Index

A

add_distance_restr() (in module SST2.tools)

add_pos_restr() (in module SST2.tools) align_traj() (in module SST2.analysis.trajectory)

C

compare_weight_RMSD() (in module SST2.analysis.data_plot) compute_all_energies() (SST2.rest2.REST2 method) compute_cluster_hdbscan() (in module SST2.analysis.data_plot) compute_cluster_kmean() (in module SST2.analysis.data_plot) compute_exchange_prob() (in module SST2.analysis.data_plot) compute_folding_fraction() (in module SST2.analysis.data_plot) compute_folding_fraction_RMSD() (in module SST2.analysis.data_plot) compute_ladder_num() (in module SST2.tools) compute_moving_average() (in module SST2.analysis.data_plot) compute_native_contact() (in module SST2.analysis.trajectory) compute_pca() (in module SST2.analysis.trajectory) compute_solute_solvent_system_energy() (SST2.rest2.REST2 method) compute_starting_weight() (SST2.sst2.SST2 method) (SST2.st.ST method)

compute_temperature_list() (in module SST2.tools) compute_Tm() (in module SST2.analysis.data_plot) compute_weight_RMSD() (in module SST2.analysis.data_plot) count_clust_transition() (in module SST2.analysis.data_plot) count_rmsd_transition() (in module SST2.analysis.data_plot) create_custom_bonded_force_rf() (in module SST2.tools) create_custom_nonbonded_force_rf() (in module SST2.tools) create_linear_peptide() (in module SST2.tools) create_rf_simulation() (SST2.rest2.REST2 method) create_sim_system() (in module SST2.tools) create_solute_solvent_simulation() (SST2.rest2.REST2 method) create_system_simulation() (in module SST2.tools) create_water_box() (in module SST2.tools)

D

describeNextReport() (SST2.rest2.Rest2Reporter method) (SST2.sst2.SST2Reporter method) (SST2.st.STReporter method)

F

filter_df() (in module SST2.analysis.data_plot)

find_nb_solute_system() (SST2.rest2.REST2 method) find_solute_nb_index() (SST2.rest2.REST2 method)

G

get_customPotEnergie() (SST2.rest2.REST2 method) get_forcefield() (in module SST2.tools)

get_forces() (in module SST2.tools) get_quant_min_max() (in module SST2.analysis.data_plot) get_specific_forces() (in module SST2.tools)

I

implicit_sim() (in module SST2.tools)

M

minimize() (in module SST2.tools) module SST2 SST2.analysis SST2.analysis.data_plot SST2.analysis.trajectory SST2.rest2 SST2.sst2 SST2.st SST2.tools

P

plot_distri_norm() (in module SST2.analysis.data_plot) plot_energie_swap_convergence() (in module SST2.analysis.data_plot) plot_energie_swap_convergence_diff() (in module SST2.analysis.data_plot) plot_energie_swap_distri_diff() (in module SST2.analysis.data_plot) plot_folding_fraction() (in module SST2.analysis.data_plot) plot_folding_fraction_convergence() (in module SST2.analysis.data_plot) plot_folding_fraction_RMSD() (in module SST2.analysis.data_plot)

plot_free_energy() (in module SST2.analysis.data_plot) plot_lineplot_avg() (in module SST2.analysis.data_plot) plot_rung_occupancy() (in module SST2.analysis.data_plot) plot_scatter() (in module SST2.analysis.data_plot) plot_weight_RMSD() (in module SST2.analysis.data_plot) prepare_pdb() (in module SST2.tools) prepare_traj() (in module SST2.analysis.trajectory) print_forces() (in module SST2.tools)

R

read_SST2_data() (in module SST2.analysis.data_plot) read_ST_data() (in module SST2.analysis.data_plot) read_traj() (in module SST2.analysis.trajectory) recompute_temp() (in module SST2.analysis.data_plot) report() (SST2.rest2.Rest2Reporter method) (SST2.sst2.SST2Reporter method) (SST2.st.STReporter method)

REST2 (class in SST2.rest2) Rest2Reporter (class in SST2.rest2) run_rest2() (in module SST2.rest2) run_sim_check_time() (in module SST2.tools) run_sst2() (in module SST2.sst2) run_st() (in module SST2.st)

S

scale_nonbonded_torsion() (SST2.rest2.REST2 method) separate_cmap_pot() (SST2.rest2.REST2 method) separate_torsion_pot() (SST2.rest2.REST2 method) setup_simulation() (in module SST2.tools) (SST2.rest2.REST2 method) show_log() (in module SST2) simulate() (in module SST2.tools) SST2 module SST2 (class in SST2.sst2) SST2.analysis module SST2.analysis.data_plot module

SST2.analysis.trajectory module SST2.rest2 module SST2.sst2 module SST2.st module SST2.tools module SST2Reporter (class in SST2.sst2) ST (class in SST2.st) step() (SST2.sst2.SST2 method) (SST2.st.ST method) STReporter (class in SST2.st)

U

update_bonded_reaction_field() (SST2.rest2.REST2 method) update_cmap() (SST2.rest2.REST2 method) update_nonbonded() (SST2.rest2.REST2 method)

update_nonbonded_reaction_field() (SST2.rest2.REST2 method) update_nonbonded_solute() (SST2.rest2.REST2 method) update_torsions() (SST2.rest2.REST2 method)

W

weights (SST2.sst2.SST2 property) (SST2.st.ST property)