README.md

ModelSEED Biochemistry Database Scripts (Biochemistry)

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:

./Reprint_Biochemistry.py

(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:

Updating

• 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

Refreshing

• Adjust_Reaction_Protons.py
• Adjust_Reaction_Water.py
• Merge_Formulas.py
• Merge_Obsolete_Aliases.py
• Merge_Reactions.py
• Rebalance_Reactions.py (pass save to write the recomputed statuses back; without it the script is a dry run. Its argument guard rejected save until 2026-09-24, so the rebalance step of Refresh_Reactions.sh had not been running.)
• Rebuild_Reactions.py
• Update_Compound_Aliases.py
• Update_Reaction_Aliases.py
• Remove_Duplicate_Aliases.py

Maintaining

• Check_Charges.py
• Check_Formulas.py
• Check_Links.py
• Check_Template_Reactions.py
• Check_Transport.py
• Fix_Values.py
• Manual_Update_Links.py