Here we have the scripts used to handle the thermodynamics data that came from both the Group Contribution approach (Jankowski et al. 2008) and from eQuilibrator (Noor et al. 2013). Our approach in handling this data is described in the paper.
The general order is that the energies from the application of the Group Contribution (GC) approach are stored in the database first, and then the energies from eQuilibrator (EQ), which, in most cases, take precedence, are used to overwrite the energies in the database
The underlying thermodynamics data is kept in
../../Biochemistry/Thermodynamics. The decomposition of molecular
structures and their resulting energies for both the older group
contribution approach and the newer eQuilibrator approach are stored in
the ModelSEED and eQuilibrator directories.
As an addendum, the two scripts used to update the energies from
eQuilibrator are in this folder, but are dependent on files in
../../Biochemistry/Structures/MetaNetX:
./Retrieve_eQuilibrator_Compound_Energies.py
./Retrieve_eQuilibrator_Reactions_Energies.py
If the underlying thermodynamics data in ../../Biochemistry/Thermodyanmics hasn't changed,
then running these six commands should not cause any changes to appear in the database.
./Update_Compound_GroupContribution_Energies.py
./Update_Reaction_GroupContribution_Energies.py
./Estimate_Reaction_Reversibility.py GC
./Update_Compound_eQuilibrator_Energies.py
./Update_Reaction_eQuilibrator_Energies.py
./Estimate_Reaction_Reversibility.py EQ
These easily run together by running:
./Rerun_Thermodynamics.sh