File Coverage

blib/lib/HackaMol/Roles/BondsAnglesDihedralsRole.pm

Criterion	Covered	Total	%
statement	6	6	100.0
branch			n/a
condition			n/a
subroutine	2	2	100.0
pod			n/a
total	8	8	100.0

$HackaMol::Roles::BondsAnglesDihedralsRole::VERSION = '0.053';
# ABSTRACT: Array traits for containers of HackaMol Bonds, Angles, Dihedrals.
use Moose::Role;

has $_ => (
    traits  => ['Array'],
    is      => 'ro',
    isa     => 'ArrayRef[Any]',
    default => sub { [] },
    lazy    => 1,
    handles => {
        "has_$_"    => 'count',
        "push_$_"   => 'push',
        "get_$_"    => 'get',
        "set_$_"    => 'set',
        "all_$_"    => 'elements',
        "count_$_"  => 'count',
        "delete_$_" => 'delete',
        "clear_$_"  => 'clear',
    },
) foreach qw(bonds angles dihedrals);

no Moose::Role;

1;


=pod

=head1 NAME

HackaMol::Roles::BondsAnglesDihedralsRole - Array traits for containers of HackaMol Bonds, Angles, Dihedrals.

=head1 VERSION

version 0.053

=head1 DESCRIPTION

The HackaMol BondsAnglesDihedralsRole provides ARRAY trait methods for interacting with
arrays of bonds angles and dihedrals. The Molecule class consumes this
role. The Atom class does not. Thus, Molecules are responsible for reporting multiple bonded
connections for any given atom.

=head1 ARRAY METHODS

=head2 push_bonds, get_bonds, set_bonds, all_bonds, count_bonds, delete_bonds, clear_bonds

ARRAY traits for the bonds attribute, respectively: push, get, set, elements, count, delete, clear

=head2 push_bonds

push bond on to bonds array

  $group->push_bonds($bond1, $bond2, @otherbonds);

=head2 all_bonds

returns array of all elements in bonds array

  print $_->bond_order, "\n" foreach $group->all_bonds;

=head2 get_bonds

return element by index from bonds array

  print $group->get_bonds(1); # returns $bond2 from that pushed above

=head2 set_bonds

set bonds array by index

  $group->set_bonds(1, $bond1);

=head2 count_bonds

return number of bonds in the array

  print $group->count_bonds;

=head2 delete_bonds

deletes bond from bonds array and returns it.

=head2 clear_bonds

clears bonds array

=head2 push_angles, get_angles, set_angles, all_angles, count_angles, delete_angles, clear_angles

ARRAY traits for the bonds attribute, respectively: push, get, set, elements, count, delete, clear

Analogous to those for bonds.

=head2 push_dihedrals, get_dihedrals, set_dihedrals, all_dihedrals, count_dihedrals, delete_dihedrals, clear_dihedrals

ARRAY traits for the bonds attribute, respectively: push, get, set, elements, count, delete, clear

Analogous to those for bonds.

=head1 SYNOPSIS
    use HackaMol::Atom;
    use HackaMol::Angle;
    use HackaMol::Dihedral;

    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 $atom4 = HackaMol::Atom->new(
        name    => 'Cl',
        coords  => [ V(-0.91386, 0.02587, -0.21792 ) ],
        Z       => 17,
    );

    my @atoms = ($atom1,$atom2,$atom3,$atom4);

    my $bond1 = HackaMol::Angle->new(name=> 'test', atoms[@atoms[0,1]]);
    my $bond2 = HackaMol::Angle->new(name=> 'test', atoms[@atoms[0,2]]);

    my @bonds = $atom1->all_bonds;

    my $angle1 = HackaMol::Angle->new(name=> 'test', atoms[@atoms[1,0,2]]);
    my $angle2 = HackaMol::Angle->new(name=> 'test', atoms[@atoms[0,1,3]]);

    my @angles = $atom1->all_angles;

    my $dihe1  = HackaMol::Dihedral->new(name=> 'test', atoms[@atoms]);
    my $dihe2  = HackaMol::Dihedral->new(name=> 'test', atoms[reverse @atoms]);

    my @dihes  = $atom1->all_dihedrals;

=head1 SEE ALSO

=over 4

=item *

L<HackaMol::Molecule>

=back

=head1 AUTHOR

Demian Riccardi <[e-mail]>

=head1 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.

=cut