Welcome to basicrta’s documentation!

basicrtakit is a package to analyze binding kinetics in molecular dynamics simulations. The analysis uses an exponential mixture model and Bayesian nonparametric inference to determine time-scales of the underlying binding processes. The output is processed to give frames belonging to a given process with an associated time-scale, which can be further analyzed.

This package was written to perform the analyses in [Sexton_2025].

Contents:

• Getting Started
• Tutorial
  • Contact Analysis
  • Gibbs Sampler
  • Clustering
  • Rate/Tau Estimates
  • Kinetic Mapping
  • Supplemental Scripts
• Combining Contact Timeseries from Multiple Repeats
  • Use Cases
  • Usage
  • Features
  • Limitations
  • Error Handling
  • Output Format
• API Documentation
  • gibbs
  • contacts
  • cluster
  • kinetics
  • combine
  • util
  • cli

Indices and tables

• Index

• Module Index

• Search Page

[Sexton_2025]

Sexton, R.; Fazel, M.; Schweiger, M.; Pressé, S.; Beckstein, O. Bayesian Nonparametric Analysis of Residence Times for Protein-Lipid Interactions in Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 2025 21 (8), 4203-4220 DOI: 10.1021/acs.jctc.4c01522