Special Functional Group List in Biochemical reactions

[0m1n0]

Dear @connorcoley,

Your team's paper on Merging enzymatic and synthetic chemistry with computational synthesis planning is absolutely excellent!
As I'm not an expert in chemoinformatics, your work helps people like me: I understand your ideas but I could never implement them so explicitly...!

I'm especially interested how you apply RDChiral on BKMS database in order to get reaction templates.
Today I'm trying to:

1. Reproduce data processing of BKMS following Jupyter Notebooks https://github.com/itai-levin/hybmind/tree/main/process_BKMS_database/Notebooks (almost done)
2. Apply the same data processing steps to MetaCyc and Rhea databases (I'm currently working on these data bases)
3. Apply RDChiral on 2

In RDChiral, you set "Special functional groups" (Table S1 of the paper, and in template_extractor.py of RDChiral).
Did you use the same list for BKMS or did you customise it for biochemical reactions? If so, how did you create this list?

Kind regards,
Min