Révision f3d1e601
| b/modules/screening.py | ||
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import logging |
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import numpy as np |
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import ase |
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logger = logging.getLogger('DockOnSurf')
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def get_atom_coords(atoms: ase.Atoms, ctrs_list): |
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pass |
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def ads_euler(site, ctr, pts_angle, neigh_ctr): |
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pass |
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def ads_chemcat(site, ctr, pts_angle): |
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pass |
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def adsorb_confs(conf_list, surf, ads_ctrs, sites, algo, num_pts, neigh_ctrs): |
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surf_ads_list = [] |
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sites_coords = get_atom_coords(surf, sites) |
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for conf in conf_list: |
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molec_ctr_coords = get_atom_coords(conf, ads_ctrs) |
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molec_neigh_coords = get_atom_coords(conf, neigh_ctrs) |
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for site in sites_coords: |
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for i, molec_ctr in enumerate(molec_ctr_coords): |
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if algo == 'euler': |
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surf_ads_list.append(ads_euler(site, molec_ctr, num_pts, |
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molec_neigh_coords[i])) |
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elif algo == 'chemcat': |
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surf_ads_list.append(ads_chemcat(site, molec_ctr, num_pts)) |
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return surf_ads_list |
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def run_screening(inp_vars): |
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"""Carry out the screening of adsorbate coordinates on a surface |
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| ... | ... | |
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""" |
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import os |
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import numpy as np |
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from modules.formats import read_coords, read_energies |
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from modules.formats import read_coords, read_energies, \ |
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rdkit_mol_to_ase_atoms, adapt_format |
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from modules.clustering import get_rmsd, clustering |
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from modules.isolated import get_moments_of_inertia |
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from modules.isolated import get_moments_of_inertia, get_neighbors |
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from modules.calculation import run_calc |
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if not os.path.isdir("isolated"):
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err = "'isolated' directory not found. It is needed in order to carry " |
| ... | ... | |
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logger.error(err) |
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raise ValueError(err) |
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ads_list = read_coords(inp_vars['code'], 'isolated', 'rdkit') |
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ads_enrgs = read_energies(inp_vars['code'], 'isolated') |
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mois = np.array([get_moments_of_inertia(ads)[0] for ads in ads_list]) |
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rmsd_mtx = get_rmsd(ads_list) |
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conf_list = read_coords(inp_vars['code'], 'isolated', 'rdkit') |
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# TODO Implement neighbors algorithm |
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# neigh_list = get_neighbors(conf_list[0], inp_vars['molec_ads_ctrs']) |
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conf_enrgs = read_energies(inp_vars['code'], 'isolated') |
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mois = np.array([get_moments_of_inertia(conf)[0] for conf in conf_list]) |
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rmsd_mtx = get_rmsd(conf_list) |
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exemplars = clustering(rmsd_mtx) |
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conf_list = [conf_list[idx] for idx in exemplars] |
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conf_list = [rdkit_mol_to_ase_atoms(conf) for conf in conf_list] |
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surf = adapt_format('ase', inp_vars['surf_file'])
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surf_ads_list = adsorb_confs(conf_list, surf, inp_vars['molec_ads_ctrs'], |
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inp_vars['sites'], inp_vars['ads_algo'], |
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inp_vars['sample_points_per_angle'], |
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inp_vars['molec_neigh_ctrs']) |
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run_calc('screening', inp_vars, surf_ads_list)
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