calcDGspA(self)

Calculates deltaGf, charge and nH of the specie when it is at least protonated state based on MFAToolkit compound data for the pKa values within the range considered (MIN_pH to MAX_pH).

These values are used as the starting point for Alberty’s calculations.

Returns

deltaGspA, sp_charge and sp_nH

Return type

tuple(float, float, int)