foldamers
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  • Installation notes
  • Coarse grained model utilities
  • Thermodynamic analysis tools for coarse grained modeling
  • Ensemble building tools
  • Utilities for the ‘foldamers’ package
  • Parameter analysis tools for coarse grained modeling
foldamers
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  • Welcome to the foldamers documentation!
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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
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© Copyright 2019, Garrett A. Meek, Michael R. Shirts Revision 905232a2.

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