NAME
HackaMol::Angle - Angle class for HackaMol
VERSION
version 0.00_02
SYNOPSIS
use HackaMol::Atom;
use HackaMol::Angle;
my $atom1 = HackaMol::Atom->new(
name => 'O1',
coords => [ V( 2.05274, 0.01959, -0.07701 ) ],
Z => 8,
);
my $atom2 = HackaMol::Atom->new(
name => 'H1',
coords => [ V( 1.08388, 0.02164, -0.12303 ) ],
Z => 1,
);
my $atom3 = HackaMol::Atom->new(
name => 'H2',
coords => [ V( 2.33092, 0.06098, -1.00332 ) ],
Z => 1,
);
my $angle1 = HackaMol::Angle->new(name=>'OH2', atoms=>[$atom1,$atom2,$atom3]);
my $angle2 = HackaMol::Angle->new(name=>'OH2', atoms=>[$atom2,$atom1,$atom3]);
foreach my $angle ($angle1, $angle2){
my $pangle = sprintf(
"Angle: %s, angle: %.2f, vector normal to angle plane: %.5 %.5 %.5 \n",
$angle->name,
$angle->ang,
@{$angle->ang_normvec},
);
print $pangle;
}
my @COM_ats = map {HackaMol::Atom->new(
name => "X".$_->name."X",
coords => [ $_->COM ],
Z => 1)
}($angle1, $angle2);
my @ang_w_HH = grep { $_->get_atoms(0)->Z == 1 and
$_->get_atoms(1)->Z == 1} ($angle1, $angle2);DESCRIPTION
The HackaMol Angle class provides a set of methods and attributes for working with two connections between three atoms. Like the Bond, the Angle class consumes the AtomGroupRole providing methods to determine the center of mass, total charge, etc (see HackaMol::AtomGroupRole). An Angle containing (atom1,atom2,atom3) produce angles between the atom21 atom23 interatomic vectors.
The Angle class also provides attributes and methods to set force_constants and measure energy. The angle_energy method calls on a CodeRef attribute that the user may define. See descriptions below.
METHODS
ang_normvec
no arguments. returns Math::Vector::Real object from the normalized cross product of the atom21 and atom23 interatomic vectors.
ang_deg
no arguments. returns the angle (degrees) between the atom21 and atom23 vectors.
ang_rad
no arguments. returns the angle (radians) between the atom21 and atom23 vectors.
angle_energy
arguments, as many as you want. Calculates energy using the angle_energy_func described below, if the attribute, angle_fc > 0. The angle_energy method calls the angle_energy_func as follows:
my $energy = &{$self->angle_energy_func}($self,@_);
which will pass $self and that in @_ array to angle_energy_func, which, similar to the Bond class, can be redefined.
ATTRIBUTES
name
isa Str that is lazy and rw. useful for labeling, bookkeeping...
angle_fc
isa Num that is lazy and rw. default = 0. force constant for harmonic potentials.
ang_eq
isa Num that is lazy and rw. default = 0. Equilibrium angle. The ang method returns angle in degrees.
angle_energy_func
isa CodeRef that is lazy and rw. default uses builder to generate harmonic potential from the angle_fc, ang_eq, and ang. See the _build_angle_energy_func, if interested in changing the function form.
SEE ALSO
EXTENDS
CONSUMES
AUTHOR
Demian Riccardi <demianriccardi@gmail.com>
COPYRIGHT AND LICENSE
This software is copyright (c) 2013 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.