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__    							= Mapping[str, np.ndarray]
UpperCamelCase__    							= Mapping[str, Any]  # Is a nested dict.
UpperCamelCase__    							= 0.0_1





@dataclasses.dataclass(frozen=_a					)
class 					A							:
   __UpperCAmelCase			:			List[str]              =      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			:			List[Any]              =      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			:			List[str]              =      42  # [num_res, num_atom_type]

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

   # Chain indices for multi-chain predictions
   __UpperCAmelCase			:			Optional[Any]              =      None

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

   # Templates used to generate this protein (prediction-only)
   __UpperCAmelCase			:			Optional[Any]              =      None

   # Chain corresponding to each parent
   __UpperCAmelCase			:			Tuple              =      None




def        lowerCAmelCase_			(					__A							)					->    Protein:







      '''simple docstring'''


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

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

      assert aatype is not None

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




def        lowerCAmelCase_			(					__A,  __A = 0							)					->    List[str]:







      '''simple docstring'''


      UpperCAmelCase__								=  []

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

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

      if parents is None or len(_lowerCAmelCase							) == 0:
            UpperCAmelCase__								=  ["""N/A"""]

      pdb_headers.append(f"""PARENT {" ".join(_lowerCAmelCase							)}"""							)

      return pdb_headers




def        lowerCAmelCase_			(					__A,  __A							)					->    str:







      '''simple docstring'''


      UpperCAmelCase__								=  []
      UpperCAmelCase__								=  pdb_str.split("\n"							)

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

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

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

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

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

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

                  out_pdb_lines.append(make_parent_line(_lowerCAmelCase							)							)

      return "\n".join(_lowerCAmelCase							)




def        lowerCAmelCase_			(					__A							)					->    str:







      '''simple docstring'''


      UpperCAmelCase__								=  residue_constants.restypes + ["""X"""]

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

      UpperCAmelCase__								=  residue_constants.atom_types

      UpperCAmelCase__								=  []

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

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

      UpperCAmelCase__								=  get_pdb_headers(_lowerCAmelCase							)
      if len(_lowerCAmelCase							) > 0:
            pdb_lines.extend(_lowerCAmelCase							)

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

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

                  UpperCAmelCase__								=  """A"""
                  if chain_index is not None:
                        UpperCAmelCase__								=  chain_tags[chain_index[i]]

                  # PDB is a columnar format, every space matters here!
                  UpperCAmelCase__								=  (
                      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(_lowerCAmelCase							)
                  atom_index += 1

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

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

      pdb_lines.append("END"							)
      pdb_lines.append(""							)
      return "\n".join(_lowerCAmelCase							)




def        lowerCAmelCase_			(					__A							)					->    np.ndarray:







      '''simple docstring'''


      return residue_constants.STANDARD_ATOM_MASK[prot.aatype]







def        lowerCAmelCase_			(					__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=_lowerCAmelCase,  remark=_lowerCAmelCase,  parents=_lowerCAmelCase,  parents_chain_index=_lowerCAmelCase,  )




import os
import zipfile

import pytest

from datasets.utils.extract import (
    BzipaExtractor,
    Extractor,
    GzipExtractor,
    LzaExtractor,
    SevenZipExtractor,
    TarExtractor,
    XzExtractor,
    ZipExtractor,
    ZstdExtractor,
)

from .utils import require_lza, require_pyazr, require_zstandard




@pytest.mark.parametrize(
    "compression_format, is_archive",  [
        ("7z", True),
        ("bz2", False),
        ("gzip", False),
        ("lz4", False),
        ("tar", True),
        ("xz", False),
        ("zip", True),
        ("zstd", False),
    ],  )
def        lowerCAmelCase_			(					__A,  __A,  __A,  __A,  __A,  __A,  __A,  __A,  __A,  __A,  __A,  __A,  )					->    Any:







      '''simple docstring'''


      UpperCAmelCase__								=  {
          "7z": (seven_zip_file, SevenZipExtractor),
          "bz2": (bza_file, BzipaExtractor),
          "gzip": (gz_file, GzipExtractor),
          "lz4": (lza_file, LzaExtractor),
          "tar": (tar_file, TarExtractor),
          "xz": (xz_file, XzExtractor),
          "zip": (zip_file, ZipExtractor),
          "zstd": (zstd_file, ZstdExtractor),
      }
      UpperCAmelCase__		,				UpperCAmelCase__								=  input_paths_and_base_extractors[compression_format]
      if input_path is None:
            UpperCAmelCase__								=  f"""for '{compression_format}' compression_format, """
            if compression_format == "7z":
                  reason += require_pyazr.kwargs["reason"]
            elif compression_format == "lz4":
                  reason += require_lza.kwargs["reason"]
            elif compression_format == "zstd":
                  reason += require_zstandard.kwargs["reason"]
            pytest.skip(__A							)
      assert base_extractor.is_extractable(__A							)
      UpperCAmelCase__								=  tmp_path / ("extracted" if is_archive else "extracted.txt")
      base_extractor.extract(__A,  __A							)
      if is_archive:
            assert output_path.is_dir()
            for file_path in output_path.iterdir():
                  assert file_path.name == text_file.name
                  UpperCAmelCase__								=  file_path.read_text(encoding="utf-8"							)
      else:
            UpperCAmelCase__								=  output_path.read_text(encoding="utf-8"							)
      UpperCAmelCase__								=  text_file.read_text(encoding="utf-8"							)
      assert extracted_file_content == expected_file_content




@pytest.mark.parametrize(
    "compression_format, is_archive",  [
        ("7z", True),
        ("bz2", False),
        ("gzip", False),
        ("lz4", False),
        ("tar", True),
        ("xz", False),
        ("zip", True),
        ("zstd", False),
    ],  )
def        lowerCAmelCase_			(					__A,  __A,  __A,  __A,  __A,  __A,  __A,  __A,  __A,  __A,  __A,  __A,  )					->    List[Any]:







      '''simple docstring'''


      UpperCAmelCase__								=  {
          "7z": seven_zip_file,
          "bz2": bza_file,
          "gzip": gz_file,
          "lz4": lza_file,
          "tar": tar_file,
          "xz": xz_file,
          "zip": zip_file,
          "zstd": zstd_file,
      }
      UpperCAmelCase__								=  input_paths[compression_format]
      if input_path is None:
            UpperCAmelCase__								=  f"""for '{compression_format}' compression_format, """
            if compression_format == "7z":
                  reason += require_pyazr.kwargs["reason"]
            elif compression_format == "lz4":
                  reason += require_lza.kwargs["reason"]
            elif compression_format == "zstd":
                  reason += require_zstandard.kwargs["reason"]
            pytest.skip(__A							)
      UpperCAmelCase__								=  Extractor.infer_extractor_format(__A							)
      assert extractor_format is not None
      UpperCAmelCase__								=  tmp_path / ("extracted" if is_archive else "extracted.txt")
      Extractor.extract(__A,  __A,  __A							)
      if is_archive:
            assert output_path.is_dir()
            for file_path in output_path.iterdir():
                  assert file_path.name == text_file.name
                  UpperCAmelCase__								=  file_path.read_text(encoding="utf-8"							)
      else:
            UpperCAmelCase__								=  output_path.read_text(encoding="utf-8"							)
      UpperCAmelCase__								=  text_file.read_text(encoding="utf-8"							)
      assert extracted_file_content == expected_file_content




@pytest.fixture
def        lowerCAmelCase_			(					__A,  __A							)					->    List[str]:







      '''simple docstring'''


      import tarfile

      UpperCAmelCase__								=  tmp_path / "data_dot_dot"
      directory.mkdir()
      UpperCAmelCase__								=  directory / "tar_file_with_dot_dot.tar"
      with tarfile.TarFile(__A,  "w"							) as f:
            f.add(__A,  arcname=os.path.join("..",  text_file.name							)							)
      return path




@pytest.fixture
def        lowerCAmelCase_			(					__A							)					->    Dict:







      '''simple docstring'''


      import tarfile

      UpperCAmelCase__								=  tmp_path / "data_sym_link"
      directory.mkdir()
      UpperCAmelCase__								=  directory / "tar_file_with_sym_link.tar"
      os.symlink("..",  directory / "subdir",  target_is_directory=__A							)
      with tarfile.TarFile(__A,  "w"							) as f:
            f.add(str(directory / "subdir"							),  arcname="subdir"							)  # str required by os.readlink on Windows and Python < 3.8
      return path




@pytest.mark.parametrize(
    "insecure_tar_file, error_log",  [("tar_file_with_dot_dot", "illegal path"), ("tar_file_with_sym_link", "Symlink")],  )
def        lowerCAmelCase_			(					__A,  __A,  __A,  __A,  __A,  __A							)					->    Dict:







      '''simple docstring'''


      UpperCAmelCase__								=  {
          "tar_file_with_dot_dot": tar_file_with_dot_dot,
          "tar_file_with_sym_link": tar_file_with_sym_link,
      }
      UpperCAmelCase__								=  insecure_tar_files[insecure_tar_file]
      UpperCAmelCase__								=  tmp_path / "extracted"
      TarExtractor.extract(__A,  __A							)
      assert caplog.text
      for record in caplog.records:
            assert record.levelname == "ERROR"
            assert error_log in record.msg







def        lowerCAmelCase_			(					__A							)					->    Any:







      '''simple docstring'''


      UpperCAmelCase__								=  tmpdir / "not_a_zip_file"
      # From: https://github.com/python/cpython/pull/5053
      UpperCAmelCase__								=  (
          B"\x89PNG\r\n\x1a\n\x00\x00\x00\rIHDR\x00\x00\x00\x01\x00\x00"
          B"\x00\x02\x08\x06\x00\x00\x00\x99\x81\xb6'\x00\x00\x00\x15I"
          B"DATx\x01\x01\n\x00\xf5\xff\x00PK\x05\x06\x00PK\x06\x06\x07"
          B"\xac\x01N\xc6|a\r\x00\x00\x00\x00IEND\xaeB`\x82"
      )
      with not_a_zip_file.open("wb"							) as f:
            f.write(__A							)
      assert zipfile.is_zipfile(str(__A							)							)  # is a false positive for `zipfile`
      assert not ZipExtractor.is_extractable(__A							)  # but we're right



