burstH2MM documentation

burstH2MM is designed to make analyzing single molecule burst experiments with H²MM easy. burstH2MM is built to work with FRETBursts, on which it depends for burst search and selection. burstH2MM serves to organize and process the results of H²MM optimizations and access the results of Viterbi analysis, which assigns each photon a state, and further processing segments the data into dwells.

Installation

To install burstH2MM simply type

pip install burstH2MM

into your terminal window. Python 3.8 or greater is required.

Please Cite

H²MM was originally introduced by Pirchi and Tsukanov et. al. 2016 and this implementation is built on the extension introduced in Harris et. al. 2022. If you use this library in a publication, please make sure to cite both these papers.

Contents

Contents:

• Tutorial
  • H²MM analysis
  • Uncertainty Estimation
  • Boostrap Uncertainty
• Divisor Approach
• How To Guides
  • Controlling Plotting Functions
  • Accessing the Results of an Optimization
  • Quantifying Accuracy/Precision of Model Parameter Values
  • Using \(\mu\)sALEX
  • Access Divisors and Models
  • Customization and Control
  • Caclulating Nanotimes with Confidence Threshold
  • Simulations
• Discussion
  • What is H²MM?
  • A Brief History of H²MM
  • Data organization
  • Divisors
• Documentation
  • BurstSort
  • BurstData
  • H2MM_list
  • H2MM_result
  • calc_dwell_nanomean()
  • calc_nanohist()
  • find_ideal()
  • make_divisors()
  • trans_stats()
  • Plotting
  • BIC_plot()
  • BICp_plot()
  • ICL_plot()
  • axline_E()
  • axline_S()
  • axline_divs()
  • axline_irf_thresh()
  • axline_nano_mean()
  • burst_ES_scatter()
  • covar_E_ll_scatter()
  • covar_S_ll_scatter()
  • covar_param_ll_scatter()
  • covar_trans_ll_scatter()
  • dwell_ES_scatter()
  • dwell_E_hist()
  • dwell_E_tau_scatter()
  • dwell_S_hist()
  • dwell_dur_hist()
  • dwell_param_hist()
  • dwell_param_transition()
  • dwell_param_transition_kde_plot()
  • dwell_params_scatter()
  • dwell_tau_hist()
  • dwell_trans_dur_hist()
  • ll_E_scatter()
  • ll_S_scatter()
  • ll_param_scatter()
  • ll_trans_scatter()
  • path_BIC_plot()
  • plot_burst_index()
  • plot_burst_path()
  • plot_burstjoin()
  • raw_nanotime_hist()
  • scatter_ES()
  • state_nanotime_hist()
  • trans_arrow_ES()
  • Selections
  • begin_dwell()
  • burst_begin_dwell()
  • burst_dwell()
  • burst_end_dwell()
  • dwell_size()
  • dwell_trans()
  • dwell_trans_from()
  • edge_dwell()
  • end_dwell()
  • mid_dwell()
  • not_mid_dwell()
  • Uncertainties
  • Bootstrap_Error
  • E_space()
  • Loglik_Error
  • ModelSet
  • S_space()
  • covar_E()
  • covar_S()
  • covar_trans()
  • err_E_search()
  • err_S_search()
  • err_param_search()
  • err_trans_search()
  • trans_space_ll()
  • Simulations
  • Sim_Result
  • simulate()
• Examples of Full Data Analysis
  • Hairpin 3 in 300 mM NaCl, nsALEX

Indices and tables

• Index

• Module Index

• Search Page

Thank you for using H²MM