Installation

Installing via conda

The more straightforward way to install peleffy along with the required dependencies is through the conda package manager.

First, you need to install the miniconda distribution, which is the minimal installation of the Anaconda Python package.

To install the Python 3 version on linux (on bash systems):

$ wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
$ bash ./Miniconda3-latest-Linux-x86_64.sh -b -p $HOME/miniconda3

It can also be installed on osx with:

$ curl https://repo.anaconda.com/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O
$ bash ./Miniconda3-latest-MacOSX-x86_64.sh -b -p $HOME/miniconda3

Once installed, the bases environment of conda can be loaded with the following commands:

$ source ~/miniconda3/etc/profile.d/conda.sh
$ conda activate base

You can also create a custom conda environment to handle peleffy:

$ conda create --name peleffy_env

which can be activated and deactivated with the two commands from below:

$ conda activate peleffy_env
$ conda deactivate

To install de dependencies of peleffy, the following conda channels need to be added and updated:

$ conda config --add channels omnia --add channels conda-forge --add channels martimunicoy
$ conda update --all

Finally, you can install the latest stable build of peleffy

$ conda install peleffy

Installing via PyPI

peleffy can also be installed through PyPI with the following command:

$ pip install peleffy

However, with PyPI some of the required dependencies of peleffy are not installed and have to be installed manually such as:

  • Open Force Field Toolkit

  • RDKit

  • AmberTools

For this reason, the installation through conda is recommended.

External dependencies

Some of the functionalities of peleffy require external dependencies. They are normally included with the standard conda installation, as explained above. However, the Schrodinger toolkit must be installed manually. It is only required when combining Open Force Field parameters with OPLS2005 (as it uses the Schrodinger’s ffld_server). Nevertheless, in case that Schrodinger dependencies are missing, peleffy can still be employed to generate pure Open Force Field parameters.

The easiest way to get a valid Schrodinger installation is downloading Free Maestro. It can be installed in both platforms that are supported by peleffy: Linux and MacOS. Once installed, peleffy will need an environment variable to be set in order to known the Schrodinger’s installation path. So, please, check that the following environment variable is set before running peleffy if you plant to work with OPLS2005 parameters:

$ export SCHRODINGER=/path/to/Schrodinger/installation/

For example, in MacOS, a typical installation path is /opt/schrodinger/suites2020-2/. Therefore:

$ export SCHRODINGER=/opt/schrodinger/suites2020-2/

This variable must be set every time peleffy is employed to work with OPLS2005 parameters in a new console session. To avoid future concerns about this issue, you can set the environment variable automatically every time you initiate a bash session in your console. You can do so by modifying your .bashrc, .bash_profile or .zshrc (in case of a zsh shell) by adding the line above.