


'''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


__UpperCAmelCase       =							Mapping[str, np.ndarray]
__UpperCAmelCase       =							Mapping[str, Any]  # Is a nested dict.
__UpperCAmelCase       =							0.01




@dataclasses.dataclass(frozen=a__  )
class 		a__    :





       '''simple docstring'''






       lowercase__      :       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'.
       lowercase__      :       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.
       lowercase__      :       np.ndarray  # [num_res, num_atom_type]

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

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

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

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

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


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

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

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

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

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

       pdb_headers.append(F"""PARENT {" ".join(A	)}"""	)

       return pdb_headers


def  _snake_case       (					A			,   A	)						->   str:
       lowerCAmelCase__	       =     []
       lowerCAmelCase__	       =     pdb_str.split('''\n'''	)

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

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

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

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

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

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

                     out_pdb_lines.append(make_parent_line(A	)	)

       return "\n".join(A	)


def  _snake_case       (					A	)						->   str:
       lowerCAmelCase__	       =     residue_constants.restypes + ['''X''']

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

       lowerCAmelCase__	       =     residue_constants.atom_types

       lowerCAmelCase__	       =     []

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

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

       lowerCAmelCase__	       =     get_pdb_headers(A	)
       if len(A	) > 0:
              pdb_lines.extend(A	)

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

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

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

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

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

              if should_terminate:
                     # Close the chain.
                     lowerCAmelCase__	       =     '''TER'''
                     lowerCAmelCase__	       =     (
                         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  _snake_case       (					A	)						->   np.ndarray:
       return residue_constants.STANDARD_ATOM_MASK[prot.aatype]






def  _snake_case       (					A			,   A			,   A = None			,   A = None			,   A = None			,   A = None			,   A = 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=A			,   remark=A			,   parents=A			,   parents_chain_index=A			,   )



'''simple docstring'''






from collections.abc import Iterable
from typing import Any




class 		a__    :





							'''simple docstring'''






							def __init__(		self ,   lowerCamelCase_ = None       )	->							List[str]:
														lowerCAmelCase__	       =     value
														lowerCAmelCase__	       =     None  # Added in order to delete a node easier
														lowerCAmelCase__	       =     None
														lowerCAmelCase__	       =     None







							def __repr__(		self       )	->							str:
														from pprint import pformat

														if self.left is None and self.right is None:
																					return str(self.value       )
														return pformat({F"""{self.value}""": (self.left, self.right)} ,   indent=1       )




class 		a__    :





							'''simple docstring'''






							def __init__(		self ,   lowerCamelCase_ = None       )	->							Union[str, Any]:
														lowerCAmelCase__	       =     root







							def __str__(		self       )	->							str:
														return str(self.root       )







							def   __SCREAMING_SNAKE_CASE							(		self ,   lowerCamelCase_ ,   lowerCamelCase_       )	->							None:
														if new_children is not None:  # reset its kids
																					lowerCAmelCase__	       =     node.parent
														if node.parent is not None:  # reset its parent
																					if self.is_right(lowerCamelCase_       ):  # If it is the right children
																												lowerCAmelCase__	       =     new_children
																					else:
																												lowerCAmelCase__	       =     new_children
														else:
																					lowerCAmelCase__	       =     new_children







							def   __SCREAMING_SNAKE_CASE							(		self ,   lowerCamelCase_       )	->							bool:
														if node.parent and node.parent.right:
																					return node == node.parent.right
														return False







							def   __SCREAMING_SNAKE_CASE							(		self       )	->							bool:
														return self.root is None







							def   __SCREAMING_SNAKE_CASE							(		self ,   lowerCamelCase_       )	->							None:
														lowerCAmelCase__	       =     Node(lowerCamelCase_       )  # create a new Node
														if self.empty():  # if Tree is empty
																					lowerCAmelCase__	       =     new_node  # set its root
														else:  # Tree is not empty
																					lowerCAmelCase__	       =     self.root  # from root
																					if parent_node is None:
																												return
																					while True:  # While we don't get to a leaf
																												if value < parent_node.value:  # We go left
																																			if parent_node.left is None:
																																										lowerCAmelCase__	       =     new_node  # We insert the new node in a leaf
																																										break
																																			else:
																																										lowerCAmelCase__	       =     parent_node.left
																												else:
																																			if parent_node.right is None:
																																										lowerCAmelCase__	       =     new_node
																																										break
																																			else:
																																										lowerCAmelCase__	       =     parent_node.right
																					lowerCAmelCase__	       =     parent_node







							def   __SCREAMING_SNAKE_CASE							(		self ,   *lowerCamelCase_       )	->							None:
														for value in values:
																					self.__insert(lowerCamelCase_       )







							def   __SCREAMING_SNAKE_CASE							(		self ,   lowerCamelCase_       )	->							Node | None:
														if self.empty():
																					raise IndexError('''Warning: Tree is empty! please use another.'''       )
														else:
																					lowerCAmelCase__	       =     self.root
																					# use lazy evaluation here to avoid NoneType Attribute error
																					while node is not None and node.value is not value:
																												lowerCAmelCase__	       =     node.left if value < node.value else node.right
																					return node







							def   __SCREAMING_SNAKE_CASE							(		self ,   lowerCamelCase_ = None       )	->							Node | None:
														if node is None:
																					if self.root is None:
																												return None
																					lowerCAmelCase__	       =     self.root

														if not self.empty():
																					while node.right is not None:
																												lowerCAmelCase__	       =     node.right
														return node







							def   __SCREAMING_SNAKE_CASE							(		self ,   lowerCamelCase_ = None       )	->							Node | None:
														if node is None:
																					lowerCAmelCase__	       =     self.root
														if self.root is None:
																					return None
														if not self.empty():
																					lowerCAmelCase__	       =     self.root
																					while node.left is not None:
																												lowerCAmelCase__	       =     node.left
														return node







							def   __SCREAMING_SNAKE_CASE							(		self ,   lowerCamelCase_       )	->							None:
														lowerCAmelCase__	       =     self.search(lowerCamelCase_       )  # Look for the node with that label
														if node is not None:
																					if node.left is None and node.right is None:  # If it has no children
																												self.__reassign_nodes(lowerCamelCase_ ,   lowerCamelCase_       )
																					elif node.left is None:  # Has only right children
																												self.__reassign_nodes(lowerCamelCase_ ,   node.right       )
																					elif node.right is None:  # Has only left children
																												self.__reassign_nodes(lowerCamelCase_ ,   node.left       )
																					else:
																												lowerCAmelCase__	       =     self.get_max(
																												    node.left       )  # Gets the max value of the left branch
																												self.remove(tmp_node.value       )  # type: ignore
																												lowerCAmelCase__	       =     (
																												    tmp_node.value  # type: ignore
																												)  # Assigns the value to the node to delete and keep tree structure







							def   __SCREAMING_SNAKE_CASE							(		self ,   lowerCamelCase_       )	->							Iterable:
														if node is not None:
																					yield node  # Preorder Traversal
																					yield from self.preorder_traverse(node.left       )
																					yield from self.preorder_traverse(node.right       )







							def   __SCREAMING_SNAKE_CASE							(		self ,   lowerCamelCase_=None       )	->							Any:
														if traversal_function is None:
																					return self.preorder_traverse(self.root       )
														else:
																					return traversal_function(self.root       )







							def   __SCREAMING_SNAKE_CASE							(		self ,   lowerCamelCase_ ,   lowerCamelCase_       )	->							None:
														if node:
																					self.inorder(lowerCamelCase_ ,   node.left       )
																					arr.append(node.value       )
																					self.inorder(lowerCamelCase_ ,   node.right       )







							def   __SCREAMING_SNAKE_CASE							(		self ,   lowerCamelCase_ ,   lowerCamelCase_       )	->							int:
														lowerCAmelCase__	       =     []
														self.inorder(lowerCamelCase_ ,   lowerCamelCase_       )  # append all values to list using inorder traversal
														return arr[k - 1]


def  _snake_case       (					A	)						->   list[Node]:
							lowerCAmelCase__	       =     []
							if curr_node is not None:
														lowerCAmelCase__	       =     postorder(curr_node.left	) + postorder(curr_node.right	) + [curr_node]
							return node_list


def  _snake_case       (					)						->   None:
							lowerCAmelCase__	       =     (8, 3, 6, 1, 10, 14, 13, 4, 7)
							lowerCAmelCase__	       =     BinarySearchTree()
							for i in testlist:
														t.insert(A	)

							# Prints all the elements of the list in order traversal
							print(A	)

							if t.search(6	) is not None:
														print('''The value 6 exists'''	)
							else:
														print('''The value 6 doesn\'t exist'''	)

							if t.search(-1	) is not None:
														print('''The value -1 exists'''	)
							else:
														print('''The value -1 doesn\'t exist'''	)

							if not t.empty():
														print('''Max Value: '''			,   t.get_max().value	)  # type: ignore
														print('''Min Value: '''			,   t.get_min().value	)  # type: ignore

							for i in testlist:
														t.remove(A	)
														print(A	)


if __name__ == "__main__":
		import doctest

		doctest.testmod(verbose=True)