Chimie Théorique » scripts_chimie4psmn » DockOnSurf

functions:

confs_to_mol_list: Converts the conformers inside a rdkit.Mol object to a list

adapt_format: Converts the coordinate files into a required library object type.

read_coords_cp2k: Reads the coordinates from a CP2K restart file and returns an

    ase.Atoms object.

read_energy_cp2k: Reads the CP2K out file and returns its final energy.

"""

import logging

    Depending on the library required to use and the file type, it converts the

    coordinate file into a library-workable object.

    @param requirement: str, the library for which the conversion should be

    @param coord_file: str, path to the coordinates file aiming to convert.

    @param spec_atms: List of tuples containing pairs of new/traditional

        chemical symbols.

    @return: an object the required library can work with.

                                        spec_atms)

            # Assign energy

            for fil in os.listdir(conf_path):

                    continue

                if conf_energy is not None:

                    ase_atms.info["energy"] = conf_energy

                    break

            logger.error(err_msg)

            raise NotImplementedError(err_msg)

    return atoms_list