thermodynamics package

Subpackages

• thermodynamics.thermodynamics_examples package
  • Submodules
  • thermodynamics.thermodynamics_examples.aerobicAnaerobic01 module
  • thermodynamics.thermodynamics_examples.aerobicAnaerobic02 module
  • thermodynamics.thermodynamics_examples.main module
  • Module contents
    • TestThermodynamics

Submodules

thermodynamics.thermodynamics_dG_f_data module

thermodynamics.thermodynamics_dG_p_data module

class thermodynamics.thermodynamics_dG_p_data.thermodynamics_dG_p_data(pathways_I={}, dG0_p_I={}, dG_p_I={})

Bases: object

Runs pathway thermodynamic analysis analysis on a cobra.Model object

#1 Calculate pathway thermodynamics

calculate_dG_p(cobra_model, dG0_r, dG_r)

calculate the Gibbs free energy of an entire pathway

Parameters:

• dG0_r (dict) –
• dG_r (dict) –

Returns:

dG0_p dict: dG_p dict: thermodynamic_consistency_check

Return type:

dict

export_dG0_p_json(filename_I)

export_dG_p_json(filename_I)

export_tcc_json(filename_I)

init_pathways()

thermodynamics.thermodynamics_dG_r_data module

thermodynamics.thermodynamics_formatter module

thermodynamics.thermodynamics_io module

helper functions for generating thermodynamic analysis input

thermodynamics.thermodynamics_io.checkInput_concentrations(measured_values_I)

check concentration data input

Parameters:measured_values (dict) – measured values with variances {metabolite.id: {‘concentration’: float, ‘concentration_var’: float, ‘concentration_units’: ‘M’} Returns:

output: measured_values_O: {metabolite.id: {‘concentration’: float,

‘concentration_var’: float, ‘concentration_units’: ‘M’}

Return type:dict

thermodynamics.thermodynamics_io.checkInput_dG_f(measured_values_I)

check dG_O_f data input

Parameters:measured_values (dict) – measured values with variances {metabolite.id: {‘dG_f’: float, ‘dG_f_var’: float, ‘dG_f_units’: ‘kJ/mol’} Returns:

output: measured_values_O: {metabolite.id: {‘dG_f’: float,

‘dG_f_var’: float, ‘dG_f_lb’: float, ‘dG_f_ub’: float, ‘dG_f_units’: ‘kJ/mol’}

Return type:dict

thermodynamics.thermodynamics_io.import_values_json(filename)

import values from a json file

class thermodynamics.thermodynamics_io.thermodynamics_io

Bases: object

base class for the input and output of data

export_values_json(filename, data)

export values to a json file

import_values_json(filename)

import values from a json file

thermodynamics.thermodynamics_metabolomicsData module

thermodynamics.thermodynamics_otherData module

thermodynamics.thermodynamics_simulatedData module

thermodynamics.thermodynamics_tfba module

thermodynamics.thermodynamics_utility module

Module contents