HackaMol-X-Vina

HackaMol extension for running Autodock Vina

VERSION

developer version 0.00_1 Available for testing from cpan.org:

please see *HackaMol::X::Vina on MetaCPAN for formatted documentation.

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",
           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, 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.