Ivan Tubert-Brohman

NAME

Chemistry::Bond - Chemical bonds as objects in molecules

SYNOPSIS

    use Chemistry::Bond;

    # assuming we have molecule $mol with atoms $a1 and $a2
    $bond = Chemistry::Bond->new(
        id => "b1", 
        type => '=', 
        atoms => [$a1, $a2]
        order => '2',
    );
    $mol->add_bond($bond);

    # simpler way of doing the same:
    $mol->new_bond(
        id => "b1", 
        type => '=', 
        atoms => [$a1, $a2]
        order => '2',
    );

DESCRIPTION

This module includes objects to describe chemical bonds. A bond is defined as a list of atoms (typically two), with some associated properties.

Bond Attributes

In addition to common attributes such as id, name, and type, bonds have the order attribute. The bond order is a number, typically the integer 1, 2, 3, or 4.

METHODS

Chemistry::Bond->new(name => value, ...)

Create a new Bond object with the specified attributes. Sensible defaults are used when possible.

$bond->order()

Sets or gets the bond order.

$bond->length

Returns the length of the bond, i.e., the distance between the two atom objects in the bond. Returns zero if the bond does not have exactly two atoms.

$bond->aromatic($bool)

Set or get whether the bond is considered to be aromatic.

$bond->print

Convert the bond to a string representation.

$bond->atoms()

If called with no parameters, return a list of atoms in the bond. If called with a list (or a reference to an array) of atom objects, define the atoms in the bond and call $atom->add_bond for each atom in the list. Note: changing the atoms in a bond may have strange side effects; it is safer to treat bonds as immutable except with respect to properties such as name and type.

$bond->delete

Calls $mol->delete_bond($bond) on the bond's parent molecule. Note that a bond should belong to only one molecule or strange things may happen.

VERSION

0.37

SEE ALSO

Chemistry::Mol, Chemistry::Atom, Chemistry::Tutorial

The PerlMol website http://www.perlmol.org/

AUTHOR

Ivan Tubert-Brohman <itub@cpan.org>

COPYRIGHT

Copyright (c) 2005 Ivan Tubert-Brohman. All rights reserved. This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.




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