Index

A

add_hyst_textbox() (in module safep.plotting) add_summary_stats() (in module safep.AFEP_parse) add_to_general_figure() (in module safep.AFEP_parse)

AFEPArgumentParser (class in safep.AFEP_parse) AFEPArguments (class in safep.AFEP_parse) alt_convergence() (in module safep.processing)

B

batch_process() (in module safep.processing)

bootstrap_estimate() (in module safep.processing)

C

convergence_plot() (in module safep.plotting)

cum_Fn() (in module safep.helpers)

D

dataroot (safep.AFEP_parse.AFEPArguments attribute) decorrelate_u_nk() (in module safep.processing) detect_equilibrium (safep.AFEP_parse.AFEPArgumentParser attribute) (safep.AFEP_parse.AFEPArguments attribute) detect_equilibrium_u_nk() (in module safep.processing) do_agg_data() (in module safep.AFEP_parse)

do_conv_plot() (in module safep.plotting) do_convergence() (in module safep.processing) do_estimation() (in module safep.estimators) do_general_figures_plot() (in module safep.AFEP_parse) do_per_lambda_convergence() (in module safep.processing) do_per_lambda_convergence_shared_axes() (in module safep.AFEP_parse) do_shared_convergence_plot() (in module safep.AFEP_parse)

F

fb_discrepancy_hist() (in module safep.plotting) fb_discrepancy_plot() (in module safep.plotting) fepoutre (safep.AFEP_parse.AFEPArgumentParser attribute)

filename_pattern (safep.AFEP_parse.AFEPArguments attribute) fittingMethod (safep.AFEP_parse.AFEPArgumentParser attribute) from_AFEPArgumentParser() (safep.AFEP_parse.AFEPArguments class method)

G

get_BAR() (in module safep.estimators) get_dG_from_data() (in module safep.estimators) get_empirical_CI() (in module safep.processing) get_exponential() (in module safep.estimators) get_limits() (in module safep.processing)

get_moving_ave_slope() (in module safep.processing) get_n_samples() (in module safep.processing) get_PDF() (in module safep.processing) get_Rsq() (in module safep.helpers) get_summary_statistics() (in module safep.AFEP_parse) guess_lambda() (in module safep.fileIO)

H

harmonicWall_dUdL() (in module safep.TI)

harmonicWall_U() (in module safep.TI)

I

initialize_general_figure() (in module safep.AFEP_parse)

M

main() (in module safep.AFEP_parse) make_figures (safep.AFEP_parse.AFEPArgumentParser attribute) (safep.AFEP_parse.AFEPArguments attribute) make_figures() (in module safep.AFEP_parse) make_harmonicWall() (in module safep.TI) make_harmonicWall_from_Colvars() (in module safep.TI) max_size (safep.AFEP_parse.AFEPArgumentParser attribute) module safep safep.AFEP_parse safep.estimators safep.fileIO safep.helpers safep.plotting safep.processing safep.TI

moving_average() (in module safep.helpers)

P

parse_Colvars_log() (in module safep.fileIO) path (safep.AFEP_parse.AFEPArgumentParser attribute) pdf_Fn() (in module safep.helpers) plot_general() (in module safep.plotting)

plot_general_legacy() (in module safep.plotting) plot_hysteresis() (in module safep.plotting) plot_samples() (in module safep.plotting) plot_TI() (in module safep.TI) process_TI() (in module safep.TI)

R

read_and_process() (in module safep.processing) read_FEPOUT() (in module safep.fileIO) read_Files() (in module safep.fileIO) read_UNK() (in module safep.fileIO)

replica_pattern (safep.AFEP_parse.AFEPArguments attribute) replicare (safep.AFEP_parse.AFEPArgumentParser attribute) replicas (safep.AFEP_parse.AFEPArguments attribute) RT_kcal_per_mol (safep.AFEP_parse.AFEPArguments attribute)

S

safep module safep.AFEP_parse module safep.estimators module safep.fileIO module safep.helpers module

safep.plotting module safep.processing module safep.TI module save_UNK() (in module safep.fileIO) subsample() (in module safep.processing)

T

temperature (safep.AFEP_parse.AFEPArgumentParser attribute) (safep.AFEP_parse.AFEPArguments attribute)

U

u_nk_from_DF() (in module safep.processing)