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Create a fingerprint database file

To create a fingerprint database file for running searches, use either:

  • The fpsim2-create-db command line tool
  • The FPSim2.io.create_db_file Python function

Both methods are described below.

Warning

FPSim2 only supports integer molecule ids.

The fingerprints are calculated with RDKit. Fingerprint types available are:

Using the command line

Run in parallel using .smi files as input. Example usage:

fpsim2-create-db smiles_file.smi fp_db.h5 --fp_type Morgan --fp_params '{"radius": 2, "fpSize": 256}' --processes 32

Using Python

Note: When using the Python library, fingerprint calculation is single-threaded.

from FPSim2.io import create_db_file

create_db_file(
    mols_source='sdf_file.sdf',
    filename='fp_db.h5',
    mol_format=None, # set to None
    fp_type='Morgan',
    fp_params={'radius': 2, 'fpSize': 256},
    mol_id_prop='mol_id'
)

from FPSim2.io import create_db_file

create_db_file(
    mols_source='smiles_file.smi',
    filename='fp_db.h5',
    mol_format=None, # set to None
    fp_type='Morgan',
    fp_params={'radius': 2, 'fpSize': 256}
)

from FPSim2.io import create_db_file

mols = [['CC', 1], ['CCC', 2], ['CCCC', 3]]
create_db_file(
    mols_source=mols,
    filename='fp_db.h5',
    mol_format='smiles', # required
    fp_type='Morgan',
    fp_params={'radius': 2, 'fpSize': 256}
)

SQLAlchemy CursorResult as an example

from FPSim2.io import create_db_file
from sqlalchemy import create_engine, text

engine = create_engine('sqlite:///test/test.db')
with engine.connect() as conn:
    sql_query = text("select molfile, mol_id from structure")
    cursor = conn.execute(sql_query)

    create_db_file(
        mols_source=cursor,
        filename='fp_db.h5',
        mol_format='molfile', # required
        fp_type='Morgan',
        fp_params={'radius': 2, 'fpSize': 256}
    )