


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_				:			str   =	Mapping[str, np.ndarray]
UpperCAmelCase_				:			Union[str, Any]   =	Mapping[str, Any]  # Is a nested dict.
UpperCAmelCase_				:			Optional[int]   =	0.0_1
@dataclasses.dataclass(frozen=_lowercase      )
class 			SCREAMING_SNAKE_CASE__  :
      snake_case__    :					List[Any]					       =						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__    :					Dict					       =						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__    :					List[Any]					       =						42  # [num_res, num_atom_type]

      # Residue index as used in PDB. It is not necessarily continuous or 0-indexed.
      snake_case__    :					Optional[Any]					       =						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__    :					int					       =						42  # [num_res, num_atom_type]

      # Chain indices for multi-chain predictions
      snake_case__    :					Tuple					       =						None

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

      # Templates used to generate this protein (prediction-only)
      snake_case__    :					Tuple					       =						None

      # Chain corresponding to each parent
      snake_case__    :					Dict					       =						None







def 	SCREAMING_SNAKE_CASE_						(      __A			:      str    )     ->		Protein:

       """simple docstring"""

       a_ :		Optional[Any]							=  R'(\[[A-Z]+\]\n)'
       a_ :		str							=  [tag.strip() for tag in re.split(a__  ,   a__    ) if len(a__    ) > 0]
       a_ :		List[str]							=  zip(tags[0::2]  ,   [l.split('\n'    ) for l in tags[1::2]]    )

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

       """simple docstring"""

       a_ :		List[str]							=  []

       a_ :		Union[str, Any]							=  prot.remark
       if remark is not None:
              pdb_headers.append(F"""REMARK {remark}"""    )

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

       if parents is None or len(a__    ) == 0:
              a_ :		List[str]							=  ['N/A']

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

       return pdb_headers







def 	SCREAMING_SNAKE_CASE_						(      __A			:      Protein  ,   __A			:      str    )     ->		str:

       """simple docstring"""

       a_ :		Tuple							=  []
       a_ :		Dict							=  pdb_str.split('\n'    )

       a_ :		Union[str, Any]							=  prot.remark
       if remark is not None:
              out_pdb_lines.append(F"""REMARK {remark}"""    )

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

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

       def make_parent_line(__A			:      Sequence[str]    ) -> str:
              return F"""PARENT {" ".join(a__    )}"""

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

       a_ :		Union[str, Any]							=  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__    ):
                            a_ :		Tuple							=  parents_per_chain[chain_counter]
                     else:
                            a_ :		Optional[int]							=  ['N/A']

                     out_pdb_lines.append(make_parent_line(a__    )    )

       return "\n".join(a__    )







def 	SCREAMING_SNAKE_CASE_						(      __A			:      Protein    )     ->		str:

       """simple docstring"""

       a_ :		Tuple							=  residue_constants.restypes + ['X']

       def res_atoa(__A			:      int    ) -> str:
              return residue_constants.restype_atoa.get(restypes[r]  ,   'UNK'    )

       a_ :		Optional[int]							=  residue_constants.atom_types

       a_ :		Union[str, Any]							=  []

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

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

       a_ :		str							=  get_pdb_headers(a__    )
       if len(a__    ) > 0:
              pdb_lines.extend(a__    )

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

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

                     a_ :		Any							=  'A'
                     if chain_index is not None:
                            a_ :		Tuple							=  chain_tags[chain_index[i]]

                     # PDB is a columnar format, every space matters here!
                     a_ :		List[str]							=  (
                         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

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

              if should_terminate:
                     # Close the chain.
                     a_ :		Any							=  'TER'
                     a_ :		Optional[Any]							=  (
                         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 	SCREAMING_SNAKE_CASE_						(      __A			:      Protein    )     ->		np.ndarray:

       """simple docstring"""

       return residue_constants.STANDARD_ATOM_MASK[prot.aatype]







def 	SCREAMING_SNAKE_CASE_						(      __A			:      FeatureDict  ,   __A			:      ModelOutput  ,   __A			:      Optional[np.ndarray] = None  ,   __A			:      Optional[np.ndarray] = None  ,   __A			:      Optional[str] = None  ,   __A			:      Optional[Sequence[str]] = None  ,   __A			:      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=a__  ,   remark=a__  ,   parents=a__  ,   parents_chain_index=a__  ,   )






def 	SCREAMING_SNAKE_CASE_						(      __A			:      int  ,   __A			:      int    )     ->		int:

       """simple docstring"""

       while b:
              a_							,		a_ :		int							=  b, a % b
       return a







def 	SCREAMING_SNAKE_CASE_						(      __A			:      int  ,   __A			:      int    )     ->		int:

       """simple docstring"""

       return a if b == 0 else euclidean_gcd_recursive(__A  ,   a % b    )







def 	SCREAMING_SNAKE_CASE_						(      )     ->		str:

       """simple docstring"""

       print(F"""euclidean_gcd(3, 5) = {euclidean_gcd(3  ,   5    )}"""    )
       print(F"""euclidean_gcd(5, 3) = {euclidean_gcd(5  ,   3    )}"""    )
       print(F"""euclidean_gcd(1, 3) = {euclidean_gcd(1  ,   3    )}"""    )
       print(F"""euclidean_gcd(3, 6) = {euclidean_gcd(3  ,   6    )}"""    )
       print(F"""euclidean_gcd(6, 3) = {euclidean_gcd(6  ,   3    )}"""    )

       print(F"""euclidean_gcd_recursive(3, 5) = {euclidean_gcd_recursive(3  ,   5    )}"""    )
       print(F"""euclidean_gcd_recursive(5, 3) = {euclidean_gcd_recursive(5  ,   3    )}"""    )
       print(F"""euclidean_gcd_recursive(1, 3) = {euclidean_gcd_recursive(1  ,   3    )}"""    )
       print(F"""euclidean_gcd_recursive(3, 6) = {euclidean_gcd_recursive(3  ,   6    )}"""    )
       print(F"""euclidean_gcd_recursive(6, 3) = {euclidean_gcd_recursive(6  ,   3    )}"""    )


if __name__ == "__main__":
   main()


