benchmate.molecule

benchmate.molecule.molecule

MoleculeInfo Objects

@dataclass(slots=True)
class MoleculeInfo()

Molecule info to store all the information related to a small molecule

get_ecfp4_fp

def get_ecfp4_fp()

get ecfp4 fingerprint for a given fingerprint radius and dimensions

Returns:

the fingerpring attribute filled in returns nothing

get_fcfp4_fp

def get_fcfp4_fp()

same as above but with fcfp

get_maccs_fp

def get_maccs_fp()

same as above but with open source maccs

Molecule Objects

class Molecule()

Molecule class to represent chemical structures using SMILES or InChI. this will include methods for different property calculations and structure comparisons using usearch molecules.

__init__

def __init__(name, smiles, fingerprint_dim=2048, radius=2)

Arguments:

• name: name of the molecule
• smiles: the smiles of the molecule
• fingerprint_dim: the dimension of the fingerprint to generate all 3 fingerprints will use the same dim
• radius: the radius (in terms of graph distance, not angstroms) to use for fingerprinting

similarity

def similarity(other, fingerprint)

get the similarity betweek two molecule instances

Arguments:

• other: other molecule instance
• fingerprint: what kind of fingerprint to use

Returns:

returns the tanimoto similarity between to molecules

generate_conformers

def generate_conformers(n, prune_thres=0.5, optimize_geom=True)

generate conformers

Arguments:

• n: number of conformers to try to generate, based on pruning they number can be smalled
• prune_thres: remove any conformer that has this much rmsd or less. So lower values will give more conformers
• optimize_geom: whether to optimize the geometry, this will also get rid of some comformers

Returns:

returns a hydrogenated mol with all the conformers that you can get with mol.GetConformers() and a list of ids

inchikey

def inchikey() -> str

generate the inchi key for the molecule

Returns:

inchikey

__eq__

def __eq__(other)

using inchi key because the molecules might not be in canonical smiles, it’s not perfect but close

benchmate.molecule.utils