===============================================================================
                                4. Rank Ligands
===============================================================================

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

PL-PatchSurfer2 provides two types of scoring function; LCS and BW.
LCS is an abbreviation of Lowest Conformer Score. It scores and ranks ligand
by finding lowest scoring conformation of each ligand.
BS is a Boltzmann-type scoring function. It uses all generated conformation of
ligand and scores a ligand by taking Boltzmann average.
Details of the scoring functions are described in reference.

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
      	    [lcs.in, bs.in]

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

receptor_file: pocket SSIC file
scoring_type: scoring function to rank ligands
	      lcs - lowest conformer score
	      bs - Boltzmann averaging type score
ligand_dir: ligand directory names that contain multiple conformations
output_file: name of output file name

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

Type in command window as below:
$python ../../scripts/rank_ligands.py bs.in (or lcs.in)

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

After finishing running scripts, the output file with the name given in input
file ranks the ligands.

In LCS type scoring output file, first column shows ligand name, second column
shows lowest scoring conformation index, and the last column shows LCS score.

BS type scoring output file has two columns showing molecule name and score.

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

