Demian Riccardi > HackaMol-0.00_07 > HackaMol::Bond

Download:
HackaMol-0.00_07.tar.gz

Dependencies

Annotate this POD

Source   Latest Release: HackaMol-0.00_21

NAME ^

HackaMol::Bond - HackaMol Bond class

VERSION ^

version 0.00_07

SYNOPSIS ^

   use HackaMol::Atom;
   use HackaMol::Bond;

   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 $bond1 = HackaMol::Bond->new(name=>'O1H1', atoms=>[$atom1,$atom2]);
   my $bond2 = HackaMol::Bond->new(name=>'O1H2', atoms=>[$atom1,$atom3]);
   my $bond3 = HackaMol::Bond->new(name=>'H1H2', atoms=>[$atom2,$atom3]);
   
   my @bonds = ($bond1, $bond2, $bond3);
   
   foreach my $bond ( @bonds ){
   
     my $pbond = sprintf(
                   "Bond: %s, Length: %.2f, Vector: %.5 %.5 %.5 \n",
                   $bond->name, 
                   $bond->bond_length, 
                   @{$bond->bond_vector},
     );

     print $pbond;
   
   }
   
   
   my @COM_ats = map {HackaMol::Atom->new(
                         name    => "X".$_->name."X",
                         coords  => [ $_->COM ],
                         Z       => 1,
                               )
                     } @bonds;
   
   my @HH_bonds = grep { $_->get_atoms(0)->Z == 1 and
                         $_->get_atoms(1)->Z == 1} @bonds;

DESCRIPTION ^

The HackaMol Bond class provides a set of methods and attributes for working with connections between two atoms. The Bond class consumes the AtomGroupRole providing Bond objects with methods to determine the center of mass, total charge, etc (see HackaMol::AtomGroupRole).

The Bond class also provides attributes and methods to set force_constants and measure energy. The bond_energy method calls on a CodeRef attribute that the user may define. See descriptions below.

METHODS ^

bond_vector

no arguments. returns Math::Vector::Real object from $atoms[0]->inter_dcoords($atoms[1]) for the two atoms in the bond.

bond_length

no arguments. returns $atoms[0]->distance($atoms[1]) for the two atoms in the bond.

bond_energy

arguments, as many as you want. Calculates energy using the bond_energy_func described below, if the attribute, bond_fc > 0. The bond_energy method calls the bond_energy_func as follows:

my $energy = &{$self->bond_energy_func}($self,@_);

which will pass $self and that in @_ array to bond_energy_func, which can be redefined.

ATTRIBUTES ^

atoms

isa ArrayRef[Atom] that is lazy with public ARRAY traits provided by the AtomGroupRole (see documentation for more details).

Pushing (atom1, atom2) on to the Bond object will produce bond_length and bond_vector from atom1 to atom2 (the atom12 interatomic vector).

name

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

bond_order

isa Num that is lazy and rw. default = 1, single bond.

bond_fc

isa Num that is lazy and rw. default = 0. force constant for harmonic bond potentials.

bond_length_eq

isa Num that is lazy and rw. default = 0. Equilibrium bond length.

bond_energy_func

isa CodeRef that is lazy and rw. default uses builder to generate harmonic potential from the bond_fc, bond_length_eq, and bond_length. See the _build_bond_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.

syntax highlighting: