

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=_UpperCAmelCase )
class   __lowercase      :
 _UpperCamelCase			  =  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'.
 _UpperCamelCase			  =  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.
 _UpperCamelCase			  =  42  # [num_res, num_atom_type]

 # Residue index as used in PDB. It is not necessarily continuous or 0-indexed.
 _UpperCamelCase			  =  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.
 _UpperCamelCase			  =  42  # [num_res, num_atom_type]

 # Chain indices for multi-chain predictions
 _UpperCamelCase			  =  None

 # Optional remark about the protein. Included as a comment in output PDB
 # files
 _UpperCamelCase			  =  None

 # Templates used to generate this protein (prediction-only)
 _UpperCamelCase			  =  None

 # Chain corresponding to each parent
 _UpperCamelCase			  =  None







def 		_lowercase (     lowercase__						):
      __lowerCAmelCase					:						Optional[int]					=					r'''(\[[A-Z]+\]\n)'''
      __lowerCAmelCase					:						List[str]					=					[tag.strip() for tag in re.split(lowercase__   ,	lowercase__						) if len(lowercase__						) > 0]
      __lowerCAmelCase					:						Iterator[Tuple[str, List[str]]]					=					zip(tags[0::2]   ,	[l.split('''\n'''						) for l in tags[1::2]]						)

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

      __lowerCAmelCase					:						Tuple					=					prot.remark
      if remark is not None:
            pdb_headers.append(f"""REMARK {remark}"""						)

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

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

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

      return pdb_headers







def 		_lowercase (     lowercase__   ,	lowercase__						):
      __lowerCAmelCase					:						List[str]					=					[]
      __lowerCAmelCase					:						str					=					pdb_str.split('''\n'''						)

      __lowerCAmelCase					:						Union[str, Any]					=					prot.remark
      if remark is not None:
            out_pdb_lines.append(f"""REMARK {remark}"""						)

      __lowerCAmelCase					:						List[List[str]]
      if prot.parents is not None and len(prot.parents						) > 0:
            __lowerCAmelCase					:						Tuple					=					[]
            if prot.parents_chain_index is not None:
                  __lowerCAmelCase					:						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__						)

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

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

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

      __lowerCAmelCase					:						Optional[Any]					=					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__						):
                        __lowerCAmelCase					:						Tuple					=					parents_per_chain[chain_counter]
                  else:
                        __lowerCAmelCase					:						Tuple					=					['''N/A''']

                  out_pdb_lines.append(make_parent_line(lowercase__						)						)

      return "\n".join(lowercase__						)







def 		_lowercase (     lowercase__						):
      __lowerCAmelCase					:						Union[str, Any]					=					residue_constants.restypes + ['''X''']

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

      __lowerCAmelCase					:						Tuple					=					residue_constants.atom_types

      __lowerCAmelCase					:						List[str]					=					[]

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

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

      __lowerCAmelCase					:						Optional[Any]					=					get_pdb_headers(lowercase__						)
      if len(lowercase__						) > 0:
            pdb_lines.extend(lowercase__						)

      __lowerCAmelCase					:						Optional[int]					=					aatype.shape[0]
      __lowerCAmelCase					:						Any					=					1
      __lowerCAmelCase					:						Optional[int]					=					0
      __lowerCAmelCase					:						Union[str, Any]					=					string.ascii_uppercase
      __lowerCAmelCase					:						List[str]					=					None
      # Add all atom sites.
      for i in range(lowercase__						):
            __lowerCAmelCase					:						Any					=					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

                  __lowerCAmelCase					:						Optional[int]					=					'''ATOM'''
                  __lowerCAmelCase					:						List[str]					=					atom_name if len(lowercase__						) == 4 else f""" {atom_name}"""
                  __lowerCAmelCase					:						List[Any]					=					''''''
                  __lowerCAmelCase					:						Optional[Any]					=					''''''
                  __lowerCAmelCase					:						Optional[int]					=					1.0_0
                  __lowerCAmelCase					:						List[Any]					=					atom_name[0]  # Protein supports only C, N, O, S, this works.
                  __lowerCAmelCase					:						List[Any]					=					''''''

                  __lowerCAmelCase					:						Tuple					=					'''A'''
                  if chain_index is not None:
                        __lowerCAmelCase					:						int					=					chain_tags[chain_index[i]]

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

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

            if should_terminate:
                  # Close the chain.
                  __lowerCAmelCase					:						Tuple					=					'''TER'''
                  __lowerCAmelCase					:						Optional[int]					=					(
                      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 		_lowercase (     lowercase__						):
      return residue_constants.STANDARD_ATOM_MASK[prot.aatype]







def 		_lowercase (     lowercase__   ,	lowercase__   ,	lowercase__ = None   ,	lowercase__ = None   ,	lowercase__ = None   ,	lowercase__ = None   ,	lowercase__ = None   ,	):
      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 		_lowercase (     lowercase__   ,	lowercase__						):

      if density <= 0:
            raise ValueError('''Impossible fluid density'''						)
      if bulk_modulus <= 0:
            raise ValueError('''Impossible bulk modulus'''						)

      return (bulk_modulus / density) ** 0.5


if __name__ == "__main__":
 import doctest

 doctest.testmod()


