


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				:       Any      =  Mapping[str, Any]  # Is a nested dict.
A				:       Dict      =  0.01






@dataclasses.dataclass(frozen=UpperCAmelCase__ )
class      UpperCamelCase:
					snake_case_		:					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'.
					snake_case_		:					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.
					snake_case_		:					np.ndarray  # [num_res, num_atom_type]

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

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

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

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

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





def 						_lowerCAmelCase							(     _lowerCAmelCase			)    ->						List[Any]:


						'''simple docstring'''






						__snake_case				=		r"(\[[A-Z]+\]\n)"
						__snake_case				=		[tag.strip() for tag in re.split(_lowerCAmelCase   ,						_lowerCAmelCase			) if len(_lowerCAmelCase			) > 0]
						__snake_case				=		zip(tags[0::2]   ,						[l.split("\n"			) for l in tags[1::2]]			)

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


						'''simple docstring'''






						__snake_case				=		[]

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

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

						if parents is None or len(_lowerCAmelCase			) == 0:
												__snake_case				=		["N/A"]

						pdb_headers.append(F'''PARENT {' '.join(_lowerCAmelCase			)}'''			)

						return pdb_headers





def 						_lowerCAmelCase							(     _lowerCAmelCase   ,						_lowerCAmelCase			)    ->						List[str]:


						'''simple docstring'''






						__snake_case				=		[]
						__snake_case				=		pdb_str.split("\n"			)

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

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

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

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

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

						__snake_case				=		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			):
																								__snake_case				=		parents_per_chain[chain_counter]
																		else:
																								__snake_case				=		["N/A"]

																		out_pdb_lines.append(make_parent_line(_lowerCAmelCase			)			)

						return "\n".join(_lowerCAmelCase			)





def 						_lowerCAmelCase							(     _lowerCAmelCase			)    ->						str:


						'''simple docstring'''






						__snake_case				=		residue_constants.restypes + ["X"]

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

						__snake_case				=		residue_constants.atom_types

						__snake_case				=		[]

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

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

						__snake_case				=		get_pdb_headers(_lowerCAmelCase			)
						if len(_lowerCAmelCase			) > 0:
												pdb_lines.extend(_lowerCAmelCase			)

						__snake_case				=		aatype.shape[0]
						__snake_case				=		1
						__snake_case				=		0
						__snake_case				=		string.ascii_uppercase
						__snake_case				=		None
						# Add all atom sites.
						for i in range(_lowerCAmelCase			):
												__snake_case				=		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

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

																		__snake_case				=		"A"
																		if chain_index is not None:
																								__snake_case				=		chain_tags[chain_index[i]]

																		# PDB is a columnar format, every space matters here!
																		__snake_case				=		(
																		    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

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

												if should_terminate:
																		# Close the chain.
																		__snake_case				=		"TER"
																		__snake_case				=		(
																		    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 						_lowerCAmelCase							(     _lowerCAmelCase			)    ->						Any:


						'''simple docstring'''






						return residue_constants.STANDARD_ATOM_MASK[prot.aatype]





def 						_lowerCAmelCase							(     _lowerCAmelCase   ,						_lowerCAmelCase   ,						_lowerCAmelCase = None   ,						_lowerCAmelCase = None   ,						_lowerCAmelCase = None   ,						_lowerCAmelCase = None   ,						_lowerCAmelCase = None   ,						)    ->						Optional[int]:


						'''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'''


from .configuration_bert_masked import MaskedBertConfig
from .modeling_bert_masked import (
    MaskedBertForMultipleChoice,
    MaskedBertForQuestionAnswering,
    MaskedBertForSequenceClassification,
    MaskedBertForTokenClassification,
    MaskedBertModel,
)
from .modules import *

