calculate_circular_fingerprint_similarity

openff.nagl.toolkits.openff.calculate_circular_fingerprint_similarity(molecule: Molecule, reference_molecule: Molecule, radius: int = 3, nbits: int = 2048, toolkit_registry=NAGL_TOOLKIT_REGISTRY) → float[source]

Compute the similarity between two molecules using a fingerprinting method. Uses a Morgan fingerprint with RDKit and a Circular fingerprint with OpenEye.

Parameters:

  • molecule (openff.toolkit.topology.Molecule) – The molecule to compute the fingerprint for.

  • reference_molecule (openff.toolkit.topology.Molecule) – The molecule to compute the fingerprint for.

  • radius (int, default 3) – The radius of the fingerprint to use.

  • nbits (int, default 2048) – The length of the fingerprint to use. Not used in RDKit.

  • toolkit_registry –

  • use (The toolkit registry to) –

Returns:

similarity (float) – The Dice similarity between the two molecules.