






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=lowercase	)
class        lowerCAmelCase_				:







				"""simple docstring"""




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

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

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

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

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

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




def 				A		(					lowercase__  :  str  )		-> Protein:
	UpperCamelCase__ :Union[str, Any]						=      r"""(\[[A-Z]+\]\n)"""
	UpperCamelCase__ :List[str]						=      [tag.strip() for tag in re.split(lowercase__ ,		lowercase__  ) if len(lowercase__  ) > 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__ :Optional[int]						=      None
	UpperCamelCase__ :Optional[int]						=      None
	UpperCamelCase__ :List[str]						=      None
	for g in groups:
		if "[PRIMARY]" == g[0]:
			UpperCamelCase__ :List[Any]						=      g[1][0].strip()
			for i in range(len(lowercase__  )  ):
				if seq[i] not in residue_constants.restypes:
					UpperCamelCase__ :List[str]						=      """X"""  # FIXME: strings are immutable
			UpperCamelCase__ :List[Any]						=      np.array(
			    [residue_constants.restype_order.get(lowercase__ ,		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(lowercase__ ,		g[1][axis].split()  )  )  )
			UpperCamelCase__ :Tuple						=      np.array(lowercase__  )
			UpperCamelCase__ :Tuple						=      np.zeros((len(tertiary[0]  ) // 3, residue_constants.atom_type_num, 3)  ).astype(np.floataa  )
			for i, atom in enumerate(lowercase__  ):
				UpperCamelCase__ :Optional[int]						=      np.transpose(tertiary_np[:, i::3]  )
			atom_positions *= PICO_TO_ANGSTROM
		elif "[MASK]" == g[0]:
			UpperCamelCase__ :Dict						=      np.array(list(map({"""-""": 0, """+""": 1}.get ,		g[1][0].strip()  )  )  )
			UpperCamelCase__ :Any						=      np.zeros(
			    (
			        len(lowercase__  ),
			        residue_constants.atom_type_num,
			    )  ).astype(np.floataa  )
			for i, atom in enumerate(lowercase__  ):
				UpperCamelCase__ :List[Any]						=      1
			atom_mask *= mask[..., None]

	assert aatype is not None

	return Protein(
	    atom_positions=lowercase__ ,		atom_mask=lowercase__ ,		aatype=lowercase__ ,		residue_index=np.arange(len(lowercase__  )  ) ,		b_factors=lowercase__ ,		)




def 				A		(					lowercase__  :  Protein ,		lowercase__  :  int = 0  )		-> List[str]:
	UpperCamelCase__ :List[str]						=      []

	UpperCamelCase__ :Optional[Any]						=      prot.remark
	if remark is not None:
		pdb_headers.append(f"""REMARK {remark}"""  )

	UpperCamelCase__ :List[Any]						=      prot.parents
	UpperCamelCase__ :List[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(lowercase__ ,		lowercase__  ) if i == chain_id]

	if parents is None or len(lowercase__  ) == 0:
		UpperCamelCase__ :str						=      ["""N/A"""]

	pdb_headers.append(f"""PARENT {" ".join(lowercase__  )}"""  )

	return pdb_headers




def 				A		(					lowercase__  :  Protein ,		lowercase__  :  str  )		-> str:
	UpperCamelCase__ :List[str]						=      []
	UpperCamelCase__ :Optional[int]						=      pdb_str.split("""\n"""  )

	UpperCamelCase__ :Tuple						=      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__ :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(lowercase__  ) ,		[]  )
				parent_dict[str(lowercase__  )].append(lowercase__  )

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

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

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

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

			out_pdb_lines.append(make_parent_line(lowercase__  )  )

	return "\n".join(lowercase__  )




def 				A		(					lowercase__  :  Protein  )		-> str:
	UpperCamelCase__ :Optional[int]						=      residue_constants.restypes + ["""X"""]

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

	UpperCamelCase__ :Optional[Any]						=      residue_constants.atom_types

	UpperCamelCase__ :List[str]						=      []

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

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

	UpperCamelCase__ :Any						=      get_pdb_headers(lowercase__  )
	if len(lowercase__  ) > 0:
		pdb_lines.extend(lowercase__  )

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

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

			UpperCamelCase__ :Union[str, Any]						=      """A"""
			if chain_index is not None:
				UpperCamelCase__ :List[Any]						=      chain_tags[chain_index[i]]

			# PDB is a columnar format, every space matters here!
			UpperCamelCase__ :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(lowercase__  )
			atom_index += 1

		UpperCamelCase__ :Dict						=      i == n - 1
		if chain_index is not None:
			if i != n - 1 and chain_index[i + 1] != prev_chain_index:
				UpperCamelCase__ :List[str]						=      True
				UpperCamelCase__ :int						=      chain_index[i + 1]

		if should_terminate:
			# Close the chain.
			UpperCamelCase__ :Tuple						=      """TER"""
			UpperCamelCase__ :Any						=      (
			    f"""{chain_end:<6}{atom_index:>5}      {res_atoa(aatype[i]  ):>3} {chain_tag:>1}{residue_index[i]:>4}"""
			)
			pdb_lines.append(lowercase__  )
			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(lowercase__ ,		lowercase__  )  )

	pdb_lines.append("""END"""  )
	pdb_lines.append(""""""  )
	return "\n".join(lowercase__  )




def 				A		(					lowercase__  :  Protein  )		-> np.ndarray:
	return residue_constants.STANDARD_ATOM_MASK[prot.aatype]




def 				A		(					lowercase__  :  FeatureDict ,		lowercase__  :  ModelOutput ,		lowercase__  :  Optional[np.ndarray] = None ,		lowercase__  :  Optional[np.ndarray] = None ,		lowercase__  :  Optional[str] = None ,		lowercase__  :  Optional[Sequence[str]] = None ,		lowercase__  :  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=lowercase__ ,		remark=lowercase__ ,		parents=lowercase__ ,		parents_chain_index=lowercase__ ,		)


def 							_lowerCamelCase   (			SCREAMING_SNAKE_CASE		,				SCREAMING_SNAKE_CASE   ):
      '''simple docstring'''







      A_							       =		len(SCREAMING_SNAKE_CASE   )
      A_							       =		len(SCREAMING_SNAKE_CASE   )
      A_							       =		(
          first_str_length if first_str_length > second_str_length else second_str_length
      )
      A_							       =		[]
      for char_count in range(SCREAMING_SNAKE_CASE   ):
            if char_count < first_str_length:
                  output_list.append(first_str[char_count]   )
            if char_count < second_str_length:
                  output_list.append(second_str[char_count]   )
      return "".join(SCREAMING_SNAKE_CASE   )


if __name__ == "__main__":
      print(alternative_string_arrange("""AB""", """XYZ"""), end=""" """)





