e3fp.conformer.protonation module

Functions for generating protonation states of molecules.

Author: Seth Axen E-mail: seth.axen@gmail.com

smiles_dict_to_proto_smiles_dict(in_smiles_dict, max_states=3, pka=7.4, dist_cutoff=20.0, add_missing=False, parallelizer=None, chunk_size=100)

Generate dict of SMILES for protonated states from SMILES dict.

smiles_list_to_proto_smiles_list(in_smiles_list, max_states=3, pka=7.4, dist_cutoff=20.0)

Generate list of SMILES for protonated states from single SMILES.

smiles_to_proto_smiles(smiles, mol_name, max_states=3, pka=7.4, dist_cutoff=20.0)

Generate list of SMILES for protonated states from single SMILES.

This is very inefficient in batch.