Reference

• mlspm.cli
  • parse_args()
• mlspm.data_generation
  • TarDataGenerator
  • TarSampleList
    • TarSampleList.hartree
    • TarSampleList.rho
    • TarSampleList.rots
  • TarWriter
    • TarWriter.add_sample()
  • get_tarinfo()
• mlspm.data_loading
  • ShardList
  • batched()
  • decode_xyz()
  • default_collate()
  • get_scan_window_from_comment()
  • rotate_and_stack
  • worker_init_fn()
  • _rotate_and_stack()
  • collate_graph()
• mlspm.datasets
  • download_dataset()
• mlspm.graph
  • Atom
    • Atom.array()
    • Atom.copy()
  • GraphStats
    • GraphStats.add_batch()
    • GraphStats.bond_count_diffs()
    • GraphStats.conf_mat_edge()
    • GraphStats.conf_mat_node()
    • GraphStats.edge_precision()
    • GraphStats.edge_recall()
    • GraphStats.extra_nodes()
    • GraphStats.graph_sizes()
    • GraphStats.hausdorff_distances()
    • GraphStats.largest_graph
    • GraphStats.matching_distances()
    • GraphStats.missing_nodes()
    • GraphStats.node_count_diffs()
    • GraphStats.node_precision()
    • GraphStats.node_recall()
    • GraphStats.plot()
    • GraphStats.report()
    • GraphStats.total_nodes
    • GraphStats.total_samples
  • MoleculeGraph
    • MoleculeGraph.add_atom()
    • MoleculeGraph.adjacency_matrix()
    • MoleculeGraph.array()
    • MoleculeGraph.copy()
    • MoleculeGraph.crop_atoms()
    • MoleculeGraph.permute()
    • MoleculeGraph.randomize_positions()
    • MoleculeGraph.remove_atoms()
    • MoleculeGraph.transform_xy()
  • add_rotation_reflection_graph()
  • crop_graph()
  • find_bonds()
  • find_gaussian_peaks()
  • make_box_borders()
  • make_position_distribution()
  • save_graphs_to_xyzs()
  • shift_mols_window()
  • threshold_atoms_bonds()
  • mlspm.graph.losses
    • GraphLoss
      • GraphLoss.forward()
  • mlspm.graph.models
    • GraphImgNet
      • GraphImgNet.encode_afm()
      • GraphImgNet.forward()
      • GraphImgNet.mpnn()
      • GraphImgNet.pred_to_graph()
      • GraphImgNet.predict_graph()
    • GraphImgNetIce
    • PosNet
      • PosNet.forward()
      • PosNet.get_positions()
• mlspm.image
  • mlspm.image.models
    • ASDAFMNet
      • ASDAFMNet.forward()
    • AttentionUNet
      • AttentionUNet.forward()
    • EDAFMNet
• mlspm.logging
  • LossLogPlot
    • LossLogPlot.add_train_loss()
    • LossLogPlot.add_val_loss()
    • LossLogPlot.get_joinable()
    • LossLogPlot.loss_str()
    • LossLogPlot.next_epoch()
    • LossLogPlot.plot_history()
  • SyncedLoss
    • SyncedLoss.append()
    • SyncedLoss.join_device
    • SyncedLoss.join_hook()
    • SyncedLoss.join_process_group
    • SyncedLoss.mean()
    • SyncedLoss.reset()
  • setup_file_logger()
• mlspm.losses
  • GraphLoss
    • GraphLoss.forward()
• mlspm.models
  • mlspm.models.PosNet
  • mlspm.models.GraphImgNet
  • mlspm.models.GraphImgNetIce
  • mlspm.models.ASDAFMNet
  • mlspm.models.AttentionUNet
  • mlspm.models.EDAFMNet
  • download_weights()
• mlspm.modules
  • AttentionConvZ
    • AttentionConvZ.forward()
  • Conv2dBlock
  • Conv3dBlock
  • UNetAttentionConv
    • UNetAttentionConv.forward()
• mlspm.preprocessing
  • add_cutout()
  • add_gradient()
  • add_noise()
  • add_norm()
  • add_rotation_reflection()
  • interpolate_and_crop()
  • minimum_to_zero()
  • rand_shift_xy_trend()
  • random_crop()
  • top_atom_to_zero()
• mlspm.utils
  • Checkpointer
    • Checkpointer.best_epoch
    • Checkpointer.best_loss
    • Checkpointer.next_epoch()
    • Checkpointer.revert_to_best_epoch()
  • batch_write_xyzs()
  • count_parameters()
  • load_checkpoint()
  • read_xyzs()
  • save_checkpoint()
  • write_to_xyz()
• mlspm.visualization
  • make_input_plots()
  • plot_confusion_matrix()
  • plot_input()
  • make_prediction_plots()
  • plot_distribution_grid()
  • plot_graphs()