text_plain_output_1.png
import ase as ase

import dscribe as ds

import pandas as pd

import pandas as pd # data processing, CSV file I/O (e.g. pd.read_csv)

structure = pd.read_csv('../input/structures.csv')

rcut = 10.0
g2_params = [[1, 2], [0.1, 2], [0.01, 2], [1, 6], [0.1, 6], [0.01, 6]]
g4_params = [[1, 4, 1], [0.1, 4, 1], [0.01, 4, 1], [1, 4, -1], [0.1, 4, -1], [0.01, 4, -1]]
g3_params = None
g5_params = None

tmp_structure = structure.loc[structure.molecule_name == 'dsgdb9nsd_000001', :].copy()
species = tmp_structure.atom.unique()
acsf = ds.descriptors.ACSF(species=species, rcut=rcut, g2_params=g2_params, g3_params=g3_params, g4_params=g4_params, g5_params=g5_params)

molecule_atoms = tmp_structure.loc[:, 'atom']
molecule_positions = tmp_structure.loc[:, ['x', 'y', 'z']]
molecule_system = ase.atoms.Atoms(symbols=molecule_atoms, positions=molecule_positions)

acsf_features = acsf.create(molecule_system, n_jobs=1)
acsf_features[0]