smiles-fp

Rust-accelerated Tanimoto similarity search over RDKit Morgan fingerprints.

Prerequisites

  • Python 3.10 to 3.14.
  • RDKit, pinned to the version a given wheel was built against.
  • To build from source: a Rust toolchain and uv (RDKit/Boost headers are fetched automatically from PyPI, no conda required).

Installation

A wheel is published to PyPI per supported RDKit release, pin the RDKit version during installation:

uv pip install smiles-fp~=0.2.1 rdkit~=2024.0 # installs smiles-fp==0.2.1.2024.9.6 and rdkit==2024.9.6

To build locally instead, build_wheel.py builds one wheel for the RDKit version you pass it, targeting whichever Python interpreter runs the script (use uv run --python to pick one):

uv run --python 3.12 smiles-fp-pypi/build_wheel.py 2024.9.6
mv ./target/wheels ./target/smiles-fp
python -m http.server --directory ./target/
uv pip install smiles-fp --extra-index-url http://localhost:8000

Usage

from smiles_fp import get_mols, get_morgan_fps, save_fingerprints
from smiles_fp.search import similarity_search

query_ids = ["aspirin", "ethanol"]
mols = get_mols(["CC(=O)OC1=CC=CC=C1C(=O)O", "CCO"])
fps = get_morgan_fps(mols)
save_fingerprints(fps, "query.fp")

db_ids = ["ethylamine", "acetylsalicylic acid"]
db_mols = get_mols(["CCN", "CC(=O)OC1=CC=CC=C1C(=O)O"])
db_fps = get_morgan_fps(db_mols)
save_fingerprints(db_fps, "db.fp")

results = similarity_search(query_ids, "query.fp", db_ids, "db.fp", k=5)

License

MIT, see LICENSE.

Project links

Data verified by PyPI on Sep 7, 2026
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Avatar for audivir from gravatar.com audivir

Credits

Author: Tim Hörmann

GitHub Statistics

Data verified by PyPI on Sep 7, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License expression

MIT
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Requires

Python <=3.15, >=3.10

Classifiers

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Uploaded CPython 3.13manylinux: glibc 2.34+ x86-64

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Uploaded CPython 3.12manylinux: glibc 2.34+ x86-64

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