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#Scripts
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post-treatment-gold.prl
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This script converts the output of a GOLD docking into a dock4 file, so it can 
be read by UCSF Chimera.

Usage: post-treatment-gold.prl <dirname> <ligname>

where <dirname> corresponds to the 'directory' keyword in the GOLD input file 
and <ligname> corresponds to the 'ligand_data_file' keyword in the GOLD input 
file, but without extension.

Note: the resulting dock4 file contains the covalent binding atoms. 
They should be removed by user for reclustering with DockRMSD.

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post-treatment-ad.prl
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This script converts the output of a AutoDock4 docking into a dock4 file, so
it can be read by UCSF Chimera.

Usage: post-treatment-ad.prl <log> 

where log corresponds to a file containing the output written by AutoDock4.

Note: the resulting dock4 file contains the covalent binding atoms. 
They should be removed by user for reclustering with DockRMSD.

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recl_dock4.prl
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This script takes a docking output in dock4 format, calculates the DockRMSD 
for each pose with respect to a reference pose with the help of the executable
DockRMSD-dock4, reclusters all poses according to the algorithm used in 
Attracting Cavities, and writes a new dock4 file with these clusters.

Usage: recl_dock4.prl <ref.mol2> <res.dock4>

where <ref.mol2> corresponds to the reference pose of the ligand and <res.dock4>
contains the results of a docking of this ligand.

If you use this script in your work, please cite

E.W. Bell and Y. Zhang, 
DockRMSD: an open-source tool for atom  mapping and RMSD calculation of 
symmetric molecules through graph isomorphism. 
J. Cheminformatics, 11:40 (2019), doi: 10.1186/s13321-019-0362-7

M. Goullieux, V. Zoete, U.F. Roehrig,
Two-Step Covalent Docking with Attracting Cavities
