



"""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


lowercase__    :  Any							    =	Mapping[str, np.ndarray]
lowercase__    :  Dict							    =	Mapping[str, Any]  # Is a nested dict.
lowercase__    :  Any							    =	0.01




@dataclasses.dataclass(frozen=lowerCAmelCase__)
class        _UpperCAmelCase       :
 _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 __lowercase			(							_a    ):
    snake_case_ :     Tuple				=	r'''(\[[A-Z]+\]\n)'''
    snake_case_ :     List[str]				=	[tag.strip() for tag in re.split(_a		,			_a    ) if len(_a    ) > 0]
    snake_case_ :     Iterator[Tuple[str, List[str]]]				=	zip(tags[0::2]		,			[l.split('''\n'''    ) for l in tags[1::2]]    )

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

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

    snake_case_ :     int				=	prot.parents
    snake_case_ :     Optional[int]				=	prot.parents_chain_index
    if parents is not None and parents_chain_index is not None:
        snake_case_ :     List[str]				=	[p for i, p in zip(_a		,			_a    ) if i == chain_id]

    if parents is None or len(_a    ) == 0:
        snake_case_ :     List[str]				=	['''N/A''']

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

    return pdb_headers




def __lowercase			(							_a		,			_a    ):
    snake_case_ :     List[str]				=	[]
    snake_case_ :     int				=	pdb_str.split('''\n'''    )

    snake_case_ :     Optional[int]				=	prot.remark
    if remark is not None:
        out_pdb_lines.append(f"REMARK {remark}"    )

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

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

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

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

    snake_case_ :     Union[str, Any]				=	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    ):
                snake_case_ :     List[Any]				=	parents_per_chain[chain_counter]
            else:
                snake_case_ :     List[str]				=	['''N/A''']

            out_pdb_lines.append(make_parent_line(_a    )    )

    return "\n".join(_a    )




def __lowercase			(							_a    ):
    snake_case_ :     str				=	residue_constants.restypes + ['''X''']

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

    snake_case_ :     Optional[int]				=	residue_constants.atom_types

    snake_case_ :     List[str]				=	[]

    snake_case_ :     List[Any]				=	prot.atom_mask
    snake_case_ :     Optional[int]				=	prot.aatype
    snake_case_ :     List[Any]				=	prot.atom_positions
    snake_case_ :     Dict				=	prot.residue_index.astype(np.intaa    )
    snake_case_ :     Tuple				=	prot.b_factors
    snake_case_ :     Tuple				=	prot.chain_index

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

    snake_case_ :     int				=	get_pdb_headers(_a    )
    if len(_a    ) > 0:
        pdb_lines.extend(_a    )

    snake_case_ :     List[str]				=	aatype.shape[0]
    snake_case_ :     Optional[Any]				=	1
    snake_case_ :     int				=	0
    snake_case_ :     Dict				=	string.ascii_uppercase
    snake_case_ :     List[str]				=	None
    # Add all atom sites.
    for i in range(_a    ):
        snake_case_ :     Optional[Any]				=	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

            snake_case_ :     Optional[int]				=	'''ATOM'''
            snake_case_ :     Any				=	atom_name if len(_a    ) == 4 else f" {atom_name}"
            snake_case_ :     int				=	''''''
            snake_case_ :     Any				=	''''''
            snake_case_ :     Tuple				=	1.00
            snake_case_ :     Tuple				=	atom_name[0]  # Protein supports only C, N, O, S, this works.
            snake_case_ :     Any				=	''''''

            snake_case_ :     Any				=	'''A'''
            if chain_index is not None:
                snake_case_ :     int				=	chain_tags[chain_index[i]]

            # PDB is a columnar format, every space matters here!
            snake_case_ :     Optional[int]				=	(
                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

        snake_case_ :     int				=	i == n - 1
        if chain_index is not None:
            if i != n - 1 and chain_index[i + 1] != prev_chain_index:
                snake_case_ :     List[Any]				=	True
                snake_case_ :     Union[str, Any]				=	chain_index[i + 1]

        if should_terminate:
            # Close the chain.
            snake_case_ :     Tuple				=	'''TER'''
            snake_case_ :     Optional[Any]				=	(
                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 __lowercase			(							_a    ):
    return residue_constants.STANDARD_ATOM_MASK[prot.aatype]






def __lowercase			(							_a		,			_a		,			_a = None		,			_a = None		,			_a = None		,			_a = None		,			_a = None		,			):
    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		,			)










"""simple docstring"""

import os
from shutil import copyfile
from typing import List, Optional, Tuple

from ...tokenization_utils_fast import PreTrainedTokenizerFast
from ...utils import is_sentencepiece_available, logging


if is_sentencepiece_available():
     from .tokenization_pegasus import PegasusTokenizer
else:
     lowercase__    :  int							    =	None


lowercase__    :  Any							    =	logging.get_logger(__name__)


lowercase__    :  List[str]							    =	'''▁'''

lowercase__    :  Optional[int]							    =	{'''vocab_file''': '''spiece.model''', '''tokenizer_file''': '''tokenizer.json'''}

lowercase__    :  str							    =	{
    '''vocab_file''': {'''google/pegasus-xsum''': '''https://huggingface.co/google/pegasus-xsum/resolve/main/spiece.model'''},
    '''tokenizer_file''': {
        '''google/pegasus-xsum''': '''https://huggingface.co/google/pegasus-xsum/resolve/main/tokenizer.json'''
    },
}

lowercase__    :  List[Any]							    =	{
    '''google/pegasus-xsum''': 5_12,
}




class        _UpperCAmelCase       (			lowerCAmelCase__):
 _lowerCAmelCase   :			List[str]							=		VOCAB_FILES_NAMES
 _lowerCAmelCase   :			List[str]							=		PRETRAINED_VOCAB_FILES_MAP
 _lowerCAmelCase   :			Any							=		PRETRAINED_POSITIONAL_EMBEDDINGS_SIZES
 _lowerCAmelCase   :			Tuple							=		PegasusTokenizer
 _lowerCAmelCase   :			str							=		["""input_ids""", """attention_mask"""]

 def __init__(     self		:       Any  ,     lowercase_		:       Optional[Any]=None  ,     lowercase_		:       int=None  ,     lowercase_		:       Tuple="<pad>"  ,     lowercase_		:       int="</s>"  ,     lowercase_		:       Tuple="<unk>"  ,     lowercase_		:       str="<mask_2>"  ,     lowercase_		:       Optional[Any]="<mask_1>"  ,     lowercase_		:       str=None  ,     lowercase_		:       List[str]=103  ,     **lowercase_		:       List[Any]  ,     ):
     snake_case_ :     Dict				=	offset

     if additional_special_tokens is not None:
         if not isinstance(lowercase_  ,     lowercase_				):
             raise TypeError(
                 f"additional_special_tokens should be of type {type(lowercase_				)}, but is"
                 f" {type(lowercase_				)}"				)

         snake_case_ :     str				=	(
             ([mask_token_sent] + additional_special_tokens)
             if mask_token_sent not in additional_special_tokens and mask_token_sent is not None
             else additional_special_tokens
         )
         # fill additional tokens with ..., <unk_token_102> in case not all additional tokens are already taken
         additional_special_tokens_extended += [
             f"<unk_{i}>" for i in range(len(lowercase_				)  ,     self.offset - 1				)
         ]

         if len(set(lowercase_				)				) != len(lowercase_				):
             raise ValueError(
                 '''Please make sure that the provided additional_special_tokens do not contain an incorrectly'''
                 f" shifted list of <unk_x> tokens. Found {additional_special_tokens_extended}."				)
         snake_case_ :     Union[str, Any]				=	additional_special_tokens_extended
     else:
         snake_case_ :     Dict				=	[mask_token_sent] if mask_token_sent is not None else []
         additional_special_tokens += [f"<unk_{i}>" for i in range(2  ,     self.offset				)]

     super().__init__(
         lowercase_  ,     tokenizer_file=lowercase_  ,     pad_token=lowercase_  ,     eos_token=lowercase_  ,     unk_token=lowercase_  ,     mask_token=lowercase_  ,     mask_token_sent=lowercase_  ,     offset=lowercase_  ,     additional_special_tokens=lowercase_  ,     **lowercase_  ,     )
     snake_case_ :     List[Any]				=	vocab_file
     snake_case_ :     List[Any]				=	False if not self.vocab_file else True

 def 						_snake_case					(     self		:       str  ,     lowercase_		:       Union[str, Any]				):
     snake_case_ :     Any				=	set(self.all_special_ids				)  # call it once instead of inside list comp
     all_special_ids.remove(self.unk_token_id				)  # <unk> is only sometimes special

     if all_special_ids != set(range(len(self.additional_special_tokens				) + 3				)				):
         raise ValueError(
             '''There should be 3 special tokens: mask_token, pad_token, and eos_token +'''
             f" {len(self.additional_special_tokens				)} additional_special_tokens, but got {all_special_ids}"				)

     return [1 if x in all_special_ids else 0 for x in seq]

 def 						_snake_case					(     self		:       int  ,     lowercase_		:       List  ,     lowercase_		:       Optional[List] = None  ,     lowercase_		:       bool = False				):
     if already_has_special_tokens:
         return self._special_token_mask(lowercase_				)
     elif token_ids_a is None:
         return self._special_token_mask(lowercase_				) + [1]
     else:
         return self._special_token_mask(token_ids_a + token_ids_a				) + [1]

 def 						_snake_case					(     self		:       List[Any]  ,     lowercase_		:       Optional[int]  ,     lowercase_		:       str=None				):
     if token_ids_a is None:
         return token_ids_a + [self.eos_token_id]
     # We don't expect to process pairs, but leave the pair logic for API consistency
     return token_ids_a + token_ids_a + [self.eos_token_id]






 def 						_snake_case					(     self		:       Optional[Any]  ,     lowercase_		:       str  ,     lowercase_		:       Optional[str] = None				):
     if not self.can_save_slow_tokenizer:
         raise ValueError(
             '''Your fast tokenizer does not have the necessary information to save the vocabulary for a slow '''
             '''tokenizer.'''				)

     if not os.path.isdir(lowercase_				):
         logger.error(f"Vocabulary path ({save_directory}) should be a directory"				)
         return
     snake_case_ :     Dict				=	os.path.join(
         lowercase_  ,     (filename_prefix + '''-''' if filename_prefix else '''''') + VOCAB_FILES_NAMES['''vocab_file''']				)

     if os.path.abspath(self.vocab_file				) != os.path.abspath(lowercase_				):
         copyfile(self.vocab_file  ,     lowercase_				)

     return (out_vocab_file,)





