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

@dataclasses.dataclass(frozen=_A  )
class        _UpperCamelCase				:






			'''simple docstring'''

			__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        A__					(						lowerCamelCase						)  ->	Protein:
				UpperCamelCase_:							Optional[Any]	=						r"""(\[[A-Z]+\]\n)"""
				UpperCamelCase_:							List[str]	=						[tag.strip() for tag in re.split(lowerCamelCase     ,    lowerCamelCase						) if len(lowerCamelCase						) > 0]
				UpperCamelCase_:							Iterator[Tuple[str, List[str]]]	=						zip(tags[0::2]     ,    [l.split("""\n"""						) for l in tags[1::2]]						)

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

				UpperCamelCase_:							List[Any]	=						prot.remark
				if remark is not None:
								pdb_headers.append(F'''REMARK {remark}'''						)

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

				if parents is None or len(lowerCamelCase						) == 0:
								UpperCamelCase_:							List[Any]	=						["""N/A"""]

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

				return pdb_headers







def        A__					(						lowerCamelCase     ,    lowerCamelCase						)  ->	str:
				UpperCamelCase_:							List[str]	=						[]
				UpperCamelCase_:							Union[str, Any]	=						pdb_str.split("""\n"""						)

				UpperCamelCase_:							Optional[int]	=						prot.remark
				if remark is not None:
								out_pdb_lines.append(F'''REMARK {remark}'''						)

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

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

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

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

				UpperCamelCase_:							Dict	=						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						):
																UpperCamelCase_:							int	=						parents_per_chain[chain_counter]
												else:
																UpperCamelCase_:							str	=						["""N/A"""]

												out_pdb_lines.append(make_parent_line(lowerCamelCase						)						)

				return "\n".join(lowerCamelCase						)







def        A__					(						lowerCamelCase						)  ->	str:
				UpperCamelCase_:							Optional[Any]	=						residue_constants.restypes + ["""X"""]

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

				UpperCamelCase_:							List[str]	=						residue_constants.atom_types

				UpperCamelCase_:							List[str]	=						[]

				UpperCamelCase_:							Dict	=						prot.atom_mask
				UpperCamelCase_:							Dict	=						prot.aatype
				UpperCamelCase_:							Union[str, Any]	=						prot.atom_positions
				UpperCamelCase_:							List[Any]	=						prot.residue_index.astype(np.intaa						)
				UpperCamelCase_:							int	=						prot.b_factors
				UpperCamelCase_:							List[Any]	=						prot.chain_index

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

				UpperCamelCase_:							Tuple	=						get_pdb_headers(lowerCamelCase						)
				if len(lowerCamelCase						) > 0:
								pdb_lines.extend(lowerCamelCase						)

				UpperCamelCase_:							Optional[int]	=						aatype.shape[0]
				UpperCamelCase_:							Any	=						1
				UpperCamelCase_:							Optional[int]	=						0
				UpperCamelCase_:							Dict	=						string.ascii_uppercase
				UpperCamelCase_:							Optional[int]	=						None
				# Add all atom sites.
				for i in range(lowerCamelCase						):
								UpperCamelCase_:							List[Any]	=						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

												UpperCamelCase_:							int	=						"""ATOM"""
												UpperCamelCase_:							Dict	=						atom_name if len(lowerCamelCase						) == 4 else F''' {atom_name}'''
												UpperCamelCase_:							Union[str, Any]	=						""""""
												UpperCamelCase_:							Optional[Any]	=						""""""
												UpperCamelCase_:							Optional[int]	=						1.00
												UpperCamelCase_:							List[str]	=						atom_name[0]  # Protein supports only C, N, O, S, this works.
												UpperCamelCase_:							Optional[int]	=						""""""

												UpperCamelCase_:							Dict	=						"""A"""
												if chain_index is not None:
																UpperCamelCase_:							Optional[int]	=						chain_tags[chain_index[i]]

												# PDB is a columnar format, every space matters here!
												UpperCamelCase_:							Optional[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(lowerCamelCase						)
												atom_index += 1

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

								if should_terminate:
												# Close the chain.
												UpperCamelCase_:							Tuple	=						"""TER"""
												UpperCamelCase_:							str	=						(
												    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        A__					(						lowerCamelCase						)  ->	np.ndarray:
				return residue_constants.STANDARD_ATOM_MASK[prot.aatype]







def        A__					(						lowerCamelCase     ,    lowerCamelCase     ,    lowerCamelCase = None     ,    lowerCamelCase = None     ,    lowerCamelCase = None     ,    lowerCamelCase = None     ,    lowerCamelCase = None     ,    )  ->	Protein:
				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     ,    )








class        _UpperCamelCase				:






			'''simple docstring'''

			def __init__(       self :       List[str]						,	snake_case_ :       int						,	snake_case_ :       Optional[Any]=None						,	snake_case_ :       List[str]=None      ):
							UpperCamelCase_:							List[Any]	=						data
							UpperCamelCase_:							List[Any]	=						previous
							UpperCamelCase_:							Tuple	=						next_node

			def __str__(       self :       Dict      ):
							return f'''{self.data}'''

			def       lowerCAmelCase__	(       self :       List[str]      ):
							return self.data

			def       lowerCAmelCase__	(       self :       Any      ):
							return self.next




			def       lowerCAmelCase__	(       self :       List[str]      ):
							return self.previous




class        _UpperCamelCase				:






			'''simple docstring'''

			def __init__(       self :       Optional[Any]						,	snake_case_ :       int      ):
							UpperCamelCase_:							Union[str, Any]	=						head

			def __iter__(       self :       Union[str, Any]      ):
							return self




			def       lowerCAmelCase__	(       self :       Union[str, Any]      ):
							if not self.current:
											raise StopIteration
							else:
											UpperCamelCase_:							Dict	=						self.current.get_data()
											UpperCamelCase_:							Tuple	=						self.current.get_next()
											return value




class        _UpperCamelCase				:






			'''simple docstring'''

			def __init__(       self :       int      ):
							UpperCamelCase_:							Optional[int]	=						None  # First node in list
							UpperCamelCase_:							Dict	=						None  # Last node in list

			def __str__(       self :       Tuple      ):
							UpperCamelCase_:							int	=						self.head
							UpperCamelCase_:							Tuple	=						[]
							while current is not None:
											nodes.append(current.get_data()      )
											UpperCamelCase_:							List[str]	=						current.get_next()
							return " ".join(str(snake_case_      ) for node in nodes      )

			def __contains__(       self :       int						,	snake_case_ :       int      ):
							UpperCamelCase_:							Optional[Any]	=						self.head
							while current:
											if current.get_data() == value:
															return True
											UpperCamelCase_:							Any	=						current.get_next()
							return False

			def __iter__(       self :       Any      ):
							return LinkedListIterator(self.head      )

			def       lowerCAmelCase__	(       self :       Tuple      ):
							if self.head:
											return self.head.get_data()
							return None

			def       lowerCAmelCase__	(       self :       Optional[Any]      ):
							if self.tail:
											return self.tail.get_data()
							return None

			def       lowerCAmelCase__	(       self :       Optional[int]						,	snake_case_ :       Node      ):
							if self.head is None:
											UpperCamelCase_:							Tuple	=						node
											UpperCamelCase_:							Optional[int]	=						node
							else:
											self.insert_before_node(self.head						,	snake_case_      )

			def       lowerCAmelCase__	(       self :       Optional[Any]						,	snake_case_ :       Node      ):
							if self.head is None:
											self.set_head(snake_case_      )
							else:
											self.insert_after_node(self.tail						,	snake_case_      )

			def       lowerCAmelCase__	(       self :       List[Any]						,	snake_case_ :       int      ):
							UpperCamelCase_:							Any	=						Node(snake_case_      )
							if self.head is None:
											self.set_head(snake_case_      )
							else:
											self.set_tail(snake_case_      )

			def       lowerCAmelCase__	(       self :       Optional[Any]						,	snake_case_ :       Node						,	snake_case_ :       Node      ):
							UpperCamelCase_:							str	=						node
							UpperCamelCase_:							int	=						node.previous

							if node.get_previous() is None:
											UpperCamelCase_:							int	=						node_to_insert
							else:
											UpperCamelCase_:							Dict	=						node_to_insert

							UpperCamelCase_:							int	=						node_to_insert

			def       lowerCAmelCase__	(       self :       Dict						,	snake_case_ :       Node						,	snake_case_ :       Node      ):
							UpperCamelCase_:							Tuple	=						node
							UpperCamelCase_:							Dict	=						node.next

							if node.get_next() is None:
											UpperCamelCase_:							Union[str, Any]	=						node_to_insert
							else:
											UpperCamelCase_:							str	=						node_to_insert

							UpperCamelCase_:							int	=						node_to_insert

			def       lowerCAmelCase__	(       self :       Tuple						,	snake_case_ :       int						,	snake_case_ :       int      ):
							UpperCamelCase_:							Union[str, Any]	=						1
							UpperCamelCase_:							List[str]	=						Node(snake_case_      )
							UpperCamelCase_:							Optional[Any]	=						self.head
							while node:
											if current_position == position:
															self.insert_before_node(snake_case_						,	snake_case_      )
															return
											current_position += 1
											UpperCamelCase_:							Dict	=						node.next
							self.insert_after_node(self.tail						,	snake_case_      )

			def       lowerCAmelCase__	(       self :       int						,	snake_case_ :       int      ):
							UpperCamelCase_:							Union[str, Any]	=						self.head
							while node:
											if node.get_data() == item:
															return node
											UpperCamelCase_:							List[Any]	=						node.get_next()
							raise Exception("""Node not found"""      )

			def       lowerCAmelCase__	(       self :       List[Any]						,	snake_case_ :       List[str]      ):
							if (node := self.get_node(snake_case_      )) is not None:
											if node == self.head:
															UpperCamelCase_:							Optional[int]	=						self.head.get_next()

											if node == self.tail:
															UpperCamelCase_:							Union[str, Any]	=						self.tail.get_previous()

											self.remove_node_pointers(snake_case_      )

			@staticmethod
			def       lowerCAmelCase__	(       snake_case_ :       Node      ):
							if node.get_next():
											UpperCamelCase_:							str	=						node.previous

							if node.get_previous():
											UpperCamelCase_:							int	=						node.next

							UpperCamelCase_:							List[str]	=						None
							UpperCamelCase_:							int	=						None




			def       lowerCAmelCase__	(       self :       str      ):
							return self.head is None







def        A__					(						)  ->	None:
				pass


if __name__ == "__main__":
							import doctest

							doctest.testmod()






