Index

_

_rotate_and_stack() (in module mlspm.data_loading)

A

add_atom() (mlspm.graph.MoleculeGraph method) add_batch() (mlspm.graph.GraphStats method) add_cutout() (in module mlspm.preprocessing) add_gradient() (in module mlspm.preprocessing) add_noise() (in module mlspm.preprocessing) add_norm() (in module mlspm.preprocessing) add_rotation_reflection() (in module mlspm.preprocessing) add_rotation_reflection_graph() (in module mlspm.graph) add_sample() (mlspm.data_generation.TarWriter method)

add_train_loss() (mlspm.logging.LossLogPlot method) add_val_loss() (mlspm.logging.LossLogPlot method) adjacency_matrix() (mlspm.graph.MoleculeGraph method) append() (mlspm.logging.SyncedLoss method) array() (mlspm.graph.Atom method) (mlspm.graph.MoleculeGraph method) ASDAFMNet (class in mlspm.image.models) Atom (class in mlspm.graph) AttentionConvZ (class in mlspm.modules) AttentionUNet (class in mlspm.image.models)

B

batch_write_xyzs() (in module mlspm.utils) batched() (in module mlspm.data_loading)

best_epoch (mlspm.utils.Checkpointer property) best_loss (mlspm.utils.Checkpointer property) bond_count_diffs() (mlspm.graph.GraphStats method)

C

Checkpointer (class in mlspm.utils) collate_graph() (in module mlspm.data_loading) conf_mat_edge() (mlspm.graph.GraphStats method) conf_mat_node() (mlspm.graph.GraphStats method) Conv2dBlock (class in mlspm.modules)

Conv3dBlock (class in mlspm.modules) copy() (mlspm.graph.Atom method) (mlspm.graph.MoleculeGraph method) count_parameters() (in module mlspm.utils) crop_atoms() (mlspm.graph.MoleculeGraph method) crop_graph() (in module mlspm.graph)

D

decode_xyz() (in module mlspm.data_loading) default_collate() (in module mlspm.data_loading)

download_dataset() (in module mlspm.datasets) download_weights() (in module mlspm.models)

E

EDAFMNet (class in mlspm.image.models) edge_precision() (mlspm.graph.GraphStats method)

edge_recall() (mlspm.graph.GraphStats method) encode_afm() (mlspm.graph.models.GraphImgNet method) extra_nodes() (mlspm.graph.GraphStats method)

F

find_bonds() (in module mlspm.graph) find_gaussian_peaks() (in module mlspm.graph) forward() (mlspm.graph.losses.GraphLoss method) (mlspm.graph.models.GraphImgNet method) (mlspm.graph.models.PosNet method) (mlspm.image.models.ASDAFMNet method) (mlspm.image.models.AttentionUNet method) (mlspm.losses.GraphLoss method) (mlspm.modules.AttentionConvZ method) (mlspm.modules.UNetAttentionConv method)

G

get_joinable() (mlspm.logging.LossLogPlot method) get_positions() (mlspm.graph.models.PosNet method) get_scan_window_from_comment() (in module mlspm.data_loading) get_tarinfo() (in module mlspm.data_generation) graph_sizes() (mlspm.graph.GraphStats method)

GraphImgNet (class in mlspm.graph.models) GraphImgNetIce (class in mlspm.graph.models) GraphLoss (class in mlspm.graph.losses) (class in mlspm.losses) GraphStats (class in mlspm.graph)

H

hartree (mlspm.data_generation.TarSampleList attribute)

hausdorff_distances() (mlspm.graph.GraphStats method)

I

interpolate_and_crop() (in module mlspm.preprocessing)

J

join_device (mlspm.logging.SyncedLoss property)

join_hook() (mlspm.logging.SyncedLoss method) join_process_group (mlspm.logging.SyncedLoss property)

L

largest_graph (mlspm.graph.GraphStats property) load_checkpoint() (in module mlspm.utils)

loss_str() (mlspm.logging.LossLogPlot method) LossLogPlot (class in mlspm.logging)

M

make_box_borders() (in module mlspm.graph) make_input_plots() (in module mlspm.visualization) make_position_distribution() (in module mlspm.graph) make_prediction_plots() (in module mlspm.visualization) matching_distances() (mlspm.graph.GraphStats method) mean() (mlspm.logging.SyncedLoss method) minimum_to_zero() (in module mlspm.preprocessing) missing_nodes() (mlspm.graph.GraphStats method) mlspm.cli module mlspm.data_generation module mlspm.data_loading module mlspm.datasets module mlspm.graph module mlspm.graph.losses module mlspm.graph.models module mlspm.image module mlspm.image.models module mlspm.logging module mlspm.models.ASDAFMNet (built-in class)

mlspm.models.AttentionUNet (built-in class) mlspm.models.EDAFMNet (built-in class) mlspm.models.GraphImgNet (built-in class) mlspm.models.GraphImgNetIce (built-in class) mlspm.models.PosNet (built-in class) mlspm.modules module mlspm.preprocessing module mlspm.utils module mlspm.visualization module module mlspm.cli mlspm.data_generation mlspm.data_loading mlspm.datasets mlspm.graph mlspm.graph.losses mlspm.graph.models mlspm.image mlspm.image.models mlspm.logging mlspm.modules mlspm.preprocessing mlspm.utils mlspm.visualization MoleculeGraph (class in mlspm.graph) mpnn() (mlspm.graph.models.GraphImgNet method)

N

next_epoch() (mlspm.logging.LossLogPlot method) (mlspm.utils.Checkpointer method)

node_count_diffs() (mlspm.graph.GraphStats method) node_precision() (mlspm.graph.GraphStats method) node_recall() (mlspm.graph.GraphStats method)

P

parse_args() (in module mlspm.cli) permute() (mlspm.graph.MoleculeGraph method) plot() (mlspm.graph.GraphStats method) plot_confusion_matrix() (in module mlspm.visualization) plot_distribution_grid() (in module mlspm.visualization)

plot_graphs() (in module mlspm.visualization) plot_history() (mlspm.logging.LossLogPlot method) plot_input() (in module mlspm.visualization) PosNet (class in mlspm.graph.models) pred_to_graph() (mlspm.graph.models.GraphImgNet method) predict_graph() (mlspm.graph.models.GraphImgNet method)

R

rand_shift_xy_trend() (in module mlspm.preprocessing) random_crop() (in module mlspm.preprocessing) randomize_positions() (mlspm.graph.MoleculeGraph method) read_xyzs() (in module mlspm.utils) remove_atoms() (mlspm.graph.MoleculeGraph method)

report() (mlspm.graph.GraphStats method) reset() (mlspm.logging.SyncedLoss method) revert_to_best_epoch() (mlspm.utils.Checkpointer method) rho (mlspm.data_generation.TarSampleList attribute) rotate_and_stack (in module mlspm.data_loading) rots (mlspm.data_generation.TarSampleList attribute)

S

save_checkpoint() (in module mlspm.utils) save_graphs_to_xyzs() (in module mlspm.graph) setup_file_logger() (in module mlspm.logging)

ShardList (class in mlspm.data_loading) shift_mols_window() (in module mlspm.graph) SyncedLoss (class in mlspm.logging)

T

TarDataGenerator (class in mlspm.data_generation) TarSampleList (class in mlspm.data_generation) TarWriter (class in mlspm.data_generation) threshold_atoms_bonds() (in module mlspm.graph)

top_atom_to_zero() (in module mlspm.preprocessing) total_nodes (mlspm.graph.GraphStats property) total_samples (mlspm.graph.GraphStats property) transform_xy() (mlspm.graph.MoleculeGraph method)

U

UNetAttentionConv (class in mlspm.modules)

W

worker_init_fn() (in module mlspm.data_loading)

write_to_xyz() (in module mlspm.utils)