
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


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





@dataclasses.dataclass(frozen=__SCREAMING_SNAKE_CASE  )
class 							UpperCAmelCase      :




	'''simple docstring'''





	snake_case_					    =     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_					    =     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_					    =     42  # [num_res, num_atom_type]

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

	# Chain indices for multi-chain predictions
	snake_case_					    =     None

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

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

	# Chain corresponding to each parent
	snake_case_					    =     None





def 						UpperCAmelCase			(	a_						)		->	Protein:







				"""simple docstring"""



				__A   			= r"(\[[A-Z]+\]\n)"
				__A   			= [tag.strip() for tag in re.split(a_		,   a_						) if len(a_						) > 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(a_						)						):
																if seq[i] not in residue_constants.restypes:
																				__A   			= "X"  # FIXME: strings are immutable
												__A   			= np.array(
												    [residue_constants.restype_order.get(a_		,   residue_constants.restype_num						) for res_symbol in seq]						)
								elif "[TERTIARY]" == g[0]:
												__A   			= []
												for axis in range(3						):
																tertiary.append(list(map(a_		,   g[1][axis].split()						)						)						)
												__A   			= np.array(a_						)
												__A   			= np.zeros((len(tertiary[0]						) // 3, residue_constants.atom_type_num, 3)						).astype(np.floataa						)
												for i, atom in enumerate(a_						):
																__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(a_						),
												        residue_constants.atom_type_num,
												    )						).astype(np.floataa						)
												for i, atom in enumerate(a_						):
																__A   			= 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 						UpperCAmelCase			(	a_		,   a_ = 0						)		->	List[str]:







				"""simple docstring"""



				__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(a_		,   a_						) if i == chain_id]

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

				pdb_headers.append(F'''PARENT {' '.join(a_						)}'''						)

				return pdb_headers


def 						UpperCAmelCase			(	a_		,   a_						)		->	str:







				"""simple docstring"""



				__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(a_						)		,   []						)
																parent_dict[str(a_						)].append(a_						)

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

				def make_parent_line(a_						) -> str:
								return F'''PARENT {' '.join(a_						)}'''

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

				__A   			= 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   			= parents_per_chain[chain_counter]
												else:
																__A   			= ["N/A"]

												out_pdb_lines.append(make_parent_line(a_						)						)

				return "\n".join(a_						)


def 						UpperCAmelCase			(	a_						)		->	str:







				"""simple docstring"""



				__A   			= residue_constants.restypes + ["X"]

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

				__A   			= aatype.shape[0]
				__A   			= 1
				__A   			= 0
				__A   			= string.ascii_uppercase
				__A   			= None
				# Add all atom sites.
				for i in range(a_						):
								__A   			= 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   			= "ATOM"
												__A   			= atom_name if len(a_						) == 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(a_						)
												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(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 						UpperCAmelCase			(	a_						)		->	np.ndarray:







				"""simple docstring"""



				return residue_constants.STANDARD_ATOM_MASK[prot.aatype]


def 						UpperCAmelCase			(	a_		,   a_		,   a_ = None		,   a_ = None		,   a_ = None		,   a_ = None		,   a_ = 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_		,   )


import dataclasses
import json
import sys
import types
from argparse import ArgumentDefaultsHelpFormatter, ArgumentParser, ArgumentTypeError
from copy import copy
from enum import Enum
from inspect import isclass
from pathlib import Path
from typing import Any, Callable, Dict, Iterable, List, Literal, NewType, Optional, Tuple, Union, get_type_hints

import yaml


SCREAMING_SNAKE_CASE							:Optional[int]							 =				NewType('DataClass', Any)
SCREAMING_SNAKE_CASE							:int							 =				NewType('DataClassType', Any)


def 						UpperCAmelCase			(	a_						)		->	Optional[int]:







				"""simple docstring"""



				if isinstance(a_		,   a_						):
								return v
				if v.lower() in ("yes", "true", "t", "y", "1"):
								return True
				elif v.lower() in ("no", "false", "f", "n", "0"):
								return False
				else:
								raise ArgumentTypeError(
								    F'''Truthy value expected: got {v} but expected one of yes/no, true/false, t/f, y/n, 1/0 (case insensitive).'''						)


def 						UpperCAmelCase			(	a_						)		->	Callable[[str], Any]:







				"""simple docstring"""



				__A   			= {str(a_						): choice for choice in choices}
				return lambda a_						: str_to_choice.get(a_		,   a_						)


def 						UpperCAmelCase			(	*,
    a_ = None		,   a_ = None		,   a_ = dataclasses.MISSING		,   a_ = dataclasses.MISSING		,   a_ = None		,   **a_		,   )		->	dataclasses.Field:







				"""simple docstring"""



				if metadata is None:
								# Important, don't use as default param in function signature because dict is mutable and shared across function calls
								__A   			= {}
				if aliases is not None:
								__A   			= aliases
				if help is not None:
								__A   			= help

				return dataclasses.field(metadata=a_		,   default=a_		,   default_factory=a_		,   **a_						)





class 							UpperCAmelCase      (  __SCREAMING_SNAKE_CASE  ):




	'''simple docstring'''





	snake_case_					    =     42






	def __init__(       self					: Union[str, Any]							,A					: Union[DataClassType, Iterable[DataClassType]]							,**A					: List[Any] ):
					# To make the default appear when using --help
					if "formatter_class" not in kwargs:
									__A   			= ArgumentDefaultsHelpFormatter
					super().__init__(**A )
					if dataclasses.is_dataclass(A ):
									__A   			= [dataclass_types]
					__A   			= list(A )
					for dtype in self.dataclass_types:
									self._add_dataclass_arguments(A )






	@staticmethod
	def 				UpperCamelCase_  (       A					: ArgumentParser							,A					: dataclasses.Field ):
					__A   			= f'''--{field.name}'''
					__A   			= field.metadata.copy()
					# field.metadata is not used at all by Data Classes,
					# it is provided as a third-party extension mechanism.
					if isinstance(field.type							,A ):
									raise RuntimeError(
									    "Unresolved type detected, which should have been done with the help of "
									    "`typing.get_type_hints` method by default" )

					__A   			= kwargs.pop("aliases"							,[] )
					if isinstance(A							,A ):
									__A   			= [aliases]

					__A   			= getattr(field.type							,"__origin__"							,field.type )
					if origin_type is Union or (hasattr(A							,"UnionType" ) and isinstance(A							,types.UnionType )):
									if str not in field.type.__args__ and (
									    len(field.type.__args__ ) != 2 or type(A ) not in field.type.__args__
									):
													raise ValueError(
													    "Only `Union[X, NoneType]` (i.e., `Optional[X]`) is allowed for `Union` because"
													    " the argument parser only supports one type per argument."
													    f''' Problem encountered in field \'{field.name}\'.''' )
									if type(A ) not in field.type.__args__:
													# filter `str` in Union
													__A   			= field.type.__args__[0] if field.type.__args__[1] == str else field.type.__args__[1]
													__A   			= getattr(field.type							,"__origin__"							,field.type )
									elif bool not in field.type.__args__:
													# filter `NoneType` in Union (except for `Union[bool, NoneType]`)
													__A   			= (
													    field.type.__args__[0] if isinstance(A							,field.type.__args__[1] ) else field.type.__args__[1]
													)
													__A   			= getattr(field.type							,"__origin__"							,field.type )

        # A variable to store kwargs for a boolean field, if needed
        # so that we can init a `no_*` complement argument (see below)
					__A   			= {}
					if origin_type is Literal or (isinstance(field.type							,A ) and issubclass(field.type							,A )):
									if origin_type is Literal:
													__A   			= field.type.__args__
									else:
													__A   			= [x.value for x in field.type]

									__A   			= make_choice_type_function(kwargs["choices"] )

									if field.default is not dataclasses.MISSING:
													__A   			= field.default
									else:
													__A   			= True
					elif field.type is bool or field.type == Optional[bool]:
									# Copy the currect kwargs to use to instantiate a `no_*` complement argument below.
									# We do not initialize it here because the `no_*` alternative must be instantiated after the real argument
									__A   			= copy(A )

									# Hack because type=bool in argparse does not behave as we want.
									__A   			= string_to_bool
									if field.type is bool or (field.default is not None and field.default is not dataclasses.MISSING):
													# Default value is False if we have no default when of type bool.
													__A   			= False if field.default is dataclasses.MISSING else field.default
													# This is the value that will get picked if we don't include --field_name in any way
													__A   			= default
													# This tells argparse we accept 0 or 1 value after --field_name
													__A   			= "?"
													# This is the value that will get picked if we do --field_name (without value)
													__A   			= True
					elif isclass(A ) and issubclass(A							,A ):
									__A   			= field.type.__args__[0]
									__A   			= "+"
									if field.default_factory is not dataclasses.MISSING:
													__A   			= field.default_factory()
									elif field.default is dataclasses.MISSING:
													__A   			= True
					else:
									__A   			= field.type
									if field.default is not dataclasses.MISSING:
													__A   			= field.default
									elif field.default_factory is not dataclasses.MISSING:
													__A   			= field.default_factory()
									else:
													__A   			= True
					parser.add_argument(A							,*A							,**A )

					# Add a complement `no_*` argument for a boolean field AFTER the initial field has already been added.
					# Order is important for arguments with the same destination!
					# We use a copy of earlier kwargs because the original kwargs have changed a lot before reaching down
					# here and we do not need those changes/additional keys.
					if field.default is True and (field.type is bool or field.type == Optional[bool]):
									__A   			= False
									parser.add_argument(f'''--no_{field.name}'''							,action="store_false"							,dest=field.name							,**A )






	def 				UpperCamelCase_  (       self					: Union[str, Any]							,A					: DataClassType ):
					if hasattr(A							,"_argument_group_name" ):
									__A   			= self.add_argument_group(dtype._argument_group_name )
					else:
									__A   			= self

					try:
									__A   			= get_type_hints(A )
					except NameError:
									raise RuntimeError(
									    f'''Type resolution failed for {dtype}. Try declaring the class in global scope or '''
									    "removing line of `from __future__ import annotations` which opts in Postponed "
									    "Evaluation of Annotations (PEP 563)" )
					except TypeError as ex:
									# Remove this block when we drop Python 3.9 support
									if sys.version_info[:2] < (3, 10) and "unsupported operand type(s) for |" in str(A ):
													__A   			= ".".join(map(A							,sys.version_info[:3] ) )
													raise RuntimeError(
													    f'''Type resolution failed for {dtype} on Python {python_version}. Try removing '''
													    "line of `from __future__ import annotations` which opts in union types as "
													    "`X | Y` (PEP 604) via Postponed Evaluation of Annotations (PEP 563). To "
													    "support Python versions that lower than 3.10, you need to use "
													    "`typing.Union[X, Y]` instead of `X | Y` and `typing.Optional[X]` instead of "
													    "`X | None`." ) from ex
									raise

					for field in dataclasses.fields(A ):
									if not field.init:
													continue
									__A   			= type_hints[field.name]
									self._parse_dataclass_field(A							,A )






	def 				UpperCamelCase_  (       self					: Union[str, Any]							,A					: List[Any]=None							,A					: List[Any]=False							,A					: Optional[Any]=True							,A					: Union[str, Any]=None							,A					: Union[str, Any]=None							,):

					if args_file_flag or args_filename or (look_for_args_file and len(sys.argv )):
									__A   			= []

									if args_filename:
													args_files.append(Path(A ) )
									elif look_for_args_file and len(sys.argv ):
													args_files.append(Path(sys.argv[0] ).with_suffix(".args" ) )

									# args files specified via command line flag should overwrite default args files so we add them last
									if args_file_flag:
													# Create special parser just to extract the args_file_flag values
													__A   			= ArgumentParser()
													args_file_parser.add_argument(A							,type=A							,action="append" )

													# Use only remaining args for further parsing (remove the args_file_flag)
													__A			,							__A   			= args_file_parser.parse_known_args(args=A )
													__A   			= vars(A ).get(args_file_flag.lstrip("-" )							,A )

													if cmd_args_file_paths:
																	args_files.extend([Path(A ) for p in cmd_args_file_paths] )

									__A   			= []
									for args_file in args_files:
													if args_file.exists():
																	file_args += args_file.read_text().split()

            # in case of duplicate arguments the last one has precedence
            # args specified via the command line should overwrite args from files, so we add them last
									__A   			= file_args + args if args is not None else file_args + sys.argv[1:]
					__A			,							__A   			= self.parse_known_args(args=A )
					__A   			= []
					for dtype in self.dataclass_types:
									__A   			= {f.name for f in dataclasses.fields(A ) if f.init}
									__A   			= {k: v for k, v in vars(A ).items() if k in keys}
									for k in keys:
													delattr(A							,A )
									__A   			= dtype(**A )
									outputs.append(A )
					if len(namespace.__dict__ ) > 0:
									# additional namespace.
									outputs.append(A )
					if return_remaining_strings:
									return (*outputs, remaining_args)
					else:
									if remaining_args:
													raise ValueError(f'''Some specified arguments are not used by the HfArgumentParser: {remaining_args}''' )

									return (*outputs,)






	def 				UpperCamelCase_  (       self					: Dict							,A					: Dict[str, Any]							,A					: bool = False ):
					__A   			= set(args.keys() )
					__A   			= []
					for dtype in self.dataclass_types:
									__A   			= {f.name for f in dataclasses.fields(A ) if f.init}
									__A   			= {k: v for k, v in args.items() if k in keys}
									unused_keys.difference_update(inputs.keys() )
									__A   			= dtype(**A )
									outputs.append(A )
					if not allow_extra_keys and unused_keys:
									raise ValueError(f'''Some keys are not used by the HfArgumentParser: {sorted(A )}''' )
					return tuple(A )






	def 				UpperCamelCase_  (       self					: List[str]							,A					: str							,A					: bool = False ):
					with open(Path(A )							,encoding="utf-8" ) as open_json_file:
									__A   			= json.loads(open_json_file.read() )
					__A   			= self.parse_dict(A							,allow_extra_keys=A )
					return tuple(A )







	def 				UpperCamelCase_  (       self					: int							,A					: str							,A					: bool = False ):
					__A   			= self.parse_dict(yaml.safe_load(Path(A ).read_text() )							,allow_extra_keys=A )
					return tuple(A )
