NAME

HackaMol::X::Vina - HackaMol extension for running Autodock Vina

VERSION

version 0.00_3

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.pdbtq",
               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_ts([0 .. $mol->tmax]);

       }

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

• Moose::Object

CONSUMES

• HackaMol::ExeRole

• HackaMol::ExeRole

• HackaMol::PathRole

• HackaMol::X::ExtensionRole

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.