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

@dataclasses.dataclass(frozen=_SCREAMING_SNAKE_CASE      )
class lowerCamelCase		:






					'''simple docstring'''


					a   	=		42  # [num_res, num_atom_type, 3]

					# Amino-acid type for each residue represented as an integer between 0 and
					# 20, where 20 is 'X'.
					a   	=		42  # [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.
					a   	=		42  # [num_res, num_atom_type]

					# Residue index as used in PDB. It is not necessarily continuous or 0-indexed.
					a   	=		42  # [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.
					a   	=		42  # [num_res, num_atom_type]

					# Chain indices for multi-chain predictions
					a   	=		None

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

					# Templates used to generate this protein (prediction-only)
					a   	=		None

					# Chain corresponding to each parent
					a   	=		None




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

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

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

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

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

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

				return pdb_headers




def 						SCREAMING_SNAKE_CASE					(  __UpperCAmelCase  ,					__UpperCAmelCase       )							->   str:
				SCREAMING_SNAKE_CASE__		  =				[]
				SCREAMING_SNAKE_CASE__		  =				pdb_str.split("\n"       )

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

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

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

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

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

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

												out_pdb_lines.append(make_parent_line(__UpperCAmelCase       )       )

				return "\n".join(__UpperCAmelCase       )




def 						SCREAMING_SNAKE_CASE					(  __UpperCAmelCase       )							->   str:
				SCREAMING_SNAKE_CASE__		  =				residue_constants.restypes + ["X"]

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

				SCREAMING_SNAKE_CASE__		  =				residue_constants.atom_types

				SCREAMING_SNAKE_CASE__		  =				[]

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

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

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

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

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

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

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

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

								if should_terminate:
												# Close the chain.
												SCREAMING_SNAKE_CASE__		  =				"TER"
												SCREAMING_SNAKE_CASE__		  =				(
												    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 						SCREAMING_SNAKE_CASE					(  __UpperCAmelCase       )							->   np.ndarray:
				return residue_constants.STANDARD_ATOM_MASK[prot.aatype]




def 						SCREAMING_SNAKE_CASE					(  __UpperCAmelCase  ,					__UpperCAmelCase  ,					__UpperCAmelCase = None  ,					__UpperCAmelCase = None  ,					__UpperCAmelCase = None  ,					__UpperCAmelCase = None  ,					__UpperCAmelCase = None  ,					)							->   Protein:
				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  ,					)





"""simple docstring"""






import os

from huggingface_hub.constants import HUGGINGFACE_HUB_CACHE, hf_cache_home


_A   					=    HUGGINGFACE_HUB_CACHE


_A   					=    'config.json'
_A   					=    'diffusion_pytorch_model.bin'
_A   					=    'diffusion_flax_model.msgpack'
_A   					=    'model.onnx'
_A   					=    'diffusion_pytorch_model.safetensors'
_A   					=    'weights.pb'
_A   					=    'https://huggingface.co'
_A   					=    default_cache_path
_A   					=    'diffusers_modules'
_A   					=    os.getenv('HF_MODULES_CACHE', os.path.join(hf_cache_home, 'modules'))
_A   					=    ['fp16', 'non-ema']
_A   					=    '.self_attn'




