
'''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


A__   :		Optional[Any] 		=Mapping[str, np.ndarray]
A__   :		Union[str, Any] 		=Mapping[str, Any]  # Is a nested dict.
A__   :		int 		=0.0_1







@dataclasses.dataclass(frozen=_SCREAMING_SNAKE_CASE			)
class  __A				:
 lowerCamelCase				       =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'.
 lowerCamelCase				       =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.
 lowerCamelCase				       =42  # [num_res, num_atom_type]

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

 # Chain indices for multi-chain predictions
 lowerCamelCase				       =None

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

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

 # Chain corresponding to each parent
 lowerCamelCase				       =None







def        A_     (						__SCREAMING_SNAKE_CASE						:  str )				->       Protein:





  """simple docstring"""

  __A		:     Optional[int]												=		R"""(\[[A-Z]+\]\n)"""
  __A		:     List[str]												=		[tag.strip() for tag in re.split(__SCREAMING_SNAKE_CASE			,     __SCREAMING_SNAKE_CASE ) if len(__SCREAMING_SNAKE_CASE ) > 0]
  __A		:     Iterator[Tuple[str, List[str]]]												=		zip(tags[0::2]			,     [l.split("""\n""" ) for l in tags[1::2]] )

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

  assert aatype is not None

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







def        A_     (						__SCREAMING_SNAKE_CASE						:  Protein			,     __SCREAMING_SNAKE_CASE						:  int = 0 )				->       List[str]:





  """simple docstring"""

  __A		:     List[str]												=		[]

  __A		:     Optional[Any]												=		prot.remark
  if remark is not None:
    pdb_headers.append(F"REMARK {remark}" )

  __A		:     int												=		prot.parents
  __A		:     Optional[Any]												=		prot.parents_chain_index
  if parents is not None and parents_chain_index is not None:
    __A		:     Optional[Any]												=		[p for i, p in zip(__SCREAMING_SNAKE_CASE			,     __SCREAMING_SNAKE_CASE ) if i == chain_id]

  if parents is None or len(__SCREAMING_SNAKE_CASE ) == 0:
    __A		:     Union[str, Any]												=		["""N/A"""]

  pdb_headers.append(F"PARENT {' '.join(__SCREAMING_SNAKE_CASE )}" )

  return pdb_headers







def        A_     (						__SCREAMING_SNAKE_CASE						:  Protein			,     __SCREAMING_SNAKE_CASE						:  str )				->       str:





  """simple docstring"""

  __A		:     List[str]												=		[]
  __A		:     Optional[int]												=		pdb_str.split("""\n""" )

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

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

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

  def make_parent_line(__SCREAMING_SNAKE_CASE						:  Sequence[str] ) -> str:
    return F"PARENT {' '.join(__SCREAMING_SNAKE_CASE )}"

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

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

      out_pdb_lines.append(make_parent_line(__SCREAMING_SNAKE_CASE ) )

  return "\n".join(__SCREAMING_SNAKE_CASE )







def        A_     (						__SCREAMING_SNAKE_CASE						:  Protein )				->       str:





  """simple docstring"""

  __A		:     Optional[Any]												=		residue_constants.restypes + ["""X"""]

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

  __A		:     Any												=		residue_constants.atom_types

  __A		:     List[str]												=		[]

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

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

  __A		:     List[str]												=		get_pdb_headers(__SCREAMING_SNAKE_CASE )
  if len(__SCREAMING_SNAKE_CASE ) > 0:
    pdb_lines.extend(__SCREAMING_SNAKE_CASE )

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

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

      __A		:     Union[str, Any]												=		"""A"""
      if chain_index is not None:
        __A		:     List[Any]												=		chain_tags[chain_index[i]]

      # PDB is a columnar format, every space matters here!
      __A		:     Tuple												=		(
          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(__SCREAMING_SNAKE_CASE )
      atom_index += 1

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

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

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







def        A_     (						__SCREAMING_SNAKE_CASE						:  Protein )				->       np.ndarray:





  """simple docstring"""

  return residue_constants.STANDARD_ATOM_MASK[prot.aatype]







def        A_     (						__SCREAMING_SNAKE_CASE						:  FeatureDict			,     __SCREAMING_SNAKE_CASE						:  ModelOutput			,     __SCREAMING_SNAKE_CASE						:  Optional[np.ndarray] = None			,     __SCREAMING_SNAKE_CASE						:  Optional[np.ndarray] = None			,     __SCREAMING_SNAKE_CASE						:  Optional[str] = None			,     __SCREAMING_SNAKE_CASE						:  Optional[Sequence[str]] = None			,     __SCREAMING_SNAKE_CASE						:  Optional[Sequence[int]] = 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=__SCREAMING_SNAKE_CASE			,     remark=__SCREAMING_SNAKE_CASE			,     parents=__SCREAMING_SNAKE_CASE			,     parents_chain_index=__SCREAMING_SNAKE_CASE			,     )





'''simple docstring'''
def        A_     (						__SCREAMING_SNAKE_CASE						:  int			,     __SCREAMING_SNAKE_CASE						:  bool = False )				->       bool:





  """simple docstring"""

  if n == 2:
    return True
  if not n % 2 or n < 2:
    return False
  if n > 5 and n % 10 not in (1, 3, 7, 9):  # can quickly check last digit
    return False
  if n > 3_3170_4406_4679_8873_8596_1981 and not allow_probable:
    raise ValueError(
        """Warning: upper bound of deterministic test is exceeded. """
        """Pass allow_probable=True to allow probabilistic test. """
        """A return value of True indicates a probable prime.""" )
  # array bounds provided by analysis
  __A		:     Optional[int]												=		[
      2047,
      137_3653,
      2532_6001,
      32_1503_1751,
      2_1523_0289_8747,
      3_4747_4966_0383,
      341_5500_7172_8321,
      1,
      382_5123_0565_4641_3051,
      1,
      1,
      3186_6585_7834_0311_5116_7461,
      3_3170_4406_4679_8873_8596_1981,
  ]

  __A		:     Optional[int]												=		[2, 3, 5, 7, 11, 13, 17, 19, 23, 29, 31, 37, 41]
  for idx, _p in enumerate(__SCREAMING_SNAKE_CASE			,     1 ):
    if n < _p:
      # then we have our last prime to check
      __A		:     Union[str, Any]												=		primes[:idx]
      break
  __A							,					__A		:     int												=		n - 1, 0
  # break up n -1 into a power of 2 (s) and
  # remaining odd component
  # essentially, solve for d * 2 ** s == n - 1
  while d % 2 == 0:
    d //= 2
    s += 1
  for prime in plist:
    __A		:     int												=		False
    for r in range(__SCREAMING_SNAKE_CASE ):
      __A		:     Optional[Any]												=		pow(__SCREAMING_SNAKE_CASE			,     d * 2**r			,     __SCREAMING_SNAKE_CASE )
      # see article for analysis explanation for m
      if (r == 0 and m == 1) or ((m + 1) % n == 0):
        __A		:     Optional[int]												=		True
        # this loop will not determine compositeness
        break
    if pr:
      continue
    # if pr is False, then the above loop never evaluated to true,
    # and the n MUST be composite
    return False
  return True







def        A_     (						)				->       None:





  """simple docstring"""

  assert not miller_rabin(561 )
  assert miller_rabin(563 )
  # 2047

  assert not miller_rabin(83_8201 )
  assert miller_rabin(83_8207 )
  # 1_373_653

  assert not miller_rabin(1731_6001 )
  assert miller_rabin(1731_6017 )
  # 25_326_001

  assert not miller_rabin(30_7838_6641 )
  assert miller_rabin(30_7838_6653 )
  # 3_215_031_751

  assert not miller_rabin(1_7130_4557_4801 )
  assert miller_rabin(1_7130_4557_4819 )
  # 2_152_302_898_747

  assert not miller_rabin(2_7797_9972_8307 )
  assert miller_rabin(2_7797_9972_8327 )
  # 3_474_749_660_383

  assert not miller_rabin(113_8500_2390_9441 )
  assert miller_rabin(113_8500_2390_9527 )
  # 341_550_071_728_321

  assert not miller_rabin(127_5041_0188_4880_4351 )
  assert miller_rabin(127_5041_0188_4880_4391 )
  # 3_825_123_056_546_413_051

  assert not miller_rabin(796_6646_4458_5077_8779_1867 )
  assert miller_rabin(796_6646_4458_5077_8779_1951 )
  # 318_665_857_834_031_151_167_461

  assert not miller_rabin(5528_4067_7446_6478_9766_0333 )
  assert miller_rabin(5528_4067_7446_6478_9766_0359 )
  # 3_317_044_064_679_887_385_961_981
  # upper limit for probabilistic test


if __name__ == "__main__":
     test_miller_rabin()



