Index

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

A

analyze_protein_and_water_interaction()
- built-in function

arranged_figure_generation()
- built-in function

B

C

calculate_representative_frame()
- built-in function
change_lig_to_residue()
- built-in function
characterize_complex()
- built-in function
cleanup()
- built-in function
cloud_json_generation()
- built-in function
combine_subdict_values()
- built-in function

convert_ligand_to_smiles()
- built-in function
copy_file()
- built-in function
create_and_merge_images()
- built-in function
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

F

ff_selection()
- built-in function
fill_missing_frames()
- built-in function
filter_and_parse_pdb()
- built-in function

filtering_values()
- built-in function
find_interacting_residues()
- built-in function

G

gather_interactions()
- built-in function
generate_bindingmode_pharmacophore()
- built-in function
generate_forcefield()
- built-in function
generate_interaction_dict()
- built-in function
generate_ligand_image()
- built-in function
generate_md_pharmacophore_cloudcenters()
- built-in function

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_transitional_forcefield()
- built-in function

H

highlight_numbers()
- built-in function

I

increase_ring_indices()
- built-in function

interacting_water_ids()
- built-in function

M

MDanalysis_conversion()
- built-in function
mdtraj_conversion()
- built-in function
min_transition_calculation()
- built-in function

module
- openmmdl
move_hydrogens_to_end()
- built-in function

O

openmmdl
- module

organize_files()
- built-in function

P

perform_clustering_and_writing()
- built-in function
plot_bacodes_grouped()
- built-in function
plot_barcodes()
- built-in function
plot_waterbridge_piechart()
- built-in function
post_md_file_movement()
- built-in function

process_frame_special()
- built-in function
process_frame_wrapper()
- built-in function
process_pdb()
- built-in function
process_pdb_file()
- built-in function
process_trajectory()
- built-in function

R

read_pdb_as_dataframe()
- built-in function
remove_duplicate_values()
- built-in function
renumber_atoms_in_residues()
- built-in function
replace_atom_type()
- built-in function
retrieve_plip_interactions()
- built-in function

retrieve_plip_interactions_peptide()
- built-in function
RMSD_dist_frames()
- built-in function
rmsd_for_atomgroups()
- built-in function
run_visualization()
- built-in function

S

save_interacting_waters_trajectory()
- built-in function
split_interaction_data()
- built-in function

stable_waters_pipeline()
- built-in function

T

trace_waters()
- built-in function

U

unique_data_generation()
- built-in function
update_dict()
- built-in function

update_values()
- built-in function

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