

'''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					:			Optional[int]							=    Mapping[str, np.ndarray]
_a					:			Optional[int]							=    Mapping[str, Any]  # Is a nested dict.
_a					:			Any							=    0.01



@dataclasses.dataclass(frozen=a			)
class 							lowercase_						:

  '''simple docstring'''





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

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

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

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

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

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




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

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

  assert aatype is not None

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


def    lowerCamelCase__		(    SCREAMING_SNAKE_CASE   : Protein							, SCREAMING_SNAKE_CASE   : int = 0    ):
  UpperCAmelCase    				=						[]

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

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

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

  pdb_headers.append(f'''PARENT {' '.join(SCREAMING_SNAKE_CASE    )}'''    )

  return pdb_headers


def    lowerCamelCase__		(    SCREAMING_SNAKE_CASE   : Protein							, SCREAMING_SNAKE_CASE   : str    ):
  UpperCAmelCase    				=						[]
  UpperCAmelCase    				=						pdb_str.split('\n'    )

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

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

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

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

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

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

      out_pdb_lines.append(make_parent_line(SCREAMING_SNAKE_CASE    )    )

  return "\n".join(SCREAMING_SNAKE_CASE    )


def    lowerCamelCase__		(    SCREAMING_SNAKE_CASE   : Protein    ):
  UpperCAmelCase    				=						residue_constants.restypes + ['X']

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

  UpperCAmelCase    				=						residue_constants.atom_types

  UpperCAmelCase    				=						[]

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

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

  UpperCAmelCase    				=						get_pdb_headers(SCREAMING_SNAKE_CASE    )
  if len(SCREAMING_SNAKE_CASE    ) > 0:
    pdb_lines.extend(SCREAMING_SNAKE_CASE    )

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

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

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

      # PDB is a columnar format, every space matters here!
      UpperCAmelCase    				=						(
          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(SCREAMING_SNAKE_CASE    )
      atom_index += 1

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

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

  pdb_lines.append('END'    )
  pdb_lines.append(''    )
  return "\n".join(SCREAMING_SNAKE_CASE    )


def    lowerCamelCase__		(    SCREAMING_SNAKE_CASE   : Protein    ):
  return residue_constants.STANDARD_ATOM_MASK[prot.aatype]



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





'''simple docstring'''




import sys
import webbrowser

import requests
from bsa import BeautifulSoup
from fake_useragent import UserAgent

if __name__ == "__main__":
  print('Googling.....')
  _a					:			List[Any]							=    'https://www.google.com/search?q=' + ' '.join(sys.argv[1:])
  _a					:			Dict							=    requests.get(url, headers={'UserAgent': UserAgent().random})
  # res.raise_for_status()
  with open('project1a.html', 'wb') as out_file:  # only for knowing the class
    for data in res.iter_content(10_000):
      out_file.write(data)
  _a					:			Any							=    BeautifulSoup(res.text, 'html.parser')
  _a					:			Optional[Any]							=    list(soup.select('.eZt8xd'))[:5]

  print(len(links))
  for link in links:
    if link.text == "Maps":
      webbrowser.open(link.get('href'))
    else:
      webbrowser.open(F'''https://google.com{link.get('href')}''')


