


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


snake_case							:       Dict     			=      Mapping[str, np.ndarray]
snake_case							:       Optional[int]     			=      Mapping[str, Any]  # Is a nested dict.
snake_case							:       Any     			=      0.01







@dataclasses.dataclass(frozen=lowerCamelCase_      )
class        snake_case_   :
					UpperCAmelCase__					:    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'.
					UpperCAmelCase__					:    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.
					UpperCAmelCase__					:    np.ndarray  # [num_res, num_atom_type]

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

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

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

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

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






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

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

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

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

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

							pdb_headers.append(F'PARENT {" ".join(__lowerCAmelCase   )}'   )

							return pdb_headers






def 							__lowercase   ( __lowerCAmelCase							:				Protein					,    __lowerCAmelCase							:				str   ):
							a__             =     []
							a__             =     pdb_str.split('\n'   )

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

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

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

							a__             =     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   ):
																												a__             =     parents_per_chain[chain_counter]
																					else:
																												a__             =     ['N/A']

																					out_pdb_lines.append(make_parent_line(__lowerCAmelCase   )   )

							return "\n".join(__lowerCAmelCase   )






def 							__lowercase   ( __lowerCAmelCase							:				Protein   ):
							a__             =     residue_constants.restypes + ['X']

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

							a__             =     residue_constants.atom_types

							a__             =     []

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

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

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

							a__             =     aatype.shape[0]
							a__             =     1
							a__             =     0
							a__             =     string.ascii_uppercase
							a__             =     None
							# Add all atom sites.
							for i in range(__lowerCAmelCase   ):
														a__             =     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

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

																					a__             =     'A'
																					if chain_index is not None:
																												a__             =     chain_tags[chain_index[i]]

																					# PDB is a columnar format, every space matters here!
																					a__             =     (
																					    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

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

														if should_terminate:
																					# Close the chain.
																					a__             =     'TER'
																					a__             =     (
																					    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 							__lowercase   ( __lowerCAmelCase							:				Protein   ):
							return residue_constants.STANDARD_ATOM_MASK[prot.aatype]






def 							__lowercase   ( __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					,    ):
							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					,    )








import copy
from dataclasses import dataclass, field
from typing import ClassVar, Dict

from ..features import Audio, ClassLabel, Features
from .base import TaskTemplate







@dataclass(frozen=lowerCamelCase_      )
class        snake_case_   (lowerCamelCase_      ):
					UpperCAmelCase__					:    str          =			field(default='''audio-classification'''	,						metadata={'''include_in_asdict_even_if_is_default''': True}      )
					UpperCAmelCase__					:    ClassVar[Features]          =			Features({'''audio''': Audio()}      )
					UpperCAmelCase__					:    ClassVar[Features]          =			Features({'''labels''': ClassLabel}      )
					UpperCAmelCase__					:    str          =			"audio"
					UpperCAmelCase__					:    str          =			"labels"
					def  lowerCamelCase__(      self   :Optional[int]			,__snake_case   :int      )					->    str:
												if self.label_column not in features:
																			raise ValueError(F'Column {self.label_column} is not present in features.'      )
												if not isinstance(features[self.label_column]			,__snake_case      ):
																			raise ValueError(F'Column {self.label_column} is not a ClassLabel.'      )
												a__             =     copy.deepcopy(self      )
												a__             =     self.label_schema.copy()
												a__             =     features[self.label_column]
												a__             =     label_schema
												return task_template



					@property
					def  lowerCamelCase__(      self   :Dict      )					->    Dict[str, str]:
												return {
												    self.audio_column: "audio",
												    self.label_column: "labels",
												}




