Firstly, locate where is the package. Generally, the package could be found in $PYTHONPATH/lib/python2.7/site-packages/dockingML/bin

Copy the files in the bin folder to your $HOME/bin/ directory. If $HOME/bin is not exisited, create one. Then add the following line in your $HOME/.bashrc

export PATH=$HOME/bin:$PATH

$ cd ~/applications
$ git clone https://github.com/zhenglz/dockingML
$ cd dockingML
$ pip install -e . 
$ export PATH=$HOME/applications/dockingML/bin:$PATH
# you could add the above line into your ~/.bashrc 

or add the following line in your ~/.bashrc file:

export PATH=$PYTHONPATH/lib/python2.7/site-packages/dockingML/bin:$PATH

The tools starting with gmx_ would be use to analyze trajectory files (xtc, multiple-frame pdb file), if reference pdb file provided. The tools could also be used to process gromacs output xvg files.

gmx_angle.py: reading xtc file to calculate angles/dihedrals of selected atoms if a gromacs index file is provided.

$ gmx_angle.py -h

gmx_index.py: reading pdb file to generate gromacs index file.

$ gmx_index.py -h

Plot gromacs output dataset files, or python generated dataset files. Plot types could be xy, xyz, histogram

$ gmx_plot.py -h</p>
$ gmx_plot.py xy -h</p>

Extract binding interation features from the protein ligand complex.

$ genfeatures.py -h