Molecule Module

This is a small module that provides some tools and methods to deal with small molecules. It includes functions to generate RDKit molecule object instances from SMILES strings, compute molecular fingerprints, and calculate various molecular properties.

Additionally, it provides searching and filtering capabilities based on molecular properties and substructure matching using the usearch-molecule packages.

Usage

from benchmate.molecule import Molecule

smiles="C1=CC=CC=C1"  # Benzene
molecule = Molecule(smiles)

# all the information is stored in the info attribute
print(molecule.info.ecfp4) #or fcfp4 or maccs
print(molecule.info.properties) #all propertires that can be calculated with rdkit are available and stored in the info attribute

You can check how similar it is to another molecule or generate conformers.

molecule.generate_conformers(n=50, optimize_geom=True)
molecule.inchikey()