Chimie Théorique » scripts_chimie4psmn » DockOnSurf

import logging

logger = logging.getLogger('DockOnSurf')

    """Carry out the screening of adsorbate coordinates on a surface

    @param inp_vars: Calculation parameters from input file.

    """

    import os

    import numpy as np

    from formats import read_coords, read_energies

    from clustering import get_rmsd, clustering

    from isolated import get_moments_of_inertia

    if not os.path.isdir("isolated"):

        err = "'isolated' directory not found. It is needed in order to carry "

        "out the screening of structures to be adsorbed"

        logger.error(err)

        raise ValueError(err)

    ads_list = read_coords(inp_vars['code'], 'isolated', 'rdkit')

    ads_enrgs = read_energies(inp_vars['code'], 'isolated')

    mois = np.array([get_moments_of_inertia(ads) for ads in ads_list])

    rmsd_mtx = get_rmsd(ads_list)

    print(len(ads_list))

    exemplars = clustering(rmsd_mtx, True, ads_enrgs, mois)