SSTMap Solvation Structure and Thermodynamic Mapping

Installing SSTMap

Written by Kamran Haider 06 Jun 2017

The main requirement for installation of SSTMap is the anaconda python distribution. If you are not familiar with Anaconda, please have a look at continuum.io/why-anaconda. SSTMap is implemented in python 2.7, so if you do not have the anaconda installation, downlaod the anaconda for python 2.7, as shown below. Alternatively, if you have a an anaconda installation for python 3.6, you can create a python 2.7 enviornment to run sstmap.

For instructions on how to download and install Anaconda, please go to Anaconda Download page. The installation is very easy and can be done with the following two steps.

For Linux-64

wget https://repo.continuum.io/archive/Anaconda2-4.3.1-Linux-x86_64.sh
bash Anaconda2-4.3.1-Linux-x86_64.sh

For MacOSX

curl -O https://repo.continuum.io/archive/Anaconda2-4.3.1-MacOSX-x86_64.sh
bash Anaconda2-4.3.1-MacOSX-x86_64.sh

If you already have an anaconda installation for python 3.6, you can install and run SSTMap in a seprate python 2.7 envioronment. The enviornment is created as follows:

conda create -n py27 python=2.7
source activate py27

Conda Installation

The anaconda python distribution comes with conda package manager, which can then be used to install SSTMap with the following commands.

conda install sstmap -c omnia -c solvationtools

GitHub Source Code

You can install the latest development version from the GitHub repository by executing

pip install git+git://github.com/kurtzmanlab/sstmap.git@v1.0#egg=sstmap

You can also download the release package manually from GitHub, unzip it, navigate into the directory, and execute the command:

https://github.com/KurtzmanLab/SSTMap/archive/v1.0.tar.gz or https://github.com/KurtzmanLab/SSTMap/archive/v1.0.zip
tar -xvf v1.0.tar.gz or unzip v1.0.zip
cd SSTMap-1.0
python setup.py install

Or you can clone the GitHub repository, navigate into the directory, and execute the command:

git clone git@github.com:KurtzmanLab/SSTMap.git
cd SSTMap

For the release version:

git checkout tags/v1.0
python setup.py install

For the developmental version:

python setup.py install

When building from the source code or using the release package, make sure that you manually install the dependencies: mdtraj and parmed. You can do this by:

conda config --add channels omnia
conda install mdtraj parmed

Or using pip:

pip install ParmEd 
pip install mdtraj

Related Posts