'''simple docstring'''





class   lowerCamelCase					:
  """simple docstring"""







  def __init__(							self :       Dict  ,     __magic_name__ :       int  ,     __magic_name__ :       Tuple=None  ,     __magic_name__ :       str=None   )  ->	List[str]:
        SCREAMING_SNAKE_CASE_          =  data
        SCREAMING_SNAKE_CASE_          =  previous
        SCREAMING_SNAKE_CASE_          =  next_node







  def __str__(							self :       Tuple   )  ->	str:
        return F'''{self.data}'''







  def    __A     (							self :       List[str]   )  ->	int:
        return self.data







  def    __A     (							self :       Optional[int]   )  ->	Union[str, Any]:
        return self.next







  def    __A     (							self :       Tuple   )  ->	List[Any]:
        return self.previous



class   lowerCamelCase					:
  """simple docstring"""







  def __init__(							self :       Optional[int]  ,     __magic_name__ :       Dict   )  ->	List[str]:
        SCREAMING_SNAKE_CASE_          =  head







  def __iter__(							self :       List[Any]   )  ->	Tuple:
        return self







  def    __A     (							self :       Optional[int]   )  ->	Optional[int]:
        if not self.current:
              raise StopIteration
        else:
              SCREAMING_SNAKE_CASE_          =  self.current.get_data()
              SCREAMING_SNAKE_CASE_          =  self.current.get_next()
              return value



class   lowerCamelCase					:
  """simple docstring"""







  def __init__(							self :       List[Any]   )  ->	int:
        SCREAMING_SNAKE_CASE_          =  None  # First node in list
        SCREAMING_SNAKE_CASE_          =  None  # Last node in list







  def __str__(							self :       Union[str, Any]   )  ->	Any:
        SCREAMING_SNAKE_CASE_          =  self.head
        SCREAMING_SNAKE_CASE_          =  []
        while current is not None:
              nodes.append(current.get_data()   )
              SCREAMING_SNAKE_CASE_          =  current.get_next()
        return " ".join(str(__magic_name__   ) for node in nodes   )







  def __contains__(							self :       Any  ,     __magic_name__ :       int   )  ->	Any:
        SCREAMING_SNAKE_CASE_          =  self.head
        while current:
              if current.get_data() == value:
                    return True
              SCREAMING_SNAKE_CASE_          =  current.get_next()
        return False







  def __iter__(							self :       Dict   )  ->	int:
        return LinkedListIterator(self.head   )







  def    __A     (							self :       Any   )  ->	Optional[int]:
        if self.head:
              return self.head.get_data()
        return None







  def    __A     (							self :       List[Any]   )  ->	List[str]:
        if self.tail:
              return self.tail.get_data()
        return None







  def    __A     (							self :       str  ,     __magic_name__ :       Node   )  ->	None:
        if self.head is None:
              SCREAMING_SNAKE_CASE_          =  node
              SCREAMING_SNAKE_CASE_          =  node
        else:
              self.insert_before_node(self.head  ,     __magic_name__   )







  def    __A     (							self :       int  ,     __magic_name__ :       Node   )  ->	None:
        if self.head is None:
              self.set_head(__magic_name__   )
        else:
              self.insert_after_node(self.tail  ,     __magic_name__   )







  def    __A     (							self :       Union[str, Any]  ,     __magic_name__ :       int   )  ->	None:
        SCREAMING_SNAKE_CASE_          =  Node(__magic_name__   )
        if self.head is None:
              self.set_head(__magic_name__   )
        else:
              self.set_tail(__magic_name__   )







  def    __A     (							self :       Any  ,     __magic_name__ :       Node  ,     __magic_name__ :       Node   )  ->	None:
        SCREAMING_SNAKE_CASE_          =  node
        SCREAMING_SNAKE_CASE_          =  node.previous

        if node.get_previous() is None:
              SCREAMING_SNAKE_CASE_          =  node_to_insert
        else:
              SCREAMING_SNAKE_CASE_          =  node_to_insert

        SCREAMING_SNAKE_CASE_          =  node_to_insert







  def    __A     (							self :       Optional[Any]  ,     __magic_name__ :       Node  ,     __magic_name__ :       Node   )  ->	None:
        SCREAMING_SNAKE_CASE_          =  node
        SCREAMING_SNAKE_CASE_          =  node.next

        if node.get_next() is None:
              SCREAMING_SNAKE_CASE_          =  node_to_insert
        else:
              SCREAMING_SNAKE_CASE_          =  node_to_insert

        SCREAMING_SNAKE_CASE_          =  node_to_insert







  def    __A     (							self :       int  ,     __magic_name__ :       int  ,     __magic_name__ :       int   )  ->	None:
        SCREAMING_SNAKE_CASE_          =  1
        SCREAMING_SNAKE_CASE_          =  Node(__magic_name__   )
        SCREAMING_SNAKE_CASE_          =  self.head
        while node:
              if current_position == position:
                    self.insert_before_node(__magic_name__  ,     __magic_name__   )
                    return
              current_position += 1
              SCREAMING_SNAKE_CASE_          =  node.next
        self.insert_after_node(self.tail  ,     __magic_name__   )







  def    __A     (							self :       str  ,     __magic_name__ :       int   )  ->	Node:
        SCREAMING_SNAKE_CASE_          =  self.head
        while node:
              if node.get_data() == item:
                    return node
              SCREAMING_SNAKE_CASE_          =  node.get_next()
        raise Exception("Node not found"   )







  def    __A     (							self :       List[Any]  ,     __magic_name__ :       int   )  ->	Optional[int]:
        if (node := self.get_node(__magic_name__   )) is not None:
              if node == self.head:
                    SCREAMING_SNAKE_CASE_          =  self.head.get_next()

              if node == self.tail:
                    SCREAMING_SNAKE_CASE_          =  self.tail.get_previous()

              self.remove_node_pointers(__magic_name__   )







  @staticmethod
  def    __A     (							__magic_name__ :       Node   )  ->	None:
        if node.get_next():
              SCREAMING_SNAKE_CASE_          =  node.previous

        if node.get_previous():
              SCREAMING_SNAKE_CASE_          =  node.next

        SCREAMING_SNAKE_CASE_          =  None
        SCREAMING_SNAKE_CASE_          =  None







  def    __A     (							self :       Dict   )  ->	Any:
        return self.head is None



def      a__ (		):
      pass


if __name__ == "__main__":
      import doctest

      doctest.testmod()



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


@dataclasses.dataclass(frozen=SCREAMING_SNAKE_CASE__					)
class   lowerCamelCase					:
  """simple docstring"""







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

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

      SCREAMING_SNAKE_CASE_          =  prot.remark
      if remark is not None:
            pdb_headers.append(F'''REMARK {remark}'''				)

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

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

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

      return pdb_headers


def      a__ (		__UpperCamelCase     ,      __UpperCamelCase				):
      SCREAMING_SNAKE_CASE_          =  []
      SCREAMING_SNAKE_CASE_          =  pdb_str.split("\n"				)

      SCREAMING_SNAKE_CASE_          =  prot.remark
      if remark is not None:
            out_pdb_lines.append(F'''REMARK {remark}'''				)

      SCREAMING_SNAKE_CASE_          =  42
      if prot.parents is not None and len(prot.parents				) > 0:
            SCREAMING_SNAKE_CASE_          =  []
            if prot.parents_chain_index is not None:
                  SCREAMING_SNAKE_CASE_          =  {}
                  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_          =  max([int(__UpperCamelCase				) for chain_idx in parent_dict]				)
                  for i in range(max_idx + 1				):
                        SCREAMING_SNAKE_CASE_          =  parent_dict.get(str(__UpperCamelCase				)     ,      ["N/A"]				)
                        parents_per_chain.append(__UpperCamelCase				)
            else:
                  parents_per_chain.append(list(prot.parents				)				)
      else:
            SCREAMING_SNAKE_CASE_          =  [["N/A"]]

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

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

      SCREAMING_SNAKE_CASE_          =  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_          =  parents_per_chain[chain_counter]
                  else:
                        SCREAMING_SNAKE_CASE_          =  ["N/A"]

                  out_pdb_lines.append(make_parent_line(__UpperCamelCase				)				)

      return "\n".join(__UpperCamelCase				)


def      a__ (		__UpperCamelCase				):
      SCREAMING_SNAKE_CASE_          =  residue_constants.restypes + ["X"]

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

      SCREAMING_SNAKE_CASE_          =  residue_constants.atom_types

      SCREAMING_SNAKE_CASE_          =  []

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

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

      SCREAMING_SNAKE_CASE_          =  get_pdb_headers(__UpperCamelCase				)
      if len(__UpperCamelCase				) > 0:
            pdb_lines.extend(__UpperCamelCase				)

      SCREAMING_SNAKE_CASE_          =  aatype.shape[0]
      SCREAMING_SNAKE_CASE_          =  1
      SCREAMING_SNAKE_CASE_          =  0
      SCREAMING_SNAKE_CASE_          =  string.ascii_uppercase
      SCREAMING_SNAKE_CASE_          =  None
      # Add all atom sites.
      for i in range(__UpperCamelCase				):
            SCREAMING_SNAKE_CASE_          =  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_          =  "ATOM"
                  SCREAMING_SNAKE_CASE_          =  atom_name if len(__UpperCamelCase				) == 4 else F''' {atom_name}'''
                  SCREAMING_SNAKE_CASE_          =  ""
                  SCREAMING_SNAKE_CASE_          =  ""
                  SCREAMING_SNAKE_CASE_          =  1.00
                  SCREAMING_SNAKE_CASE_          =  atom_name[0]  # Protein supports only C, N, O, S, this works.
                  SCREAMING_SNAKE_CASE_          =  ""

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

                  # PDB is a columnar format, every space matters here!
                  SCREAMING_SNAKE_CASE_          =  (
                      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_          =  i == n - 1
            if chain_index is not None:
                  if i != n - 1 and chain_index[i + 1] != prev_chain_index:
                        SCREAMING_SNAKE_CASE_          =  True
                        SCREAMING_SNAKE_CASE_          =  chain_index[i + 1]

            if should_terminate:
                  # Close the chain.
                  SCREAMING_SNAKE_CASE_          =  "TER"
                  SCREAMING_SNAKE_CASE_          =  (
                      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				):
      return residue_constants.STANDARD_ATOM_MASK[prot.aatype]





def      a__ (		__UpperCamelCase     ,      __UpperCamelCase     ,      __UpperCamelCase = None     ,      __UpperCamelCase = None     ,      __UpperCamelCase = None     ,      __UpperCamelCase = None     ,      __UpperCamelCase = 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=__UpperCamelCase     ,      remark=__UpperCamelCase     ,      parents=__UpperCamelCase     ,      parents_chain_index=__UpperCamelCase     ,      )


