Welcome to the foldamers documentation!

This documentation is generated automatically using Sphinx, which reads all docstring-formatted comments from Python functions in the ‘foldamers’ repository. (See foldamers/doc for Sphinx source files.)

• Installation notes
  • Dependencies for the foldamers package
  • Recommended installation steps
• Coarse grained model utilities
  • Using the ‘CGModel()’ class to build coarse grained heteropolymers
  • ‘basic_cgmodel’: a simple function to build coarse grained homopolymers
• Thermodynamic analysis tools for coarse grained modeling
  • Using MBAR to compute expectation values for structural & thermodynamic properties
  • Evaluating thermodynamic properties with ‘pymbar’
  • Tools to evaluate thermodynamic properties with ‘pymbar’
  • Calculating the heat capacity with pymbar
• Ensemble building tools
  • Using MSMBuilder to generate conformational ensembles
  • Native structure-based ensemble generation tools
  • Energy-based ensemble generation tools
  • Writing and reading ensemble data from the ‘foldamers’ database
• Utilities for the ‘foldamers’ package
  • Random structure generation in ‘foldamers’
  • Reading and writing to output within the ‘foldamers’ package
• Parameter analysis tools for coarse grained modeling