



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


UpperCAmelCase_							:      Optional[Any]      =  Mapping[str, np.ndarray]
UpperCAmelCase_							:      Optional[int]      =  Mapping[str, Any]  # Is a nested dict.
UpperCAmelCase_							:      int      =  0.01
@dataclasses.dataclass(frozen=_UpperCAmelCase     )
class      UpperCamelCase    :
	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  UpperCamelCase						(       _A			:				Tuple    )->       Protein:





						"""simple docstring"""





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

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

						assert aatype is not None

						return Protein(
						    atom_positions=__UpperCAmelCase			,							atom_mask=__UpperCAmelCase			,							aatype=__UpperCAmelCase			,							residue_index=np.arange(len(__UpperCAmelCase    )    )			,							b_factors=__UpperCAmelCase			,							)
def  UpperCamelCase						(       _A			:				Union[str, Any]			,							_A			:				Optional[Any] = 0    )->       List[str]:





						"""simple docstring"""





						A__							=       []

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

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

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

						pdb_headers.append(f"""PARENT {" ".join(__UpperCAmelCase    )}"""    )

						return pdb_headers
def  UpperCamelCase						(       _A			:				str			,							_A			:				Tuple    )->       str:





						"""simple docstring"""





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

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

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

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

						def make_parent_line(_A			:				Union[str, Any]    ) -> str:
												return f"""PARENT {" ".join(__UpperCAmelCase    )}"""

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

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

																		out_pdb_lines.append(make_parent_line(__UpperCAmelCase    )    )

						return "\n".join(__UpperCAmelCase    )
def  UpperCamelCase						(       _A			:				Dict    )->       str:





						"""simple docstring"""





						A__							=       residue_constants.restypes + ['''X''']

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

						A__							=       residue_constants.atom_types

						A__							=       []

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

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

						A__							=       get_pdb_headers(__UpperCAmelCase    )
						if len(__UpperCAmelCase    ) > 0:
												pdb_lines.extend(__UpperCAmelCase    )

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

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

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

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

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

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

						pdb_lines.append("END"    )
						pdb_lines.append(""    )
						return "\n".join(__UpperCAmelCase    )
def  UpperCamelCase						(       _A			:				List[str]    )->       np.ndarray:





						"""simple docstring"""





						return residue_constants.STANDARD_ATOM_MASK[prot.aatype]
def  UpperCamelCase						(       _A			:				Optional[int]			,							_A			:				List[str]			,							_A			:				List[Any] = None			,							_A			:				Any = None			,							_A			:				Optional[int] = None			,							_A			:				str = None			,							_A			:				Dict = None			,							)->       Protein:





						"""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=__UpperCAmelCase			,							remark=__UpperCAmelCase			,							parents=__UpperCAmelCase			,							parents_chain_index=__UpperCAmelCase			,							)










import os
import zipfile

import requests
from get_ci_error_statistics import download_artifact, get_artifacts_links
def  UpperCamelCase						(       _A			:				List[Any]			,							_A			:				List[str]=7    )->       Optional[Any]:





						"""simple docstring"""





						A__							=       None
						if token is not None:
												A__							=       {"Accept": "application/vnd.github+json", "Authorization": f"""Bearer {token}"""}

						# The id of a workflow (not of a workflow run)
						A__							=       "636036"

						A__							=       f"""https://api.github.com/repos/huggingface/transformers/actions/workflows/{workflow_id}/runs"""
						# On `main` branch + event being `schedule` + not returning PRs + only `num_runs` results
						url += f"""?branch=main&event=schedule&exclude_pull_requests=true&per_page={num_runs}"""

						A__							=       requests.get(_A			,							headers=_A    ).json()

						return result["workflow_runs"]
def  UpperCamelCase						(       _A			:				str    )->       Dict:





						"""simple docstring"""





						A__							=       get_daily_ci_runs(_A    )
						A__							=       None
						for workflow_run in workflow_runs:
												if workflow_run["status"] == "completed":
																		A__							=       workflow_run["id"]
																		break

						return workflow_run_id
def  UpperCamelCase						(       _A			:				int			,							_A			:				List[str]			,							_A			:				str    )->       Any:





						"""simple docstring"""





						A__							=       get_last_daily_ci_runs(_A    )
						if workflow_run_id is not None:
												A__							=       get_artifacts_links(worflow_run_id=_A			,							token=_A    )
												for artifact_name in artifact_names:
																		if artifact_name in artifacts_links:
																								A__							=       artifacts_links[artifact_name]
																								download_artifact(
																								    artifact_name=_A			,							artifact_url=_A			,							output_dir=_A			,							token=_A    )
def  UpperCamelCase						(       _A			:				Optional[Any]			,							_A			:				Any			,							_A			:				List[Any]    )->       Optional[int]:





						"""simple docstring"""





						get_last_daily_ci_artifacts(_A			,							_A			,							_A    )

						A__							=       {}
						for artifact_name in artifact_names:
												A__							=       os.path.join(_A			,							f"""{artifact_name}.zip"""    )
												if os.path.isfile(_A    ):
																		A__							=       {}
																		with zipfile.ZipFile(_A    ) as z:
																								for filename in z.namelist():
																														if not os.path.isdir(_A    ):
																																				# read the file
																																				with z.open(_A    ) as f:
																																										A__							=       f.read().decode("UTF-8"    )

						return results





