NAME
HackaMol::AtomGroup - HackaMol AtomGroup class
VERSION
version 0.00_18
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
EXTENDS
CONSUMES
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.