






import copy

from ...configuration_utils import PretrainedConfig
from ...utils import add_start_docstrings


A_       :Tuple       =						R'\n    [`RagConfig`] stores the configuration of a *RagModel*. Configuration objects inherit from [`PretrainedConfig`] and\n    can be used to control the model outputs. Read the documentation from [`PretrainedConfig`] for more information.\n\n    Args:\n        title_sep (`str`, *optional*, defaults to  `" / "`):\n            Separator inserted between the title and the text of the retrieved document when calling [`RagRetriever`].\n        doc_sep (`str`, *optional*, defaults to  `" // "`):\n            Separator inserted between the text of the retrieved document and the original input when calling\n            [`RagRetriever`].\n        n_docs (`int`, *optional*, defaults to 5):\n            Number of documents to retrieve.\n        max_combined_length (`int`, *optional*, defaults to 300):\n            Max length of contextualized input returned by [`~RagRetriever.__call__`].\n        retrieval_vector_size (`int`, *optional*, defaults to 768):\n            Dimensionality of the document embeddings indexed by [`RagRetriever`].\n        retrieval_batch_size (`int`, *optional*, defaults to 8):\n            Retrieval batch size, defined as the number of queries issues concurrently to the faiss index encapsulated\n            [`RagRetriever`].\n        dataset (`str`, *optional*, defaults to `"wiki_dpr"`):\n            A dataset identifier of the indexed dataset in HuggingFace Datasets (list all available datasets and ids\n            using `datasets.list_datasets()`).\n        dataset_split (`str`, *optional*, defaults to `"train"`)\n            Which split of the `dataset` to load.\n        index_name (`str`, *optional*, defaults to `"compressed"`)\n            The index name of the index associated with the `dataset`. One can choose between `"legacy"`, `"exact"` and\n            `"compressed"`.\n        index_path (`str`, *optional*)\n            The path to the serialized faiss index on disk.\n        passages_path (`str`, *optional*):\n            A path to text passages compatible with the faiss index. Required if using\n            [`~models.rag.retrieval_rag.LegacyIndex`]\n        use_dummy_dataset (`bool`, *optional*, defaults to `False`)\n            Whether to load a "dummy" variant of the dataset specified by `dataset`.\n        label_smoothing (`float`, *optional*, defaults to 0.0):\n            Only relevant if `return_loss` is set to `True`. Controls the `epsilon` parameter value for label smoothing\n            in the loss calculation. If set to 0, no label smoothing is performed.\n        do_marginalize (`bool`, *optional*, defaults to `False`):\n            If `True`, the logits are marginalized over all documents by making use of\n            `torch.nn.functional.log_softmax`.\n        reduce_loss (`bool`, *optional*, defaults to `False`):\n            Whether or not to reduce the NLL loss using the `torch.Tensor.sum` operation.\n        do_deduplication (`bool`, *optional*, defaults to `True`):\n            Whether or not to deduplicate the generations from different context documents for a given input. Has to be\n            set to `False` if used while training with distributed backend.\n        exclude_bos_score (`bool`, *optional*, defaults to `False`):\n            Whether or not to disregard the BOS token when computing the loss.\n        output_retrieved(`bool`, *optional*, defaults to `False`):\n            If set to `True`, `retrieved_doc_embeds`, `retrieved_doc_ids`, `context_input_ids` and\n            `context_attention_mask` are returned. See returned tensors for more detail.\n        use_cache (`bool`, *optional*, defaults to `True`):\n            Whether or not the model should return the last key/values attentions (not used by all models).\n        forced_eos_token_id (`int`, *optional*):\n            The id of the token to force as the last generated token when `max_length` is reached. Usually set to\n            `eos_token_id`.\n'




@add_start_docstrings(lowercase_ )
class 				__A     (			lowercase_ ):





				"""simple docstring"""







				UpperCamelCase__ :      Any			 ="""rag"""
				UpperCamelCase__ :      List[Any]			 =True


				def __init__( self							,  lowerCamelCase__=None							,  lowerCamelCase__=True							,  lowerCamelCase__=None							,  lowerCamelCase__=None							,  lowerCamelCase__=None							,  lowerCamelCase__=None							,  lowerCamelCase__=None							,  lowerCamelCase__=" / "							,  lowerCamelCase__=" // "							,  lowerCamelCase__=5							,  lowerCamelCase__=300							,  lowerCamelCase__=768							,  lowerCamelCase__=8							,  lowerCamelCase__="wiki_dpr"							,  lowerCamelCase__="train"							,  lowerCamelCase__="compressed"							,  lowerCamelCase__=None							,  lowerCamelCase__=None							,  lowerCamelCase__=False							,  lowerCamelCase__=False							,  lowerCamelCase__=0.0							,  lowerCamelCase__=True							,  lowerCamelCase__=False							,  lowerCamelCase__=False							,  lowerCamelCase__=False							,  lowerCamelCase__=True							,  lowerCamelCase__=None							,  **lowerCamelCase__							,  ):




									"""simple docstring"""

									super().__init__(
									    bos_token_id=lowerCamelCase__							,  pad_token_id=lowerCamelCase__							,  eos_token_id=lowerCamelCase__							,  decoder_start_token_id=lowerCamelCase__							,  forced_eos_token_id=lowerCamelCase__							,  is_encoder_decoder=lowerCamelCase__							,  prefix=lowerCamelCase__							,  vocab_size=lowerCamelCase__							,  **lowerCamelCase__							,  )
									assert (
									    "question_encoder" in kwargs and "generator" in kwargs
									), "Config has to be initialized with question_encoder and generator config"
									__UpperCamelCase      :					Dict       		=kwargs.pop('question_encoder'    )
									__UpperCamelCase      :					Any       		=question_encoder_config.pop('model_type'    )
									__UpperCamelCase      :					Optional[Any]       		=kwargs.pop('generator'    )
									__UpperCamelCase      :					Union[str, Any]       		=decoder_config.pop('model_type'    )

									from ..auto.configuration_auto import AutoConfig

									__UpperCamelCase      :					List[str]       		=AutoConfig.for_model(lowerCamelCase__							,  **lowerCamelCase__    )
									__UpperCamelCase      :					Tuple       		=AutoConfig.for_model(lowerCamelCase__							,  **lowerCamelCase__    )

									__UpperCamelCase      :					Optional[Any]       		=reduce_loss
									__UpperCamelCase      :					Optional[int]       		=label_smoothing
									__UpperCamelCase      :					Optional[int]       		=exclude_bos_score
									__UpperCamelCase      :					int       		=do_marginalize

									__UpperCamelCase      :					str       		=title_sep
									__UpperCamelCase      :					Tuple       		=doc_sep
									__UpperCamelCase      :					List[str]       		=n_docs
									__UpperCamelCase      :					List[str]       		=max_combined_length

									__UpperCamelCase      :					Any       		=dataset
									__UpperCamelCase      :					Union[str, Any]       		=dataset_split
									__UpperCamelCase      :					List[str]       		=index_name

									__UpperCamelCase      :					List[Any]       		=retrieval_vector_size
									__UpperCamelCase      :					str       		=retrieval_batch_size
									__UpperCamelCase      :					List[str]       		=passages_path
									__UpperCamelCase      :					Union[str, Any]       		=index_path
									__UpperCamelCase      :					List[str]       		=use_dummy_dataset

									__UpperCamelCase      :					Union[str, Any]       		=output_retrieved

									__UpperCamelCase      :					List[str]       		=do_deduplication

									__UpperCamelCase      :					Tuple       		=use_cache

									if self.forced_eos_token_id is None:
														__UpperCamelCase      :					int       		=getattr(self.generator							,  'forced_eos_token_id'							,  lowerCamelCase__    )


				@classmethod
				def       __lowercase							( cls							,  lowerCamelCase__							,  lowerCamelCase__							,  **lowerCamelCase__    ):




									"""simple docstring"""

									return cls(question_encoder=question_encoder_config.to_dict()							,  generator=generator_config.to_dict()							,  **lowerCamelCase__    )







				def       __lowercase							( self    ):




									"""simple docstring"""

									__UpperCamelCase      :					List[Any]       		=copy.deepcopy(self.__dict__    )
									__UpperCamelCase      :					Any       		=self.question_encoder.to_dict()
									__UpperCamelCase      :					Optional[Any]       		=self.generator.to_dict()
									__UpperCamelCase      :					Optional[int]       		=self.__class__.model_type
									return output





'''simple docstring'''

import dataclasses
import re
import string
from typing import Any, Dict, Iterator, List, Mapping, Optional, Sequence, Tuple

import numpy as np

from . import residue_constants


lowerCamelCase							:   str  						=	Mapping[str, np.ndarray]
lowerCamelCase							:   List[Any]  						=	Mapping[str, Any]  # Is a nested dict.
lowerCamelCase							:   Any  						=	0.0_1
@dataclasses.dataclass(frozen=lowercase_     )
class   __lowerCAmelCase						:





      '''simple docstring'''






      lowerCAmelCase__					:     np.ndarray  # [num_res, num_atom_type, 3]

      # Amino-acid type for each residue represented as an integer between 0 and
      # 20, where 20 is 'X'.
      lowerCAmelCase__					:     np.ndarray  # [num_res]

      # Binary float mask to indicate presence of a particular atom. 1.0 if an atom
      # is present and 0.0 if not. This should be used for loss masking.
      lowerCAmelCase__					:     np.ndarray  # [num_res, num_atom_type]

      # Residue index as used in PDB. It is not necessarily continuous or 0-indexed.
      lowerCAmelCase__					:     np.ndarray  # [num_res]

      # B-factors, or temperature factors, of each residue (in sq. angstroms units),
      # representing the displacement of the residue from its ground truth mean
      # value.
      lowerCAmelCase__					:     np.ndarray  # [num_res, num_atom_type]

      # Chain indices for multi-chain predictions
      lowerCAmelCase__					:     Optional[np.ndarray]  					=							None

      # Optional remark about the protein. Included as a comment in output PDB
      # files
      lowerCAmelCase__					:     Optional[str]  					=							None

      # Templates used to generate this protein (prediction-only)
      lowerCAmelCase__					:     Optional[Sequence[str]]  					=							None

      # Chain corresponding to each parent
      lowerCAmelCase__					:     Optional[Sequence[int]]  					=							None






def _SCREAMING_SNAKE_CASE      (A       )       ->       Protein:






       """simple docstring"""







       lowercase__      			= R'''(\[[A-Z]+\]\n)'''
       lowercase__      			= [tag.strip() for tag in re.split(A  , A       ) if len(A       ) > 0]
       lowercase__      			= zip(tags[0::2]  , [l.split('''\n'''       ) for l in tags[1::2]]       )

       lowercase__      			= ["N", "CA", "C"]
       lowercase__      			= None
       lowercase__      			= None
       lowercase__      			= None
       for g in groups:
              if "[PRIMARY]" == g[0]:
                     lowercase__      			= g[1][0].strip()
                     for i in range(len(A       )       ):
                            if seq[i] not in residue_constants.restypes:
                                   lowercase__      			= '''X'''  # FIXME: strings are immutable
                     lowercase__      			= np.array(
                         [residue_constants.restype_order.get(A  , residue_constants.restype_num       ) for res_symbol in seq]       )
              elif "[TERTIARY]" == g[0]:
                     lowercase__      			= []
                     for axis in range(3       ):
                            tertiary.append(list(map(A  , g[1][axis].split()       )       )       )
                     lowercase__      			= np.array(A       )
                     lowercase__      			= np.zeros((len(tertiary[0]       ) // 3, residue_constants.atom_type_num, 3)       ).astype(np.floataa       )
                     for i, atom in enumerate(A       ):
                            lowercase__      			= np.transpose(tertiary_np[:, i::3]       )
                     atom_positions *= PICO_TO_ANGSTROM
              elif "[MASK]" == g[0]:
                     lowercase__      			= np.array(list(map({'''-''': 0, '''+''': 1}.get  , g[1][0].strip()       )       )       )
                     lowercase__      			= np.zeros(
                         (
                             len(A       ),
                             residue_constants.atom_type_num,
                         )       ).astype(np.floataa       )
                     for i, atom in enumerate(A       ):
                            lowercase__      			= 1
                     atom_mask *= mask[..., None]

       assert aatype is not None

       return Protein(
           atom_positions=A  , atom_mask=A  , aatype=A  , residue_index=np.arange(len(A       )       )  , b_factors=A  , )

def _SCREAMING_SNAKE_CASE      (A  , A = 0       )       ->       List[str]:






       """simple docstring"""







       lowercase__      			= []

       lowercase__      			= prot.remark
       if remark is not None:
              pdb_headers.append(f"REMARK {remark}"       )

       lowercase__      			= prot.parents
       lowercase__      			= prot.parents_chain_index
       if parents is not None and parents_chain_index is not None:
              lowercase__      			= [p for i, p in zip(A  , A       ) if i == chain_id]

       if parents is None or len(A       ) == 0:
              lowercase__      			= ['''N/A''']

       pdb_headers.append(f"PARENT {' '.join(A       )}"       )

       return pdb_headers

def _SCREAMING_SNAKE_CASE      (A  , A       )       ->       str:






       """simple docstring"""







       lowercase__      			= []
       lowercase__      			= pdb_str.split('''\n'''       )

       lowercase__      			= prot.remark
       if remark is not None:
              out_pdb_lines.append(f"REMARK {remark}"       )

       lowercase__      			= 42
       if prot.parents is not None and len(prot.parents       ) > 0:
              lowercase__      			= []
              if prot.parents_chain_index is not None:
                     lowercase__      			= {}
                     for p, i in zip(prot.parents  , prot.parents_chain_index       ):
                            parent_dict.setdefault(str(A       )  , []       )
                            parent_dict[str(A       )].append(A       )

                     lowercase__      			= max([int(A       ) for chain_idx in parent_dict]       )
                     for i in range(max_idx + 1       ):
                            lowercase__      			= parent_dict.get(str(A       )  , ['''N/A''']       )
                            parents_per_chain.append(A       )
              else:
                     parents_per_chain.append(list(prot.parents       )       )
       else:
              lowercase__      			= [['''N/A''']]

       def make_parent_line(A       ) -> str:
              return f"PARENT {' '.join(A       )}"

       out_pdb_lines.append(make_parent_line(parents_per_chain[0]       )       )

       lowercase__      			= 0
       for i, l in enumerate(A       ):
              if "PARENT" not in l and "REMARK" not in l:
                     out_pdb_lines.append(A       )
              if "TER" in l and "END" not in lines[i + 1]:
                     chain_counter += 1
                     if not chain_counter >= len(A       ):
                            lowercase__      			= parents_per_chain[chain_counter]
                     else:
                            lowercase__      			= ['''N/A''']

                     out_pdb_lines.append(make_parent_line(A       )       )

       return "\n".join(A       )

def _SCREAMING_SNAKE_CASE      (A       )       ->       str:






       """simple docstring"""







       lowercase__      			= residue_constants.restypes + ['''X''']

       def res_atoa(A       ) -> str:
              return residue_constants.restype_atoa.get(restypes[r]  , '''UNK'''       )

       lowercase__      			= residue_constants.atom_types

       lowercase__      			= []

       lowercase__      			= prot.atom_mask
       lowercase__      			= prot.aatype
       lowercase__      			= prot.atom_positions
       lowercase__      			= prot.residue_index.astype(np.intaa       )
       lowercase__      			= prot.b_factors
       lowercase__      			= prot.chain_index

       if np.any(aatype > residue_constants.restype_num       ):
              raise ValueError('''Invalid aatypes.'''       )

       lowercase__      			= get_pdb_headers(A       )
       if len(A       ) > 0:
              pdb_lines.extend(A       )

       lowercase__      			= aatype.shape[0]
       lowercase__      			= 1
       lowercase__      			= 0
       lowercase__      			= string.ascii_uppercase
       lowercase__      			= None
       # Add all atom sites.
       for i in range(A       ):
              lowercase__      			= res_atoa(aatype[i]       )
              for atom_name, pos, mask, b_factor in zip(A  , atom_positions[i]  , atom_mask[i]  , b_factors[i]       ):
                     if mask < 0.5:
                            continue

                     lowercase__      			= '''ATOM'''
                     lowercase__      			= atom_name if len(A       ) == 4 else f" {atom_name}"
                     lowercase__      			= ''''''
                     lowercase__      			= ''''''
                     lowercase__      			= 1.00
                     lowercase__      			= atom_name[0]  # Protein supports only C, N, O, S, this works.
                     lowercase__      			= ''''''

                     lowercase__      			= '''A'''
                     if chain_index is not None:
                            lowercase__      			= chain_tags[chain_index[i]]

                     # PDB is a columnar format, every space matters here!
                     lowercase__      			= (
                         f"{record_type:<6}{atom_index:>5} {name:<4}{alt_loc:>1}"
                         f"{res_name_a:>3} {chain_tag:>1}"
                         f"{residue_index[i]:>4}{insertion_code:>1}   "
                         f"{pos[0]:>8.3f}{pos[1]:>8.3f}{pos[2]:>8.3f}"
                         f"{occupancy:>6.2f}{b_factor:>6.2f}          "
                         f"{element:>2}{charge:>2}"
                     )
                     pdb_lines.append(A       )
                     atom_index += 1

              lowercase__      			= i == n - 1
              if chain_index is not None:
                     if i != n - 1 and chain_index[i + 1] != prev_chain_index:
                            lowercase__      			= True
                            lowercase__      			= chain_index[i + 1]

              if should_terminate:
                     # Close the chain.
                     lowercase__      			= '''TER'''
                     lowercase__      			= (
                         f"{chain_end:<6}{atom_index:>5}      {res_atoa(aatype[i]       ):>3} {chain_tag:>1}{residue_index[i]:>4}"
                     )
                     pdb_lines.append(A       )
                     atom_index += 1

                     if i != n - 1:
                            # "prev" is a misnomer here. This happens at the beginning of
                            # each new chain.
                            pdb_lines.extend(get_pdb_headers(A  , A       )       )

       pdb_lines.append('''END'''       )
       pdb_lines.append(''''''       )
       return "\n".join(A       )

def _SCREAMING_SNAKE_CASE      (A       )       ->       np.ndarray:






       """simple docstring"""







       return residue_constants.STANDARD_ATOM_MASK[prot.aatype]

def _SCREAMING_SNAKE_CASE      (A  , A  , A = None  , A = None  , A = None  , A = None  , A = None  , )       ->       Protein:






       """simple docstring"""







       return Protein(
           aatype=features['''aatype''']  , atom_positions=result['''final_atom_positions''']  , atom_mask=result['''final_atom_mask''']  , residue_index=features['''residue_index'''] + 1  , b_factors=b_factors if b_factors is not None else np.zeros_like(result['''final_atom_mask''']       )  , chain_index=A  , remark=A  , parents=A  , parents_chain_index=A  , )




