NAME
HackaMol::X::Vina - HackaMol extension for running Autodock Vina
VERSION
version 0.00_4
SYNOPSIS
use Modern::Perl;
use HackaMol;
use HackaMol::X::Vina;
use Math::Vector::Real;
my $receptor = "receptor.pdbqt";
my $ligand = "lig.pdbqt",
my $rmol = HackaMol -> new( hush_read=>1 ) -> read_file_mol( $receptor );
my $lmol = HackaMol -> new( hush_read=>1 ) -> read_file_mol( $ligand );
my $fh = $lmol->print_pdb("lig_out.pdb");
my @centers = map {$_ -> xyz}
grep {$_ -> name eq "OH" }
grep {$_ -> resname eq "TYR"} $rmol -> all_atoms;
foreach my $center ( @centers ){
my $vina = HackaMol::X::Vina -> new(
receptor => $receptor,
ligand => $ligand,
center => $center,
size => V( 20, 20, 20 ),
cpu => 4,
exhaustiveness => 12,
exe => '~/bin/vina',
scratch => 'tmp',
);
my $mol = $vina->dock_mol(3); # fill mol with 3 binding configurations
printf ("Score: %6.1f\n", $mol->get_score($_) ) foreach (0 .. $mol->tmax);
$mol->print_pdb_ts([0 .. $mol->tmax], $fh);
}
$_->segid("hgca") foreach $rmol->all_atoms; #for vmd rendering cartoons.. etc
$rmol->print_pdb("receptor.pdb");DESCRIPTION
HackaMol::X::Vina provides an interface to AutoDock Vina. This class does not include the AutoDock Vina program, which is <released under a very permissive Apache license|http://vina.scripps.edu/manual.html#license>, with few restrictions on commercial or non-commercial use, or on the derivative works, such is this. Follow these <instructions | http://vina.scripps.edu/manual.html#installation> to acquire the program. Most importantly, if you use this interface effectively, please be sure to cite AutoDock Vina in your work:
O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461
Since HackaMol has no pdbqt writing capabilities (yet, HackaMol can read pdbqt files), the user is required to provide those files. This is still a work in progress and the API may still change. Documentation will improve as API gets more stable... comments welcome!
EXTENDS
CONSUMES
AUTHOR
Demian Riccardi <demianriccardi@gmail.com>
COPYRIGHT AND LICENSE
This software is copyright (c) 2014 by Demian Riccardi.
This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.