Installation

Download the binary release from the release page then extract it. In the extracted folder you will find an executable file named with pilah and an example folder which contain configuration and input files for the following usage guidelines.

You can execute PiLAH directly from the extraction folder as such:

./pilah --help

It is highly recommended to copy PiLAH to one of your executable path. You can check your available executable path by running the command echo $PATH. Some path that you can use are /home/$USER/.local/bin or usr/local/bin.

After copying PiLAH to your executable path, go to PiLAH’s example directory and run PiLAH again:

pilah --help

If it runs properly, the next step is to run PiLAH using one of the provided example. Still in the example directory run PiLAH with the following command:

pilah run config_pdb_hux.txt

Normally it will take between 5-15 seconds for PiLAH to complete the protein ligand extraction and protonation. After PiLAH finished the processing, PiLAH will generate four files. One for the isolated protein molecule, protein_1e66.pdb. Second one for the extracted ligand molecule, HUX.pdb. Third one for the ligand image in 2D representation, HUX.png. The last one for the log file which is named with the date and time when PiLAH was executed, such as log_20240815_172113.txt

Now PiLAH is ready to be used on your system.