mirror of
https://github.com/baker-laboratory/RoseTTAFold-All-Atom.git
synced 2024-11-24 22:37:20 +00:00
202 lines
8.4 KiB
Python
202 lines
8.4 KiB
Python
import torch
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from dataclasses import dataclass, fields
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from typing import Optional, List
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from rf2aa.chemical import ChemicalData as ChemData
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from rf2aa.data.data_loader_utils import MSAFeaturize, get_bond_distances, generate_xyz_prev
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from rf2aa.kinematics import xyz_to_t2d
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from rf2aa.util import get_prot_sm_mask, xyz_t_to_frame_xyz, same_chain_from_bond_feats, \
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Ls_from_same_chain_2d, idx_from_Ls, is_atom
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@dataclass
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class RawInputData:
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msa: torch.Tensor
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ins: torch.Tensor
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bond_feats: torch.Tensor
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xyz_t: torch.Tensor
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mask_t: torch.Tensor
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t1d: torch.Tensor
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chirals: torch.Tensor
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atom_frames: torch.Tensor
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taxids: Optional[List[str]] = None
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term_info: Optional[torch.Tensor] = None
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chain_lengths: Optional[List] = None
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idx: Optional[List] = None
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def query_sequence(self):
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return self.msa[0]
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def sequence_string(self):
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three_letter_sequence = [ChemData().num2aa[num] for num in self.query_sequence()]
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return "".join([ChemData().aa_321[three] for three in three_letter_sequence])
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def is_atom(self):
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return is_atom(self.query_sequence())
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def length(self):
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return self.msa.shape[1]
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def get_chain_bins_from_chain_lengths(self):
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if self.chain_lengths is None:
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raise ValueError("Cannot call get_chain_bins_from_chain_lengths without \
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setting chain_lengths. Chain_lengths is set in merge_inputs")
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chain_bins = {}
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running_length = 0
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for chain, length in self.chain_lengths:
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chain_bins[chain] = (running_length, running_length+length)
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running_length = running_length + length
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return chain_bins
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def update_protein_features_after_atomize(self, residues_to_atomize):
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if self.chain_lengths is None:
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raise("Cannot update protein features without chain_lengths. \
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merge_inputs must be called before this function")
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chain_bins = self.get_chain_bins_from_chain_lengths()
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keep = torch.ones(self.length())
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prev_absolute_index = None
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prev_C = None
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#need to atomize residues from N term to Cterm to handle atomizing neighbors
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residues_to_atomize = sorted(residues_to_atomize, key= lambda x: x.original_chain +str(x.index_in_original_chain))
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for residue in residues_to_atomize:
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original_chain_start_index, original_chain_end_index = chain_bins[residue.original_chain]
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absolute_index_in_combined_input = original_chain_start_index + residue.index_in_original_chain
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atomized_chain_start_index, atomized_chain_end_index = chain_bins[residue.chain]
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N_index = atomized_chain_start_index + residue.absolute_N_index_in_chain
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C_index = atomized_chain_start_index + residue.absolute_C_index_in_chain
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# if residue is first in the chain, no extra bond feats to following residue
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if absolute_index_in_combined_input != original_chain_start_index:
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self.bond_feats[absolute_index_in_combined_input-1, N_index] = ChemData().RESIDUE_ATOM_BOND
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self.bond_feats[N_index, absolute_index_in_combined_input-1] = ChemData().RESIDUE_ATOM_BOND
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# if residue is last in chain, no extra bonds feats to following residue
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if absolute_index_in_combined_input != original_chain_end_index-1:
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self.bond_feats[absolute_index_in_combined_input+1, C_index] = ChemData().RESIDUE_ATOM_BOND
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self.bond_feats[C_index,absolute_index_in_combined_input+1] = ChemData().RESIDUE_ATOM_BOND
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keep[absolute_index_in_combined_input] = 0
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# find neighboring residues that were atomized
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if prev_absolute_index is not None:
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if prev_absolute_index + 1 == absolute_index_in_combined_input:
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self.bond_feats[prev_C, N_index] = 1
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self.bond_feats[N_index, prev_C] = 1
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prev_absolute_index = absolute_index_in_combined_input
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prev_C = C_index
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# remove protein features
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self.keep_features(keep.bool())
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def keep_features(self, keep):
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if not torch.all(keep[self.is_atom()]):
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raise ValueError("cannot remove atoms")
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self.msa = self.msa[:,keep]
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self.ins = self.ins[:,keep]
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self.bond_feats = self.bond_feats[keep][:,keep]
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self.xyz_t = self.xyz_t[:,keep]
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self.t1d = self.t1d[:,keep]
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self.mask_t = self.mask_t[:,keep]
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if self.term_info is not None:
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self.term_info = self.term_info[keep]
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if self.idx is not None:
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self.idx = self.idx[keep]
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# assumes all chirals are after all protein residues
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self.chirals[...,:-1] = self.chirals[...,:-1] - torch.sum(~keep)
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def construct_features(self, model_runner):
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loader_params = model_runner.config.loader_params
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B, L = 1, self.length()
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seq, msa_clust, msa_seed, msa_extra, mask_pos = MSAFeaturize(
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self.msa.long(),
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self.ins.long(),
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loader_params,
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p_mask=loader_params.get("p_msa_mask", 0),
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term_info=self.term_info,
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deterministic=model_runner.deterministic,
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)
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dist_matrix = get_bond_distances(self.bond_feats)
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# xyz_prev, mask_prev = generate_xyz_prev(self.xyz_t, self.mask_t, loader_params)
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# xyz_prev = torch.nan_to_num(xyz_prev)
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# NOTE: The above is the way things "should" be done, this is for compatability with training.
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xyz_prev = ChemData().INIT_CRDS.reshape(1,ChemData().NTOTAL,3).repeat(L,1,1)
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self.xyz_t = torch.nan_to_num(self.xyz_t)
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mask_t_2d = get_prot_sm_mask(self.mask_t, seq[0])
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mask_t_2d = mask_t_2d[:,None]*mask_t_2d[:,:,None] # (B, T, L, L)
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xyz_t_frame = xyz_t_to_frame_xyz(self.xyz_t[None], self.msa[0], self.atom_frames)
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t2d = xyz_to_t2d(xyz_t_frame, mask_t_2d[None])
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t2d = t2d[0]
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# get torsion angles from templates
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seq_tmp = self.t1d[...,:-1].argmax(dim=-1)
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alpha, _, alpha_mask, _ = model_runner.xyz_converter.get_torsions(self.xyz_t.reshape(-1,L,ChemData().NTOTAL,3),
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seq_tmp, mask_in=self.mask_t.reshape(-1,L,ChemData().NTOTAL))
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alpha = alpha.reshape(B,-1,L,ChemData().NTOTALDOFS,2)
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alpha_mask = alpha_mask.reshape(B,-1,L,ChemData().NTOTALDOFS,1)
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alpha_t = torch.cat((alpha, alpha_mask), dim=-1).reshape(B, -1, L, 3*ChemData().NTOTALDOFS)
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alpha_t = alpha_t[0]
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alpha_prev = torch.zeros((L,ChemData().NTOTALDOFS,2))
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same_chain = same_chain_from_bond_feats(self.bond_feats)
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return RFInput(
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msa_latent=msa_seed,
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msa_full=msa_extra,
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seq=seq,
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seq_unmasked=self.query_sequence(),
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bond_feats=self.bond_feats,
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dist_matrix=dist_matrix,
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chirals=self.chirals,
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atom_frames=self.atom_frames.long(),
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xyz_prev=xyz_prev,
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alpha_prev=alpha_prev,
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t1d=self.t1d,
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t2d=t2d,
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xyz_t=self.xyz_t[..., 1, :],
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alpha_t=alpha_t.float(),
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mask_t=mask_t_2d.float(),
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same_chain=same_chain.long(),
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idx=self.idx
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)
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@dataclass
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class RFInput:
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msa_latent: torch.Tensor
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msa_full: torch.Tensor
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seq: torch.Tensor
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seq_unmasked: torch.Tensor
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idx: torch.Tensor
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bond_feats: torch.Tensor
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dist_matrix: torch.Tensor
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chirals: torch.Tensor
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atom_frames: torch.Tensor
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xyz_prev: torch.Tensor
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alpha_prev: torch.Tensor
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t1d: torch.Tensor
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t2d: torch.Tensor
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xyz_t: torch.Tensor
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alpha_t: torch.Tensor
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mask_t: torch.Tensor
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same_chain: torch.Tensor
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msa_prev: Optional[torch.Tensor] = None
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pair_prev: Optional[torch.Tensor] = None
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state_prev: Optional[torch.Tensor] = None
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mask_recycle: Optional[torch.Tensor] = None
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def to(self, gpu):
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for field in fields(self):
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field_value = getattr(self, field.name)
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if torch.is_tensor(field_value):
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setattr(self, field.name, field_value.to(gpu))
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def add_batch_dim(self):
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""" mimic pytorch dataloader at inference time"""
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for field in fields(self):
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field_value = getattr(self, field.name)
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if torch.is_tensor(field_value):
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setattr(self, field.name, field_value[None])
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