Installation notes

The foldamers package will eventually be available for installation via Anaconda. This will make resolution of software conflicts much easier. However, at present, because the package has not been made public, Anaconda installation is not yet possible, and software conflicts must be resolved by the individual.

Here we provide installation instructions which have been tested on multiple platforms.

Dependencies for the foldamers package

Due to conflicts among dependencies for the foldamers package with other Python versions, we recommend using Python version 3.6.

The following is a list of software dependencies for the foldamers package, with recommended version numbers in parentheses:

1. cg_openmm (version 0.0)

   Dependencies for the ‘cg_openmm’ software package: 2) OpenMM (version 7.3.1) 3) Yank (version 0.24.1)

4. pymbar (version 3.0.3)
5. MDTraj (version 1.9.3)
6. MSMBuilder (version 3.8)
7. scikit-learn (version 0.18.1)
8. sklearn-genetic (version 0.2)
9. kHelios

Recommended installation steps

We recommend installation of Anaconda prior to installation of the ‘foldamers’ package, as this makes resolution of conflicts between dependencies much easier.

We direct users that have not installed Anaconda to the Download page in order to select the appropriate version for your platform (Windows, Linux, Mac). (It shouldn’t matter which version of Anaconda is installed.)

The following installation steps are recommended for users that have already installed Anaconda on their system:

1. Install ‘sklearn-genetic’ (used for genetic algorithm optimization of model parameters):

   pip install sklearn-genetic
   

2. Create an Anaconda environment for Python version 3.6 (the most stable Python version for ‘foldamers’):

   conda create -n foldamers python=3.6 mdtraj=1.9.3 openmm=7.3.1 pymbar=3.0.3 msmbuilder=3.8 scikit-learn=0.18.1 yank=0.21.2
   

3. Activate this new environment:

   conda activate foldamers
   

4. Clone and install a fresh copy of ‘cg_openmm’:

   git clone https://github.com/shirtsgroup/cg_openmm.git
   cd cg_openmm
   python setup.py install
   

5. Clone and install a fresh copy of ‘foldamers’ to your system:

   git clone https://github.com/shirtsgroup/foldamers.git
   cd foldamers
   python setup.py install