"""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       :			Any   	=Mapping[str, np.ndarray]
__lowerCAmelCase       :			Union[str, Any]   	=Mapping[str, Any]  # Is a nested dict.
__lowerCAmelCase       :			List[Any]   	=0.01





@dataclasses.dataclass(frozen=lowerCAmelCase      )
class 					_A		:
      snake_case__     :  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'.
      snake_case__     :  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.
      snake_case__     :  np.ndarray  # [num_res, num_atom_type]

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

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

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

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

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






def      UpperCAmelCase__			(							lowerCAmelCase__	:str						)					->       Protein:
      '''simple docstring'''


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

      assert aatype is not None

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


def      UpperCAmelCase__			(							lowerCAmelCase__	:Protein   ,						lowerCAmelCase__	:int = 0						)					->       List[str]:
      '''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(lowerCAmelCase__   ,						lowerCAmelCase__						) if i == chain_id]

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

      pdb_headers.append(f'PARENT {" ".join(lowerCAmelCase__						)}'						)

      return pdb_headers


def      UpperCAmelCase__			(							lowerCAmelCase__	:Protein   ,						lowerCAmelCase__	:str						)					->       str:
      '''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(lowerCAmelCase__						)   ,						[]						)
                        parent_dict[str(lowerCAmelCase__						)].append(lowerCAmelCase__						)

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

      def make_parent_line(lowerCAmelCase__	:Sequence[str]						) -> str:
            return f'PARENT {" ".join(lowerCAmelCase__						)}'

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

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

                  out_pdb_lines.append(make_parent_line(lowerCAmelCase__						)						)

      return "\n".join(lowerCAmelCase__						)


def      UpperCAmelCase__			(							lowerCAmelCase__	:Protein						)					->       str:
      '''simple docstring'''


      lowercase								=      residue_constants.restypes + ["""X"""]

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

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

                  lowercase								=      """ATOM"""
                  lowercase								=      atom_name if len(lowerCAmelCase__						) == 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(lowerCAmelCase__						)
                  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(lowerCAmelCase__						)
                  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(lowerCAmelCase__   ,						lowerCAmelCase__						)						)

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


def      UpperCAmelCase__			(							lowerCAmelCase__	:Protein						)					->       np.ndarray:
      '''simple docstring'''


      return residue_constants.STANDARD_ATOM_MASK[prot.aatype]






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




"""simple docstring"""






import os
import unittest

from transformers.models.transfo_xl.tokenization_transfo_xl import VOCAB_FILES_NAMES, TransfoXLTokenizer

from ...test_tokenization_common import TokenizerTesterMixin





class 					_A		(			lowerCAmelCase    ,       unittest.TestCase      ):
      snake_case__     :  str				    =      TransfoXLTokenizer
      snake_case__     :  Union[str, Any]				    =      False
      snake_case__     :  Union[str, Any]				    =      False

      def 							A__			(		self		):







            """simple docstring"""



            super().setUp()

            lowercase								=      [
                """<unk>""",
                """[CLS]""",
                """[SEP]""",
                """want""",
                """unwanted""",
                """wa""",
                """un""",
                """running""",
                """,""",
                """low""",
                """l""",
            ]
            lowercase								=      os.path.join(self.tmpdirname						,			VOCAB_FILES_NAMES["""vocab_file"""]		)
            with open(self.vocab_file						,			"""w"""						,			encoding="""utf-8"""		) as vocab_writer:
                  vocab_writer.write("""""".join([x + """\n""" for x in vocab_tokens]		)		)

      def 							A__			(		self						,			**__lowerCAmelCase		):







            """simple docstring"""



            lowercase								=      True
            return TransfoXLTokenizer.from_pretrained(self.tmpdirname						,			**__lowerCAmelCase		)

      def 							A__			(		self						,			__lowerCAmelCase		):







            """simple docstring"""



            lowercase								=      """<unk> UNwanted , running"""
            lowercase								=      """<unk> unwanted, running"""
            return input_text, output_text

      def 							A__			(		self		):







            """simple docstring"""



            lowercase								=      TransfoXLTokenizer(vocab_file=self.vocab_file						,			lower_case=__lowerCAmelCase		)

            lowercase								=      tokenizer.tokenize("""<unk> UNwanted , running"""		)
            self.assertListEqual(__lowerCAmelCase						,			["""<unk>""", """unwanted""", """,""", """running"""]		)

            self.assertListEqual(tokenizer.convert_tokens_to_ids(__lowerCAmelCase		)						,			[0, 4, 8, 7]		)

      def 							A__			(		self		):







            """simple docstring"""



            lowercase								=      TransfoXLTokenizer(lower_case=__lowerCAmelCase		)

            self.assertListEqual(
                tokenizer.tokenize(""" \tHeLLo ! how  \n Are yoU ?  """		)						,			["""hello""", """!""", """how""", """are""", """you""", """?"""]		)

      def 							A__			(		self		):







            """simple docstring"""



            lowercase								=      TransfoXLTokenizer(lower_case=__lowerCAmelCase		)

            self.assertListEqual(
                tokenizer.tokenize(""" \tHeLLo ! how  \n Are yoU ?  """		)						,			["""HeLLo""", """!""", """how""", """Are""", """yoU""", """?"""]		)

      def 							A__			(		self		):







            """simple docstring"""



            lowercase								=      TransfoXLTokenizer(lower_case=__lowerCAmelCase		)
            lowercase								=      """Hello (bracket) and side-scrolled [and] Henry's $5,000 with 3.34 m. What's up!?"""
            lowercase								=      [
                """Hello""",
                """(""",
                """bracket""",
                """)""",
                """and""",
                """side""",
                """@-@""",
                """scrolled""",
                """[""",
                """and""",
                """]""",
                """Henry""",
                """'s""",
                """$""",
                """5""",
                """@,@""",
                """000""",
                """with""",
                """3""",
                """@.@""",
                """34""",
                """m""",
                """.""",
                """What""",
                """'s""",
                """up""",
                """!""",
                """?""",
            ]

            self.assertListEqual(tokenizer.tokenize(__lowerCAmelCase		)						,			__lowerCAmelCase		)

            self.assertEqual(tokenizer.convert_tokens_to_string(__lowerCAmelCase		)						,			__lowerCAmelCase		)







      def 							A__			(		self		):







            """simple docstring"""



            lowercase								=      self.get_tokenizer()
            lowercase								=      len(__lowerCAmelCase		)

            tokenizer.add_tokens(["""new1""", """new2"""]		)
            tokenizer.move_added_token("""new1"""						,			1		)

            # Check that moved token is not copied (duplicate)
            self.assertEqual(len(__lowerCAmelCase		)						,			original_len + 2		)
            # Check that token is moved to specified id
            self.assertEqual(tokenizer.encode("""new1"""		)						,			[1]		)
            self.assertEqual(tokenizer.decode([1]		)						,			"""new1"""		)



