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.\" ========================================================================
.\"
.IX Title "Chemistry::Bond 3pm"
.TH Chemistry::Bond 3pm "2022-07-14" "perl v5.34.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
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.SH "NAME"
Chemistry::Bond \- Chemical bonds as objects in molecules
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&    use Chemistry::Bond;
\&
\&    # assuming we have molecule $mol with atoms $a1 and $a2
\&    $bond = Chemistry::Bond\->new(
\&        id => "b1", 
\&        type => \*(Aq=\*(Aq, 
\&        atoms => [$a1, $a2]
\&        order => \*(Aq2\*(Aq,
\&    );
\&    $mol\->add_bond($bond);
\&
\&    # simpler way of doing the same:
\&    $mol\->new_bond(
\&        id => "b1", 
\&        type => \*(Aq=\*(Aq, 
\&        atoms => [$a1, $a2]
\&        order => \*(Aq2\*(Aq,
\&    );
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This module includes objects to describe chemical bonds.
A bond is defined as a list of atoms (typically two), with some
associated properties.
.SS "Bond Attributes"
.IX Subsection "Bond Attributes"
In addition to common attributes such as id, name, and type, 
bonds have the order attribute. The bond order is a number, typically the
integer 1, 2, 3, or 4.
.SH "METHODS"
.IX Header "METHODS"
.IP "Chemistry::Bond\->new(name => value, ...)" 4
.IX Item "Chemistry::Bond->new(name => value, ...)"
Create a new Bond object with the specified attributes. Sensible defaults
are used when possible.
.ie n .IP "$bond\->\fBorder()\fR" 4
.el .IP "\f(CW$bond\fR\->\fBorder()\fR" 4
.IX Item "$bond->order()"
Sets or gets the bond order.
.ie n .IP "$bond\->length" 4
.el .IP "\f(CW$bond\fR\->length" 4
.IX Item "$bond->length"
Returns the length of the bond, i.e., the distance between the two atom
objects in the bond. Returns zero if the bond does not have exactly two atoms.
.ie n .IP "$bond\->aromatic($bool)" 4
.el .IP "\f(CW$bond\fR\->aromatic($bool)" 4
.IX Item "$bond->aromatic($bool)"
Set or get whether the bond is considered to be aromatic.
.ie n .IP "$bond\->print" 4
.el .IP "\f(CW$bond\fR\->print" 4
.IX Item "$bond->print"
Convert the bond to a string representation.
.ie n .IP "$bond\->\fBatoms()\fR" 4
.el .IP "\f(CW$bond\fR\->\fBatoms()\fR" 4
.IX Item "$bond->atoms()"
If called with no parameters, return a list of atoms in the bond.  If called
with a list (or a reference to an array) of atom objects, define the atoms in
the bond and call \f(CW$atom\fR\->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.
.ie n .IP "$bond\->delete" 4
.el .IP "\f(CW$bond\fR\->delete" 4
.IX Item "$bond->delete"
Calls \f(CW$mol\fR\->delete_bond($bond) on the bond's parent molecule. Note that a bond
should belong to only one molecule or strange things may happen.
.SH "SOURCE CODE REPOSITORY"
.IX Header "SOURCE CODE REPOSITORY"
<https://github.com/perlmol/Chemistry\-Mol>
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Chemistry::Mol, Chemistry::Atom, Chemistry::Tutorial
.SH "AUTHOR"
.IX Header "AUTHOR"
Ivan Tubert-Brohman <itub@cpan.org>
.SH "COPYRIGHT"
.IX Header "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.