



'''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


__lowerCAmelCase		     =  Mapping[str, np.ndarray]
__lowerCAmelCase		     =  Mapping[str, Any]  # Is a nested dict.
__lowerCAmelCase		     =  0.01

@dataclasses.dataclass(frozen=__snake_case  )
class       __magic_name__		:
							lowerCAmelCase			:       Tuple  							=   4_2  # [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			:       List[Any]  							=   4_2  # [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			:       Union[str, Any]  							=   4_2  # [num_res, num_atom_type]

							# Residue index as used in PDB. It is not necessarily continuous or 0-indexed.
							lowerCAmelCase			:       Tuple  							=   4_2  # [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			:       Dict  							=   4_2  # [num_res, num_atom_type]

							# Chain indices for multi-chain predictions
							lowerCAmelCase			:       Dict  							=   None

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

							# Templates used to generate this protein (prediction-only)
							lowerCAmelCase			:       int  							=   None

							# Chain corresponding to each parent
							lowerCAmelCase			:       str  							=   None



def 	__lowerCamelCase	( lowerCAmelCase_    )     -> Tuple:
		_a	: Union[str, Any]								=				R'''(\[[A-Z]+\]\n)'''
		_a	: List[str]								=				[tag.strip() for tag in re.split(snake_case__		,     snake_case__    ) if len(snake_case__    ) > 0]
		_a	: Iterator[Tuple[str, List[str]]]								=				zip(tags[0::2]		,     [l.split('\n'    ) for l in tags[1::2]]    )

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

		assert aatype is not None

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



def 	__lowerCamelCase	( lowerCAmelCase_		,     lowerCAmelCase_ = 0    )     -> str:
		_a	: List[str]								=				[]

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

		_a	: int								=				prot.parents
		_a	: Any								=				prot.parents_chain_index
		if parents is not None and parents_chain_index is not None:
				_a	: Dict								=				[p for i, p in zip(snake_case__		,     snake_case__    ) if i == chain_id]

		if parents is None or len(snake_case__    ) == 0:
				_a	: Tuple								=				['''N/A''']

		pdb_headers.append(f"""PARENT {' '.join(snake_case__    )}"""    )

		return pdb_headers



def 	__lowerCamelCase	( lowerCAmelCase_		,     lowerCAmelCase_    )     -> Optional[int]:
		_a	: List[str]								=				[]
		_a	: str								=				pdb_str.split('\n'    )

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

		_a	: List[List[str]]
		if prot.parents is not None and len(prot.parents    ) > 0:
				_a	: Tuple								=				[]
				if prot.parents_chain_index is not None:
						_a	: Dict[str, List[str]]								=				{}
						for p, i in zip(prot.parents		,     prot.parents_chain_index    ):
								parent_dict.setdefault(str(snake_case__    )		,     []    )
								parent_dict[str(snake_case__    )].append(snake_case__    )

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

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

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

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

						out_pdb_lines.append(make_parent_line(snake_case__    )    )

		return "\n".join(snake_case__    )



def 	__lowerCamelCase	( lowerCAmelCase_    )     -> Union[str, Any]:
		_a	: Optional[int]								=				residue_constants.restypes + ['''X''']

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

		_a	: Tuple								=				residue_constants.atom_types

		_a	: List[str]								=				[]

		_a	: Optional[Any]								=				prot.atom_mask
		_a	: Union[str, Any]								=				prot.aatype
		_a	: List[str]								=				prot.atom_positions
		_a	: int								=				prot.residue_index.astype(np.intaa    )
		_a	: Tuple								=				prot.b_factors
		_a	: Tuple								=				prot.chain_index

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

		_a	: int								=				get_pdb_headers(snake_case__    )
		if len(snake_case__    ) > 0:
				pdb_lines.extend(snake_case__    )

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

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

						_a	: Union[str, Any]								=				'''A'''
						if chain_index is not None:
								_a	: int								=				chain_tags[chain_index[i]]

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

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

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

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



def 	__lowerCamelCase	( lowerCAmelCase_    )     -> int:
		return residue_constants.STANDARD_ATOM_MASK[prot.aatype]



def 	__lowerCamelCase	( lowerCAmelCase_		,     lowerCAmelCase_		,     lowerCAmelCase_ = None		,     lowerCAmelCase_ = None		,     lowerCAmelCase_ = None		,     lowerCAmelCase_ = None		,     lowerCAmelCase_ = None		,     )     -> Any:
		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=snake_case__		,     remark=snake_case__		,     parents=snake_case__		,     parents_chain_index=snake_case__		,     )






'''simple docstring'''




lowercase     :							dict[str, float]       						=     {
    "joule": 1.0,
    "kilojoule": 10_00,
    "megajoule": 1_00_00_00,
    "gigajoule": 10_00_00_00_00,
    "wattsecond": 1.0,
    "watthour": 36_00,
    "kilowatthour": 3_60_00_00,
    "newtonmeter": 1.0,
    "calorie_nutr": 41_86.8,
    "kilocalorie_nutr": 4_18_68_00.00,
    "electronvolt": 1.6_02_17_66_34e-19,
    "britishthermalunit_it": 10_55.0_55_85,
    "footpound": 1.35_58_18,
}







def 						lowerCAmelCase_							(  snake_case__						,							snake_case__						,							snake_case__		):




    '''simple docstring'''



    if to_type not in ENERGY_CONVERSION or from_type not in ENERGY_CONVERSION:
        A			:  int   =		(
            F'Incorrect \'from_type\' or \'to_type\' value: {from_type!r}, {to_type!r}\n'
            F'Valid values are: {", ".join(snake_case__		)}'
        )
        raise ValueError(snake_case__		)
    return value * ENERGY_CONVERSION[from_type] / ENERGY_CONVERSION[to_type]


if __name__ == "__main__":
      import doctest

      doctest.testmod()




