
'''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


_lowercase			:  str   							=	Mapping[str, np.ndarray]
_lowercase			:  str   							=	Mapping[str, Any]  # Is a nested dict.
_lowercase			:  Optional[Any]   							=	0.0_1






@dataclasses.dataclass(frozen=lowerCamelCase_					)
class 			lowerCAmelCase__       :






					"""simple docstring"""




					lowerCAmelCase_					       =					4_2  # [num_res, num_atom_type, 3]

					# Amino-acid type for each residue represented as an integer between 0 and
					# 20, where 20 is 'X'.
					lowerCAmelCase_					       =					4_2  # [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.
					lowerCAmelCase_					       =					4_2  # [num_res, num_atom_type]

					# Residue index as used in PDB. It is not necessarily continuous or 0-indexed.
					lowerCAmelCase_					       =					4_2  # [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.
					lowerCAmelCase_					       =					4_2  # [num_res, num_atom_type]

					# Chain indices for multi-chain predictions
					lowerCAmelCase_					       =					None

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

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

					# Chain corresponding to each parent
					lowerCAmelCase_					       =					None







def  snake_case_		(    __SCREAMING_SNAKE_CASE :			str							):



						"""simple docstring"""





						lowercase_     :					int													=	R'''(\[[A-Z]+\]\n)'''
						lowercase_     :					List[str]													=	[tag.strip() for tag in re.split(__SCREAMING_SNAKE_CASE				,				__SCREAMING_SNAKE_CASE							) if len(__SCREAMING_SNAKE_CASE							) > 0]
						lowercase_     :					Iterator[Tuple[str, List[str]]]													=	zip(tags[0::2]				,				[l.split('''\n'''							) for l in tags[1::2]]							)

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

						assert aatype is not None

						return Protein(
						    atom_positions=__SCREAMING_SNAKE_CASE				,				atom_mask=__SCREAMING_SNAKE_CASE				,				aatype=__SCREAMING_SNAKE_CASE				,				residue_index=np.arange(len(__SCREAMING_SNAKE_CASE							)							)				,				b_factors=__SCREAMING_SNAKE_CASE				,				)
def  snake_case_		(    __SCREAMING_SNAKE_CASE :			Protein				,				__SCREAMING_SNAKE_CASE :			int = 0							):



						"""simple docstring"""





						lowercase_     :					List[str]													=	[]

						lowercase_     :					Union[str, Any]													=	prot.remark
						if remark is not None:
												pdb_headers.append(F'''REMARK {remark}'''							)

						lowercase_     :					int													=	prot.parents
						lowercase_     :					int													=	prot.parents_chain_index
						if parents is not None and parents_chain_index is not None:
												lowercase_     :					Union[str, Any]													=	[p for i, p in zip(__SCREAMING_SNAKE_CASE				,				__SCREAMING_SNAKE_CASE							) if i == chain_id]

						if parents is None or len(__SCREAMING_SNAKE_CASE							) == 0:
												lowercase_     :					Union[str, Any]													=	['''N/A''']

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

						return pdb_headers
def  snake_case_		(    __SCREAMING_SNAKE_CASE :			Protein				,				__SCREAMING_SNAKE_CASE :			str							):



						"""simple docstring"""





						lowercase_     :					List[str]													=	[]
						lowercase_     :					Optional[Any]													=	pdb_str.split('''\n'''							)

						lowercase_     :					Union[str, Any]													=	prot.remark
						if remark is not None:
												out_pdb_lines.append(F'''REMARK {remark}'''							)

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

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

						def make_parent_line(__SCREAMING_SNAKE_CASE :			Sequence[str]							) -> str:
												return F'''PARENT {' '.join(__SCREAMING_SNAKE_CASE							)}'''

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

						lowercase_     :					List[str]													=	0
						for i, l in enumerate(__SCREAMING_SNAKE_CASE							):
												if "PARENT" not in l and "REMARK" not in l:
																		out_pdb_lines.append(__SCREAMING_SNAKE_CASE							)
												if "TER" in l and "END" not in lines[i + 1]:
																		chain_counter += 1
																		if not chain_counter >= len(__SCREAMING_SNAKE_CASE							):
																								lowercase_     :					int													=	parents_per_chain[chain_counter]
																		else:
																								lowercase_     :					List[Any]													=	['''N/A''']

																		out_pdb_lines.append(make_parent_line(__SCREAMING_SNAKE_CASE							)							)

						return "\n".join(__SCREAMING_SNAKE_CASE							)
def  snake_case_		(    __SCREAMING_SNAKE_CASE :			Protein							):



						"""simple docstring"""





						lowercase_     :					Any													=	residue_constants.restypes + ['''X''']

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

						lowercase_     :					Union[str, Any]													=	residue_constants.atom_types

						lowercase_     :					List[str]													=	[]

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

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

						lowercase_     :					Optional[Any]													=	get_pdb_headers(__SCREAMING_SNAKE_CASE							)
						if len(__SCREAMING_SNAKE_CASE							) > 0:
												pdb_lines.extend(__SCREAMING_SNAKE_CASE							)

						lowercase_     :					List[str]													=	aatype.shape[0]
						lowercase_     :					List[str]													=	1
						lowercase_     :					Tuple													=	0
						lowercase_     :					int													=	string.ascii_uppercase
						lowercase_     :					Union[str, Any]													=	None
						# Add all atom sites.
						for i in range(__SCREAMING_SNAKE_CASE							):
												lowercase_     :					Optional[Any]													=	res_atoa(aatype[i]							)
												for atom_name, pos, mask, b_factor in zip(__SCREAMING_SNAKE_CASE				,				atom_positions[i]				,				atom_mask[i]				,				b_factors[i]							):
																		if mask < 0.5:
																								continue

																		lowercase_     :					List[str]													=	'''ATOM'''
																		lowercase_     :					Tuple													=	atom_name if len(__SCREAMING_SNAKE_CASE							) == 4 else F''' {atom_name}'''
																		lowercase_     :					int													=	''''''
																		lowercase_     :					Dict													=	''''''
																		lowercase_     :					Dict													=	1.00
																		lowercase_     :					Tuple													=	atom_name[0]  # Protein supports only C, N, O, S, this works.
																		lowercase_     :					int													=	''''''

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

																		# PDB is a columnar format, every space matters here!
																		lowercase_     :					Any													=	(
																		    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(__SCREAMING_SNAKE_CASE							)
																		atom_index += 1

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

												if should_terminate:
																		# Close the chain.
																		lowercase_     :					List[str]													=	'''TER'''
																		lowercase_     :					Union[str, Any]													=	(
																		    F'''{chain_end:<6}{atom_index:>5}      {res_atoa(aatype[i]							):>3} {chain_tag:>1}{residue_index[i]:>4}'''
																		)
																		pdb_lines.append(__SCREAMING_SNAKE_CASE							)
																		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(__SCREAMING_SNAKE_CASE				,				__SCREAMING_SNAKE_CASE							)							)

						pdb_lines.append('''END'''							)
						pdb_lines.append(''''''							)
						return "\n".join(__SCREAMING_SNAKE_CASE							)
def  snake_case_		(    __SCREAMING_SNAKE_CASE :			Protein							):



						"""simple docstring"""





						return residue_constants.STANDARD_ATOM_MASK[prot.aatype]




def  snake_case_		(    __SCREAMING_SNAKE_CASE :			FeatureDict				,				__SCREAMING_SNAKE_CASE :			ModelOutput				,				__SCREAMING_SNAKE_CASE :			Optional[np.ndarray] = None				,				__SCREAMING_SNAKE_CASE :			Optional[np.ndarray] = None				,				__SCREAMING_SNAKE_CASE :			Optional[str] = None				,				__SCREAMING_SNAKE_CASE :			Optional[Sequence[str]] = None				,				__SCREAMING_SNAKE_CASE :			Optional[Sequence[int]] = None				,				):



						"""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=__SCREAMING_SNAKE_CASE				,				remark=__SCREAMING_SNAKE_CASE				,				parents=__SCREAMING_SNAKE_CASE				,				parents_chain_index=__SCREAMING_SNAKE_CASE				,				)





'''simple docstring'''







from __future__ import annotations






class 			lowerCAmelCase__       :






					def __init__(       self    ,							__SCREAMING_SNAKE_CASE = 0		):


											"""simple docstring"""





											lowercase_     :					Any													=	key






					def      _snake_case   (       self    ,							__SCREAMING_SNAKE_CASE    ,							__SCREAMING_SNAKE_CASE		):


											"""simple docstring"""





											assert isinstance(__SCREAMING_SNAKE_CASE    ,							__SCREAMING_SNAKE_CASE		) and isinstance(__SCREAMING_SNAKE_CASE    ,							__SCREAMING_SNAKE_CASE		)

											lowercase_     :					List[str]													=	key or self.__key or 1

											# make sure key is an appropriate size
											key %= 2_55

											return [chr(ord(__SCREAMING_SNAKE_CASE		) ^ key		) for ch in content]






					def      _snake_case   (       self    ,							__SCREAMING_SNAKE_CASE    ,							__SCREAMING_SNAKE_CASE		):


											"""simple docstring"""





											assert isinstance(__SCREAMING_SNAKE_CASE    ,							__SCREAMING_SNAKE_CASE		) and isinstance(__SCREAMING_SNAKE_CASE    ,							__SCREAMING_SNAKE_CASE		)

											lowercase_     :					Optional[int]													=	key or self.__key or 1

											# make sure key is an appropriate size
											key %= 2_55

											return [chr(ord(__SCREAMING_SNAKE_CASE		) ^ key		) for ch in content]






					def      _snake_case   (       self    ,							__SCREAMING_SNAKE_CASE    ,							__SCREAMING_SNAKE_CASE = 0		):


											"""simple docstring"""





											assert isinstance(__SCREAMING_SNAKE_CASE    ,							__SCREAMING_SNAKE_CASE		) and isinstance(__SCREAMING_SNAKE_CASE    ,							__SCREAMING_SNAKE_CASE		)

											lowercase_     :					List[Any]													=	key or self.__key or 1

											# make sure key can be any size
											while key > 2_55:
																	key -= 2_55

											# This will be returned
											lowercase_     :					str													=	''''''

											for ch in content:
																	ans += chr(ord(__SCREAMING_SNAKE_CASE		) ^ key		)

											return ans






					def      _snake_case   (       self    ,							__SCREAMING_SNAKE_CASE    ,							__SCREAMING_SNAKE_CASE = 0		):


											"""simple docstring"""





											assert isinstance(__SCREAMING_SNAKE_CASE    ,							__SCREAMING_SNAKE_CASE		) and isinstance(__SCREAMING_SNAKE_CASE    ,							__SCREAMING_SNAKE_CASE		)

											lowercase_     :					Any													=	key or self.__key or 1

											# make sure key can be any size
											while key > 2_55:
																	key -= 2_55

											# This will be returned
											lowercase_     :					Dict													=	''''''

											for ch in content:
																	ans += chr(ord(__SCREAMING_SNAKE_CASE		) ^ key		)

											return ans






					def      _snake_case   (       self    ,							__SCREAMING_SNAKE_CASE    ,							__SCREAMING_SNAKE_CASE = 0		):


											"""simple docstring"""





											assert isinstance(__SCREAMING_SNAKE_CASE    ,							__SCREAMING_SNAKE_CASE		) and isinstance(__SCREAMING_SNAKE_CASE    ,							__SCREAMING_SNAKE_CASE		)

											try:
																	with open(__SCREAMING_SNAKE_CASE		) as fin, open('''encrypt.out'''    ,							'''w+'''		) as fout:
																							# actual encrypt-process
																							for line in fin:
																													fout.write(self.encrypt_string(__SCREAMING_SNAKE_CASE    ,							__SCREAMING_SNAKE_CASE		)		)

											except OSError:
																	return False

											return True






					def      _snake_case   (       self    ,							__SCREAMING_SNAKE_CASE    ,							__SCREAMING_SNAKE_CASE		):


											"""simple docstring"""





											assert isinstance(__SCREAMING_SNAKE_CASE    ,							__SCREAMING_SNAKE_CASE		) and isinstance(__SCREAMING_SNAKE_CASE    ,							__SCREAMING_SNAKE_CASE		)

											try:
																	with open(__SCREAMING_SNAKE_CASE		) as fin, open('''decrypt.out'''    ,							'''w+'''		) as fout:
																							# actual encrypt-process
																							for line in fin:
																													fout.write(self.decrypt_string(__SCREAMING_SNAKE_CASE    ,							__SCREAMING_SNAKE_CASE		)		)

											except OSError:
																	return False

											return True


# Tests
# crypt = XORCipher()
# key = 67

# # test encrypt
# print(crypt.encrypt("hallo welt",key))
# # test decrypt
# print(crypt.decrypt(crypt.encrypt("hallo welt",key), key))

# # test encrypt_string
# print(crypt.encrypt_string("hallo welt",key))

# # test decrypt_string
# print(crypt.decrypt_string(crypt.encrypt_string("hallo welt",key),key))

# if (crypt.encrypt_file("test.txt",key)):
#       print("encrypt successful")
# else:
#       print("encrypt unsuccessful")

# if (crypt.decrypt_file("encrypt.out",key)):
#       print("decrypt successful")
# else:
#       print("decrypt unsuccessful")



