Source code for mofdscribe.featurizers.chemistry.partialchargestats

# -*- coding: utf-8 -*-
"""Partial charge statistics featurizer."""
from typing import List, Tuple, Union

import numpy as np
from pymatgen.core import IStructure, Structure

from mofdscribe.featurizers.base import MOFBaseFeaturizer
from mofdscribe.featurizers.utils.aggregators import ARRAY_AGGREGATORS
from mofdscribe.featurizers.utils.eqeq import get_eqeq_charges
from mofdscribe.featurizers.utils.extend import operates_on_istructure, operates_on_structure

__all__ = ["PartialChargeStats"]


[docs]@operates_on_istructure @operates_on_structure class PartialChargeStats(MOFBaseFeaturizer): """Compute partial charges using the EqEq charge equilibration method [Ongari2019]_. Then derive a fix-length feature vector from the partial charges using aggregative statistics. They have, for instance, been used as "maximum positive charge" and "mininum negative charge" in `Moosavi et al. (2020) <https://www.nature.com/articles/s41467-020-17755-8>`_ """ def __init__( self, aggregations: Tuple[str] = ("max", "min", "std"), primitive: bool = True ) -> None: """ Initialize the PartialChargeStats featurizer. Args: aggregations (Tuple[str]): Aggregations to compute. For available methods, see :py:obj:`mofdscribe.featurizers.utils.aggregators.ARRAY_AGGREGATORS`. Defaults to ("max", "min", "std"). primitive (bool): If True, the structure is reduced to its primitive form before the descriptor is computed. Defaults to True. """ self.aggregations = aggregations super().__init__(primitive=primitive)
[docs] def feature_labels(self) -> List[str]: return [f"chargestat_{agg}" for agg in self.aggregations]
def _featurize(self, s: Union[Structure, IStructure]) -> np.ndarray: if isinstance(s, Structure): s = IStructure.from_sites(s.sites) _, results = get_eqeq_charges(s) aggregated = [ARRAY_AGGREGATORS[agg](results) for agg in self.aggregations] return np.array(aggregated)
[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"]