diffalign package

Subpackages

• diffalign.models package
  • Subpackages
    • diffalign.models.encoder package
      • Submodules
      • diffalign.models.encoder.edge module
        • MLPEdgeEncoder
          • MLPEdgeEncoder.forward()
          • MLPEdgeEncoder.out_channels
      • diffalign.models.encoder.egnn module
        • EGNN
          • EGNN.forward()
        • EGNN_old
          • EGNN_old.forward()
        • E_GCL
          • E_GCL.coord2radial()
          • E_GCL.coord_model()
          • E_GCL.edge_model()
          • E_GCL.forward()
          • E_GCL.node_model()
        • GNN
          • GNN.forward()
        • MLP
          • MLP.forward()
        • TransformerNN
          • TransformerNN.SetDecoder
            • TransformerNN.SetDecoder.forward()
          • TransformerNN.forward()
        • unsorted_segment_sum()
      • Module contents
    • diffalign.models.epsnet package
      • Submodules
      • diffalign.models.epsnet.diffusion module
        • DiffAlign
          • DiffAlign.DDIM_CFG_Sampling()
          • DiffAlign.DDPM_CFG_Sampling()
          • DiffAlign.DDPM_Sampling()
          • DiffAlign.forward()
          • DiffAlign.get_loss()
        • SinusoidalTimeEmbeddings
          • SinusoidalTimeEmbeddings.forward()
        • get_distance()
        • merge_graphs_in_batch()
      • Module contents
  • Submodules
  • diffalign.models.common module
    • MultiLayerPerceptron
      • MultiLayerPerceptron.forward()
    • extend_graph_order_radius()
    • extend_to_cross_attention()
  • Module contents
• diffalign.utils package
  • Subpackages
    • diffalign.utils.evaluation package
      • Submodules
      • diffalign.utils.evaluation.covmat module
        • CovMatEvaluator
        • evaluate_conf()
        • get_rmsd_confusion_matrix()
        • print_covmat_results()
      • Module contents
  • Submodules
  • diffalign.utils.chem module
    • bond_type_to_int()
    • draw_mol_svg()
    • get_2D_mol()
    • get_atom_symbol()
    • get_atoms_in_ring()
    • get_best_rmsd()
    • mol_to_graph_data_obj()
    • mol_to_smiles()
    • mol_to_smiles_without_Hs()
    • remove_duplicate_mols()
    • set_conformer_positions()
    • set_rdmol_positions()
    • set_rdmol_positions_()
    • update_data_pos_from_rdmol()
    • update_data_rdmol_positions()
  • diffalign.utils.common module
    • ExponentialLR_with_minLr
      • ExponentialLR_with_minLr.get_lr()
    • get_optimizer()
    • get_scheduler()
    • repeat_batch()
    • repeat_data()
  • diffalign.utils.dataloader module
    • Collater
    • DataLoader
  • diffalign.utils.datasets module
    • ConformationDataset
      • ConformationDataset.get()
      • ConformationDataset.len()
    • MolClusterData
    • PackedConformationDataset
    • SidechainConformationDataset
      • SidechainConformationDataset.collate_fn()
    • accumulate_grad_from_subgraph()
    • get_test_set_with_large_num_conf()
    • pdb_to_data()
    • prepare_pdb2()
    • prepare_pdb_valtest()
    • prepare_pdblarge()
    • preprocess_GEOM_dataset()
    • preprocess_GEOM_dataset_with_fixed_num_conf()
    • preprocess_iso17_dataset()
    • rdmol_cluster_to_data()
    • rdmol_to_data()
  • diffalign.utils.misc module
    • BlackHole
    • get_checkpoint_path()
    • get_logger()
    • get_new_log_dir()
    • inf_iterator()
    • int_tuple()
    • log_hyperparams()
    • repeat_batch()
    • repeat_data()
    • seed_all()
    • str_tuple()
  • diffalign.utils.transforms module
    • AddAngleDihedral
      • AddAngleDihedral.iter_angle_triplet()
      • AddAngleDihedral.iter_dihedral_quartet()
    • AddEdgeLength
    • AddEdgeName
    • AddHigherOrderEdges
      • AddHigherOrderEdges.binarize()
      • AddHigherOrderEdges.get_higher_order_adj_matrix()
    • AddPlaceHolder
    • CountNodesPerGraph
  • diffalign.utils.visualize module
    • visualize_mol()
  • Module contents

Submodules

diffalign.train module

Module contents