





'''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=_snake_case      )
class __a			:
   __UpperCamelCase :			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'.
   __UpperCamelCase :			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.
   __UpperCamelCase :			np.ndarray  # [num_res, num_atom_type]

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

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

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

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

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





def     __magic_name__							(				__UpperCAmelCase   )    ->       Protein:

   '''simple docstring'''







   __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     __magic_name__							(				__UpperCAmelCase				,						__UpperCAmelCase = 0   )    ->       List[str]:

   '''simple docstring'''







   __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     __magic_name__							(				__UpperCAmelCase				,						__UpperCAmelCase   )    ->       str:

   '''simple docstring'''







   __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     __magic_name__							(				__UpperCAmelCase   )    ->       str:

   '''simple docstring'''







   __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   				=							1.0_0
         __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     __magic_name__							(				__UpperCAmelCase   )    ->       np.ndarray:

   '''simple docstring'''







   return residue_constants.STANDARD_ATOM_MASK[prot.aatype]







def     __magic_name__							(				__UpperCAmelCase				,						__UpperCAmelCase				,						__UpperCAmelCase = None				,						__UpperCAmelCase = None				,						__UpperCAmelCase = None				,						__UpperCAmelCase = None				,						__UpperCAmelCase = 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=__UpperCAmelCase				,						remark=__UpperCAmelCase				,						parents=__UpperCAmelCase				,						parents_chain_index=__UpperCAmelCase				,						)









import baseaa





def 						_lowerCAmelCase							(     _lowerCAmelCase			)    ->						bytes:


						'''simple docstring'''






						return baseaa.baaencode(string.encode("utf-8"			)			)





def 						_lowerCAmelCase							(     _lowerCAmelCase			)    ->						str:


						'''simple docstring'''






						return baseaa.baadecode(_lowerCAmelCase			).decode("utf-8"			)


if __name__ == "__main__":
	A				:       Dict      =  'Hello World!'
	A				:       Any      =  baseaa_encode(test)
	print(encoded)

	A				:       Optional[int]      =  baseaa_decode(encoded)
	print(decoded)





