promptbind package

Subpackages

• promptbind.data package
  • Submodules
  • promptbind.data.data module
    • FABindDataSet
      • FABindDataSet.get()
      • FABindDataSet.len()
      • FABindDataSet.processed_file_names
    • get_data()
  • promptbind.data.inference_preprocess_mol_confs module
  • promptbind.data.inference_preprocess_protein module
  • Module contents
• promptbind.models package
  • Submodules
  • promptbind.models.att_model module
    • ComplexGraph
      • ComplexGraph.construct_edges()
      • ComplexGraph.forward()
    • EfficientMCAttModel
      • EfficientMCAttModel.forward()
    • sequential_and()
    • sequential_or()
  • promptbind.models.cross_att module
    • CrossAttentionModule
      • CrossAttentionModule.forward()
    • RowAttentionBlock
      • RowAttentionBlock.forward()
      • RowAttentionBlock.inf
    • RowTriangleAttentionBlock
      • RowTriangleAttentionBlock.forward()
      • RowTriangleAttentionBlock.inf
  • promptbind.models.egnn module
    • MCAttEGNN
      • MCAttEGNN.forward()
    • MC_Att_L
      • MC_Att_L.att_model()
      • MC_Att_L.coord_model()
      • MC_Att_L.forward()
      • MC_Att_L.node_model()
      • MC_Att_L.trio_encoder()
    • MC_E_GCL
      • MC_E_GCL.coord_model()
      • MC_E_GCL.edge_model()
      • MC_E_GCL.forward()
      • MC_E_GCL.node_model()
    • MC_E_GCL_Prompt
      • MC_E_GCL_Prompt.coord_model()
      • MC_E_GCL_Prompt.edge_model()
      • MC_E_GCL_Prompt.forward()
      • MC_E_GCL_Prompt.node_model()
      • MC_E_GCL_Prompt.prompt_generation_module()
      • MC_E_GCL_Prompt.prompt_interaction_module()
    • coord2radial()
    • get_edges()
    • get_edges_batch()
    • unsorted_segment_mean()
    • unsorted_segment_sum()
  • promptbind.models.model module
    • IaBNet_mean_and_pocket_prediction_cls_coords_dependent
      • IaBNet_mean_and_pocket_prediction_cls_coords_dependent.forward()
      • IaBNet_mean_and_pocket_prediction_cls_coords_dependent.inference()
    • Transition_diff_out_dim
      • Transition_diff_out_dim.forward()
    • get_model()
  • promptbind.models.model_utils module
    • Attention
      • Attention.forward()
    • GaussianSmearing
      • GaussianSmearing.forward()
    • InteractionModule
      • InteractionModule.forward()
    • RBFDistanceModule
      • RBFDistanceModule.forward()
    • Transition
      • Transition.forward()
    • flatten_final_dims()
    • permute_final_dims()
  • Module contents
• promptbind.utils package
  • Submodules
  • promptbind.utils.fabind_inference_dataset module
    • InferenceDataset
      • InferenceDataset.get()
      • InferenceDataset.len()
  • promptbind.utils.feature_utils module
    • Seed_everything()
    • binarize()
    • extract_torchdrug_feature_from_mol()
    • extract_torchdrug_feature_from_mol_E3Bind()
    • generate_and_write_sdf_from_smiles_using_rdkit_E3Bind()
    • generate_conformation()
    • generate_rdkit_conformation_v2()
    • generate_sdf_from_smiles_using_rdkit()
    • generate_sdf_from_smiles_using_rdkit_E3Bind()
    • get_LAS_distance_constraint_mask()
    • get_canonical_smiles()
    • get_clean_res_list()
    • get_compound_pair_dis_distribution()
    • get_protein_feature()
    • get_res_unique_id()
    • n_hops_adj()
    • read_mol()
    • remove_hetero_and_extract_ligand()
    • save_cleaned_protein()
    • select_chain_within_cutoff_to_ligand_v2()
    • split_protein_and_ligand()
    • write_renumbered_sdf()
    • write_with_new_coords()
  • promptbind.utils.generation_utils module
    • binarize()
    • compute_RMSD()
    • distance_loss_function()
    • distance_optimize_compound_coords()
    • get_LAS_distance_constraint_mask()
    • get_info_pred_distance()
    • n_hops_adj()
    • read_mol()
    • write_with_new_coords()
  • promptbind.utils.inference_mol_utils module
    • binarize()
    • extract_torchdrug_feature_from_mol()
    • generate_conformation()
    • get_LAS_distance_constraint_mask()
    • get_compound_pair_dis_distribution()
    • n_hops_adj()
    • read_mol_and_renumber()
    • read_smiles()
    • write_mol()
  • promptbind.utils.inference_pdb_utils module
    • extract_esm_feature()
    • extract_protein_structure()
    • get_clean_res_list()
    • get_protein_structure()
  • promptbind.utils.logging_utils module
    • Logger
      • Logger.log_message()
      • Logger.log_stats()
  • promptbind.utils.metrics module
    • affinity_metrics()
    • cls_metric()
    • compute_individual_metrics()
    • myMetric()
    • pocket_direct_metrics()
    • pocket_metrics()
    • print_metrics()
  • promptbind.utils.metrics_to_tsb module
    • metrics_runtime_no_prefix()
  • promptbind.utils.post_optim_utils module
    • compute_RMSD()
    • post_optimize_compound_coords()
    • post_optimize_compound_coords_lbfgs()
    • post_optimize_loss_function()
    • read_molecule()
    • write_mol()
  • promptbind.utils.utils module
    • SetDihedral()
    • compute_dis_between_two_vector()
    • compute_dis_between_two_vector_tensor()
    • construct_data_from_graph_gvp_mean()
    • evaluate_mean_pocket_cls_coord_multi_task()
    • evaluate_mean_pocket_cls_coord_pocket_pred()
    • get_keepNode()
    • get_keepNode_tensor()
    • get_protein_edge_features_and_index()
    • get_torsions()
    • gumbel_softmax_no_random()
    • post_optim_mol()
    • read_mol()
    • read_pdbbind_data()
    • uniform_random_rotation()
  • Module contents

Submodules

promptbind.test_promptbind module

class promptbind.test_promptbind.PromptBindInference(config_path='args.yml')

Bases: object

load_args()

load_model()

run_inference()

Runs the inference process for the model.

This method sets the model to evaluation mode, logs the beginning of the test, and if the current process is the main process, it evaluates the model using the provided evaluation function. The evaluation metrics are then logged.

The method waits for all processes to complete before finishing.

Returns:

None

setup_accelerator()

setup_criterions()

setup_data_loaders()

setup_logger()

promptbind.train_promptbind module

promptbind.visualize_prompt_components module

promptbind.visualize_prompt_components.main(opt)

Module contents