






'''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


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


@dataclasses.dataclass(frozen=snake_case      )
class 							_UpperCAmelCase    :
    __lowerCamelCase: np.ndarray  # [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: np.ndarray  # [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: np.ndarray  # [num_res, num_atom_type]

    # Residue index as used in PDB. It is not necessarily continuous or 0-indexed.
    __lowerCamelCase: np.ndarray  # [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: np.ndarray  # [num_res, num_atom_type]

    # Chain indices for multi-chain predictions
    __lowerCamelCase: Optional[np.ndarray]									=     None

    # Optional remark about the protein. Included as a comment in output PDB
    # files
    __lowerCamelCase: Optional[str]									=     None

    # Templates used to generate this protein (prediction-only)
    __lowerCamelCase: Optional[Sequence[str]]									=     None

    # Chain corresponding to each parent
    __lowerCamelCase: Optional[Sequence[int]]									=     None




def 		__SCREAMING_SNAKE_CASE       (	_UpperCamelCase				):


   """simple docstring"""




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

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


   """simple docstring"""




   lowercase_						:     List[str]							     =  []

   lowercase_						:     List[str]							     =  prot.remark
   if remark is not None:
      pdb_headers.append(F"""REMARK {remark}"""				)

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

   if parents is None or len(_UpperCamelCase				) == 0:
      lowercase_						:     str							     =  ["N/A"]

   pdb_headers.append(F"""PARENT {" ".join(_UpperCamelCase				)}"""				)

   return pdb_headers




def 		__SCREAMING_SNAKE_CASE       (	_UpperCamelCase    ,		_UpperCamelCase				):


   """simple docstring"""




   lowercase_						:     List[str]							     =  []
   lowercase_						:     Optional[Any]							     =  pdb_str.split("\n"				)

   lowercase_						:     List[Any]							     =  prot.remark
   if remark is not None:
      out_pdb_lines.append(F"""REMARK {remark}"""				)

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

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

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

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

   lowercase_						:     List[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				):
            lowercase_						:     List[Any]							     =  parents_per_chain[chain_counter]
         else:
            lowercase_						:     Optional[Any]							     =  ["N/A"]

         out_pdb_lines.append(make_parent_line(_UpperCamelCase				)				)

   return "\n".join(_UpperCamelCase				)




def 		__SCREAMING_SNAKE_CASE       (	_UpperCamelCase				):


   """simple docstring"""




   lowercase_						:     Dict							     =  residue_constants.restypes + ["X"]

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

   lowercase_						:     Dict							     =  residue_constants.atom_types

   lowercase_						:     List[str]							     =  []

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

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

   lowercase_						:     Union[str, Any]							     =  get_pdb_headers(_UpperCamelCase				)
   if len(_UpperCamelCase				) > 0:
      pdb_lines.extend(_UpperCamelCase				)

   lowercase_						:     Any							     =  aatype.shape[0]
   lowercase_						:     Dict							     =  1
   lowercase_						:     Dict							     =  0
   lowercase_						:     List[str]							     =  string.ascii_uppercase
   lowercase_						:     Dict							     =  None
   # Add all atom sites.
   for i in range(_UpperCamelCase				):
      lowercase_						:     Union[str, 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

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

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

         # PDB is a columnar format, every space matters here!
         lowercase_						:     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

      lowercase_						:     Any							     =  i == n - 1
      if chain_index is not None:
         if i != n - 1 and chain_index[i + 1] != prev_chain_index:
            lowercase_						:     Optional[int]							     =  True
            lowercase_						:     List[Any]							     =  chain_index[i + 1]

      if should_terminate:
         # Close the chain.
         lowercase_						:     List[str]							     =  "TER"
         lowercase_						:     Tuple							     =  (
             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 		__SCREAMING_SNAKE_CASE       (	_UpperCamelCase				):


   """simple docstring"""




   return residue_constants.STANDARD_ATOM_MASK[prot.aatype]





def 		__SCREAMING_SNAKE_CASE       (	_UpperCamelCase    ,		_UpperCamelCase    ,		_UpperCamelCase = None    ,		_UpperCamelCase = None    ,		_UpperCamelCase = None    ,		_UpperCamelCase = None    ,		_UpperCamelCase = 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'''
UpperCamelCase__			=      {
    "joule": 1.0,
    "kilojoule": 1000,
    "megajoule": 1000000,
    "gigajoule": 1000000000,
    "wattsecond": 1.0,
    "watthour": 3600,
    "kilowatthour": 3600000,
    "newtonmeter": 1.0,
    "calorie_nutr": 4186.8,
    "kilocalorie_nutr": 4186800.00,
    "electronvolt": 1.602176634e-19,
    "britishthermalunit_it": 1055.05585,
    "footpound": 1.35_58_18,
}




def 		__SCREAMING_SNAKE_CASE       (	_UpperCamelCase    ,		_UpperCamelCase    ,		_UpperCamelCase				):


   """simple docstring"""




   if to_type not in ENERGY_CONVERSION or from_type not in ENERGY_CONVERSION:
      lowercase_						:     Union[str, Any]							     =  (
          F"""Incorrect 'from_type' or 'to_type' value: {from_type!r}, {to_type!r}\n"""
          F"""Valid values are: {", ".join(_UpperCamelCase				)}"""
      )
      raise ValueError(_UpperCamelCase				)
   return value * ENERGY_CONVERSION[from_type] / ENERGY_CONVERSION[to_type]


if __name__ == "__main__":
 import doctest

 doctest.testmod()




