BONAFIDE is a Python-based package for calculating features for atoms and bonds in molecules by providing a consistent API to popular featurization libraries and packages. It can calculate descriptors based on both 2D and 3D molecular representations depending on the provided user input. It aims to simplify the process of calculating local features for machine learning and cheminformatics applications.
For any further details, please visit the documentation.
- Python 3.12
- Conda (for environment management)
- Key dependencies: alfabet, ase, dbstep, dscribe, kallisto, mendeleev, morfeus-ml, numpy, pandas, py3Dmol, qmdesc, rdkit, scipy
- Optional external programs: Multiwfn, Psi4, xtb
For further details, please see the
installation guide and the
environment .yml files.
from bonafide import AtomBondFeaturizer
f = AtomBondFeaturizer()
# Get the list of the desired feature indices (all 2D atom features from RDKit)
fdf = f.list_atom_features(origin="RDKit", dimensionality="2D")
fidx_list = fdf.index.to_list()
# Read in the molecule and calculate the features
f.read_input(input_value="O=C(O)Cc1ccccc1Nc1c(Cl)cccc1Cl", namespace="diclofenac")
f.featurize_atoms(atom_indices="all", feature_indices=fidx_list)
# Retrieve results as a DataFrame
f.return_atom_features()For more details and examples, see the examples folder and the documentation.
- Lukas Sigmund
- Michele Assante
- Matt Ball
For any further details, please refer to our preprint.