\brief Hamiltonian Monte Carlo for Integrative Modeling

This module provides functionality for using Dynamic/Adaptive Hamiltonian Monte Carlo (HMC) to sample IMP Models. This interface is experimental and can change at any time.

Installing Dependencies

The package currently has several dependencies in the Julia language. Follow the following steps to install IMP.hmc's dependencies:

1. Install Julia

2. Install the Python/Julia interface with

$ pip install julia
$ python -c 'import julia; julia.install()'

3. Install the HMCUtilities.jl package from the command line with

$ julia -e 'using Pkg; Pkg.add(PackageSpec(url="https://github.com/salilab/HMCUtilities.jl", rev="v0.2.2"))'

Then install this module using the standard approach.

For some configurations, you may need to use python-jl instead of python. The usage is identical.

Examples

See examples/notebooks for example usage.

Info

Author(s): Seth Axen

Maintainer: sethaxen

License: LGPL This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Publications:

• None