"""Identification of symmetry equivalent positions in 2D mol objects."""
import copy
from collections import defaultdict
from typing import Dict, List, Union, cast
from bonafide.utils.base_featurizer import BaseFeaturizer
from bonafide.utils.helper_functions_chemistry import get_symmetric_atom_sites
[docs]
class Bonafide2DAtomIsSymmetricTo(BaseFeaturizer):
"""Feature factory for the 2D atom feature "is_symmetric_to", implemented within this
package.
The index of this feature is 30 (see the ``list_atom_features()`` and
``list_bond_features()`` method). The corresponding configuration settings can be found
under "bonafide.symmetry" in the _feature_config.toml file.
"""
includeAtomMaps: bool
includeChirality: bool
includeChiralPresence: bool
includeIsotopes: bool
reduce_to_canonical: bool
consider_resonance: bool
resonance_ALLOW_CHARGE_SEPARATION: bool
resonance_ALLOW_INCOMPLETE_OCTETS: bool
resonance_KEKULE_ALL: bool
resonance_UNCONSTRAINED_ANIONS: bool
resonance_UNCONSTRAINED_CATIONS: bool
def __init__(self) -> None:
self.extraction_mode = "multi"
super().__init__()
[docs]
def calculate(self) -> None:
"""Calculate the ``bonafide2D-atom-is_symmetric_to`` feature."""
# Get the symmetric atom sites
sites = get_symmetric_atom_sites(
mol=self.mol,
# Configuration settings for Chem.CanonicalRankAtoms
include_chirality=self.includeChirality,
include_isotopes=self.includeIsotopes,
include_atom_maps=self.includeAtomMaps,
include_chiral_presence=self.includeChiralPresence,
# Configuration settings for Chem.ResonanceMolSupplier
consider_resonance=self.consider_resonance,
resonance_ALLOW_CHARGE_SEPARATION=self.resonance_ALLOW_CHARGE_SEPARATION,
resonance_ALLOW_INCOMPLETE_OCTETS=self.resonance_ALLOW_INCOMPLETE_OCTETS,
resonance_KEKULE_ALL=self.resonance_KEKULE_ALL,
resonance_UNCONSTRAINED_ANIONS=self.resonance_UNCONSTRAINED_ANIONS,
resonance_UNCONSTRAINED_CATIONS=self.resonance_UNCONSTRAINED_CATIONS,
)
# Handle missing indices in initial sites dictionary
new_sites = cast(Dict[int, Union[List[int], str]], copy.deepcopy(sites))
for idx_list in sites.values():
if len(idx_list) == 1:
continue
for atom_idx in idx_list:
if atom_idx not in sites:
if self.reduce_to_canonical is True:
new_sites[atom_idx] = "_inaccessible"
else:
new_sites[atom_idx] = idx_list
# Write values to the results dictionary
for atom_idx, idx_list2 in new_sites.items():
if isinstance(idx_list2, str) and idx_list2 == "_inaccessible":
self.results[atom_idx] = {self.feature_name: "_inaccessible"}
else:
self.results[atom_idx] = {self.feature_name: ",".join([str(i) for i in idx_list2])}
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class Bonafide2DBondIsSymmetricTo(BaseFeaturizer):
"""Feature factory for the 2D bond feature "is_symmetric_to", implemented within this
package.
The index of this feature is 52 (see the ``list_atom_features()`` and
``list_bond_features()`` method). The corresponding configuration settings can be found
under "bonafide.symmetry" in the _feature_config.toml file.
"""
includeAtomMaps: bool
includeChirality: bool
includeChiralPresence: bool
includeIsotopes: bool
reduce_to_canonical: bool
consider_resonance: bool
resonance_ALLOW_CHARGE_SEPARATION: bool
resonance_ALLOW_INCOMPLETE_OCTETS: bool
resonance_KEKULE_ALL: bool
resonance_UNCONSTRAINED_ANIONS: bool
resonance_UNCONSTRAINED_CATIONS: bool
def __init__(self) -> None:
self.extraction_mode = "multi"
super().__init__()
[docs]
def calculate(self) -> None:
"""Calculate the ``bonafide2D-bond-is_symmetric_to`` feature."""
# Get the symmetric atom sites
atom_sites = get_symmetric_atom_sites(
mol=self.mol,
# Configuration settings for Chem.CanonicalRankAtoms
include_chirality=self.includeChirality,
include_isotopes=self.includeIsotopes,
include_atom_maps=self.includeAtomMaps,
include_chiral_presence=self.includeChiralPresence,
# Configuration settings for Chem.ResonanceMolSupplier
consider_resonance=self.consider_resonance,
resonance_ALLOW_CHARGE_SEPARATION=self.resonance_ALLOW_CHARGE_SEPARATION,
resonance_ALLOW_INCOMPLETE_OCTETS=self.resonance_ALLOW_INCOMPLETE_OCTETS,
resonance_KEKULE_ALL=self.resonance_KEKULE_ALL,
resonance_UNCONSTRAINED_ANIONS=self.resonance_UNCONSTRAINED_ANIONS,
resonance_UNCONSTRAINED_CATIONS=self.resonance_UNCONSTRAINED_CATIONS,
)
# Get dictionary of symmetry equivalent bond sites defined by the representative atom
# indices for the symmetry groups of their begin and end atoms
bond_sites_ = defaultdict(list)
for bond in self.mol.GetBonds():
rank_begin_idx = self._get_rank_idx(rank_dict=atom_sites, idx=bond.GetBeginAtomIdx())
rank_end_idx = self._get_rank_idx(rank_dict=atom_sites, idx=bond.GetEndAtomIdx())
bond_id = [rank_begin_idx, rank_end_idx]
bond_id.sort()
bond_id_str = "-".join([str(x) for x in bond_id])
bond_sites_[bond_id_str].append(bond.GetIdx())
bond_sites = {indices[0]: indices for indices in bond_sites_.values()}
# Handle missing indices in bond sites dictionary
new_sites = cast(Dict[int, Union[List[int], str]], copy.deepcopy(bond_sites))
for idx_list in bond_sites.values():
if len(idx_list) == 1:
continue
for bond_idx in idx_list:
if bond_idx not in bond_sites:
if self.reduce_to_canonical is True:
new_sites[bond_idx] = "_inaccessible"
else:
new_sites[bond_idx] = idx_list
# Write values to the results dictionary
for bond_idx, idx_list2 in new_sites.items():
if isinstance(idx_list2, str) and idx_list2 == "_inaccessible":
self.results[bond_idx] = {self.feature_name: "_inaccessible"}
else:
self.results[bond_idx] = {self.feature_name: ",".join([str(i) for i in idx_list2])}
[docs]
@staticmethod
def _get_rank_idx(rank_dict: Dict[int, List[int]], idx: int) -> int:
"""Get the rank index for a given atom index from the rank dictionary.
Parameters
----------
rank_dict : Dict[int, List[int]]
The rank dictionary mapping rank indices to lists of atom indices.
idx : int
The atom index for which to find the rank index.
Returns
-------
int
The rank index corresponding to the given atom index.
"""
for rank_idx, atom_indices in rank_dict.items():
if idx in atom_indices:
return rank_idx
return -1 # Return -1 if the atom index is not found in the rank dictionary