safep

• safep package
  • Submodules
  • safep.AFEP_parse module
    • AFEPArgumentParser
      • AFEPArgumentParser.path
      • AFEPArgumentParser.fepoutre
      • AFEPArgumentParser.replicare
      • AFEPArgumentParser.temperature
      • AFEPArgumentParser.detect_equilibrium
      • AFEPArgumentParser.fittingMethod
      • AFEPArgumentParser.max_size
      • AFEPArgumentParser.make_figures
    • AFEPArguments
      • AFEPArguments.RT_kcal_per_mol
      • AFEPArguments.dataroot
      • AFEPArguments.detect_equilibrium
      • AFEPArguments.filename_pattern
      • AFEPArguments.from_AFEPArgumentParser()
      • AFEPArguments.make_figures
      • AFEPArguments.replica_pattern
      • AFEPArguments.replicas
      • AFEPArguments.temperature
    • add_summary_stats()
    • add_to_general_figure()
    • do_agg_data()
    • do_general_figures_plot()
    • do_per_lambda_convergence_shared_axes()
    • do_shared_convergence_plot()
    • get_summary_statistics()
    • initialize_general_figure()
    • main()
    • make_figures()
  • safep.TI module
    • harmonicWall_U()
    • harmonicWall_dUdL()
    • make_harmonicWall()
    • make_harmonicWall_from_Colvars()
    • plot_TI()
    • process_TI()
  • safep.estimators module
    • do_estimation()
    • get_BAR()
    • get_dG_from_data()
    • get_exponential()
  • safep.fileIO module
    • guess_lambda()
    • parse_Colvars_log()
    • read_FEPOUT()
    • read_Files()
    • read_UNK()
    • save_UNK()
  • safep.helpers module
    • cum_Fn()
    • get_Rsq()
    • moving_average()
    • pdf_Fn()
  • safep.plotting module
    • add_hyst_textbox()
    • convergence_plot()
    • do_conv_plot()
    • fb_discrepancy_hist()
    • fb_discrepancy_plot()
    • plot_general()
    • plot_general_legacy()
    • plot_hysteresis()
    • plot_samples()
  • safep.processing module
    • alt_convergence()
    • batch_process()
    • bootstrap_estimate()
    • decorrelate_u_nk()
    • detect_equilibrium_u_nk()
    • do_convergence()
    • do_per_lambda_convergence()
    • get_PDF()
    • get_empirical_CI()
    • get_limits()
    • get_moving_ave_slope()
    • get_n_samples()
    • read_and_process()
    • subsample()
    • u_nk_from_DF()
  • Module contents