Download and Installation¶
Quick Installation using
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)
- 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 python3command to install Python3.
- Install gmx_clusterByFeatrues by
sudo pip3 install gmx-clusterByFeaturescommand.
- Python3 is available through Homebrew package manager. After installing Homebrew, run
brew install python3command to install Python3.
- Install gmx_clusterByFeatrues by
pip3 install gmx-clusterByFeaturescommand.
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.
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
update of dependent packages like numpy, scipy, matplotlib etc.
Installation from source-code¶
- It depends on following two packages:
- GROMACS : 2016 and above version
- Python : 3.4 and above version
A standard installation of GROMACS is sufficient. GROMACS library
libgromacs.so) and header files are required for compilation.
If GROMACS is not installed at standard location, define
GMX_PATH environment variable as follows:
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
sudo pip3 install numpy scipy sklearn matplotlib
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
/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
needs to be added manually.