Index _ | A | B | C | D | E | F | G | I | L | M | N | P | R | S | V | W _ __init__() (AtomEmpty method), [1], [2] (Base method), [1], [2], [3] (FrameEmpty method), [1], [2] (InvalidRoutine method), [1], [2] (MultiFrameTraj method), [1], [2], [3] (NoResidues method), [1], [2], [3] (ResEmpty method), [1], [2] (SmartIndexingAction method), [1], [2], [3], [4] (Vector method), [1], [2], [3] _get_args() (SmartIndexingAction method), [1], [2], [3], [4] _get_kwargs() (SmartIndexingAction method), [1], [2], [3], [4] A add_note() (AtomEmpty method), [1], [2] (FrameEmpty method), [1], [2] (InvalidRoutine method), [1], [2] (MultiFrameTraj method), [1], [2], [3] (NoResidues method), [1], [2], [3] (ResEmpty method), [1], [2] args (AtomEmpty attribute), [1], [2] (FrameEmpty attribute), [1], [2] (InvalidRoutine attribute), [1], [2] (MultiFrameTraj attribute), [1], [2], [3] (NoResidues attribute), [1], [2], [3] (ResEmpty attribute), [1], [2] AtomEmpty, [1], [2] B Base (class in stacker.residue_movement), [1], [2], [3] block_printing() (in module stacker), [1], [2] bottaro_routine() (in module stacker), [1], [2] C calc_center_3pts() (in module stacker.residue_movement), [1], [2], [3] calculate_bottaro_values_for_frame() (in module stacker.residue_movement), [1], [2], [3] calculate_cross_product() (Vector method), [1], [2], [3], [4] calculate_projection() (Vector method), [1], [2], [3], [4] calculate_residue_distance() (in module stacker.pairwise_distance), [1], [2], [3] collect_atom_locations_by_frame() (in module stacker.residue_movement), [1], [2], [3] combine_frames() (in module stacker), [1], [2] compare_routine() (in module stacker), [1], [2] convert_to_python_command() (in module stacker), [1], [2] correct_theta_sign() (in module stacker.residue_movement), [1], [2], [3] create_axis_labels() (in module stacker.visualization), [1], [2], [3] create_base_from_coords_list() (in module stacker.residue_movement), [1], [2], [3] create_kmeans_input() (in module stacker.kmeans), [1], [2], [3] create_parent_directories() (in module stacker.visualization), [1], [2], [3] D display_arrays_as_video() (in module stacker.visualization), [1], [2], [3] display_psf_heatmap() (in module stacker.visualization), [1], [2], [3] display_psf_scatter() (in module stacker.visualization), [1], [2], [3] display_ssfs() (in module stacker.visualization), [1], [2], [3] E enable_printing() (in module stacker), [1], [2] F file_convert() (in module stacker.file_manipulation), [1], [2], [3] filter_traj() (in module stacker.file_manipulation), [1], [2], [3] filter_traj_routine() (in module stacker), [1], [2] filter_traj_to_pdb() (in module stacker.file_manipulation), [1], [2], [3] format_usage() (SmartIndexingAction method), [1], [2], [3], [4], [5], [6] FrameEmpty, [1], [2] G get_frame_average() (in module stacker.pairwise_distance), [1], [2], [3] get_residue_distance_for_frame() (in module stacker.pairwise_distance), [1], [2], [3] get_residue_distance_for_trajectory() (in module stacker.pairwise_distance), [1], [2], [3] get_top_stacking() (in module stacker.pairwise_distance), [1], [2], [3] I increment_residue() (in module stacker.pairwise_distance), [1], [2], [3] InvalidRoutine, [1], [2] L load_ssfs() (in module stacker.pairwise_distance), [1], [2], [3] M magnitude() (Vector method), [1], [2], [3], [4] module stacker, [1] stacker.file_manipulation, [1], [2] stacker.kmeans, [1], [2] stacker.pairwise_distance, [1], [2] stacker.residue_movement, [1], [2] stacker.vector, [1], [2] stacker.visualization, [1], [2] MultiFrameTraj, [1], [2], [3] N NoResidues, [1], [2], [3] P parse_smart_index() (SmartIndexingAction static method), [1], [2], [3], [4], [5], [6] plot_cluster_trj_data() (in module stacker.kmeans), [1], [2], [3] plot_pca() (in module stacker.kmeans), [1], [2], [3] plot_silhouette() (in module stacker.kmeans), [1], [2], [3] R read_and_preprocess_data() (in module stacker.kmeans), [1], [2], [3] res_distance_routine() (in module stacker), [1], [2] ResEmpty, [1], [2] run_kmeans() (in module stacker.kmeans), [1], [2], [3] run_python_command() (in module stacker), [1], [2] S scale() (Vector method), [1], [2], [3], [4] set_polar_grid() (in module stacker.visualization), [1], [2], [3] SmartIndexingAction (class in stacker) (class in stacker.file_manipulation), [1], [2], [3] stack_events_routine() (in module stacker), [1], [2] stacker module, [1] stacker.file_manipulation module, [1], [2] stacker.kmeans module, [1], [2] stacker.pairwise_distance module, [1], [2] stacker.residue_movement module, [1], [2] stacker.vector module, [1], [2] stacker.visualization module, [1], [2] system_routine() (in module stacker), [1], [2] system_stacking_fingerprints() (in module stacker.pairwise_distance), [1], [2], [3] V Vector (class in stacker.vector), [1], [2], [3] visualize_two_residue_movement_heatmap() (in module stacker.visualization), [1], [2], [3] visualize_two_residue_movement_scatterplot() (in module stacker.visualization), [1], [2], [3] W with_traceback() (AtomEmpty method), [1], [2] (FrameEmpty method), [1], [2] (InvalidRoutine method), [1], [2] (MultiFrameTraj method), [1], [2], [3] (NoResidues method), [1], [2], [3] (ResEmpty method), [1], [2] write_bottaro_to_csv() (in module stacker.residue_movement), [1], [2], [3] write_psf_data() (in module stacker.residue_movement), [1], [2], [3]
