Here we keep the scripts for loading and manipulating the biochemistry
database, we separate them into several categories depending on how we
use them. The "parent" script, which does the simple job of loading
the data from the original *.tsv
files and some supplemental files,
then re-printing them, is the one we re-run every time to double-check
that everything is in place:
(What we look for is if this script runs silently, and git status -s
shows no change)
The categories in which we sort the other scripts are:
Add_New_Biochemistry_Attribute.py
Remove_Biochemistry_Attribute.py
Add_New_Compounds.py
Add_New_Reactions.py
Remove_Newly_Obsolescent_Compounds.py
Remove_Newly_Obsolescent_Reactions.py
Adjust_Reaction_Protons.py
Adjust_Reaction_Water.py
Merge_Formulas.py
Merge_Obsolete_Aliases.py
Merge_Reactions.py
Rebalance_Reactions.py
Rebuild_Reactions.py
Update_Compound_Aliases.py
Update_Reaction_Aliases.py
Remove_Duplicate_Aliases.py
Check_Charges.py
Check_Formulas.py
Check_Links.py
Check_Template_Reactions.py
Check_Transport.py
Fix_Values.py
Manual_Update_Links.py