"""simple docstring"""

# flake8: noqa
# Lint as: python3

from typing import Dict, List, Optional, Type

from .. import config
from ..utils import logging
from .formatting import (
    ArrowFormatter,
    CustomFormatter,
    Formatter,
    PandasFormatter,
    PythonFormatter,
    TensorFormatter,
    format_table,
    query_table,
)
from .np_formatter import NumpyFormatter


UpperCAmelCase       =  logging.get_logger(__name__)

UpperCAmelCase       =  {}
UpperCAmelCase       =  {}
UpperCAmelCase       =  {}






def      lowercase		(						a__	:		Any ,  a__	:		str ,  a__	:		List[Any] = None ,  )						->   int:
					_UpperCamelCase      						=	aliases if aliases is not None else []
					if format_type in _FORMAT_TYPES:
										logger.warning(
										    F'''Overwriting format type \'{format_type}\' ({_FORMAT_TYPES[format_type].__name__} -> {formatter_cls.__name__})'''     )
					_UpperCamelCase      						=	formatter_cls
					for alias in set(aliases + [format_type]     ):
										if alias in _FORMAT_TYPES_ALIASES:
															logger.warning(
															    F'''Overwriting format type alias \'{alias}\' ({_FORMAT_TYPES_ALIASES[alias]} -> {format_type})'''     )
										_UpperCamelCase      						=	format_type






def      lowercase		(						a__	:		int ,  a__	:		Union[str, Any] ,  a__	:		List[Any] = None     )						->   List[Any]:
					_UpperCamelCase      						=	aliases if aliases is not None else []
					for alias in set(aliases + [format_type]     ):
										_UpperCamelCase      						=	unavailable_error


# Here we define all the available formatting functions that can be used by `Dataset.set_format`
_register_formatter(PythonFormatter, None, aliases=["""python"""])
_register_formatter(ArrowFormatter, """arrow""", aliases=["""pa""", """pyarrow"""])
_register_formatter(NumpyFormatter, """numpy""", aliases=["""np"""])
_register_formatter(PandasFormatter, """pandas""", aliases=["""pd"""])
_register_formatter(CustomFormatter, """custom""")

if config.TORCH_AVAILABLE:
		from .torch_formatter import TorchFormatter

		_register_formatter(TorchFormatter, """torch""", aliases=["""pt""", """pytorch"""])
else:
		UpperCAmelCase       =  ValueError("""PyTorch needs to be installed to be able to return PyTorch tensors.""")
		_register_unavailable_formatter(_torch_error, """torch""", aliases=["""pt""", """pytorch"""])

if config.TF_AVAILABLE:
		from .tf_formatter import TFFormatter

		_register_formatter(TFFormatter, """tensorflow""", aliases=["""tf"""])
else:
		UpperCAmelCase       =  ValueError("""Tensorflow needs to be installed to be able to return Tensorflow tensors.""")
		_register_unavailable_formatter(_tf_error, """tensorflow""", aliases=["""tf"""])

if config.JAX_AVAILABLE:
		from .jax_formatter import JaxFormatter

		_register_formatter(JaxFormatter, """jax""", aliases=[])
else:
		UpperCAmelCase       =  ValueError("""JAX needs to be installed to be able to return JAX arrays.""")
		_register_unavailable_formatter(_jax_error, """jax""", aliases=[])






def      lowercase		(						a__	:		List[Any]     )						->   Any:
					if format_type in _FORMAT_TYPES_ALIASES:
										return _FORMAT_TYPES_ALIASES[format_type]
					else:
										return format_type






def      lowercase		(						a__	:		Tuple ,  **a__	:		List[Any]     )						->   Optional[int]:
					_UpperCamelCase      						=	get_format_type_from_alias(lowercase__     )
					if format_type in _FORMAT_TYPES:
										return _FORMAT_TYPES[format_type](**lowercase__     )
					if format_type in _FORMAT_TYPES_ALIASES_UNAVAILABLE:
										raise _FORMAT_TYPES_ALIASES_UNAVAILABLE[format_type]
					else:
										raise ValueError(
										    F'''Return type should be None or selected in {list(type for type in _FORMAT_TYPES.keys() if type != None     )}, but got \'{format_type}\''''     )



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 		_lowercase (     lowercase__						):
      __lowerCAmelCase					:						str					=					[]
      __lowerCAmelCase					:						List[Any]					=					[]
      __lowerCAmelCase					:						str					=					[]

      for rt in rc.restypes:
            __lowerCAmelCase					:						List[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					:						List[str]					=					{name: i for i, name in enumerate(lowercase__						)}
            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] * 1_4						)
      restype_atomaa_to_atomaa_list.append([0] * 3_7						)
      restype_atomaa_mask_list.append([0.0] * 1_4						)

      __lowerCAmelCase					:						List[Any]					=					torch.tensor(
          lowercase__   ,	dtype=torch.intaa   ,	device=protein['''aatype'''].device   ,	)
      __lowerCAmelCase					:						Optional[Any]					=					torch.tensor(
          lowercase__   ,	dtype=torch.intaa   ,	device=protein['''aatype'''].device   ,	)
      __lowerCAmelCase					:						Tuple					=					torch.tensor(
          lowercase__   ,	dtype=torch.floataa   ,	device=protein['''aatype'''].device   ,	)
      __lowerCAmelCase					:						List[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					:						Any					=					restype_atomaa_to_atomaa[protein_aatype]
      __lowerCAmelCase					:						Union[str, Any]					=					restype_atomaa_mask[protein_aatype]

      __lowerCAmelCase					:						int					=					residx_atomaa_mask
      __lowerCAmelCase					:						List[str]					=					residx_atomaa_to_atomaa.long()

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

      # create the corresponding mask
      __lowerCAmelCase					:						str					=					torch.zeros([2_1, 3_7]   ,	dtype=torch.floataa   ,	device=protein['''aatype'''].device						)
      for restype, restype_letter in enumerate(rc.restypes						):
            __lowerCAmelCase					:						Optional[int]					=					rc.restype_atoa[restype_letter]
            __lowerCAmelCase					:						Optional[Any]					=					rc.residue_atoms[restype_name]
            for atom_name in atom_names:
                  __lowerCAmelCase					:						str					=					rc.atom_order[atom_name]
                  __lowerCAmelCase					:						List[Any]					=					1

      __lowerCAmelCase					:						Union[str, Any]					=					restype_atomaa_mask[protein_aatype]
      __lowerCAmelCase					:						Any					=					residx_atomaa_mask

      return protein







def 		_lowercase (     lowercase__						):
      __lowerCAmelCase					:						Dict					=					tree_map(lambda lowercase__						: torch.tensor(lowercase__   ,	device=batch['''aatype'''].device						)   ,	lowercase__   ,	np.ndarray						)
      __lowerCAmelCase					:						Tuple					=					tensor_tree_map(lambda lowercase__						: np.array(lowercase__						)   ,	make_atomaa_masks(lowercase__						)						)
      return out


