Installation

Currently, only the development version of analyze_foldamers is available.

Download analyze_foldamers from GitHub using:

git clone https://github.com/shirtsgroup/analyze_foldamers.git

In the base directory of analyze_foldamers, install using:

python setup.py install

Note

A working version of VMD is required to use the molecular snapshot tools in analyze_foldamers

Conda environment

analyze_foldamers is currently tested and maintained on Python 3.6, 3.7, and 3.8.

With CGModel support

To use CGModel objects created with cg_openmm, additional dependencies need to be specified when creating an anaconda environment for analyze_foldamers:

conda create -n cg_openmm_env python=3.X mdtraj mpi4py numpy openmm openmmtools physical_validation
pymbar scikit-learn scikit-learn-extra scipy

In addition, an installed version of cg_openmm is required to use CGModel objects.

Download cg_openmm from GitHub using:

git clone https://github.com/shirtsgroup/cg_openmm.git

In the base directory of cg_openmm, install using:

python setup.py install

Without CGModel support

Note

We are currently working on eliminating the dependency of analyze_foldamers on cg_openmm. This option is not yet supported.