Chimie Théorique » scripts_chimie4psmn » DockOnSurf

import logging

import numpy as np

import ase

logger = logging.getLogger('DockOnSurf')

def get_atom_coords(atoms: ase.Atoms, ctrs_list):

    pass

def ads_euler(site, ctr, pts_angle, neigh_ctr):

    pass

def ads_chemcat(site, ctr, pts_angle):

    pass

def adsorb_confs(conf_list, surf, ads_ctrs, sites, algo, num_pts, neigh_ctrs):

    surf_ads_list = []

    sites_coords = get_atom_coords(surf, sites)

    for conf in conf_list:

        molec_ctr_coords = get_atom_coords(conf, ads_ctrs)

        molec_neigh_coords = get_atom_coords(conf, neigh_ctrs)

        for site in sites_coords:

            for i, molec_ctr in enumerate(molec_ctr_coords):

                if algo == 'euler':

                    surf_ads_list.append(ads_euler(site, molec_ctr, num_pts,

                                                   molec_neigh_coords[i]))

                elif algo == 'chemcat':

                    surf_ads_list.append(ads_chemcat(site, molec_ctr, num_pts))

    return surf_ads_list

def run_screening(inp_vars):

    """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 modules.formats import read_coords, read_energies, \

        rdkit_mol_to_ase_atoms, adapt_format

    from modules.clustering import get_rmsd, clustering

    from modules.isolated import get_moments_of_inertia, get_neighbors

    from modules.calculation import run_calc

    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)

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

    # TODO Implement neighbors algorithm

    # neigh_list = get_neighbors(conf_list[0], inp_vars['molec_ads_ctrs'])

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

    mois = np.array([get_moments_of_inertia(conf)[0] for conf in conf_list])

    rmsd_mtx = get_rmsd(conf_list)

    exemplars = clustering(rmsd_mtx)

    conf_list = [conf_list[idx] for idx in exemplars]

    conf_list = [rdkit_mol_to_ase_atoms(conf) for conf in conf_list]

    surf = adapt_format('ase', inp_vars['surf_file'])

    surf_ads_list = adsorb_confs(conf_list, surf, inp_vars['molec_ads_ctrs'],

                                 inp_vars['sites'], inp_vars['ads_algo'],

                                 inp_vars['sample_points_per_angle'],

                                 inp_vars['molec_neigh_ctrs'])

    run_calc('screening', inp_vars, surf_ads_list)