


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


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



@dataclasses.dataclass(frozen=_a						)
class 	__lowerCamelCase			:
       _lowercase											=     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'.
       _lowercase											=     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.
       _lowercase											=     42  # [num_res, num_atom_type]

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

       # Chain indices for multi-chain predictions
       _lowercase											=     None

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

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

       # Chain corresponding to each parent
       _lowercase											=     None






def 		_A		(		_lowercase )					-> Protein:


     """simple docstring"""


     __UpperCamelCase =			r'(\[[A-Z]+\]\n)'
     __UpperCamelCase =			[tag.strip() for tag in re.split(_lowercase					,  _lowercase ) if len(_lowercase ) > 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(_lowercase ) ):
                    if seq[i] not in residue_constants.restypes:
                         __UpperCamelCase =			'X'  # FIXME: strings are immutable
               __UpperCamelCase =			np.array(
                   [residue_constants.restype_order.get(_lowercase					,  residue_constants.restype_num ) for res_symbol in seq] )
          elif "[TERTIARY]" == g[0]:
               __UpperCamelCase =			[]
               for axis in range(3 ):
                    tertiary.append(list(map(_lowercase					,  g[1][axis].split() ) ) )
               __UpperCamelCase =			np.array(_lowercase )
               __UpperCamelCase =			np.zeros((len(tertiary[0] ) // 3, residue_constants.atom_type_num, 3) ).astype(np.floataa )
               for i, atom in enumerate(_lowercase ):
                    __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(_lowercase ),
                       residue_constants.atom_type_num,
                   ) ).astype(np.floataa )
               for i, atom in enumerate(_lowercase ):
                    __UpperCamelCase =			1
               atom_mask *= mask[..., None]

     assert aatype is not None

     return Protein(
         atom_positions=_lowercase					,  atom_mask=_lowercase					,  aatype=_lowercase					,  residue_index=np.arange(len(_lowercase ) )					,  b_factors=_lowercase					,  )






def 		_A		(		_lowercase					,  _lowercase = 0 )					-> List[str]:


     """simple docstring"""


     __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(_lowercase					,  _lowercase ) if i == chain_id]

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

     pdb_headers.append(f'''PARENT {' '.join(_lowercase )}''' )

     return pdb_headers






def 		_A		(		_lowercase					,  _lowercase )					-> str:


     """simple docstring"""


     __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(_lowercase )					,  [] )
                    parent_dict[str(_lowercase )].append(_lowercase )

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

     def make_parent_line(_lowercase ) -> str:
          return f'''PARENT {' '.join(_lowercase )}'''

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

     __UpperCamelCase =			0
     for i, l in enumerate(_lowercase ):
          if "PARENT" not in l and "REMARK" not in l:
               out_pdb_lines.append(_lowercase )
          if "TER" in l and "END" not in lines[i + 1]:
               chain_counter += 1
               if not chain_counter >= len(_lowercase ):
                    __UpperCamelCase =			parents_per_chain[chain_counter]
               else:
                    __UpperCamelCase =			['N/A']

               out_pdb_lines.append(make_parent_line(_lowercase ) )

     return "\n".join(_lowercase )






def 		_A		(		_lowercase )					-> str:


     """simple docstring"""


     __UpperCamelCase =			residue_constants.restypes + ['X']

     def res_atoa(_lowercase ) -> 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(_lowercase )
     if len(_lowercase ) > 0:
          pdb_lines.extend(_lowercase )

     __UpperCamelCase =			aatype.shape[0]
     __UpperCamelCase =			1
     __UpperCamelCase =			0
     __UpperCamelCase =			string.ascii_uppercase
     __UpperCamelCase =			None
     # Add all atom sites.
     for i in range(_lowercase ):
          __UpperCamelCase =			res_atoa(aatype[i] )
          for atom_name, pos, mask, b_factor in zip(_lowercase					,  atom_positions[i]					,  atom_mask[i]					,  b_factors[i] ):
               if mask < 0.5:
                    continue

               __UpperCamelCase =			'ATOM'
               __UpperCamelCase =			atom_name if len(_lowercase ) == 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(_lowercase )
               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(_lowercase )
               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(_lowercase					,  _lowercase ) )

     pdb_lines.append('END' )
     pdb_lines.append('' )
     return "\n".join(_lowercase )






def 		_A		(		_lowercase )					-> np.ndarray:


     """simple docstring"""


     return residue_constants.STANDARD_ATOM_MASK[prot.aatype]






def 		_A		(		_lowercase					,  _lowercase					,  _lowercase = None					,  _lowercase = None					,  _lowercase = None					,  _lowercase = None					,  _lowercase = 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=_lowercase					,  remark=_lowercase					,  parents=_lowercase					,  parents_chain_index=_lowercase					,  )






import string






def 		_A		(		_lowercase )					-> None:


     """simple docstring"""


     for key in range(len(string.ascii_uppercase ) ):
          __UpperCamelCase =			''
          for symbol in message:
               if symbol in string.ascii_uppercase:
                    __UpperCamelCase =			string.ascii_uppercase.find(_lowercase )
                    __UpperCamelCase =			num - key
                    if num < 0:
                         __UpperCamelCase =			num + len(string.ascii_uppercase )
                    __UpperCamelCase =			translated + string.ascii_uppercase[num]
               else:
                    __UpperCamelCase =			translated + symbol
          print(f'''Decryption using Key #{key}: {translated}''' )






def 		_A		(		)					-> None:


     """simple docstring"""


     __UpperCamelCase =			input('Encrypted message: ' )
     __UpperCamelCase =			message.upper()
     decrypt(_lowercase )


if __name__ == "__main__":
    import doctest

    doctest.testmod()
    main()


