

from typing import Dict

import numpy as np
import torch

from . import residue_constants as rc
from .tensor_utils import tensor_tree_map, tree_map







def 	_snake_case		(    SCREAMING_SNAKE_CASE				)       ->      Dict[str, torch.Tensor]:

     """simple docstring"""







     _lowerCAmelCase   :					int        =    []
     _lowerCAmelCase   :					Tuple        =    []
     _lowerCAmelCase   :					List[Any]        =    []

     for rt in rc.restypes:
          _lowerCAmelCase   :					int        =    rc.restype_name_to_atomaa_names[rc.restype_atoa[rt]]
          restype_atomaa_to_atomaa_list.append([(rc.atom_order[name] if name else 0) for name in atom_names]				)
          _lowerCAmelCase   :					str        =    {name: i for i, name in enumerate(SCREAMING_SNAKE_CASE				)}
          restype_atomaa_to_atomaa_list.append(
              [(atom_name_to_idxaa[name] if name in atom_name_to_idxaa else 0) for name in rc.atom_types]				)

          restype_atomaa_mask_list.append([(1.0 if name else 0.0) for name in atom_names]				)

     # Add dummy mapping for restype 'UNK'
     restype_atomaa_to_atomaa_list.append([0] * 14				)
     restype_atomaa_to_atomaa_list.append([0] * 37				)
     restype_atomaa_mask_list.append([0.0] * 14				)

     _lowerCAmelCase   :					List[str]        =    torch.tensor(
         SCREAMING_SNAKE_CASE		,							dtype=torch.intaa		,							device=protein["aatype"].device		,							)
     _lowerCAmelCase   :					str        =    torch.tensor(
         SCREAMING_SNAKE_CASE		,							dtype=torch.intaa		,							device=protein["aatype"].device		,							)
     _lowerCAmelCase   :					Optional[Any]        =    torch.tensor(
         SCREAMING_SNAKE_CASE		,							dtype=torch.floataa		,							device=protein["aatype"].device		,							)
     _lowerCAmelCase   :					List[str]        =    protein["aatype"].to(torch.long				)

     # create the mapping for (residx, atom14) --> atom37, i.e. an array
     # with shape (num_res, 14) containing the atom37 indices for this protein
     _lowerCAmelCase   :					Dict        =    restype_atomaa_to_atomaa[protein_aatype]
     _lowerCAmelCase   :					Optional[Any]        =    restype_atomaa_mask[protein_aatype]

     _lowerCAmelCase   :					Any        =    residx_atomaa_mask
     _lowerCAmelCase   :					Dict        =    residx_atomaa_to_atomaa.long()

     # create the gather indices for mapping back
     _lowerCAmelCase   :					Optional[int]        =    restype_atomaa_to_atomaa[protein_aatype]
     _lowerCAmelCase   :					str        =    residx_atomaa_to_atomaa.long()

     # create the corresponding mask
     _lowerCAmelCase   :					Dict        =    torch.zeros([21, 37]		,							dtype=torch.floataa		,							device=protein["aatype"].device				)
     for restype, restype_letter in enumerate(rc.restypes				):
          _lowerCAmelCase   :					Optional[Any]        =    rc.restype_atoa[restype_letter]
          _lowerCAmelCase   :					int        =    rc.residue_atoms[restype_name]
          for atom_name in atom_names:
               _lowerCAmelCase   :					Union[str, Any]        =    rc.atom_order[atom_name]
               _lowerCAmelCase   :					Dict        =    1

     _lowerCAmelCase   :					Tuple        =    restype_atomaa_mask[protein_aatype]
     _lowerCAmelCase   :					List[str]        =    residx_atomaa_mask

     return protein







def 	_snake_case		(    SCREAMING_SNAKE_CASE				)       ->      Dict[str, np.ndarray]:

     """simple docstring"""







     _lowerCAmelCase   :					Any        =    tree_map(lambda SCREAMING_SNAKE_CASE				: torch.tensor(SCREAMING_SNAKE_CASE		,							device=batch["aatype"].device				)		,							SCREAMING_SNAKE_CASE		,							np.ndarray				)
     _lowerCAmelCase   :					Optional[int]        =    tensor_tree_map(lambda SCREAMING_SNAKE_CASE				: np.array(SCREAMING_SNAKE_CASE				)		,							make_atomaa_masks(SCREAMING_SNAKE_CASE				)				)
     return out









# Author: OMKAR PATHAK, Nwachukwu Chidiebere

# Use a Python dictionary to construct the graph.
from __future__ import annotations

from pprint import pformat
from typing import Generic, TypeVar

__UpperCAmelCase    				=     TypeVar('T')





class A__    ( Generic[T] ):



 """simple docstring"""







 def __init__(		self :	Optional[int]     ,						A_ :	bool = True       ):






      '''simple docstring'''




      _lowerCAmelCase   :					dict[T, list[T]]        =    {}  # dictionary of lists
      _lowerCAmelCase   :					List[Any]        =    directed

 def    __magic_name__       (		self :	Any     ,						A_ :	T     ,						A_ :	T       ):






      '''simple docstring'''




      if not self.directed:  # For undirected graphs
           # if both source vertex and destination vertex are both present in the
           # adjacency list, add destination vertex to source vertex list of adjacent
           # vertices and add source vertex to destination vertex list of adjacent
           # vertices.
           if source_vertex in self.adj_list and destination_vertex in self.adj_list:
                self.adj_list[source_vertex].append(A_       )
                self.adj_list[destination_vertex].append(A_       )
           # if only source vertex is present in adjacency list, add destination vertex
           # to source vertex list of adjacent vertices, then create a new vertex with
           # destination vertex as key and assign a list containing the source vertex
           # as it's first adjacent vertex.
           elif source_vertex in self.adj_list:
                self.adj_list[source_vertex].append(A_       )
                _lowerCAmelCase   :					List[Any]        =    [source_vertex]
           # if only destination vertex is present in adjacency list, add source vertex
           # to destination vertex list of adjacent vertices, then create a new vertex
           # with source vertex as key and assign a list containing the source vertex
           # as it's first adjacent vertex.
           elif destination_vertex in self.adj_list:
                self.adj_list[destination_vertex].append(A_       )
                _lowerCAmelCase   :					List[str]        =    [destination_vertex]
           # if both source vertex and destination vertex are not present in adjacency
           # list, create a new vertex with source vertex as key and assign a list
           # containing the destination vertex as it's first adjacent vertex also
           # create a new vertex with destination vertex as key and assign a list
           # containing the source vertex as it's first adjacent vertex.
           else:
                _lowerCAmelCase   :					List[str]        =    [destination_vertex]
                _lowerCAmelCase   :					Dict        =    [source_vertex]
      else:  # For directed graphs
           # if both source vertex and destination vertex are present in adjacency
           # list, add destination vertex to source vertex list of adjacent vertices.
           if source_vertex in self.adj_list and destination_vertex in self.adj_list:
                self.adj_list[source_vertex].append(A_       )
           # if only source vertex is present in adjacency list, add destination
           # vertex to source vertex list of adjacent vertices and create a new vertex
           # with destination vertex as key, which has no adjacent vertex
           elif source_vertex in self.adj_list:
                self.adj_list[source_vertex].append(A_       )
                _lowerCAmelCase   :					Tuple        =    []
           # if only destination vertex is present in adjacency list, create a new
           # vertex with source vertex as key and assign a list containing destination
           # vertex as first adjacent vertex
           elif destination_vertex in self.adj_list:
                _lowerCAmelCase   :					Dict        =    [destination_vertex]
           # if both source vertex and destination vertex are not present in adjacency
           # list, create a new vertex with source vertex as key and a list containing
           # destination vertex as it's first adjacent vertex. Then create a new vertex
           # with destination vertex as key, which has no adjacent vertex
           else:
                _lowerCAmelCase   :					Any        =    [destination_vertex]
                _lowerCAmelCase   :					Union[str, Any]        =    []

      return self


 def __repr__(		self :	List[str]       ):






      '''simple docstring'''




      return pformat(self.adj_list       )






