






'''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_					=	Mapping[str, np.ndarray]
a_					=	Mapping[str, Any]  # Is a nested dict.
a_					=	0.01






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

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

 # Chain indices for multi-chain predictions
 snake_case_												=							None

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

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

 # Chain corresponding to each parent
 snake_case_												=							None





def 	_a(					UpperCamelCase__			:  str							):




      '''simple docstring'''






      SCREAMING_SNAKE_CASE__       :			List[Any]													=R'''(\[[A-Z]+\]\n)'''
      SCREAMING_SNAKE_CASE__       :			List[str]													=[tag.strip() for tag in re.split(UpperCamelCase__,		UpperCamelCase__							) if len(UpperCamelCase__							) > 0]
      SCREAMING_SNAKE_CASE__       :			Iterator[Tuple[str, List[str]]]													=zip(tags[0::2],		[l.split('''\n'''							) for l in tags[1::2]]							)

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




      '''simple docstring'''






      SCREAMING_SNAKE_CASE__       :			List[str]													=[]

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

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

      if parents is None or len(UpperCamelCase__							) == 0:
            SCREAMING_SNAKE_CASE__       :			Union[str, Any]													=['''N/A''']

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

      return pdb_headers





def 	_a(					UpperCamelCase__			:  Protein,		UpperCamelCase__			:  str							):




      '''simple docstring'''






      SCREAMING_SNAKE_CASE__       :			List[str]													=[]
      SCREAMING_SNAKE_CASE__       :			Any													=pdb_str.split('''\n'''							)

      SCREAMING_SNAKE_CASE__       :			Union[str, Any]													=prot.remark
      if remark is not None:
            out_pdb_lines.append(f"REMARK {remark}"							)

      SCREAMING_SNAKE_CASE__       :			List[List[str]]
      if prot.parents is not None and len(prot.parents							) > 0:
            SCREAMING_SNAKE_CASE__       :			Tuple													=[]
            if prot.parents_chain_index is not None:
                  SCREAMING_SNAKE_CASE__       :			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__							)

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

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

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

      SCREAMING_SNAKE_CASE__       :			str													=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__							):
                        SCREAMING_SNAKE_CASE__       :			Union[str, Any]													=parents_per_chain[chain_counter]
                  else:
                        SCREAMING_SNAKE_CASE__       :			int													=['''N/A''']

                  out_pdb_lines.append(make_parent_line(UpperCamelCase__							)							)

      return "\n".join(UpperCamelCase__							)





def 	_a(					UpperCamelCase__			:  Protein							):




      '''simple docstring'''






      SCREAMING_SNAKE_CASE__       :			List[str]													=residue_constants.restypes + ['''X''']

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

      SCREAMING_SNAKE_CASE__       :			str													=residue_constants.atom_types

      SCREAMING_SNAKE_CASE__       :			List[str]													=[]

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

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

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

      SCREAMING_SNAKE_CASE__       :			Tuple													=aatype.shape[0]
      SCREAMING_SNAKE_CASE__       :			str													=1
      SCREAMING_SNAKE_CASE__       :			Any													=0
      SCREAMING_SNAKE_CASE__       :			Tuple													=string.ascii_uppercase
      SCREAMING_SNAKE_CASE__       :			Optional[int]													=None
      # Add all atom sites.
      for i in range(UpperCamelCase__							):
            SCREAMING_SNAKE_CASE__       :			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

                  SCREAMING_SNAKE_CASE__       :			int													='''ATOM'''
                  SCREAMING_SNAKE_CASE__       :			str													=atom_name if len(UpperCamelCase__							) == 4 else f" {atom_name}"
                  SCREAMING_SNAKE_CASE__       :			str													=''''''
                  SCREAMING_SNAKE_CASE__       :			Optional[Any]													=''''''
                  SCREAMING_SNAKE_CASE__       :			Any													=1.0_0
                  SCREAMING_SNAKE_CASE__       :			Union[str, Any]													=atom_name[0]  # Protein supports only C, N, O, S, this works.
                  SCREAMING_SNAKE_CASE__       :			str													=''''''

                  SCREAMING_SNAKE_CASE__       :			List[str]													='''A'''
                  if chain_index is not None:
                        SCREAMING_SNAKE_CASE__       :			Tuple													=chain_tags[chain_index[i]]

                  # PDB is a columnar format, every space matters here!
                  SCREAMING_SNAKE_CASE__       :			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(UpperCamelCase__							)
                  atom_index += 1

            SCREAMING_SNAKE_CASE__       :			Optional[Any]													=i == n - 1
            if chain_index is not None:
                  if i != n - 1 and chain_index[i + 1] != prev_chain_index:
                        SCREAMING_SNAKE_CASE__       :			Union[str, Any]													=True
                        SCREAMING_SNAKE_CASE__       :			Tuple													=chain_index[i + 1]

            if should_terminate:
                  # Close the chain.
                  SCREAMING_SNAKE_CASE__       :			Union[str, Any]													='''TER'''
                  SCREAMING_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(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 	_a(					UpperCamelCase__			:  Protein							):




      '''simple docstring'''






      return residue_constants.STANDARD_ATOM_MASK[prot.aatype]







def 	_a(					UpperCamelCase__			:  FeatureDict,		UpperCamelCase__			:  ModelOutput,		UpperCamelCase__			:  Optional[np.ndarray] = None,		UpperCamelCase__			:  Optional[np.ndarray] = None,		UpperCamelCase__			:  Optional[str] = None,		UpperCamelCase__			:  Optional[Sequence[str]] = None,		UpperCamelCase__			:  Optional[Sequence[int]] = None,		):




      '''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=UpperCamelCase__,		remark=UpperCamelCase__,		parents=UpperCamelCase__,		parents_chain_index=UpperCamelCase__,		)







'''simple docstring'''
def 	_a(					UpperCamelCase__			:  Optional[Any]=2_8_1_2_3							):




      '''simple docstring'''






      SCREAMING_SNAKE_CASE__       :			List[Any]													=[1] * (limit + 1)

      for i in range(2,		int(limit**0.5							) + 1							):
            sum_divs[i * i] += i
            for k in range(i + 1,		limit // i + 1							):
                  sum_divs[k * i] += k + i

      SCREAMING_SNAKE_CASE__       :			List[str]													=set()
      SCREAMING_SNAKE_CASE__       :			str													=0

      for n in range(1,		limit + 1							):
            if sum_divs[n] > n:
                  abundants.add(UpperCamelCase__							)

            if not any((n - a in abundants) for a in abundants							):
                  res += n

      return res


if __name__ == "__main__":
  print(solution())