===============================================================================
                                3. Compare Seed
===============================================================================

This part shows how to prepare an input file for ligand pocket with
'compare_seed.py' in 'scripts' directory.

Three files are required (file names in this directory is shown between []):

Receptor SSIC file: receptor pocket SSIC file generated from first stage
	      	    [rec.ssic]
Ligand conformation directories: SSIC files for multiple conformations of
       		    		 ligands from second stage
				 [ZINC01484895, ZINC03833861]
Input file: contains input parameters
      	    [compare_seed.in]

===============================================================================
                    Description of parameters in input file
===============================================================================

PLPS_path: path of PL-PatchSurfer2 package
receptor_file: pocket SSIC file
n_conf: maximum number of conformations for each ligand
ligand_dir: ligand directory names that contain multiple conformations

===============================================================================
                                Runnung Scripts
===============================================================================

Type in command window as below:
$python ../../scripts/compare_seeds.py compare_seeds.in

===============================================================================
                                  Output file
===============================================================================

After finishing running scripts, DAT files are generated in the ligand
directories. The files are named by combining the receptor and ligand
conformation file names.

===============================================================================

