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This file gives an overview of the data and scripts available for the self-docking test of the rDock program.  The distribution consists of
two top level directories.  The Scripts directory contains scripts which can be used to automatically run the test.  The astex_diverse_smile
directory contains sub-directories of data files.  Each sub-directory contains data files for the receptor, crystallographic ligand pose and
SMILES generated ligand conformation, as well as rDock input files.

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The astex_diverse_smiles folder contains 85 directories, one each for
the proteins that make up the test set.

Each directory contains three data files which are as follows:

      - Receptor (.mol2 file)
      - Reference ligand (_c.sd file)
      - Ligand to be docked (_l.sd file).


The ligand to be docked has been generated from a SMILES representation by using accelrys Discovery studio and Open Babel.  

The script runit (see below) generates a receptor cavity file (.as) for each receptor.  The program using the parameter file (.prm) to run the
docking.

During the calculations, the following files are generated:

_rmsd.sd
        The output file generated by rDrms command. It has the RMS Difference between each conformation predicted by rDock and the crystallographic reference conformation contained in the _c.sd file, and the respective scores assigned to that conformation.

_sorted.sd
        The same as above but with the conformations sorted according to the overall score (the lowest score is the best). The overall score corresponds to the validity of the prediction.

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The Scripts folder contains three scripts:

1. The script runit

This script uses the rDock input files to generate a description of the cavity and perform the docking.

From a directory (such as astex_diverse_smile) its usage is:

 > foreach file ( ???? )
foreach? source runit > output.txt
foreach? end

The terminal output is piped into an output file for subsequent processing.

2. A perl script for processing the output file -- rmsd_lowest.pl

Usage:

 > chmod a+x rmsd_lowest.pl
 > Perl rmsd_lowest.pl

This generates a file named lowest_rmsd.txt output file which contains a list of the PDB IDs along with the pose number, the scores and the corresponding lowest RMSD value for the particular receptor-ligand docked complex. This helps in assessing the 'Docking accuracy' of the rdock program.

3. A perl script for processing the output file -- topscored.pl

Usage:
 > chmod a+x topscored.pl
 > Perl topscored.pl

This generates the best_scored.txt output file which contains list of the PDB IDs along with the pose number, the best overall score and the RMSD value for the particular receptor-ligand docked complex.  This helps in assessing the 'Scoring efficiency' of the rDock program.


