Substructure Database#

To make the label command possible, we created a database using data from PubChem and RDKit’s SMARTS-based substructure matching functionality.

Current Supported Functional Groups / Substructures

hydroxyl, carbonyl, carboxyl, amine, alcohol, ether, ketone, halide, ester, amide, aldehyde, aromatic, amino acid, nitrate, phenol, nitro, phosphoric acid, phosphoric ester, sulfate, sulfonate, thiol, carbothioester

Add another substructure to the database#

  1. Clone our repo to your machine

  2. Install RDKit

  3. Navigate to the tofspec/db folder

  4. Open the substructures.yml file

  5. Add your substructure(s) and the corresponding SMARTS string to the list, and save changes

  6. Run build_db.py

It might take a few minutes, but database.feather will be updated with your substructure(s) of choice!