Object-oriented Perl 5, Moose library for molecular hacking on multiple scales
developer version 0.00_21 Available for testing from cpan.org:
please see *HackaMol on MetaCPAN for formatted documentation.
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);
}
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 HackaMol::X, the extensions, such as HackaMol::X::PDB (TODO), a parser for protein databank files, and HackaMol::X::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.
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.
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.
-
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.
-
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.
-
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!!!
-
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_21.tar.gz
HackaMol is too fun to not be experimental! Feedback and contributions welcome!