



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__   :					int 						=      Mapping[str, np.ndarray]
a__   :					Tuple 						=      Mapping[str, Any]  # Is a nested dict.
a__   :					int 						=      0.0_1



@dataclasses.dataclass(frozen=lowerCamelCase						)
class    UpperCAmelCase__:

   '''simple docstring'''




   A     :	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'.
   A     :	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.
   A     :	np.ndarray  # [num_res, num_atom_type]

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

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

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

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

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

def 	_lowerCAmelCase (    A__						):
      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 	_lowerCAmelCase (    A__    ,	A__ = 0						):
      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 	_lowerCAmelCase (    A__    ,	A__						):
      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 	_lowerCAmelCase (    A__						):
      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 	_lowerCAmelCase (    A__						):
      return residue_constants.STANDARD_ATOM_MASK[prot.aatype]

def 	_lowerCAmelCase (    A__    ,	A__    ,	A__ = None    ,	A__ = None    ,	A__ = None    ,	A__ = None    ,	A__ = None    ,	):
      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__    ,	)





import json
import os
import unittest

from transformers.models.ctrl.tokenization_ctrl import VOCAB_FILES_NAMES, CTRLTokenizer

from ...test_tokenization_common import TokenizerTesterMixin



class    UpperCAmelCase__(				lowerCamelCase  ,				unittest.TestCase						):

   '''simple docstring'''




   A     :	int												=     CTRLTokenizer
   A     :	Tuple												=     False
   A     :	Any												=     False


   def       UpperCAmelCase		(    self	:      int)						->					Any:




         """simple docstring"""

         super().setUp()

         # Adapted from Sennrich et al. 2015 and https://github.com/rsennrich/subword-nmt
         lowercase__  =	['adapt', 're@@', 'a@@', 'apt', 'c@@', 't', '<unk>']
         lowercase__  =	dict(zip(lowerCAmelCase      ,					range(len(lowerCAmelCase))))
         lowercase__  =	['#version: 0.2', 'a p', 'ap t</w>', 'r e', 'a d', 'ad apt</w>', '']
         lowercase__  =	{'unk_token': '<unk>'}

         lowercase__  =	os.path.join(self.tmpdirname      ,					VOCAB_FILES_NAMES['vocab_file'])
         lowercase__  =	os.path.join(self.tmpdirname      ,					VOCAB_FILES_NAMES['merges_file'])
         with open(self.vocab_file      ,					'w'      ,					encoding='utf-8') as fp:
               fp.write(json.dumps(lowerCAmelCase) + '\n')
         with open(self.merges_file      ,					'w'      ,					encoding='utf-8') as fp:
               fp.write('\n'.join(lowerCAmelCase))


   def       UpperCAmelCase		(    self	:      int      ,					**lowerCAmelCase	:      str)						->					Dict:




         """simple docstring"""

         kwargs.update(self.special_tokens_map)
         return CTRLTokenizer.from_pretrained(self.tmpdirname      ,					**lowerCAmelCase)


   def       UpperCAmelCase		(    self	:      List[str]      ,					lowerCAmelCase	:      Optional[int])						->					Optional[Any]:




         """simple docstring"""

         lowercase__  =	'adapt react readapt apt'
         lowercase__  =	'adapt react readapt apt'
         return input_text, output_text



   def       UpperCAmelCase		(    self	:      Optional[int])						->					str:




         """simple docstring"""

         lowercase__  =	CTRLTokenizer(self.vocab_file      ,					self.merges_file      ,					**self.special_tokens_map)
         lowercase__  =	'adapt react readapt apt'
         lowercase__  =	'adapt re@@ a@@ c@@ t re@@ adapt apt'.split()
         lowercase__  =	tokenizer.tokenize(lowerCAmelCase)
         self.assertListEqual(lowerCAmelCase      ,					lowerCAmelCase)

         lowercase__  =	tokens + [tokenizer.unk_token]

         lowercase__  =	[0, 1, 2, 4, 5, 1, 0, 3, 6]
         self.assertListEqual(tokenizer.convert_tokens_to_ids(lowerCAmelCase)      ,					lowerCAmelCase)
