





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      	=		Mapping[str, np.ndarray]
_SCREAMING_SNAKE_CASE      	=		Mapping[str, Any]  # Is a nested dict.
_SCREAMING_SNAKE_CASE      	=		0.0_1
@dataclasses.dataclass(frozen=snake_case_					)
class SCREAMING_SNAKE_CASE_						:
						__magic_name__:			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'.
						__magic_name__:			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.
						__magic_name__:			np.ndarray  # [num_res, num_atom_type]

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

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

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

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

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


def 							SCREAMING_SNAKE_CASE__						(    __a   ):
	snake_case_		:			Optional[Any]											=	r'(\[[A-Z]+\]\n)'
	snake_case_		:			List[str]											=	[tag.strip() for tag in re.split(__a   , __a   ) if len(__a   ) > 0]
	snake_case_		:			Iterator[Tuple[str, List[str]]]											=	zip(tags[0::2]   , [l.split('\n'   ) for l in tags[1::2]]   )

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

	snake_case_		:			Dict											=	prot.remark
	if remark is not None:
		pdb_headers.append(f"""REMARK {remark}"""   )

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

	if parents is None or len(__a   ) == 0:
		snake_case_		:			Dict											=	['N/A']

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

	return pdb_headers


def 							SCREAMING_SNAKE_CASE__						(    __a   , __a   ):
	snake_case_		:			List[str]											=	[]
	snake_case_		:			Tuple											=	pdb_str.split('\n'   )

	snake_case_		:			Dict											=	prot.remark
	if remark is not None:
		out_pdb_lines.append(f"""REMARK {remark}"""   )

	snake_case_		:			List[List[str]]
	if prot.parents is not None and len(prot.parents   ) > 0:
		snake_case_		:			Optional[Any]											=	[]
		if prot.parents_chain_index is not None:
			snake_case_		:			Dict[str, List[str]]											=	{}
			for p, i in zip(prot.parents   , prot.parents_chain_index   ):
				parent_dict.setdefault(str(__a   )   , []   )
				parent_dict[str(__a   )].append(__a   )

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

	def make_parent_line(__a   ) -> str:
		return f"""PARENT {' '.join(__a   )}"""

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

	snake_case_		:			Optional[int]											=	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   ):
				snake_case_		:			List[Any]											=	parents_per_chain[chain_counter]
			else:
				snake_case_		:			str											=	['N/A']

			out_pdb_lines.append(make_parent_line(__a   )   )

	return "\n".join(__a   )


def 							SCREAMING_SNAKE_CASE__						(    __a   ):
	snake_case_		:			Dict											=	residue_constants.restypes + ['X']

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

	snake_case_		:			str											=	residue_constants.atom_types

	snake_case_		:			List[str]											=	[]

	snake_case_		:			Any											=	prot.atom_mask
	snake_case_		:			Optional[Any]											=	prot.aatype
	snake_case_		:			Optional[Any]											=	prot.atom_positions
	snake_case_		:			Optional[Any]											=	prot.residue_index.astype(np.intaa   )
	snake_case_		:			Dict											=	prot.b_factors
	snake_case_		:			int											=	prot.chain_index

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

	snake_case_		:			Union[str, Any]											=	get_pdb_headers(__a   )
	if len(__a   ) > 0:
		pdb_lines.extend(__a   )

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

			snake_case_		:			Tuple											=	'ATOM'
			snake_case_		:			Union[str, Any]											=	atom_name if len(__a   ) == 4 else f""" {atom_name}"""
			snake_case_		:			Optional[int]											=	''
			snake_case_		:			Tuple											=	''
			snake_case_		:			Union[str, Any]											=	1.00
			snake_case_		:			Optional[int]											=	atom_name[0]  # Protein supports only C, N, O, S, this works.
			snake_case_		:			int											=	''

			snake_case_		:			Union[str, Any]											=	'A'
			if chain_index is not None:
				snake_case_		:			int											=	chain_tags[chain_index[i]]

			# PDB is a columnar format, every space matters here!
			snake_case_		:			int											=	(
			    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

		snake_case_		:			str											=	i == n - 1
		if chain_index is not None:
			if i != n - 1 and chain_index[i + 1] != prev_chain_index:
				snake_case_		:			Optional[int]											=	True
				snake_case_		:			List[str]											=	chain_index[i + 1]

		if should_terminate:
			# Close the chain.
			snake_case_		:			str											=	'TER'
			snake_case_		:			int											=	(
			    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   ):
	return residue_constants.STANDARD_ATOM_MASK[prot.aatype]


def 							SCREAMING_SNAKE_CASE__						(    __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   , )








from ....utils import logging


_SCREAMING_SNAKE_CASE      	=		logging.get_logger(__name__)
class SCREAMING_SNAKE_CASE_						(					snake_case_					):






						def __init__(      self      :      str		,   _A      :      List[Any]		,   _A      :      List[Any]=None		,   _A      :      str=2048	)							->    Optional[int]:







							"""simple docstring"""


							snake_case_		:			Tuple											=	config.__dict__
							snake_case_		:			List[str]											=	modal_hidden_size
							if num_labels:
								snake_case_		:			int											=	num_labels

