





'''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__				:   List[Any]      =Mapping[str, np.ndarray]
A__				:   Dict      =Mapping[str, Any]  # Is a nested dict.
A__				:   Optional[Any]      =0.01




@dataclasses.dataclass(frozen=snake_case_   )
class  UpperCAmelCase     :
      _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    UpperCamelCase__      (		lowerCAmelCase  ):





      """simple docstring"""


      _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    UpperCamelCase__      (		lowerCAmelCase							,	lowerCAmelCase = 0  ):





      """simple docstring"""


      _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    UpperCamelCase__      (		lowerCAmelCase							,	lowerCAmelCase  ):





      """simple docstring"""


      _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    UpperCamelCase__      (		lowerCAmelCase  ):





      """simple docstring"""


      _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    UpperCamelCase__      (		lowerCAmelCase  ):





      """simple docstring"""


      return residue_constants.STANDARD_ATOM_MASK[prot.aatype]





def    UpperCamelCase__      (		lowerCAmelCase							,	lowerCAmelCase							,	lowerCAmelCase = None							,	lowerCAmelCase = None							,	lowerCAmelCase = None							,	lowerCAmelCase = None							,	lowerCAmelCase = 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=lowerCAmelCase							,	remark=lowerCAmelCase							,	parents=lowerCAmelCase							,	parents_chain_index=lowerCAmelCase							,	)







'''simple docstring'''




__SCREAMING_SNAKE_CASE       :     Dict     =  8.3_1_4_4_6_2  # Unit - J mol-1 K-1

def 	UpperCamelCase_							(					_UpperCAmelCase  :      float			,	_UpperCAmelCase  :      float			,	_UpperCAmelCase  :      float    )    ->    float:


       """simple docstring"""







       if moles < 0 or kelvin < 0 or volume < 0:
              raise ValueError("Invalid inputs. Enter positive value."    )
       return moles * kelvin * UNIVERSAL_GAS_CONSTANT / volume

def 	UpperCamelCase_							(					_UpperCAmelCase  :      float			,	_UpperCAmelCase  :      float			,	_UpperCAmelCase  :      float    )    ->    float:


       """simple docstring"""







       if moles < 0 or kelvin < 0 or pressure < 0:
              raise ValueError("Invalid inputs. Enter positive value."    )
       return moles * kelvin * UNIVERSAL_GAS_CONSTANT / pressure


if __name__ == "__main__":
  from doctest import testmod

  testmod()

