



"""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


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







@dataclasses.dataclass(frozen=SCREAMING_SNAKE_CASE_    )
class 				A_      :



      """simple docstring"""
      __UpperCamelCase		    =							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'.
      __UpperCamelCase		    =							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.
      __UpperCamelCase		    =							42  # [num_res, num_atom_type]

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

      # Chain indices for multi-chain predictions
      __UpperCamelCase		    =							None

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

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

      # Chain corresponding to each parent
      __UpperCamelCase		    =							None


def 			_lowerCAmelCase				(       lowercase_						):
      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 			_lowerCAmelCase				(       lowercase_		,     lowercase_ = 0						):
      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 			_lowerCAmelCase				(       lowercase_		,     lowercase_						):
      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 			_lowerCAmelCase				(       lowercase_						):
      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 			_lowerCAmelCase				(       lowercase_						):
      return residue_constants.STANDARD_ATOM_MASK[prot.aatype]






def 			_lowerCAmelCase				(       lowercase_		,     lowercase_		,     lowercase_ = None		,     lowercase_ = None		,     lowercase_ = None		,     lowercase_ = None		,     lowercase_ = None		,     ):
      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_		,     )










"""simple docstring"""


import re

import jax.numpy as jnp
from flax.traverse_util import flatten_dict, unflatten_dict
from jax.random import PRNGKey

from ..utils import logging


snake_case_    					=	logging.get_logger(__name__)

def 			_lowerCAmelCase				(       lowercase_						):
						UpperCAmelCase					=			R'\w+[.]\d+'
						UpperCAmelCase					=			re.findall(lowercase_		,     lowercase_						)
						for pat in pats:
												UpperCAmelCase					=			key.replace(lowercase_		,     '_'.join(pat.split('.'						)						)						)
						return key

def 			_lowerCAmelCase				(       lowercase_		,     lowercase_		,     lowercase_						):
						UpperCAmelCase					=			pt_tuple_key[:-1] + ('scale',)
						if (
						    any('norm' in str_ for str_ in pt_tuple_key						)
						    and (pt_tuple_key[-1] == "bias")
						    and (pt_tuple_key[:-1] + ("bias",) not in random_flax_state_dict)
						    and (pt_tuple_key[:-1] + ("scale",) in random_flax_state_dict)
						):
												UpperCAmelCase					=			pt_tuple_key[:-1] + ('scale',)
												return renamed_pt_tuple_key, pt_tensor
						elif pt_tuple_key[-1] in ["weight", "gamma"] and pt_tuple_key[:-1] + ("scale",) in random_flax_state_dict:
												UpperCAmelCase					=			pt_tuple_key[:-1] + ('scale',)
												return renamed_pt_tuple_key, pt_tensor

						# embedding
						if pt_tuple_key[-1] == "weight" and pt_tuple_key[:-1] + ("embedding",) in random_flax_state_dict:
												UpperCAmelCase					=			pt_tuple_key[:-1] + ('embedding',)
												return renamed_pt_tuple_key, pt_tensor

						# conv layer
						UpperCAmelCase					=			pt_tuple_key[:-1] + ('kernel',)
						if pt_tuple_key[-1] == "weight" and pt_tensor.ndim == 4:
												UpperCAmelCase					=			pt_tensor.transpose(2		,     3		,     1		,     0						)
												return renamed_pt_tuple_key, pt_tensor

						# linear layer
						UpperCAmelCase					=			pt_tuple_key[:-1] + ('kernel',)
						if pt_tuple_key[-1] == "weight":
												UpperCAmelCase					=			pt_tensor.T
												return renamed_pt_tuple_key, pt_tensor

						# old PyTorch layer norm weight
						UpperCAmelCase					=			pt_tuple_key[:-1] + ('weight',)
						if pt_tuple_key[-1] == "gamma":
												return renamed_pt_tuple_key, pt_tensor

						# old PyTorch layer norm bias
						UpperCAmelCase					=			pt_tuple_key[:-1] + ('bias',)
						if pt_tuple_key[-1] == "beta":
												return renamed_pt_tuple_key, pt_tensor

						return pt_tuple_key, pt_tensor






def 			_lowerCAmelCase				(       lowercase_		,     lowercase_		,     lowercase_=42						):
						# Step 1: Convert pytorch tensor to numpy
						UpperCAmelCase					=			{k: v.numpy() for k, v in pt_state_dict.items()}

						# Step 2: Since the model is stateless, get random Flax params
						UpperCAmelCase					=			flax_model.init_weights(PRNGKey(lowercase_						)						)

						UpperCAmelCase					=			flatten_dict(lowercase_						)
						UpperCAmelCase					=			{}

						# Need to change some parameters name to match Flax names
						for pt_key, pt_tensor in pt_state_dict.items():
												UpperCAmelCase					=			rename_key(lowercase_						)
												UpperCAmelCase					=			tuple(renamed_pt_key.split('.'						)						)

												# Correctly rename weight parameters
												UpperCAmelCase				,   UpperCAmelCase					=			rename_key_and_reshape_tensor(lowercase_		,     lowercase_		,     lowercase_						)

												if flax_key in random_flax_state_dict:
																		if flax_tensor.shape != random_flax_state_dict[flax_key].shape:
																								raise ValueError(
																								    F"""PyTorch checkpoint seems to be incorrect. Weight {pt_key} was expected to be of shape """
																								    F"""{random_flax_state_dict[flax_key].shape}, but is {flax_tensor.shape}."""						)

        # also add unexpected weight so that warning is thrown
												UpperCAmelCase					=			jnp.asarray(lowercase_						)

						return unflatten_dict(lowercase_						)





