HackaMol::AtomGroup - HackaMol AtomGroup class
version 0.022
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;
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.
no arguments. returns the scalar radius of gyration for the group of atoms
isa Str that is lazy and rw. useful for labeling, bookkeeping...
HackaMol::Molecule
HackaMol::AtomGroupRole
Moose::Object
HackaMol::Roles::AtomGroupRole
HackaMol::Roles::NameRole
Demian Riccardi <demianriccardi@gmail.com>
This software is copyright (c) 2015 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.
To install HackaMol, copy and paste the appropriate command in to your terminal.
cpanm
cpanm HackaMol
CPAN shell
perl -MCPAN -e shell install HackaMol
For more information on module installation, please visit the detailed CPAN module installation guide.