





"""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


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




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







     '''simple docstring'''




     __lowerCAmelCase					=					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'.
     __lowerCAmelCase					=					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.
     __lowerCAmelCase					=					42  # [num_res, num_atom_type]

     # Residue index as used in PDB. It is not necessarily continuous or 0-indexed.
     __lowerCAmelCase					=					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.
     __lowerCAmelCase					=					42  # [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       __A (     a_  :str)						->						Protein:
    __a	:  int         =					R'''(\[[A-Z]+\]\n)'''
    __a	:  List[str]         =					[tag.strip() for tag in re.split(a_				,    a_) if len(a_) > 0]
    __a	:  Iterator[Tuple[str, List[str]]]         =					zip(tags[0::2]				,    [l.split('''\n''') for l in tags[1::2]])

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

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

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

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

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

    return pdb_headers

def       __A (     a_  :Protein				,    a_  :str)						->						str:
    __a	:  List[str]         =					[]
    __a	:  str         =					pdb_str.split('''\n''')

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

    __a	:  List[List[str]]
    if prot.parents is not None and len(prot.parents) > 0:
        __a	:  Union[str, Any]         =					[]
        if prot.parents_chain_index is not None:
            __a	:  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_)

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

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

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

    __a	:  str         =					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	:  Union[str, Any]         =					parents_per_chain[chain_counter]
            else:
                __a	:  Union[str, Any]         =					['''N/A''']

            out_pdb_lines.append(make_parent_line(a_))

    return "\n".join(a_)

def       __A (     a_  :Protein)						->						str:
    __a	:  List[Any]         =					residue_constants.restypes + ['''X''']

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

    __a	:  int         =					residue_constants.atom_types

    __a	:  List[str]         =					[]

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

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

    __a	:  str         =					get_pdb_headers(a_)
    if len(a_) > 0:
        pdb_lines.extend(a_)

    __a	:  Optional[int]         =					aatype.shape[0]
    __a	:  Any         =					1
    __a	:  Any         =					0
    __a	:  Optional[Any]         =					string.ascii_uppercase
    __a	:  List[str]         =					None
    # Add all atom sites.
    for i in range(a_):
        __a	:  Dict         =					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	:  str         =					'''ATOM'''
            __a	:  Any         =					atom_name if len(a_) == 4 else F""" {atom_name}"""
            __a	:  Union[str, Any]         =					''''''
            __a	:  List[str]         =					''''''
            __a	:  Optional[Any]         =					1.0_0
            __a	:  Optional[int]         =					atom_name[0]  # Protein supports only C, N, O, S, this works.
            __a	:  Tuple         =					''''''

            __a	:  Any         =					'''A'''
            if chain_index is not None:
                __a	:  Optional[int]         =					chain_tags[chain_index[i]]

            # PDB is a columnar format, every space matters here!
            __a	:  Union[str, 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(a_)
            atom_index += 1

        __a	:  Dict         =					i == n - 1
        if chain_index is not None:
            if i != n - 1 and chain_index[i + 1] != prev_chain_index:
                __a	:  Union[str, Any]         =					True
                __a	:  str         =					chain_index[i + 1]

        if should_terminate:
            # Close the chain.
            __a	:  Tuple         =					'''TER'''
            __a	:  Dict         =					(
                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       __A (     a_  :Protein)						->						np.ndarray:
    return residue_constants.STANDARD_ATOM_MASK[prot.aatype]






def       __A (     a_  :FeatureDict				,    a_  :ModelOutput				,    a_  :Optional[np.ndarray] = None				,    a_  :Optional[np.ndarray] = None				,    a_  :Optional[str] = None				,    a_  :Optional[Sequence[str]] = None				,    a_  :Optional[Sequence[int]] = 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 __future__ import annotations

import sys
from collections import deque
from typing import Generic, TypeVar

A	     =					TypeVar('''T''')




class 			__lowercase     (     Generic[T]							):







					'''simple docstring'''




					__lowerCAmelCase					=					42  # Cache store of keys
					__lowerCAmelCase					=					42  # References of the keys in cache
					__lowerCAmelCase					=					10  # Maximum capacity of cache







					def __init__(  self		,     _UpperCAmelCase       ):
									__a	:  Optional[int]         =					deque()
									__a	:  Dict         =					set()
									if not n:
													__a	:  List[Any]         =					sys.maxsize
									elif n < 0:
													raise ValueError('''n should be an integer greater than 0.'''       )
									else:
													__a	:  str         =					n







					def 	_lowerCamelCase						(  self		,     _UpperCAmelCase       ):
									if x not in self.key_reference:
													if len(self.dq_store       ) == LRUCache._MAX_CAPACITY:
																	__a	:  int         =					self.dq_store.pop()
																	self.key_reference.remove(_UpperCAmelCase       )
									else:
													self.dq_store.remove(_UpperCAmelCase       )

									self.dq_store.appendleft(_UpperCAmelCase       )
									self.key_reference.add(_UpperCAmelCase       )







					def 	_lowerCamelCase						(  self       ):
									for k in self.dq_store:
													print(_UpperCAmelCase       )







					def __repr__(  self       ):
									return f"""LRUCache({self._MAX_CAPACITY}) => {list(self.dq_store       )}"""


if __name__ == "__main__":
		import doctest

		doctest.testmod()

		A	     =					LRUCache(4)
		lru_cache.refer('''A''')
		lru_cache.refer(2)
		lru_cache.refer(3)
		lru_cache.refer('''A''')
		lru_cache.refer(4)
		lru_cache.refer(5)
		lru_cache.display()

		print(lru_cache)
		assert str(lru_cache) == "LRUCache(4) => [5, 4, 'A', 3]"