




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__  :  Optional[int]					=       Mapping[str, np.ndarray]
__magic_name__  :  str					=       Mapping[str, Any]  # Is a nested dict.
__magic_name__  :  Union[str, Any]					=       0.01





@dataclasses.dataclass(frozen=_a			)
class     SCREAMING_SNAKE_CASE__		:
     lowercase_ :      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'.
     lowercase_ :      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.
     lowercase_ :      np.ndarray  # [num_res, num_atom_type]

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

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

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

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

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



def 		a_							( __lowerCAmelCase				):
  lowerCAmelCase__										=      r'''(\[[A-Z]+\]\n)'''
  lowerCAmelCase__										=      [tag.strip() for tag in re.split(__lowerCAmelCase   , __lowerCAmelCase				) if len(__lowerCAmelCase				) > 0]
  lowerCAmelCase__										=      zip(tags[0::2]   , [l.split('''\n'''				) for l in tags[1::2]]				)

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

  assert aatype is not None

  return Protein(
      atom_positions=__lowerCAmelCase   , atom_mask=__lowerCAmelCase   , aatype=__lowerCAmelCase   , residue_index=np.arange(len(__lowerCAmelCase				)				)   , b_factors=__lowerCAmelCase   , )
def 		a_							( __lowerCAmelCase   , __lowerCAmelCase = 0				):
  lowerCAmelCase__										=      []

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

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

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

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

  return pdb_headers
def 		a_							( __lowerCAmelCase   , __lowerCAmelCase				):
  lowerCAmelCase__										=      []
  lowerCAmelCase__										=      pdb_str.split('''\n'''				)

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

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

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

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

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

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

      out_pdb_lines.append(make_parent_line(__lowerCAmelCase				)				)

  return "\n".join(__lowerCAmelCase				)
def 		a_							( __lowerCAmelCase				):
  lowerCAmelCase__										=      residue_constants.restypes + ['''X''']

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

  lowerCAmelCase__										=      residue_constants.atom_types

  lowerCAmelCase__										=      []

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

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

  lowerCAmelCase__										=      get_pdb_headers(__lowerCAmelCase				)
  if len(__lowerCAmelCase				) > 0:
    pdb_lines.extend(__lowerCAmelCase				)

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

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

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

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

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

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

  pdb_lines.append('''END'''				)
  pdb_lines.append(''''''				)
  return "\n".join(__lowerCAmelCase				)
def 		a_							( __lowerCAmelCase				):
  return residue_constants.STANDARD_ATOM_MASK[prot.aatype]




def 		a_							( __lowerCAmelCase   , __lowerCAmelCase   , __lowerCAmelCase = None   , __lowerCAmelCase = None   , __lowerCAmelCase = None   , __lowerCAmelCase = None   , __lowerCAmelCase = 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=__lowerCAmelCase   , remark=__lowerCAmelCase   , parents=__lowerCAmelCase   , parents_chain_index=__lowerCAmelCase   , )







import torch
from torch import nn
from transformers import CLIPPreTrainedModel, CLIPVisionModel

from ...models.attention import BasicTransformerBlock
from ...utils import logging


__magic_name__  :  List[str]					=       logging.get_logger(__name__)  # pylint: disable=invalid-name





class     SCREAMING_SNAKE_CASE__		(_a			):
     def __init__(						self	:		List[Any]       ,						__lowerCamelCase	:		Tuple       ,						__lowerCamelCase	:		List[Any]=7_68						):



       """simple docstring"""
       super().__init__(__lowerCamelCase						)
       lowerCAmelCase__										=      proj_size

       lowerCAmelCase__										=      CLIPVisionModel(__lowerCamelCase						)
       lowerCAmelCase__										=      PaintByExampleMapper(__lowerCamelCase						)
       lowerCAmelCase__										=      nn.LayerNorm(config.hidden_size						)
       lowerCAmelCase__										=      nn.Linear(config.hidden_size       ,						self.proj_size						)

       # uncondition for scaling
       lowerCAmelCase__										=      nn.Parameter(torch.randn((1, 1, self.proj_size)						)						)



     def        A__      (						self	:		Tuple       ,						__lowerCamelCase	:		int       ,						__lowerCamelCase	:		str=False						):



       """simple docstring"""
       lowerCAmelCase__										=      self.model(pixel_values=__lowerCamelCase						)
       lowerCAmelCase__										=      clip_output.pooler_output
       lowerCAmelCase__										=      self.mapper(latent_states[:, None]						)
       lowerCAmelCase__										=      self.final_layer_norm(__lowerCamelCase						)
       lowerCAmelCase__										=      self.proj_out(__lowerCamelCase						)
       if return_uncond_vector:
         return latent_states, self.uncond_vector

       return latent_states





class     SCREAMING_SNAKE_CASE__		(nn.Module			):
     def __init__(						self	:		Optional[Any]       ,						__lowerCamelCase	:		Tuple						):



       """simple docstring"""
       super().__init__()
       lowerCAmelCase__										=      (config.num_hidden_layers + 1) // 5
       lowerCAmelCase__										=      config.hidden_size
       lowerCAmelCase__										=      1
       lowerCAmelCase__										=      nn.ModuleList(
           [
               BasicTransformerBlock(__lowerCamelCase       ,						__lowerCamelCase       ,						__lowerCamelCase       ,						activation_fn='''gelu'''       ,						attention_bias=__lowerCamelCase						)
               for _ in range(__lowerCamelCase						)
           ]						)



     def        A__      (						self	:		str       ,						__lowerCamelCase	:		Optional[Any]						):



       """simple docstring"""
       for block in self.blocks:
         lowerCAmelCase__										=      block(__lowerCamelCase						)

       return hidden_states

