NAME

HackaMol::AtomGroup - HackaMol AtomGroup class

VERSION

version 0.042

SYNOPSIS

use HackaMol::AtomGroup;
use Math::Vector::Real;
use Math::Vector::Real::Random;

my $radius = 16;
my $natoms = int(0.0334*($radius**3)*4*pi/3);

my @atoms = map {Atom->new(Z => 8, charges=> [0], coords => [$_]) }
            map {$_*$radius}
            map {Math::Vector::Real->random_in_sphere(3)} 1 .. $natoms;

my $group = AtomGroup->new(gname => 'biggroup', atoms=> [@atoms]);

print $group->count_atoms . "\n";

print $group->count_unique_atoms . "\n";

print $group->Rg . "\n";

my $numerical_error = $radius*sqrt($radius*3/5) - $group->Rg;

DESCRIPTION

The HackaMol AtomGroup class provides methods and attributes for groups of atoms. Atom groupings can be defined to mimic conventional forcefields or manipulated to generate novel analytical tools. For example, with a trajectory loaded, a dynamic cluster of atoms can be placed in a group and monitored in time. Or, perhaps, track regional charges of a quantum mechanical molecule with changes in configuration or external field. The AtomGroup class consumes the AtomGroupRole and provides the parent class for the Molecule class.

METHODS

Rg

no arguments. returns the scalar radius of gyration for the group of atoms

ATTRIBUTES

name

isa Str that is lazy and rw. useful for labeling, bookkeeping...

SEE ALSO

• HackaMol::Molecule

• HackaMol::AtomGroupRole

EXTENDS

• Moose::Object

CONSUMES

• HackaMol::Roles::AtomGroupRole

• HackaMol::Roles::NameRole

• HackaMol::Roles::NameRole

AUTHOR

Demian Riccardi <demianriccardi@gmail.com>

COPYRIGHT AND LICENSE

This software is copyright (c) 2017 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.