# -*- coding: utf-8 -*-
"""Partial charge histogram featurizer."""
from typing import List, Union
import numpy as np
from pymatgen.core import IStructure, Structure
from mofdscribe.featurizers.base import MOFBaseFeaturizer
from mofdscribe.featurizers.utils.eqeq import get_eqeq_charges
from mofdscribe.featurizers.utils.extend import operates_on_istructure, operates_on_structure
from mofdscribe.featurizers.utils.histogram import get_rdf
__all__ = ["PartialChargeHistogram"]
[docs]@operates_on_istructure
@operates_on_structure
class PartialChargeHistogram(MOFBaseFeaturizer):
"""Compute partial charges using the EqEq charge equilibration method [Ongari2019]_.
Then derive a fix-length feature vector from the partial charges by binning
charges in a histogram.
"""
def __init__(
self,
min_charge: float = -4,
max_charge: float = 4,
bin_size: float = 0.5,
primitive: bool = False,
) -> None:
"""Construct a new PartialChargeHistogram featurizer.
Args:
min_charge (float): Minimum limit of bin grid.
Defaults to -4.
max_charge (float): Maximum limit of bin grid.
Defaults to 4.
bin_size (float): Bin size.
Defaults to 0.5.
primitive (bool): If True, the structure is reduced to its primitive
form before the descriptor is computed. Defaults to True.
"""
self.min_charge = min_charge
self.max_charge = max_charge
self.bin_size = bin_size
super().__init__(primitive=primitive)
def _get_grid(self):
return np.arange(self.min_charge, self.max_charge, self.bin_size)
[docs] def feature_labels(self) -> List[str]:
return [f"chargehist_{val}" for val in self._get_grid()]
def _featurize(self, s: Union[Structure, IStructure]) -> np.ndarray:
if isinstance(s, Structure):
s = IStructure.from_sites(s.sites)
_, results = get_eqeq_charges(s)
hist = get_rdf(results, self.min_charge, self.max_charge, self.bin_size, None, None, False)
return hist
[docs] def citations(self) -> List[str]:
return [
"@article{Ongari2018,"
"doi = {10.1021/acs.jctc.8b00669},"
"url = {https://doi.org/10.1021/acs.jctc.8b00669},"
"year = {2018},"
"month = nov,"
"publisher = {American Chemical Society ({ACS})},"
"volume = {15},"
"number = {1},"
"pages = {382--401},"
"author = {Daniele Ongari and Peter G. Boyd and Ozge Kadioglu and "
"Amber K. Mace and Seda Keskin and Berend Smit},"
"title = {Evaluating Charge Equilibration Methods To Generate "
"Electrostatic Fields in Nanoporous Materials},"
"journal = {Journal of Chemical Theory and Computation}"
"}",
"@article{Wilmer2012,"
"doi = {10.1021/jz3008485},"
"url = {https://doi.org/10.1021/jz3008485},"
"year = {2012},"
"month = aug,"
"publisher = {American Chemical Society ({ACS})},"
"volume = {3},"
"number = {17},"
"pages = {2506--2511},"
"author = {Christopher E. Wilmer and Ki Chul Kim and Randall Q. Snurr},"
"title = {An Extended Charge Equilibration Method},"
"journal = {The Journal of Physical Chemistry Letters}"
"}",
]
[docs] def implementors(self):
return ["Kevin Maik Jablonka", "Daniele Ongari", "Christopher Wilmer"]