Index

_ | A | B | C | D | E | F | G | H | I | L | M | O | P | R | S | T | U | V | W

_

A

analyze_protein_and_water_interaction()
- built-in function
analyze_protein_and_water_interaction() (StableWaters method)

arranged_figure_generation()
- built-in function
arranged_figure_generation() (FigureArranger method)

B

C

calc_rmsd_2frames_jit()
- built-in function
calculate_distance_matrix() (RMSDAnalyzer method)
calculate_representative_frame()
- built-in function
calculate_representative_frame() (RMSDAnalyzer method)
change_lig_to_residue()
- built-in function
characterize_complex()
- built-in function
cleanup_post_md()
- built-in function
close_reporters()
- built-in function, [1]

cloud_json_generation()
- built-in function
combine_subdict_values()
- built-in function, [1]
convert_ligand_to_smiles()
- built-in function
copy_file()
- built-in function
create_and_merge_images()
- built-in function
create_and_merge_images() (FigureMerger method)
create_df_from_binding_site()
- built-in function
create_directory_if_not_exists()
- built-in function

D

df_iteration_numbering()
- built-in function

E

extract_and_save_ligand_as_sdf()
- built-in function

extract_and_save_ligand_as_sdf() (Preprocessing method)

F

ff_selection()
- built-in function
FigureArranger (built-in class)
FigureHighlighter (built-in class)
FigureMerger (built-in class)
fill_missing_frames()
- built-in function

filter_and_parse_pdb()
- built-in function, [1]
filtering_values()
- built-in function
find_interacting_residues()
- built-in function

G

gather_interactions()
- built-in function
generate_barcode() (BarcodeGenerator method)
generate_bindingmode_pharmacophore()
- built-in function
generate_bindingmode_pharmacophore() (PharmacophoreGenerator method)
generate_forcefield()
- built-in function
generate_image() (LigandImageGenerator method)
generate_interaction_dict()
- built-in function
generate_interaction_dict() (FigureHighlighter method)
generate_ligand_image()
- built-in function

generate_md_pharmacophore_cloudcenters()
- built-in function
generate_md_pharmacophore_cloudcenters() (PharmacophoreGenerator method)
generate_pharmacophore_centers()
- built-in function
generate_pharmacophore_centers_all_points()
- built-in function
generate_pharmacophore_vectors()
- built-in function
generate_point_cloud_pml()
- built-in function
generate_point_cloud_pml() (PharmacophoreGenerator method)
generate_transition_graph() (MarkovChainAnalysis method)
generate_transitional_forcefield()
- built-in function

H

highlight_numbers()
- built-in function

highlight_numbers() (FigureHighlighter method)

I

increase_ring_indices()
- built-in function
increase_ring_indices() (Preprocessing method)

interacting_water_ids()
- built-in function
interacting_water_ids() (BarcodeGenerator method)
InteractionAnalyzer (built-in class)

L

LigandImageGenerator (built-in class)

M

MarkovChainAnalysis (built-in class)
MDanalysis_conversion()
- built-in function
mdtraj_conversion()
- built-in function

min_transition_calculation()
- built-in function
move_hydrogens_to_end()
- built-in function

O

organize_files()
- built-in function

P

perform_clustering_and_writing()
- built-in function
PharmacophoreGenerator (built-in class)
plot_bacodes_grouped()
- built-in function
plot_barcodes()
- built-in function
plot_barcodes_grouped() (BarcodePlotter method)
plot_waterbridge_piechart()
- built-in function
plot_waterbridge_piechart() (BarcodePlotter method)
post_md_file_movement()
- built-in function

Preprocessing (built-in class)
process_frame_special()
- built-in function
process_frame_wrapper()
- built-in function
process_pdb()
- built-in function
process_pdb() (Preprocessing method)
process_pdb_file()
- built-in function
process_pdb_file() (Preprocessing method)
process_trajectory()
- built-in function

R

read_pdb_as_dataframe()
- built-in function, [1]
remove_duplicate_values()
- built-in function, [1]
renumber_atoms_in_residues()
- built-in function
renumber_atoms_in_residues() (Preprocessing method)
renumber_protein_residues() (Preprocessing method)
replace_atom_type()
- built-in function
replace_atom_type() (Preprocessing method)
retrieve_plip_interactions()
- built-in function

retrieve_plip_interactions_peptide()
- built-in function
RMSD_dist_frames()
- built-in function
rmsd_dist_frames() (RMSDAnalyzer method)
rmsd_for_atomgroups()
- built-in function
rmsd_for_atomgroups() (RMSDAnalyzer method)
RMSDAnalyzer (built-in class)
run_visualization()
- built-in function, [1]

S

save_frame() (TrajectorySaver method)
save_interacting_waters_trajectory()
- built-in function
save_interacting_waters_trajectory() (TrajectorySaver method)
split_interaction_data()
- built-in function

split_interaction_data() (FigureHighlighter method)
stable_waters_pipeline()
- built-in function
stable_waters_pipeline() (StableWaters method)
StableWaters (built-in class)

T

to_dict() (PharmacophoreGenerator method)
trace_waters()
- built-in function

TrajectorySaver (built-in class)

U

unique_data_generation()
- built-in function
update_dict()
- built-in function, [1]

update_values()
- built-in function, [1]

V

visualization()
- built-in function

W

water_forcefield_selection()
- built-in function
water_model_selection()
- built-in function

waterids_barcode_generator()
- built-in function
write_pdb_clusters_and_representatives()
- built-in function