6.1.1.6.1.3. pytfa.thermo.reaction

Thermodynamic computations for reactions

6.1.1.6.1.3.1. Module Contents

6.1.1.6.1.3.1.1. Functions

calcDGtpt_rhs(reaction, compartmentsData, thermo_units)

Calculates the RHS of the deltaG constraint, i.e. the sum of the

calcDGR_cues(reaction, reaction_cues_data)

Calculates the deltaG reaction and error of the reaction using the

calcDGF_cues(cues, reaction_cues_data)

Calculates the deltaG formation and error of the compound using its

get_debye_huckel_b(T)

The Debye-Huckel A and B do depend on the temperature
pytfa.calcDGtpt_rhs(reaction, compartmentsData, thermo_units)

Calculates the RHS of the deltaG constraint, i.e. the sum of the non-concentration terms

Parameters

  • reaction (cobra.thermo.reaction.Reaction) – The reaction to compute the data for

  • compartmentsData (dict(float)) – Data of the compartments of the cobra_model

  • thermo_units (str) – The thermodynamic database of the cobra_model

Returns

deltaG_tpt and the breakdown of deltaG_tpt

Return type

tuple(float, dict(float))

Example:

ATP Synthase reaction:

reaction = cpd00008 + 4 cpd00067 + cpd00009 <=> cpd00002 + 3 cpd00067 + cpd00001
compartments =  'c'       'e'        'c'           'c'         'c'         'c'
If there are any metabolites with unknown energies then returns

(0, None).

pytfa.calcDGR_cues(reaction, reaction_cues_data)

Calculates the deltaG reaction and error of the reaction using the constituent structural cues changes and returns also the error if any.

Parameters

  • reaction (cobra.thermo.reaction.Reaction) – The reaction to compute deltaG for

  • reaction_cues_data (dict) –

Returns

deltaGR, error on deltaGR, the cues in the reaction (keys of the dictionnary) and their indices (values of the dictionnary), and the error code if any.

If everything went right, the error code is an empty string

Return type

tuple(float, float, dict(float), str)

pytfa.calcDGF_cues(cues, reaction_cues_data)

Calculates the deltaG formation and error of the compound using its constituent structural cues.

Parameters

  • cues (list(str)) – A list of cues’ names

  • reaction_cues_data (dict) –

Returns

deltaG formation, the error on deltaG formation, and a dictionnary with the cues’ names as key and their coefficient as value

Return type

tuple(float, float, dict(float)).

pytfa.get_debye_huckel_b(T)

The Debye-Huckel A and B do depend on the temperature As for now though they are returned as a constant (value at 298.15K)

Parameters

T – Temperature in Kelvin

Returns

Debye_Huckel_B