Index

A

align_homologues() (in module util)

all_post_hist() (in module util)

B

b_color_structure() (cluster.ProcessProtein method)

C

check_results() (in module util) cli module cluster module cluster() (gibbs.Gibbs method) collect_n_plot() (in module util)

combine module CombineContacts (class in combine) (class in contacts) confidence_interval() (in module util) contacts module create_traj() (kinetics.MapKinetics method)

E

estimate_tau() (gibbs.Gibbs method)

expand_times() (in module util) extract_data() (in module util)

G

get_bars() (in module util) get_bins() (in module util) get_code() (in module util) get_color() (in module util) get_dec() (in module util) get_delta_tau() (in module util) get_diffcode() (in module util) get_fa_sel() (in module util) get_fa_sel_match() (in module util) get_indices() (in module util) get_parser() (in module cluster) (in module combine) (in module contacts) (in module gibbs) (in module kinetics)

get_remaining_residue_inds() (in module util) get_s() (in module util) get_start_stop_frames() (in module util) get_taus() (cluster.ProcessProtein method) get_write_frames() (in module util) gibbs module Gibbs (class in gibbs)

K

kinetics module

L

load() (gibbs.Gibbs static method)

M

main() (in module cli) (in module cluster) (in module combine) (in module contacts) (in module gibbs) (in module kinetics) make_residue_plots() (in module util) make_surv() (in module util) MapContacts (class in contacts)

MapKinetics (class in kinetics) mixture_and_plot() (in module util) module cli cluster combine contacts gibbs kinetics util

P

ParallelGibbs (class in gibbs) plot_delta_tau() (in module util) plot_gibbs() (gibbs.Gibbs method) plot_hist() (gibbs.Gibbs method) plot_hists() (in module util) plot_post() (in module util) plot_protein() (cluster.ProcessProtein method) (in module util)

plot_r_vs_w() (in module util) plot_results() (in module util) plot_surv() (gibbs.Gibbs method) plot_tau_hist() (gibbs.Gibbs method) plot_trace() (in module util) process_gibbs() (gibbs.Gibbs method) ProcessContacts (class in contacts) ProcessProtein (class in cluster)

R

reprocess() (cluster.ProcessProtein method) result_plot() (gibbs.Gibbs method) run() (combine.CombineContacts method) (contacts.CombineContacts method) (contacts.MapContacts method) (contacts.ProcessContacts method) (gibbs.Gibbs method) (gibbs.ParallelGibbs method)

run_residue() (in module gibbs)

S

save() (gibbs.Gibbs method) siground() (in module util)

simulate_hn() (in module util) slice_trajectory() (in module util)

T

tm() (in module util)

U

unique_rates() (in module util)

util module

W

weighted_densities() (kinetics.MapKinetics method)

write_data() (cluster.ProcessProtein method) write_trajs() (in module util)