The repository of useful scripts to manipulate SQLite DB using Chemicalite

Normally you should create DB from SMILES, add the mol field and add desired fingerprints:
create_db.py - create DB from SMILES file
create_mol_field.py - create Mol objects in DB
add_fp_to_db.py - add chosen fingerprints to DB - morgan, atom-pairs or pattern (for substructure search) are supported.

After that you may perform similarity of substructure search:
sim_search.py - perform similarity search using the chosen fingerprints
substr_search.py - perform substructure search (after pattern fp were added)

Examples:

create_db.py -i input.smi -o database.db
create_mol_field.py -d database.db
add_fp_to_db.py -d database.db -f pattern
add_fp_to_db.py -d database.db -f morgan

sim_search.py -d database.db -q 'CCO' -f morgan
substr_search.py -d database.db -q 'CCO' 

Dependency

rdkit - https://www.rdkit.org/
Chemicalite - SQLite cartridge for RDKit - https://github.com/rvianello/chemicalite