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


@dataclasses.dataclass(frozen=_SCREAMING_SNAKE_CASE   )
class 				lowercase					:
		__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       A       (					lowercase )   ->  Protein:
		'''simple docstring'''

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

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

		assert aatype is not None

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


def       A       (					lowercase    ,       lowercase = 0 )   ->  List[str]:
		'''simple docstring'''

		UpperCamelCase		=     []

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

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

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

		pdb_headers.append(f'''PARENT {' '.join(lowercase )}''' )

		return pdb_headers


def       A       (					lowercase    ,       lowercase )   ->  str:
		'''simple docstring'''

		UpperCamelCase		=     []
		UpperCamelCase		=     pdb_str.split('\n' )

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

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

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

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

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

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

						out_pdb_lines.append(make_parent_line(lowercase ) )

		return "\n".join(lowercase )


def       A       (					lowercase )   ->  str:
		'''simple docstring'''

		UpperCamelCase		=     residue_constants.restypes + ['X']

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

		UpperCamelCase		=     residue_constants.atom_types

		UpperCamelCase		=     []

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

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

		UpperCamelCase		=     get_pdb_headers(lowercase )
		if len(lowercase ) > 0:
				pdb_lines.extend(lowercase )

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

						UpperCamelCase		=     'ATOM'
						UpperCamelCase		=     atom_name if len(lowercase ) == 4 else f''' {atom_name}'''
						UpperCamelCase		=     ''
						UpperCamelCase		=     ''
						UpperCamelCase		=     1.0_0
						UpperCamelCase		=     atom_name[0]  # Protein supports only C, N, O, S, this works.
						UpperCamelCase		=     ''

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

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

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

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

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


def       A       (					lowercase )   ->  np.ndarray:
		'''simple docstring'''

		return residue_constants.STANDARD_ATOM_MASK[prot.aatype]


def       A       (					lowercase    ,       lowercase    ,       lowercase = None    ,       lowercase = None    ,       lowercase = None    ,       lowercase = None    ,       lowercase = 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=lowercase    ,       remark=lowercase    ,       parents=lowercase    ,       parents_chain_index=lowercase    ,       )


from unittest import TestCase

from datasets import Dataset
from minhash_deduplication import deduplicate_dataset, make_duplicate_clusters


def       A       (					)   ->  Union[str, Any]:
		'''simple docstring'''

		UpperCamelCase		=     {
		    'repo_name': ['test_repo1', 'test_repo2', 'test_repo3'],
		    'path': ['test_1.py', 'test_2.py', 'unit_test.py'],
		    'content': ['a ' * 20, 'a ' * 30, 'b ' * 7],
		}
		UpperCamelCase		=     Dataset.from_dict(lowercase )
		return dataset


class 				lowercase					(		_SCREAMING_SNAKE_CASE   ):



		def __UpperCamelCase ( self       )  ->					Tuple:
				"""simple docstring"""
				UpperCamelCase		=     get_dataset()
				UpperCamelCase		=     make_duplicate_clusters(A_				,      0.85       )
				self.assertEqual(len(duplicate_clusters[0]       )				,      2       )



		def __UpperCamelCase ( self       )  ->					Any:
				"""simple docstring"""
				UpperCamelCase		=     get_dataset()
				UpperCamelCase	,  UpperCamelCase		=     deduplicate_dataset(A_       )
				self.assertEqual(len(A_       )				,      2       )
				print(A_       )
				self.assertEqual(duplicate_clusters[0][0]['copies']				,      2       )
				self.assertEqual(duplicate_clusters[0][0]['is_extreme']				,      A_       )
