"""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


lowerCAmelCase_:					List[Any]     =					Mapping[str, np.ndarray]
lowerCAmelCase_:					Tuple     =					Mapping[str, Any]  # Is a nested dict.
lowerCAmelCase_:					str     =					0.01






@dataclasses.dataclass(frozen=_a	)
class    a__    :
   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   (		A      ):






     '''simple docstring'''



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

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

     assert aatype is not None

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







def 					__a   (		A    ,				A = 0      ):






     '''simple docstring'''



     lowercase__				 =							[]

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

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

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

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

     return pdb_headers







def 					__a   (		A    ,				A      ):






     '''simple docstring'''



     lowercase__				 =							[]
     lowercase__				 =							pdb_str.split("\n"      )

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

     lowercase__				 =							42
     if prot.parents is not None and len(prot.parents      ) > 0:
          lowercase__				 =							[]
          if prot.parents_chain_index is not None:
               lowercase__				 =							{}
               for p, i in zip(prot.parents    ,				prot.parents_chain_index      ):
                    parent_dict.setdefault(str(A      )    ,				[]      )
                    parent_dict[str(A      )].append(A      )

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

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

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

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

               out_pdb_lines.append(make_parent_line(A      )      )

     return "\n".join(A      )







def 					__a   (		A      ):






     '''simple docstring'''



     lowercase__				 =							residue_constants.restypes + ["X"]

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

     lowercase__				 =							residue_constants.atom_types

     lowercase__				 =							[]

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

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

     lowercase__				 =							get_pdb_headers(A      )
     if len(A      ) > 0:
          pdb_lines.extend(A      )

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

               lowercase__				 =							"ATOM"
               lowercase__				 =							atom_name if len(A      ) == 4 else f''' {atom_name}'''
               lowercase__				 =							""
               lowercase__				 =							""
               lowercase__				 =							1.00
               lowercase__				 =							atom_name[0]  # Protein supports only C, N, O, S, this works.
               lowercase__				 =							""

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

               # PDB is a columnar format, every space matters here!
               lowercase__				 =							(
                   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(A      )
               atom_index += 1

          lowercase__				 =							i == n - 1
          if chain_index is not None:
               if i != n - 1 and chain_index[i + 1] != prev_chain_index:
                    lowercase__				 =							True
                    lowercase__				 =							chain_index[i + 1]

          if should_terminate:
               # Close the chain.
               lowercase__				 =							"TER"
               lowercase__				 =							(
                   f'''{chain_end:<6}{atom_index:>5}      {res_atoa(aatype[i]      ):>3} {chain_tag:>1}{residue_index[i]:>4}'''
               )
               pdb_lines.append(A      )
               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(A    ,				A      )      )

     pdb_lines.append("END"      )
     pdb_lines.append(""      )
     return "\n".join(A      )







def 					__a   (		A      ):






     '''simple docstring'''



     return residue_constants.STANDARD_ATOM_MASK[prot.aatype]







def 					__a   (		A    ,				A    ,				A = None    ,				A = None    ,				A = None    ,				A = None    ,				A = 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=A    ,				remark=A    ,				parents=A    ,				parents_chain_index=A    ,				)





"""simple docstring"""


from __future__ import annotations







def 					__a   (		A    ,				A      ):






     '''simple docstring'''



     if partitions <= 0:
          raise ValueError("partitions must be a positive number!"      )
     if partitions > number_of_bytes:
          raise ValueError("partitions can not > number_of_bytes!"      )
     lowercase__				 =							number_of_bytes // partitions
     lowercase__				 =							[]
     for i in range(A      ):
          lowercase__				 =							i * bytes_per_partition + 1
          lowercase__				 =							(
              number_of_bytes if i == partitions - 1 else (i + 1) * bytes_per_partition
          )
          allocation_list.append(f'''{start_bytes}-{end_bytes}'''      )
     return allocation_list


if __name__ == "__main__":
 import doctest

 doctest.testmod()




