

'''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 :      int					 =     Mapping[str, np.ndarray]
lowerCamelCase :      Union[str, Any]					 =     Mapping[str, Any]  # Is a nested dict.
lowerCamelCase :      Dict					 =     0.0_1







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

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

  # Chain indices for multi-chain predictions
  A__		 =				None

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

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

  # Chain corresponding to each parent
  A__		 =				None


def        _lowerCAmelCase					(						_UpperCamelCase						:     str				)      ->			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        _lowerCAmelCase					(						_UpperCamelCase						:     Protein							, _UpperCamelCase						:     int = 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        _lowerCAmelCase					(						_UpperCamelCase						:     Protein							, _UpperCamelCase						:     str				)      ->			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						:     Sequence[str]				) -> 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        _lowerCAmelCase					(						_UpperCamelCase						:     Protein				)      ->			str:
     """simple docstring"""




     _SCREAMING_SNAKE_CASE							    =residue_constants.restypes + ['X']

     def res_atoa(_UpperCamelCase						:     int				) -> 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        _lowerCAmelCase					(						_UpperCamelCase						:     Protein				)      ->			np.ndarray:
     """simple docstring"""




     return residue_constants.STANDARD_ATOM_MASK[prot.aatype]







def        _lowerCAmelCase					(						_UpperCamelCase						:     FeatureDict							, _UpperCamelCase						:     ModelOutput							, _UpperCamelCase						:     Optional[np.ndarray] = None							, _UpperCamelCase						:     Optional[np.ndarray] = None							, _UpperCamelCase						:     Optional[str] = None							, _UpperCamelCase						:     Optional[Sequence[str]] = None							, _UpperCamelCase						:     Optional[Sequence[int]] = 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							, )







"""simple docstring"""
# Copyright 2021 The HuggingFace Team. All rights reserved.
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#     http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

from argparse import ArgumentParser

from accelerate.commands.config import get_config_parser
from accelerate.commands.env import env_command_parser
from accelerate.commands.launch import launch_command_parser
from accelerate.commands.test import test_command_parser
from accelerate.commands.tpu import tpu_command_parser



def      __lowerCamelCase   (							)			->      Any:
      __SCREAMING_SNAKE_CASE   :Tuple						=  ArgumentParser('''Accelerate CLI tool''' ,   usage='''accelerate <command> [<args>]''' ,   allow_abbrev=a_							)
      __SCREAMING_SNAKE_CASE   :str						=  parser.add_subparsers(help='''accelerate command helpers'''							)

      # Register commands
      get_config_parser(subparsers=a_							)
      env_command_parser(subparsers=a_							)
      launch_command_parser(subparsers=a_							)
      tpu_command_parser(subparsers=a_							)
      test_command_parser(subparsers=a_							)

      # Let's go
      __SCREAMING_SNAKE_CASE   :int						=  parser.parse_args()

      if not hasattr(a_ ,   '''func'''							):
            parser.print_help()
            exit(1							)

      # Run
      args.func(a_							)


if __name__ == "__main__":
  main()