Introduction

H2MM_C is a python package that implements the H²MM algorithm. This was initially designed for analyzing confocal based single-molecule FRET data to detect transitions between different states, characterizing the rate of transitions, and the FRET efficiencies. The data comes in the form of photon arrival times, and indices to indicate at which detector the photon arrived. While originally designed for confocal smFRET, in principle H²MM can be used to assess any other sort of data where data is composed of pairs of times and indices.

H²MM was originally developed by Pirchi and Tsukanov et. al. 2016 and this package was developed by Harris et. al. 2022 who also demonstrated additional statistical discriminators that clarified model selection. If you use H2MM_C, please cite both of these papers. For a more detailed description of the purpose and nature of H²MM see AboutH2MM.

Installation

For most systems, simply typing

pip install h2mm-c

into the console window will install H2MM_C. We supply wheels built with cibuildwheel for Python 3.7 to 3.10. Note that you are required to have numpy version 1.20.1 or greater to use these wheels. On Linux distributions, older versions of numpy have incompatibilities with the size of certain data-types.

H2MM_C

Contents:

• About H²MM
  • What is H²MM?
  • A Brief History of H²MM
• Tutorials
  • Function Based Tutorials
  • Object Oriented Tutorials
  • Simulations Tutorial
• How To
  • H2MM_C Secondary Control Features
  • Customizing Optimization Progress Display
• Documentation
  • Data Analysis Functions
  • Simulation Functions
  • Classes

Indices and tables

• Index

• Module Index

• Search Page