GSP
Quick Navigator

Search Site

Unix VPS
A - Starter
B - Basic
C - Preferred
D - Commercial
MPS - Dedicated
Previous VPSs
* Sign Up! *

Support
Contact Us
Online Help
Handbooks
Domain Status
Man Pages

FAQ
Virtual Servers
Pricing
Billing
Technical

Network
Facilities
Connectivity
Topology Map

Miscellaneous
Server Agreement
Year 2038
Credits
 

USA Flag

 

 

Man Pages
Bond(3) User Contributed Perl Documentation Bond(3)
 

Chemistry::Bond - Chemical bonds as objects in molecules

    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',
    );

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

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.

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.

0.37

Chemistry::Mol, Chemistry::Atom, Chemistry::Tutorial
The PerlMol website <http://www.perlmol.org/>

Ivan Tubert-Brohman <itub@cpan.org>

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.
2009-05-10 perl v5.28.1

Search for    or go to Top of page |  Section 3 |  Main Index

Powered by GSP Visit the GSP FreeBSD Man Page Interface.
Output converted with ManDoc.