Chimie Théorique » scripts_chimie4psmn » DockOnSurf

def read_coords(requirement, coord_file):

    from ase.io.formats import filetype

    req_vals = ['rdkit', 'ase']

    file_type_vals = ['xyz', 'mol']

    assert requirement in req_vals, ValueError('Not an adequate requirement.\n'

                                    f'adequate requirements: {req_vals}')

    assert filetype(coord_file) in file_type_vals, TypeError('The file formnat '

                                                             'is not supported')

    if requirement == 'rdkit':

        if filetype(coord_file) == 'xyz':

            from xyz2mol import xyz2mol, read_xyz_file

            atoms, charge, xyz_coordinates = read_xyz_file(coord_file)

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

            return rd_mol_obj

        elif filetype(coord_file) == 'mol':

            from rdkit.Chem import MolFromMolFile

            return MolFromMolFile(coord_file)

    if requirement == 'ase':

        import ase.io

        return ase.io.read(coord_file)