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Getting Started
API Documentation
Create System Stacking Fingerprints (SSFs)
Create Pairwise Stacking Fingerprints (PSFs)
More
Command Line Options
Molecular Dynamics
GitHub
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Getting Started
API Documentation
Create System Stacking Fingerprints (SSFs)
Create Pairwise Stacking Fingerprints (PSFs)
Command Line Options
Molecular Dynamics
GitHub
Search
Ctrl
+
K
GitHub
Search
Ctrl
+
K
StACKER documentation
Contents:
Getting Started
API Documentation
stacker
stacker.block_printing
stacker.bottaro_routine
stacker.combine_frames
stacker.compare_routine
stacker.convert_to_python_command
stacker.enable_printing
stacker.filter_traj_routine
stacker.res_distance_routine
stacker.run_python_command
stacker.stack_events_routine
stacker.system_routine
stacker.AtomEmpty
stacker.FrameEmpty
stacker.InvalidRoutine
stacker.ResEmpty
file_manipulation
stacker.file_manipulation.file_convert
stacker.file_manipulation.filter_traj
stacker.file_manipulation.filter_traj_to_pdb
SmartIndexingAction
kmeans
stacker.kmeans.create_kmeans_input
stacker.kmeans.plot_cluster_trj_data
stacker.kmeans.plot_pca
stacker.kmeans.plot_silhouette
stacker.kmeans.read_and_preprocess_data
stacker.kmeans.run_kmeans
pairwise_distance
stacker.pairwise_distance.calculate_residue_distance
stacker.pairwise_distance.get_frame_average
stacker.pairwise_distance.get_residue_distance_for_frame
stacker.pairwise_distance.get_residue_distance_for_trajectory
stacker.pairwise_distance.get_top_stacking
stacker.pairwise_distance.increment_residue
stacker.pairwise_distance.load_ssfs
stacker.pairwise_distance.system_stacking_fingerprints
stacker.pairwise_distance.MultiFrameTraj
residue_movement
stacker.residue_movement.calc_center_3pts
stacker.residue_movement.calculate_bottaro_values_for_frame
stacker.residue_movement.collect_atom_locations_by_frame
stacker.residue_movement.correct_theta_sign
stacker.residue_movement.create_base_from_coords_list
stacker.residue_movement.write_bottaro_to_csv
stacker.residue_movement.write_psf_data
Base
vector
Vector
visualization
stacker.visualization.create_axis_labels
stacker.visualization.create_parent_directories
stacker.visualization.display_arrays_as_video
stacker.visualization.display_psf_heatmap
stacker.visualization.display_psf_scatter
stacker.visualization.display_ssfs
stacker.visualization.set_polar_grid
stacker.visualization.visualize_two_residue_movement_heatmap
stacker.visualization.visualize_two_residue_movement_scatterplot
stacker.visualization.NoResidues
file_manipulation
stacker.file_manipulation.file_convert
stacker.file_manipulation.filter_traj
stacker.file_manipulation.filter_traj_to_pdb
SmartIndexingAction
pairwise_distance
stacker.pairwise_distance.calculate_residue_distance
stacker.pairwise_distance.get_frame_average
stacker.pairwise_distance.get_residue_distance_for_frame
stacker.pairwise_distance.get_residue_distance_for_trajectory
stacker.pairwise_distance.get_top_stacking
stacker.pairwise_distance.increment_residue
stacker.pairwise_distance.load_ssfs
stacker.pairwise_distance.system_stacking_fingerprints
stacker.pairwise_distance.MultiFrameTraj
residue_movement
stacker.residue_movement.calc_center_3pts
stacker.residue_movement.calculate_bottaro_values_for_frame
stacker.residue_movement.collect_atom_locations_by_frame
stacker.residue_movement.correct_theta_sign
stacker.residue_movement.create_base_from_coords_list
stacker.residue_movement.write_bottaro_to_csv
stacker.residue_movement.write_psf_data
Base
visualization
stacker.visualization.create_axis_labels
stacker.visualization.create_parent_directories
stacker.visualization.display_arrays_as_video
stacker.visualization.display_psf_heatmap
stacker.visualization.display_psf_scatter
stacker.visualization.display_ssfs
stacker.visualization.set_polar_grid
stacker.visualization.visualize_two_residue_movement_heatmap
stacker.visualization.visualize_two_residue_movement_scatterplot
stacker.visualization.NoResidues
kmeans
stacker.kmeans.create_kmeans_input
stacker.kmeans.plot_cluster_trj_data
stacker.kmeans.plot_pca
stacker.kmeans.plot_silhouette
stacker.kmeans.read_and_preprocess_data
stacker.kmeans.run_kmeans
vector
Vector
Create System Stacking Fingerprints (SSFs)
Create Pairwise Stacking Fingerprints (PSFs)
Command Line Options
Molecular Dynamics
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