HackaMol

Object-oriented Perl 5, Moose library for molecular hacking on multiple scales

VERSION

developer version 0.00_13 Available for testing from cpan.org:

please see *HackaMol on MetaCPAN for formatted documentation.

SYNOPSIS

   use HackaMol;
   use Math::Vector::Real;

   my $hack = HackaMol->new( name => "hackitup" );

   # all coordinates from NMR ensemble are loaded into atoms
   my $mol  = $hack->read_file_mol("1L2Y.pdb");

   #recenter all coordinates to center of mass
   foreach my $t ( 0 .. $mol->tmax) {
       $mol->t($t);
       $mol->translate( -$mol->COM );
   }

   #create array of CA atoms with full occupancy 

   my @CAs = grep {
                    $_->name    eq 'CA'  and
                    $_->occ == 1 
                  } $mol->all_atoms;

   #print out the pdb with CA for several models from the NMR 
   HackaMol::Molecule->new( 
                            atoms=>[@CAs] 
                          )-> print_pdb_ts([8,2,4,6,8,0], 'some.pdb');

   # print coordinates to trp-cage.xyz and return filehandle for future
   # writing
   my $fh = $mol->print_xyz( $mol->name . ".xyz" );
   foreach ( 1 .. 10 ) {
       $mol->rotate(
           V( 0, 0, 1 ),    # rotation vector
           36,              # rotate by 36 degrees
           V( 5, 0, 0 )     # origin of rotation
       );
       $mol->print_xyz($fh); 
   }

   # translate/rotate method is provided by AtomGroupRole
   # populate groups byatom resid attr
   my @groups = $hack->group_by_atom_attr( 'resid', $mol->all_atoms );
   $mol->push_groups(@groups);

   foreach my $ang ( 1 .. 10 ) {
       $_->rotate( V( 1, 1, 1 ), 36, $_->COM ) foreach $mol->all_groups;
       $mol->print_xyz($fh);
   }

DESCRIPTION

The HackaMol library enables users to build simple, yet powerful scripts for carrying out computational work on molecules at multiple scales. The molecular object system organizes atoms within molecules using groups, bonds, angles, and dihedrals. HackaMol seeks to provide intuitive attributes and methods that may be harnessed to coerce computational chemistry through a common core. The library is inspired by PerlMol, BioPerl, MMTSB, and my own experiences as a researcher. A goal of this library is to reduce the "viscosity" of setting up computations and managing data.

The library is organized into two regions: HackaMol, the core (contained here) that has classes for atoms and molecules, and HackaMolX, the extensions, such as HackaMolX::PDB, a parser for protein databank files, and HackaMolX::Calculator, an abstract calculator for coercing computational chemistry, that use the core. The three major goals of the core are for it to be well-tested, well-documented, and easy to install. The goal of the extensions is to provide a more flexible space for researchers to develop and share new methods that use the core. Extensions are in the works, but the HackaMolX namespace has not been established yet!

HackaMol uses Math::Vector::Real (MVR) for all the vector operations. MVR is a lightweight solution with a fast XS dropin that overlaps very well with the desirables for working with atomic coordinates. Extensions that treat much larger systems will definitely benefit from the capabilities Perl Data Language (PDL) or Math::GSL.

INSTALLATION

To install HackaMol, I recommend using cpanminus and local::lib. This approach avoids the need for root privileges and uses the system Perl (available on most systems; see Strawberry Perl for Windows). I use Perlbrew to manage local versions of Perl, but Perlbrew is overkill unless your system Perl is very old (if you do use Perlbrew, you won't need local::lib).

Here is a quick summary of a [step by step post on installing Perl modules] (http://perlmaven.com/install-perl-modules-without-root-rights-on-linux-ubuntu-13-10). Below, prompt> denotes your terminal prompt.

1. install cpanminus

   prompt> curl -L http://cpanmin.us | perl - App::cpanminus

   Execution without superuser privileges will complain about not being to write to a path. This is ok! It will create a perl5 directory in your home directory, in which all modules will be installed. Thus, an uninstall involves deleting the ~/perl5 directory.

2. install local::lib

   prompt> ~/perl5/bin/cpanm --local-lib=~/perl5 local::lib && eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)

   Execution should install local::lib and configure the cpanm command to know about the ~/perl5 directory in the local shell.

3. configure .bash_profile

   prompt> echo 'eval $(perl -I ~/perl5/lib/perl5/ -Mlocal::lib)' >> ~/.bash_profile

   Execution will add the stuff between the quotes to your bash_profile, which enables automatic configuration of cpanminus and local::lib with every new terminal shell. To uninstall, delete this line from .bash_profile

   You are now ready to install anything installable from CPAN!!!

4. install HackaMol

   prompt> cpanm HackaMol

   Execution will fail to find HackaMol until it is officially released. For now, you can install the developer release:

   prompt> cpanm DEMIAN/HackaMol-0.00_13.tar.gz

HackaMol is too fun to not be experimental! Feedback and contributions welcome!