

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






@dataclasses.dataclass(frozen=_snake_case    )
class 						__magic_name__    :
 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      _lowerCAmelCase(	__A			):
  UpperCAmelCase					      =  r"(\[[A-Z]+\]\n)"
  UpperCAmelCase					      =  [tag.strip() for tag in re.split(__A   ,       __A			) if len(__A			) > 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(__A			)			):
        if seq[i] not in residue_constants.restypes:
          UpperCAmelCase					      =  "X"  # FIXME: strings are immutable
      UpperCAmelCase					      =  np.array(
          [residue_constants.restype_order.get(__A   ,       residue_constants.restype_num			) for res_symbol in seq]			)
    elif "[TERTIARY]" == g[0]:
      UpperCAmelCase					      =  []
      for axis in range(3			):
        tertiary.append(list(map(__A   ,       g[1][axis].split()			)			)			)
      UpperCAmelCase					      =  np.array(__A			)
      UpperCAmelCase					      =  np.zeros((len(tertiary[0]			) // 3, residue_constants.atom_type_num, 3)			).astype(np.floataa			)
      for i, atom in enumerate(__A			):
        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(__A			),
              residue_constants.atom_type_num,
          )			).astype(np.floataa			)
      for i, atom in enumerate(__A			):
        UpperCAmelCase					      =  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      _lowerCAmelCase(	__A   ,       __A = 0			):
  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(__A   ,       __A			) if i == chain_id]

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

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

  return pdb_headers
def      _lowerCAmelCase(	__A   ,       __A			):
  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(__A			)   ,       []			)
        parent_dict[str(__A			)].append(__A			)

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

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

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

  UpperCAmelCase					      =  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			):
        UpperCAmelCase					      =  parents_per_chain[chain_counter]
      else:
        UpperCAmelCase					      =  ["N/A"]

      out_pdb_lines.append(make_parent_line(__A			)			)

  return "\n".join(__A			)
def      _lowerCAmelCase(	__A			):
  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(__A			)
  if len(__A			) > 0:
    pdb_lines.extend(__A			)

  UpperCAmelCase					      =  aatype.shape[0]
  UpperCAmelCase					      =  1
  UpperCAmelCase					      =  0
  UpperCAmelCase					      =  string.ascii_uppercase
  UpperCAmelCase					      =  None
  # Add all atom sites.
  for i in range(__A			):
    UpperCAmelCase					      =  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

      UpperCAmelCase					      =  "ATOM"
      UpperCAmelCase					      =  atom_name if len(__A			) == 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(__A			)
      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(__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      _lowerCAmelCase(	__A			):
  return residue_constants.STANDARD_ATOM_MASK[prot.aatype]





def      _lowerCAmelCase(	__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   ,       )






def      _lowerCAmelCase(	__A			):
  UpperCAmelCase					      =  0
  while num > 0:
    digit_sum += num % 10
    num //= 10
  return digit_sum
def      _lowerCAmelCase(	__A = 100			):
  UpperCAmelCase					      =  1
  UpperCAmelCase					      =  2

  for i in range(2   ,       max_n + 1			):
    UpperCAmelCase					      =  pre_numerator
    UpperCAmelCase					      =  2 * i // 3 if i % 3 == 0 else 1
    UpperCAmelCase					      =  cur_numerator
    UpperCAmelCase					      =  e_cont * pre_numerator + temp

  return sum_digits(__A			)


if __name__ == "__main__":
      print(f"{solution() = }")



