





import asyncio
import os
import re
import sys
import tempfile
import unittest
from contextlib import contextmanager
from copy import deepcopy
from distutils.util import strtobool
from enum import Enum
from importlib.util import find_spec
from pathlib import Path
from unittest.mock import patch

import pyarrow as pa
import pytest
import requests
from packaging import version

from datasets import config


if config.PY_VERSION < version.parse("""3.8"""):
    import importlib_metadata
else:
    import importlib.metadata as importlib_metadata


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase		,			_UpperCAmelCase=False				)    ->  Tuple:
    try:
        lowerCamelCase__					:   Dict      				=	os.environ[key]
    except KeyError:
        # KEY isn't set, default to `default`.
        lowerCamelCase__					:   str      				=	default
    else:
        # KEY is set, convert it to True or False.
        try:
            lowerCamelCase__					:   Optional[Any]      				=	strtobool(_UpperCAmelCase				)
        except ValueError:
            # More values are supported, but let's keep the message simple.
            raise ValueError(F"""If set, {key} must be yes or no."""				)
    return _value


_UpperCAmelCase       : Tuple			     =       parse_flag_from_env("""RUN_SLOW""", default=False)
_UpperCAmelCase       : Union[str, Any]			     =       parse_flag_from_env("""RUN_REMOTE""", default=False)
_UpperCAmelCase       : Optional[Any]			     =       parse_flag_from_env("""RUN_LOCAL""", default=True)
_UpperCAmelCase       : Dict			     =       parse_flag_from_env("""RUN_PACKAGED""", default=True)

# Compression
_UpperCAmelCase       : int			     =       pytest.mark.skipif(not config.LZ4_AVAILABLE, reason="""test requires lz4""")
_UpperCAmelCase       : Optional[Any]			     =       pytest.mark.skipif(not config.PY7ZR_AVAILABLE, reason="""test requires py7zr""")
_UpperCAmelCase       : str			     =       pytest.mark.skipif(not config.ZSTANDARD_AVAILABLE, reason="""test requires zstandard""")

# Audio
_UpperCAmelCase       : int			     =       pytest.mark.skipif(
    # On Windows and OS X, soundfile installs sndfile
    find_spec("""soundfile""") is None or version.parse(importlib_metadata.version("""soundfile""")) < version.parse("""0.12.0"""),
    reason="""test requires sndfile>=0.12.1: 'pip install \"soundfile>=0.12.1\"'; """,
)

# Beam
_UpperCAmelCase       : List[str]			     =       pytest.mark.skipif(
    not config.BEAM_AVAILABLE or config.DILL_VERSION >= version.parse("""0.3.2"""),
    reason="""test requires apache-beam and a compatible dill version""",
)

# Dill-cloudpickle compatibility
_UpperCAmelCase       : List[str]			     =       pytest.mark.skipif(
    config.DILL_VERSION <= version.parse("""0.3.2"""),
    reason="""test requires dill>0.3.2 for cloudpickle compatibility""",
)

# Windows
_UpperCAmelCase       : int			     =       pytest.mark.skipif(
    sys.platform == """win32""",
    reason="""test should not be run on Windows""",
)


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase				)    ->  Dict:
    try:
        import faiss  # noqa
    except ImportError:
        lowerCamelCase__					:   List[Any]      				=	unittest.skip('test requires faiss'				)(_UpperCAmelCase				)
    return test_case


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase				)    ->  Union[str, Any]:
    try:
        import regex  # noqa
    except ImportError:
        lowerCamelCase__					:   int      				=	unittest.skip('test requires regex'				)(_UpperCAmelCase				)
    return test_case


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase				)    ->  str:
    try:
        import elasticsearch  # noqa
    except ImportError:
        lowerCamelCase__					:   Optional[Any]      				=	unittest.skip('test requires elasticsearch'				)(_UpperCAmelCase				)
    return test_case


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase				)    ->  str:
    try:
        import sqlalchemy  # noqa
    except ImportError:
        lowerCamelCase__					:   Dict      				=	unittest.skip('test requires sqlalchemy'				)(_UpperCAmelCase				)
    return test_case


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase				)    ->  List[Any]:
    if not config.TORCH_AVAILABLE:
        lowerCamelCase__					:   int      				=	unittest.skip('test requires PyTorch'				)(_UpperCAmelCase				)
    return test_case


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase				)    ->  Union[str, Any]:
    if not config.TF_AVAILABLE:
        lowerCamelCase__					:   List[Any]      				=	unittest.skip('test requires TensorFlow'				)(_UpperCAmelCase				)
    return test_case


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase				)    ->  str:
    if not config.JAX_AVAILABLE:
        lowerCamelCase__					:   Any      				=	unittest.skip('test requires JAX'				)(_UpperCAmelCase				)
    return test_case


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase				)    ->  Tuple:
    if not config.PIL_AVAILABLE:
        lowerCamelCase__					:   Optional[int]      				=	unittest.skip('test requires Pillow'				)(_UpperCAmelCase				)
    return test_case


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase				)    ->  Optional[int]:
    try:
        import transformers  # noqa F401
    except ImportError:
        return unittest.skip('test requires transformers'				)(_UpperCAmelCase				)
    else:
        return test_case


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase				)    ->  int:
    try:
        import tiktoken  # noqa F401
    except ImportError:
        return unittest.skip('test requires tiktoken'				)(_UpperCAmelCase				)
    else:
        return test_case


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase				)    ->  Union[str, Any]:
    try:
        import spacy  # noqa F401
    except ImportError:
        return unittest.skip('test requires spacy'				)(_UpperCAmelCase				)
    else:
        return test_case


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase				)    ->  Optional[Any]:

    def _require_spacy_model(_UpperCAmelCase				):
        try:
            import spacy  # noqa F401

            spacy.load(_UpperCAmelCase				)
        except ImportError:
            return unittest.skip('test requires spacy'				)(_UpperCAmelCase				)
        except OSError:
            return unittest.skip('test requires spacy model \'{}\''.format(_UpperCAmelCase				)				)(_UpperCAmelCase				)
        else:
            return test_case

    return _require_spacy_model


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase				)    ->  int:
    try:
        import pyspark  # noqa F401
    except ImportError:
        return unittest.skip('test requires pyspark'				)(_UpperCAmelCase				)
    else:
        return test_case


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase				)    ->  List[Any]:
    try:
        import joblibspark  # noqa F401
    except ImportError:
        return unittest.skip('test requires joblibspark'				)(_UpperCAmelCase				)
    else:
        return test_case


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase				)    ->  Optional[int]:
    if not _run_slow_tests or _run_slow_tests == 0:
        lowerCamelCase__					:   List[str]      				=	unittest.skip('test is slow'				)(_UpperCAmelCase				)
    return test_case


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase				)    ->  Union[str, Any]:
    if not _run_local_tests or _run_local_tests == 0:
        lowerCamelCase__					:   Union[str, Any]      				=	unittest.skip('test is local'				)(_UpperCAmelCase				)
    return test_case


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase				)    ->  Union[str, Any]:
    if not _run_packaged_tests or _run_packaged_tests == 0:
        lowerCamelCase__					:   Union[str, Any]      				=	unittest.skip('test is packaged'				)(_UpperCAmelCase				)
    return test_case


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase				)    ->  Dict:
    if not _run_remote_tests or _run_remote_tests == 0:
        lowerCamelCase__					:   List[str]      				=	unittest.skip('test requires remote'				)(_UpperCAmelCase				)
    return test_case


def  SCREAMING_SNAKE_CASE   ( *_UpperCAmelCase				)    ->  Union[str, Any]:
    def decorate(cls				):
        for name, fn in cls.__dict__.items():
            if callable(_UpperCAmelCase				) and name.startswith('test'				):
                for decorator in decorators:
                    lowerCamelCase__					:   int      				=	decorator(_UpperCAmelCase				)
                setattr(cls		,			_UpperCAmelCase		,			_UpperCAmelCase				)
        return cls

    return decorate

class      lowerCAmelCase							(      __UpperCamelCase    ):
 pass


class      lowerCAmelCase							(      __UpperCamelCase    ):
 UpperCAmelCase__									=	0
 UpperCAmelCase__									=	1
 UpperCAmelCase__									=	2


@contextmanager
def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase=OfflineSimulationMode.CONNECTION_FAILS		,			_UpperCAmelCase=1e-16				)    ->  str:
    lowerCamelCase__					:   List[Any]      				=	requests.Session().request

    def timeout_request(_UpperCAmelCase		,			_UpperCAmelCase		,			_UpperCAmelCase		,			**_UpperCAmelCase				):
        # Change the url to an invalid url so that the connection hangs
        lowerCamelCase__					:   Optional[Any]      				=	'https://10.255.255.1'
        if kwargs.get('timeout'				) is None:
            raise RequestWouldHangIndefinitelyError(
                F"""Tried a call to {url} in offline mode with no timeout set. Please set a timeout."""				)
        lowerCamelCase__					:   Union[str, Any]      				=	timeout
        try:
            return online_request(_UpperCAmelCase		,			_UpperCAmelCase		,			**_UpperCAmelCase				)
        except Exception as e:
            # The following changes in the error are just here to make the offline timeout error prettier
            lowerCamelCase__					:   Tuple      				=	url
            lowerCamelCase__					:   int      				=	e.args[0]
            lowerCamelCase__					:   Any      				=	(max_retry_error.args[0].replace('10.255.255.1'		,			F"""OfflineMock[{url}]"""				),)
            lowerCamelCase__					:   int      				=	(max_retry_error,)
            raise

    def raise_connection_error(_UpperCAmelCase		,			_UpperCAmelCase		,			**_UpperCAmelCase				):
        raise requests.ConnectionError('Offline mode is enabled.'		,			request=_UpperCAmelCase				)

    if mode is OfflineSimulationMode.CONNECTION_FAILS:
        with patch('requests.Session.send'		,			_UpperCAmelCase				):
            yield
    elif mode is OfflineSimulationMode.CONNECTION_TIMES_OUT:
        # inspired from https://stackoverflow.com/a/904609
        with patch('requests.Session.request'		,			_UpperCAmelCase				):
            yield
    elif mode is OfflineSimulationMode.HF_DATASETS_OFFLINE_SET_TO_1:
        with patch('datasets.config.HF_DATASETS_OFFLINE'		,			_UpperCAmelCase				):
            yield
    else:
        raise ValueError('Please use a value from the OfflineSimulationMode enum.'				)


@contextmanager
def  SCREAMING_SNAKE_CASE   ( *_UpperCAmelCase		,			**_UpperCAmelCase				)    ->  Optional[int]:
    lowerCamelCase__					:   Dict      				=	str(Path().resolve()				)
    with tempfile.TemporaryDirectory(*_UpperCAmelCase		,			**_UpperCAmelCase				) as tmp_dir:
        try:
            os.chdir(_UpperCAmelCase				)
            yield
        finally:
            os.chdir(_UpperCAmelCase				)


@contextmanager
def  SCREAMING_SNAKE_CASE   ( )    ->  Dict:
    import gc

    gc.collect()
    lowerCamelCase__					:   str      				=	pa.total_allocated_bytes()
    yield
    assert pa.total_allocated_bytes() - previous_allocated_memory > 0, "Arrow memory didn't increase."


@contextmanager
def  SCREAMING_SNAKE_CASE   ( )    ->  Union[str, Any]:
    import gc

    gc.collect()
    lowerCamelCase__					:   Tuple      				=	pa.total_allocated_bytes()
    yield
    assert pa.total_allocated_bytes() - previous_allocated_memory <= 0, "Arrow memory wasn't expected to increase."


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase		,			_UpperCAmelCase				)    ->  str:
    return deepcopy(_UpperCAmelCase				).integers(0		,			100		,			10				).tolist() == deepcopy(_UpperCAmelCase				).integers(0		,			100		,			10				).tolist()


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase				)    ->  int:
    import decorator
    from requests.exceptions import HTTPError

    def _wrapper(_UpperCAmelCase		,			*_UpperCAmelCase		,			**_UpperCAmelCase				):
        try:
            return func(*_UpperCAmelCase		,			**_UpperCAmelCase				)
        except HTTPError as err:
            if str(_UpperCAmelCase				).startswith('500'				) or str(_UpperCAmelCase				).startswith('502'				):
                pytest.xfail(str(_UpperCAmelCase				)				)
            raise err

    return decorator.decorator(_wrapper		,			_UpperCAmelCase				)

class      lowerCAmelCase							:
 def __init__(   self						:   List[str]    ,  UpperCAmelCase						:   Any    ,  UpperCAmelCase						:   Union[str, Any]    ,  UpperCAmelCase						:   int			)    ->			Optional[Any]:
     lowerCamelCase__					:   Optional[int]      				=	returncode
     lowerCamelCase__					:   str      				=	stdout
     lowerCamelCase__					:   Dict      				=	stderr


async def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase		,			_UpperCAmelCase				)    ->  Optional[Any]:
    while True:
        lowerCamelCase__					:   Dict      				=	await stream.readline()
        if line:
            callback(_UpperCAmelCase				)
        else:
            break


async def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase		,			_UpperCAmelCase=None		,			_UpperCAmelCase=None		,			_UpperCAmelCase=None		,			_UpperCAmelCase=False		,			_UpperCAmelCase=False				)    ->  _RunOutput:
    if echo:
        print('\nRunning: '		,			' '.join(_UpperCAmelCase				)				)

    lowerCamelCase__					:   Dict      				=	await asyncio.create_subprocess_exec(
        cmd[0]		,			*cmd[1:]		,			stdin=_UpperCAmelCase		,			stdout=asyncio.subprocess.PIPE		,			stderr=asyncio.subprocess.PIPE		,			env=_UpperCAmelCase		,			)

    # note: there is a warning for a possible deadlock when using `wait` with huge amounts of data in the pipe
    # https://docs.python.org/3/library/asyncio-subprocess.html#asyncio.asyncio.subprocess.Process.wait
    #
    # If it starts hanging, will need to switch to the following code. The problem is that no data
    # will be seen until it's done and if it hangs for example there will be no debug info.
    # out, err = await p.communicate()
    # return _RunOutput(p.returncode, out, err)

    lowerCamelCase__					:   Optional[int]      				=	[]
    lowerCamelCase__					:   List[Any]      				=	[]

    def tee(_UpperCAmelCase		,			_UpperCAmelCase		,			_UpperCAmelCase		,			_UpperCAmelCase=""				):
        lowerCamelCase__					:   int      				=	line.decode('utf-8'				).rstrip()
        sink.append(_UpperCAmelCase				)
        if not quiet:
            print(_UpperCAmelCase		,			_UpperCAmelCase		,			file=_UpperCAmelCase				)

    # XXX: the timeout doesn't seem to make any difference here
    await asyncio.wait(
        [
            _read_stream(p.stdout		,			lambda _UpperCAmelCase				: tee(_UpperCAmelCase		,			_UpperCAmelCase		,			sys.stdout		,			label='stdout:'				)				),
            _read_stream(p.stderr		,			lambda _UpperCAmelCase				: tee(_UpperCAmelCase		,			_UpperCAmelCase		,			sys.stderr		,			label='stderr:'				)				),
        ]		,			timeout=_UpperCAmelCase		,			)
    return _RunOutput(await p.wait()		,			_UpperCAmelCase		,			_UpperCAmelCase				)


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase		,			_UpperCAmelCase=None		,			_UpperCAmelCase=None		,			_UpperCAmelCase=180		,			_UpperCAmelCase=False		,			_UpperCAmelCase=True				)    ->  _RunOutput:
    lowerCamelCase__					:   Tuple      				=	asyncio.get_event_loop()
    lowerCamelCase__					:   Optional[int]      				=	loop.run_until_complete(
        _stream_subprocess(_UpperCAmelCase		,			env=_UpperCAmelCase		,			stdin=_UpperCAmelCase		,			timeout=_UpperCAmelCase		,			quiet=_UpperCAmelCase		,			echo=_UpperCAmelCase				)				)

    lowerCamelCase__					:   Any      				=	' '.join(_UpperCAmelCase				)
    if result.returncode > 0:
        lowerCamelCase__					:   List[str]      				=	'\n'.join(result.stderr				)
        raise RuntimeError(
            F"""'{cmd_str}' failed with returncode {result.returncode}\n\n"""
            F"""The combined stderr from workers follows:\n{stderr}"""				)

    # check that the subprocess actually did run and produced some output, should the test rely on
    # the remote side to do the testing
    if not result.stdout and not result.stderr:
        raise RuntimeError(F"""'{cmd_str}' produced no output."""				)

    return result


def  SCREAMING_SNAKE_CASE   ( )    ->  List[Any]:
    lowerCamelCase__					:   List[Any]      				=	os.environ.get('PYTEST_XDIST_WORKER'		,			'gw0'				)
    lowerCamelCase__					:   Dict      				=	re.sub(r'^gw'		,			''		,			_UpperCAmelCase		,			0		,			re.M				)
    return int(_UpperCAmelCase				)


def  SCREAMING_SNAKE_CASE   ( )    ->  Optional[int]:
    lowerCamelCase__					:   Any      				=	2_9500
    lowerCamelCase__					:   List[str]      				=	pytest_xdist_worker_id()
    return port + uniq_delta












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


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

@dataclasses.dataclass(frozen=__UpperCamelCase    )
class      lowerCAmelCase							:
 UpperCAmelCase__									=	42  # [num_res, num_atom_type, 3]

 # Amino-acid type for each residue represented as an integer between 0 and
 # 20, where 20 is 'X'.
 UpperCAmelCase__									=	42  # [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.
 UpperCAmelCase__									=	42  # [num_res, num_atom_type]

 # Residue index as used in PDB. It is not necessarily continuous or 0-indexed.
 UpperCAmelCase__									=	42  # [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.
 UpperCAmelCase__									=	42  # [num_res, num_atom_type]

 # Chain indices for multi-chain predictions
 UpperCAmelCase__									=	None

 # Optional remark about the protein. Included as a comment in output PDB
 # files
 UpperCAmelCase__									=	None

 # Templates used to generate this protein (prediction-only)
 UpperCAmelCase__									=	None

 # Chain corresponding to each parent
 UpperCAmelCase__									=	None


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase				)    ->  Protein:
    lowerCamelCase__					:   Optional[int]      				=	r'(\[[A-Z]+\]\n)'
    lowerCamelCase__					:   List[str]      				=	[tag.strip() for tag in re.split(_UpperCAmelCase		,			_UpperCAmelCase				) if len(_UpperCAmelCase				) > 0]
    lowerCamelCase__					:   Iterator[Tuple[str, List[str]]]      				=	zip(tags[0::2]		,			[l.split('\n'				) for l in tags[1::2]]				)

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

    assert aatype is not None

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


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase		,			_UpperCAmelCase = 0				)    ->  List[str]:
    lowerCamelCase__					:   List[str]      				=	[]

    lowerCamelCase__					:   Dict      				=	prot.remark
    if remark is not None:
        pdb_headers.append(F"""REMARK {remark}"""				)

    lowerCamelCase__					:   str      				=	prot.parents
    lowerCamelCase__					:   Union[str, Any]      				=	prot.parents_chain_index
    if parents is not None and parents_chain_index is not None:
        lowerCamelCase__					:   Any      				=	[p for i, p in zip(_UpperCAmelCase		,			_UpperCAmelCase				) if i == chain_id]

    if parents is None or len(_UpperCAmelCase				) == 0:
        lowerCamelCase__					:   List[Any]      				=	['N/A']

    pdb_headers.append(F"""PARENT {" ".join(_UpperCAmelCase				)}"""				)

    return pdb_headers


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase		,			_UpperCAmelCase				)    ->  str:
    lowerCamelCase__					:   List[str]      				=	[]
    lowerCamelCase__					:   str      				=	pdb_str.split('\n'				)

    lowerCamelCase__					:   int      				=	prot.remark
    if remark is not None:
        out_pdb_lines.append(F"""REMARK {remark}"""				)

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

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

    def make_parent_line(_UpperCAmelCase				) -> str:
        return F"""PARENT {" ".join(_UpperCAmelCase				)}"""

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

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

            out_pdb_lines.append(make_parent_line(_UpperCAmelCase				)				)

    return "\n".join(_UpperCAmelCase				)


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase				)    ->  str:
    lowerCamelCase__					:   Tuple      				=	residue_constants.restypes + ['X']

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

    lowerCamelCase__					:   int      				=	residue_constants.atom_types

    lowerCamelCase__					:   List[str]      				=	[]

    lowerCamelCase__					:   Union[str, Any]      				=	prot.atom_mask
    lowerCamelCase__					:   Union[str, Any]      				=	prot.aatype
    lowerCamelCase__					:   int      				=	prot.atom_positions
    lowerCamelCase__					:   List[Any]      				=	prot.residue_index.astype(np.intaa				)
    lowerCamelCase__					:   Optional[int]      				=	prot.b_factors
    lowerCamelCase__					:   Any      				=	prot.chain_index

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

    lowerCamelCase__					:   List[Any]      				=	get_pdb_headers(_UpperCAmelCase				)
    if len(_UpperCAmelCase				) > 0:
        pdb_lines.extend(_UpperCAmelCase				)

    lowerCamelCase__					:   Union[str, Any]      				=	aatype.shape[0]
    lowerCamelCase__					:   Optional[Any]      				=	1
    lowerCamelCase__					:   str      				=	0
    lowerCamelCase__					:   Tuple      				=	string.ascii_uppercase
    lowerCamelCase__					:   str      				=	None
    # Add all atom sites.
    for i in range(_UpperCAmelCase				):
        lowerCamelCase__					:   List[Any]      				=	res_atoa(aatype[i]				)
        for atom_name, pos, mask, b_factor in zip(_UpperCAmelCase		,			atom_positions[i]		,			atom_mask[i]		,			b_factors[i]				):
            if mask < 0.5:
                continue

            lowerCamelCase__					:   Union[str, Any]      				=	'ATOM'
            lowerCamelCase__					:   Optional[int]      				=	atom_name if len(_UpperCAmelCase				) == 4 else F""" {atom_name}"""
            lowerCamelCase__					:   Any      				=	''
            lowerCamelCase__					:   Optional[Any]      				=	''
            lowerCamelCase__					:   str      				=	1.00
            lowerCamelCase__					:   str      				=	atom_name[0]  # Protein supports only C, N, O, S, this works.
            lowerCamelCase__					:   List[str]      				=	''

            lowerCamelCase__					:   str      				=	'A'
            if chain_index is not None:
                lowerCamelCase__					:   List[Any]      				=	chain_tags[chain_index[i]]

            # PDB is a columnar format, every space matters here!
            lowerCamelCase__					:   Union[str, Any]      				=	(
                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(_UpperCAmelCase				)
            atom_index += 1

        lowerCamelCase__					:   Dict      				=	i == n - 1
        if chain_index is not None:
            if i != n - 1 and chain_index[i + 1] != prev_chain_index:
                lowerCamelCase__					:   List[Any]      				=	True
                lowerCamelCase__					:   List[str]      				=	chain_index[i + 1]

        if should_terminate:
            # Close the chain.
            lowerCamelCase__					:   int      				=	'TER'
            lowerCamelCase__					:   Any      				=	(
                F"""{chain_end:<6}{atom_index:>5}      {res_atoa(aatype[i]				):>3} {chain_tag:>1}{residue_index[i]:>4}"""
            )
            pdb_lines.append(_UpperCAmelCase				)
            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(_UpperCAmelCase		,			_UpperCAmelCase				)				)

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


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase				)    ->  np.ndarray:
    return residue_constants.STANDARD_ATOM_MASK[prot.aatype]


def  SCREAMING_SNAKE_CASE   ( _UpperCAmelCase		,			_UpperCAmelCase		,			_UpperCAmelCase = None		,			_UpperCAmelCase = None		,			_UpperCAmelCase = None		,			_UpperCAmelCase = None		,			_UpperCAmelCase = None		,			)    ->  Protein:
    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=_UpperCAmelCase		,			remark=_UpperCAmelCase		,			parents=_UpperCAmelCase		,			parents_chain_index=_UpperCAmelCase		,			)





