6.1.1.6.1.1. pytfa.thermo.equilibrator¶
Thermodynamic information for metabolites from eQuilibrator.
6.1.1.6.1.1.1. Module Contents¶
6.1.1.6.1.1.1.1. Functions¶
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Build thermo_data structure from a cobra Model. |
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Get ΔGf from equilibrator compound. |
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Build thermo structure entry from a equilibrator_cache.Compound. |
6.1.1.6.1.1.1.2. Attributes¶
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- pytfa.ccache¶
- pytfa.logger¶
- pytfa.build_thermo_from_equilibrator(model, T=TEMPERATURE_0)¶
Build thermo_data structure from a cobra Model.
The structure of the returned dictionary is specified in the pyTFA [documentation](https://pytfa.readthedocs.io/en/latest/thermoDB.html).
- Parameters
model – cobra.Model
- Return thermo_data
dict to be passed as argument to initialize a ThermoModel.
- pytfa.compute_dGf(compound, cc)¶
Get ΔGf from equilibrator compound.
- pytfa.compound_to_entry(compound, cc)¶
Build thermo structure entry from a equilibrator_cache.Compound.
eQuilibrator works with Component Contribution instead of groups, so it is not possible to generate cues from it.
- Parameters
compound – equilibrator_cache.Compound
- Returns
dict with keys [‘deltaGf_std’, ‘deltaGf_err’, ‘error’, ‘struct_cues’, ‘id’, ‘pKa’, ‘mass_std’, ‘charge_std’, ‘nH_std’, ‘name’, ‘formula’, ‘other_names’]