Chimie Théorique » scripts_chimie4psmn » DockOnSurf

"""Module for the conversion of coordinate files to library-workable objects

functions:

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

"""

import logging

logger = logging.getLogger('DockOnSurf')

def adapt_format(requirement, coord_file):

    """Converts the coordinate files into a required library object type.

    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

    made. Accepted values: 'ase', 'rdkit'.

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

    Accepted file tyoes: 'xyz', 'mol'.

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

    """

    from ase.io.formats import filetype

    req_vals = ['rdkit', 'ase']

    file_type_vals = ['xyz', 'mol']

    lib_err = f"The conversion to the '{requirement}' library object type" \

              f" has not yet been implemented"

    conv_info = f"Converted {coord_file} to {requirement} object type"

    fil_type_err = f'The {filetype( coord_file )} file formnat is not supported'

    if requirement not in req_vals:

        logger.error(lib_err)

        raise NotImplementedError(lib_err)

    if filetype(coord_file) not in file_type_vals:

        logger.error(fil_type_err)

        raise NotImplementedError(fil_type_err)

    if requirement == 'rdkit':

        if filetype(coord_file) == 'xyz':

            from xyz2mol import read_xyz_file, xyz2mol

            atoms, charge, xyz_coordinates = read_xyz_file(coord_file)

            rd_mol_obj = xyz2mol(atoms, xyz_coordinates, charge=charge)

            logger.debug(conv_info)

            return rd_mol_obj

        elif filetype(coord_file) == 'mol':

            from rdkit.Chem import MolFromMolFile

            logger.debug(conv_info)

            return MolFromMolFile(coord_file, removeHs=False)

    if requirement == 'ase':

        import ase.io

        logger.debug(conv_info)

        return ase.io.read(coord_file)