





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 			SCREAMING_SNAKE_CASE (			_UpperCAmelCase					)     ->	Dict[str, torch.Tensor]:
    lowerCamelCase__       : Optional[int]   					=						[]
    lowerCamelCase__       : Tuple   					=						[]
    lowerCamelCase__       : List[Any]   					=						[]

    for rt in rc.restypes:
        lowerCamelCase__       : Optional[Any]   					=						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__       : Optional[int]   					=						{name: i for i, name in enumerate(_UpperCAmelCase					)}
        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__       : Optional[Any]   					=						torch.tensor(
        _UpperCAmelCase		,      dtype=torch.intaa		,      device=protein['aatype'].device		,      )
    lowerCamelCase__       : str   					=						torch.tensor(
        _UpperCAmelCase		,      dtype=torch.intaa		,      device=protein['aatype'].device		,      )
    lowerCamelCase__       : Optional[int]   					=						torch.tensor(
        _UpperCAmelCase		,      dtype=torch.floataa		,      device=protein['aatype'].device		,      )
    lowerCamelCase__       : Optional[Any]   					=						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__       : Optional[Any]   					=						restype_atomaa_to_atomaa[protein_aatype]
    lowerCamelCase__       : Any   					=						restype_atomaa_mask[protein_aatype]

    lowerCamelCase__       : List[Any]   					=						residx_atomaa_mask
    lowerCamelCase__       : Optional[int]   					=						residx_atomaa_to_atomaa.long()

    # create the gather indices for mapping back
    lowerCamelCase__       : Union[str, Any]   					=						restype_atomaa_to_atomaa[protein_aatype]
    lowerCamelCase__       : int   					=						residx_atomaa_to_atomaa.long()

    # create the corresponding mask
    lowerCamelCase__       : List[Any]   					=						torch.zeros([21, 37]		,      dtype=torch.floataa		,      device=protein['aatype'].device					)
    for restype, restype_letter in enumerate(rc.restypes					):
        lowerCamelCase__       : Tuple   					=						rc.restype_atoa[restype_letter]
        lowerCamelCase__       : Tuple   					=						rc.residue_atoms[restype_name]
        for atom_name in atom_names:
            lowerCamelCase__       : Optional[Any]   					=						rc.atom_order[atom_name]
            lowerCamelCase__       : List[Any]   					=						1

    lowerCamelCase__       : Any   					=						restype_atomaa_mask[protein_aatype]
    lowerCamelCase__       : Tuple   					=						residx_atomaa_mask

    return protein


def 			SCREAMING_SNAKE_CASE (			_UpperCAmelCase					)     ->	Dict[str, np.ndarray]:
    lowerCamelCase__       : str   					=						tree_map(lambda _UpperCAmelCase					: torch.tensor(_UpperCAmelCase		,      device=batch['aatype'].device					)		,      _UpperCAmelCase		,      np.ndarray					)
    lowerCamelCase__       : List[str]   					=						tensor_tree_map(lambda _UpperCAmelCase					: np.array(_UpperCAmelCase					)		,      make_atomaa_masks(_UpperCAmelCase					)					)
    return out












def 			SCREAMING_SNAKE_CASE (			_UpperCAmelCase					)     ->	str:
    lowerCamelCase__       : Dict   					=						''
    for ch in key:
        if ch == " " or ch not in key_no_dups and ch.isalpha():
            key_no_dups += ch
    return key_no_dups


def 			SCREAMING_SNAKE_CASE (			_UpperCAmelCase					)     ->	dict[str, str]:
    lowerCamelCase__       : List[str]   					=						[chr(i + 65					) for i in range(26					)]
    # Remove duplicate characters from key
    lowerCamelCase__       : Any   					=						remove_duplicates(key.upper()					)
    lowerCamelCase__       : List[Any]   					=						len(_UpperCAmelCase					)
    # First fill cipher with key characters
    lowerCamelCase__       : Optional[int]   					=						{alphabet[i]: char for i, char in enumerate(_UpperCAmelCase					)}
    # Then map remaining characters in alphabet to
    # the alphabet from the beginning
    for i in range(len(_UpperCAmelCase					)		,      26					):
        lowerCamelCase__       : Any   					=						alphabet[i - offset]
        # Ensure we are not mapping letters to letters previously mapped
        while char in key:
            offset -= 1
            lowerCamelCase__       : Union[str, Any]   					=						alphabet[i - offset]
        lowerCamelCase__       : int   					=						char
    return cipher_alphabet


def 			SCREAMING_SNAKE_CASE (			_UpperCAmelCase		,      _UpperCAmelCase					)     ->	str:
    return "".join(cipher_map.get(_UpperCAmelCase		,      _UpperCAmelCase					) for ch in message.upper()					)


def 			SCREAMING_SNAKE_CASE (			_UpperCAmelCase		,      _UpperCAmelCase					)     ->	str:
    lowerCamelCase__       : List[str]   					=						{v: k for k, v in cipher_map.items()}
    return "".join(rev_cipher_map.get(_UpperCAmelCase		,      _UpperCAmelCase					) for ch in message.upper()					)


def 			SCREAMING_SNAKE_CASE (			)     ->	None:
    lowerCamelCase__       : str   					=						input('Enter message to encode or decode: '					).strip()
    lowerCamelCase__       : Union[str, Any]   					=						input('Enter keyword: '					).strip()
    lowerCamelCase__       : Dict   					=						input('Encipher or decipher? E/D:'					).strip()[0].lower()
    try:
        lowerCamelCase__       : Dict   					=						{'e': encipher, 'd': decipher}[option]
    except KeyError:
        raise KeyError('invalid input option'					)
    lowerCamelCase__       : int   					=						create_cipher_map(_UpperCAmelCase					)
    print(func(_UpperCAmelCase		,      _UpperCAmelCase					)					)


if __name__ == "__main__":
    import doctest

    doctest.testmod()
    main()





