NAME
HackaMol::X::Vina - HackaMol extension for running Autodock Vina
VERSION
version 0.00_1
SYNOPSIS
use HackaMol;
use HackaMol::X::Vina;
use Math::Vector::Real;
my $receptor = "receptor.pdbqt";
my $rmol = HackaMol -> new( hush_read=>1 ) -> read_file_mol($receptor);
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.pdbt",
in_fn => "conf.txt",
out_fn => "ligand_out.pdbqt",
center => $center,
size => V( 20, 20, 20 ),
cpu => 4,
num_modes => 1,
exhaustiveness => 12,
exe => '~/bin/vina',
scratch => 'tmp',
);
$vina->map_input;
my @bes = $vina->map_output;
}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.
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.