


'''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


__magic_name__ : int					=Mapping[str, np.ndarray]
__magic_name__ : Tuple					=Mapping[str, Any]  # Is a nested dict.
__magic_name__ : int					=0.0_1






@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   __snake_case							(							lowerCamelCase_			:					Any    ):
				'''simple docstring'''




				__magic_name__							=			R"(\[[A-Z]+\]\n)"
				__magic_name__							=			[tag.strip() for tag in re.split(A__						,	A__    ) if len(A__    ) > 0]
				__magic_name__							=			zip(tags[0::2]						,	[l.split("\n"    ) for l in tags[1::2]]    )

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




				__magic_name__							=			[]

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

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

				if parents is None or len(A__    ) == 0:
								__magic_name__							=			["N/A"]

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

				return pdb_headers




def   __snake_case							(							lowerCamelCase_			:					List[str]						,	lowerCamelCase_			:					Optional[Any]    ):
				'''simple docstring'''




				__magic_name__							=			[]
				__magic_name__							=			pdb_str.split("\n"    )

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

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

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

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

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

				__magic_name__							=			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__    ):
																__magic_name__							=			parents_per_chain[chain_counter]
												else:
																__magic_name__							=			["N/A"]

												out_pdb_lines.append(make_parent_line(A__    )    )

				return "\n".join(A__    )




def   __snake_case							(							lowerCamelCase_			:					Union[str, Any]    ):
				'''simple docstring'''




				__magic_name__							=			residue_constants.restypes + ["X"]

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

				__magic_name__							=			residue_constants.atom_types

				__magic_name__							=			[]

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

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

				__magic_name__							=			get_pdb_headers(A__    )
				if len(A__    ) > 0:
								pdb_lines.extend(A__    )

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

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

												__magic_name__							=			"A"
												if chain_index is not None:
																__magic_name__							=			chain_tags[chain_index[i]]

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

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

								if should_terminate:
												# Close the chain.
												__magic_name__							=			"TER"
												__magic_name__							=			(
												    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							(							lowerCamelCase_			:					Any    ):
				'''simple docstring'''




				return residue_constants.STANDARD_ATOM_MASK[prot.aatype]




def   __snake_case							(							lowerCamelCase_			:					Dict						,	lowerCamelCase_			:					Tuple						,	lowerCamelCase_			:					List[str] = None						,	lowerCamelCase_			:					Tuple = None						,	lowerCamelCase_			:					int = None						,	lowerCamelCase_			:					Optional[int] = None						,	lowerCamelCase_			:					Optional[Any] = 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=A__						,	remark=A__						,	parents=A__						,	parents_chain_index=A__						,	)








from math import sqrt

def 	_lowerCAmelCase (    A__						):
      assert isinstance(A__    ,	A__						) and (
          number >= 0
      ), "'number' must been an int and positive"

      lowercase__  =	True

      # 0 and 1 are none primes.
      if number <= 1:
            lowercase__  =	False

      for divisor in range(2    ,	int(round(sqrt(A__						)						)						) + 1						):
            # if 'number' divisible by 'divisor' then sets 'status'
            # of false and break up the loop.
            if number % divisor == 0:
                  lowercase__  =	False
                  break

    # precondition
      assert isinstance(A__    ,	A__						), "'status' must been from type bool"

      return status

def 	_lowerCAmelCase (    A__						):
      assert isinstance(A__    ,	A__						) and (n > 2), "'N' must been an int and > 2"

      # beginList: contains all natural numbers from 2 up to N
      lowercase__  =	list(range(2    ,	n + 1						)						)

      lowercase__  =	[]  # this list will be returns.

      # actual sieve of erathostenes
      for i in range(len(A__						)						):
            for j in range(i + 1    ,	len(A__						)						):
                  if (begin_list[i] != 0) and (begin_list[j] % begin_list[i] == 0):
                        lowercase__  =	0

    # filters actual prime numbers.
      lowercase__  =	[x for x in begin_list if x != 0]

      # precondition
      assert isinstance(A__    ,	A__						), "'ans' must been from type list"

      return ans

def 	_lowerCAmelCase (    A__						):
      assert isinstance(A__    ,	A__						) and (n > 2), "'N' must been an int and > 2"

      lowercase__  =	[]

      # iterates over all numbers between 2 up to N+1
      # if a number is prime then appends to list 'ans'
      for number in range(2    ,	n + 1						):
            if is_prime(A__						):
                  ans.append(A__						)

    # precondition
      assert isinstance(A__    ,	A__						), "'ans' must been from type list"

      return ans

def 	_lowerCAmelCase (    A__						):
      assert isinstance(A__    ,	A__						) and number >= 0, "'number' must been an int and >= 0"

      lowercase__  =	[]  # this list will be returns of the function.

      # potential prime number factors.

      lowercase__  =	2

      lowercase__  =	number

      if number == 0 or number == 1:
            ans.append(A__						)

      # if 'number' not prime then builds the prime factorization of 'number'
      elif not is_prime(A__						):
            while quotient != 1:
                  if is_prime(A__						) and (quotient % factor == 0):
                        ans.append(A__						)
                        quotient /= factor
                  else:
                        factor += 1

      else:
            ans.append(A__						)

      # precondition
      assert isinstance(A__    ,	A__						), "'ans' must been from type list"

      return ans

def 	_lowerCAmelCase (    A__						):
      assert isinstance(A__    ,	A__						) and (
          number >= 0
      ), "'number' bust been an int and >= 0"

      lowercase__  =	0

      # prime factorization of 'number'
      lowercase__  =	prime_factorization(A__						)

      lowercase__  =	max(A__						)

      # precondition
      assert isinstance(A__    ,	A__						), "'ans' must been from type int"

      return ans

def 	_lowerCAmelCase (    A__						):
      assert isinstance(A__    ,	A__						) and (
          number >= 0
      ), "'number' bust been an int and >= 0"

      lowercase__  =	0

      # prime factorization of 'number'
      lowercase__  =	prime_factorization(A__						)

      lowercase__  =	min(A__						)

      # precondition
      assert isinstance(A__    ,	A__						), "'ans' must been from type int"

      return ans

def 	_lowerCAmelCase (    A__						):
      assert isinstance(A__    ,	A__						), "'number' must been an int"
      assert isinstance(number % 2 == 0    ,	A__						), "compare bust been from type bool"

      return number % 2 == 0

def 	_lowerCAmelCase (    A__						):
      assert isinstance(A__    ,	A__						), "'number' must been an int"
      assert isinstance(number % 2 != 0    ,	A__						), "compare bust been from type bool"

      return number % 2 != 0

def 	_lowerCAmelCase (    A__						):
      assert (
          isinstance(A__    ,	A__						) and (number > 2) and is_even(A__						)
      ), "'number' must been an int, even and > 2"

      lowercase__  =	[]  # this list will returned

      # creates a list of prime numbers between 2 up to 'number'
      lowercase__  =	get_prime_numbers(A__						)
      lowercase__  =	len(A__						)

      # run variable for while-loops.
      lowercase__  =	0
      lowercase__  =	None

      # exit variable. for break up the loops
      lowercase__  =	True

      while i < len_pn and loop:
            lowercase__  =	i + 1

            while j < len_pn and loop:
                  if prime_numbers[i] + prime_numbers[j] == number:
                        lowercase__  =	False
                        ans.append(prime_numbers[i]						)
                        ans.append(prime_numbers[j]						)

                  j += 1

            i += 1

      # precondition
      assert (
          isinstance(A__    ,	A__						)
          and (len(A__						) == 2)
          and (ans[0] + ans[1] == number)
          and is_prime(ans[0]						)
          and is_prime(ans[1]						)
      ), "'ans' must contains two primes. And sum of elements must been eq 'number'"

      return ans

def 	_lowerCAmelCase (    A__    ,	A__						):
      assert (
          isinstance(A__    ,	A__						)
          and isinstance(A__    ,	A__						)
          and (numbera >= 0)
          and (numbera >= 0)
      ), "'number1' and 'number2' must been positive integer."

      lowercase__  =	0

      while numbera != 0:
            lowercase__  =	numbera % numbera
            lowercase__  =	numbera
            lowercase__  =	rest

      # precondition
      assert isinstance(A__    ,	A__						) and (
          numbera >= 0
      ), "'number' must been from type int and positive"

      return numbera

def 	_lowerCAmelCase (    A__    ,	A__						):
      assert (
          isinstance(A__    ,	A__						)
          and isinstance(A__    ,	A__						)
          and (numbera >= 1)
          and (numbera >= 1)
      ), "'number1' and 'number2' must been positive integer."

      lowercase__  =	1  # actual answer that will be return.

      # for kgV (x,1)
      if numbera > 1 and numbera > 1:
            # builds the prime factorization of 'number1' and 'number2'
            lowercase__  =	prime_factorization(A__						)
            lowercase__  =	prime_factorization(A__						)

      elif numbera == 1 or numbera == 1:
            lowercase__  =	[]
            lowercase__  =	[]
            lowercase__  =	max(A__    ,	A__						)

      lowercase__  =	0
      lowercase__  =	0

      lowercase__  =	[]  # captured numbers int both 'primeFac1' and 'primeFac2'

      # iterates through primeFac1
      for n in prime_fac_a:
            if n not in done:
                  if n in prime_fac_a:
                        lowercase__  =	prime_fac_a.count(A__						)
                        lowercase__  =	prime_fac_a.count(A__						)

                        for _ in range(max(A__    ,	A__						)						):
                              ans *= n

                  else:
                        lowercase__  =	prime_fac_a.count(A__						)

                        for _ in range(A__						):
                              ans *= n

                  done.append(A__						)

    # iterates through primeFac2
      for n in prime_fac_a:
            if n not in done:
                  lowercase__  =	prime_fac_a.count(A__						)

                  for _ in range(A__						):
                        ans *= n

                  done.append(A__						)

    # precondition
      assert isinstance(A__    ,	A__						) and (
          ans >= 0
      ), "'ans' must been from type int and positive"

      return ans

def 	_lowerCAmelCase (    A__						):
      assert isinstance(A__    ,	A__						) and (n >= 0), "'number' must been a positive int"

      lowercase__  =	0
      lowercase__  =	2  # this variable holds the answer

      while index < n:
            index += 1

            ans += 1  # counts to the next number

            # if ans not prime then
            # runs to the next prime number.
            while not is_prime(A__						):
                  ans += 1

    # precondition
      assert isinstance(A__    ,	A__						) and is_prime(
          A__						), "'ans' must been a prime number and from type int"

      return ans

def 	_lowerCAmelCase (    A__    ,	A__						):
      assert (
          is_prime(A__						) and is_prime(A__						) and (p_number_a < p_number_a)
      ), "The arguments must been prime numbers and 'pNumber1' < 'pNumber2'"

      lowercase__  =	p_number_a + 1  # jump to the next number

      lowercase__  =	[]  # this list will be returns.

      # if number is not prime then
      # fetch the next prime number.
      while not is_prime(A__						):
            number += 1

      while number < p_number_a:
            ans.append(A__						)

            number += 1

            # fetch the next prime number.
            while not is_prime(A__						):
                  number += 1

    # precondition
      assert (
          isinstance(A__    ,	A__						)
          and ans[0] != p_number_a
          and ans[len(A__						) - 1] != p_number_a
      ), "'ans' must been a list without the arguments"

      # 'ans' contains not 'pNumber1' and 'pNumber2' !
      return ans

def 	_lowerCAmelCase (    A__						):
      assert isinstance(A__    ,	A__						) and (n >= 1), "'n' must been int and >= 1"

      lowercase__  =	[]  # will be returned.

      for divisor in range(1    ,	n + 1						):
            if n % divisor == 0:
                  ans.append(A__						)

    # precondition
      assert ans[0] == 1 and ans[len(A__						) - 1] == n, "Error in function getDivisiors(...)"

      return ans

def 	_lowerCAmelCase (    A__						):
      assert isinstance(A__    ,	A__						) and (
          number > 1
      ), "'number' must been an int and >= 1"

      lowercase__  =	get_divisors(A__						)

      # precondition
      assert (
          isinstance(A__    ,	A__						)
          and (divisors[0] == 1)
          and (divisors[len(A__						) - 1] == number)
      ), "Error in help-function getDivisiors(...)"

      # summed all divisors up to 'number' (exclusive), hence [:-1]
      return sum(divisors[:-1]						) == number

def 	_lowerCAmelCase (    A__    ,	A__						):
      assert (
          isinstance(A__    ,	A__						)
          and isinstance(A__    ,	A__						)
          and (denominator != 0)
      ), "The arguments must been from type int and 'denominator' != 0"

      # build the greatest common divisor of numerator and denominator.
      lowercase__  =	gcd(abs(A__						)    ,	abs(A__						)						)

      # precondition
      assert (
          isinstance(A__    ,	A__						)
          and (numerator % gcd_of_fraction == 0)
          and (denominator % gcd_of_fraction == 0)
      ), "Error in function gcd(...,...)"

      return (numerator // gcd_of_fraction, denominator // gcd_of_fraction)

def 	_lowerCAmelCase (    A__						):
      assert isinstance(A__    ,	A__						) and (n >= 0), "'n' must been a int and >= 0"

      lowercase__  =	1  # this will be return.

      for factor in range(1    ,	n + 1						):
            ans *= factor

      return ans

def 	_lowerCAmelCase (    A__						):
      assert isinstance(A__    ,	A__						) and (n >= 0), "'n' must been an int and >= 0"

      lowercase__  =	0
      lowercase__  =	1
      lowercase__  =	1  # this will be return

      for _ in range(n - 1						):
            lowercase__  =	ans
            ans += fiba
            lowercase__  =	tmp

      return ans
