Download and Installation¶

Quick Installation using `pip`¶

It is recommended method to install gmx_clusterByFeatrues.

Not require to install GROMACS

Only available on Linux, MacOS-10.12 (Sierra), MacOS-10.13 (High Sierra) and MacOS-10.14 (Mojave)

On Linux¶

Python3 is available through package managers such as yum (Fedora, CentOs), YaST (OpenSuse) and apt-get (Ubuntu, Linux Mint). For example on ubuntu: run sudo apt-get install python3 command to install Python3.
Install gmx_clusterByFeatrues by sudo pip3 install gmx-clusterByFeatures command.

On MacOS¶

Python3 is available through Homebrew package manager. After installing Homebrew, run brew install python3 command to install Python3.
Install gmx_clusterByFeatrues by pip3 install gmx-clusterByFeatures command.

Note

Presently, installation with pip on MacOS is restricted to 10.12 (Sierra), 10.13 (High Sierra) and 10.14 (Mojave) versions. For other MacOS versions, install gmx_clusterByFeatrues from source as described further below.

Updating gmx_clusterByFeatrues¶

To update the gmx_clusterByFeatrues package use following command:

pip3 install --upgrade --no-deps gmx-clusterByFeatures

--upgrade flag is used to update the package and --no-deps prevents update of dependent packages like numpy, scipy, matplotlib etc.

Installation from source-code¶

Requirements¶

It depends on following two packages:

GROMACS : 2016 and above version
Python : 3.4 and above version

GROMACS¶

A standard installation of GROMACS is sufficient. GROMACS library (libgromacs.a or libgromacs.so) and header files are required for compilation.

If GROMACS is not installed at standard location, define GMX_PATH environment variable as follows:

export GMX_PATH=/path/to/installed/gromacs

Python3¶

To compile gmx_clusterByFeatures, Python3 development files should be installed previously.

On Debian like distribution (Debian, Ubuntu, Linux Mint etc.), which uses apt as package manager, python3-development files can be installed as follows:

sudo apt-get install python3 python3-dev

On OS such as fedora/centos/RHEL, which uses yum as package manager, python3- development files can be installed as follows:

sudo yum install python3 python3-devel

Four other Python packages numpy , scipy , scikit-learn , and matplotlib are required that can be installed as follows:

sudo pip3 install numpy scipy sklearn matplotlib

Downloading source-code¶

It can be downloaded using git as follows

git clone -b master https://github.com/rjdkmr/gmx_clusterByFeatures

It can be also downloaded as zip file.

Compilation and Installation using python¶

Clone the repository from github as directed above then follow these steps.

cd gmx_clusterByFeatures # or gmx_clusterByFeatures-master (zip file download)
export GMX_PATH=/path/to/installed/gromacs
sudo GMX_PATH=$GMX_PATH python3 setup.py install

Now, gmx_clusterByFeatures command will be accessible in terminal.

Compilation and Installation using cmake for C++ IDEs¶

This method can be used for development purpose using C++ IDE like QT creator and KDevelop etc.

To install and use gmx_clusterByFeatrues from source location:

cd gmx_clusterByFeatures # or gmx_clusterByFeatures-master (zip file download)
mkdir build
cd build
cmake -DGMX_PATH=/path/to/installed/gromacs -DINPLACE=ON ..
make
sudo make install  # Only needed for first time install

In this installation, only gmx_clusterByFeatures executable file is installed at default location (mostly /usr/local/bin) while whole package remains at the source location.

This method is extremely useful for development because make install is only required for first time to install executable file. During subsequent development, only command make need to be repeated. In IDEs make command is executed by build. In IDEs project build setting, cmake arguments -DGMX_PATH=/path/to/installed/gromacs -DINPLACE=ON needs to be added manually.