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| import traceback |
| from typing import Union |
| import logging |
|
|
| import torch |
|
|
| from src.utils.permutation.utils import save_permutation_error |
| from src.api.model_interface import PermutationInput, GroundTruth |
| from .heuristic import correct_symmetric_chains |
| from .pocket_based_permutation import permute_pred_to_optimize_pocket_aligned_rmsd |
|
|
| logger = logging.getLogger(__name__) |
|
|
|
|
| def run( |
| pred_coord: torch.Tensor, |
| input_data: PermutationInput, |
| ground_truth: GroundTruth, |
| max_num_chains: int = -1, |
| permute_label: bool = True, |
| permute_by_pocket: bool = False, |
| error_dir: str = None, |
| **kwargs, |
| ) -> tuple[dict]: |
| """ |
| Run chain permutation. |
| |
| |
| Args: |
| pred_coord (torch.Tensor): The predicted coordinates. Shape: [N_atoms, 3]. |
| input_data (PermutationInput): A dictionary containing input features. |
| label_full_dict (dict[str, Union[torch.Tensor, int, float, dict]]): A dictionary containing full label information. |
| max_num_chains (int, optional): The maximum number of chains to consider. Defaults to -1 (no limit). |
| permute_label (bool, optional): Whether to permute the label. Defaults to True. |
| permute_by_pocket (bool, optional): Whether to permute by pocket (for PoseBusters dataset). Defaults to False. |
| error_dir (str, optional): Directory to save error data. Defaults to None. |
| **kwargs: Additional keyword arguments. |
| |
| Returns: |
| tuple[dict]: A tuple containing the output dictionary, log dictionary, permuted prediction indices, and permuted label indices. |
| """ |
|
|
| if pred_coord.dim() > 2: |
| assert ( |
| permute_label is False |
| ), "Only supports prediction permutations in batch mode." |
|
|
| try: |
|
|
| if permute_by_pocket: |
| """Optimize the chain assignment on pocket-ligand interface""" |
| assert not permute_label |
|
|
| if ground_truth.pocket_mask.dim() == 2: |
| |
| pocket_mask = ground_truth.pocket_mask[0] |
| ligand_mask = ground_truth.interested_ligand_mask[0] |
| else: |
| pocket_mask = ground_truth.pocket_mask |
| ligand_mask = ground_truth.interested_ligand_mask |
|
|
| permute_pred_indices, permuted_aligned_pred_coord, log_dict = ( |
| permute_pred_to_optimize_pocket_aligned_rmsd( |
| pred_coord=pred_coord, |
| true_coord=ground_truth.coordinate, |
| true_coord_mask=ground_truth.coordinate_mask, |
| true_pocket_mask=pocket_mask, |
| true_ligand_mask=ligand_mask, |
| atom_entity_id=input_data.entity_mol_id, |
| atom_asym_id=input_data.mol_id, |
| mol_atom_index=input_data.mol_atom_index, |
| use_center_rmsd=kwargs.get("use_center_rmsd", False), |
| ) |
| ) |
| output_dict = {"coordinate": permuted_aligned_pred_coord} |
| permute_label_indices = [] |
|
|
| else: |
| """Optimize the chain assignment on all chains""" |
| output_dict, log_dict, permute_pred_indices, permute_label_indices = ( |
| correct_symmetric_chains( |
| pred_dict={**input_data.to_dict(), "coordinate": pred_coord}, |
| ground_truth=ground_truth, |
| max_num_chains=max_num_chains, |
| permute_label=permute_label, |
| **kwargs, |
| ) |
| ) |
|
|
| except Exception as e: |
| error_message = f"{e}:\n{traceback.format_exc()}" |
| logger.warning(error_message) |
| save_permutation_error( |
| data={ |
| "error_message": error_message, |
| }, |
| error_dir=error_dir, |
| ) |
| output_dict, log_dict, permute_pred_indices, permute_label_indices = ( |
| {}, |
| {}, |
| [], |
| [], |
| ) |
|
|
| return output_dict, log_dict, permute_pred_indices, permute_label_indices |
|
|
