6.1.1.6.1.3. pytfa.thermo.reaction
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Thermodynamic computations for reactions
6.1.1.6.1.3.1. Module Contents¶
6.1.1.6.1.3.1.1. Functions¶
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Calculates the RHS of the deltaG constraint, i.e. the sum of the |
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Calculates the deltaG reaction and error of the reaction using the |
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Calculates the deltaG formation and error of the compound using its |
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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
- Returns
deltaG_tpt and the breakdown of deltaG_tpt
- Return type
- 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
- pytfa.calcDGF_cues(cues, reaction_cues_data)¶
Calculates the deltaG formation and error of the compound using its constituent structural cues.
- 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