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Thermodynamic Calculations

Overview of Thermodynamics Module

eQuilibrator

Built into Pickaxe is the ability to estimate the Gibbs free energy of compounds and reactions. Pickaxe uses eQuilibrator to calculate thermodynamic values. More information about eQuilibrator can be found here.

Calculable Values

Pickaxe calculates the following values for compounds and reactions. More information about these conditions can be found here.

  1. Compounds
    • : ΔfG’°: The Standard Gibbs Free Energy of Formation
      1. Uses pH = 7 and ionic strength = 0.1M
  2. Reactions
    • ΔrG’°: The Standard Gibbs Free Energy of Reaction
      1. Uses pH = 7 and ionic strength = 0.1M
    • ΔrG’m: The Physiological Gibbs Free Energy of Reaction
      1. Uses pH = 7 and ionic strength = 0.1M
      2. Assumes concentrations are 1mM.
    • ΔrG’: Adjusted Gibbs Free Energy of Reaction
      1. User-specified conditions

Calculating Thermodynamics of a Pickaxe Run

Set-up

Thermodynamics.py uses the compound ids (c_id) and reaction ids (r_id) of pickaxe runs to calculate values. This example assumes you have run a pickaxe run and have it accessible either from a MongoDB or in memory in a pickaxe object. Pickaxe runs can be stored later by using the pickleing functionality.

Additionally, an eQuilibrator database must be loaded.

Compound Value Calculations

If there is no eQuilibrator compounds.sqlite file present, generate one first.

>>> from equilibrator_assets.local_compound_cache import LocalCompoundCache
>>> lc = LocalCompoundCache()
>>> lc.generate_local_cache_from_default_zenodo("compounds.sqlite")
Copying default Zenodo compound cache to compounds.sqlite

Next, the thermodynamics class must be loaded and initialized, where mongo_uri is the uri to your mongo server. Providing None will use the default localhost.

>>> from minedatabase.thermodynamics import Thermodynamics
>>> thermo = Thermodynamics()
>>> thermo.load_thermo_from_sqlite("compounds.sqlite")
Loading compounds from compounds.sqlite
>>> thermo.load_mongo(mongo_uri=mongo_uri)

The following assumes you have a valid pickaxe object or a database to cross-reference the c_id and r_id from. No c_id or r_id is given here, but example outputs are.

Calculating ∆Gf'°

>>> thermo.standard_dg_formation_from_cid(c_id=c_id, pickaxe=pickaxe, db_name=db_name)
-724.5684043965385

Calculating ΔrG’m

>>> thermo.physiological_dg_prime_from_rid(r_id, pickaxe=pickaxe, db_name=db_name)
<Measurement(-5.432945798382008, 3.37496192184388, kilojoule / mole)>

Calculating ΔrG’ at pH = 4, ionic strength = 0.05M

>>> from equilibrator_api import Q_
>>> p_h = Q_("4")
>>> ionic_strength = Q_("0.05M)
>>> thermo.dg_prime_from_rid(r_id=r_id, db_name=db_name, p_h=p_h, ionic_strength=ionic_strength)
<Measurement(11.68189173633911, 3.37496192184388, kilojoule / mole)>