Chemistry::File::InternalCoords - Internal coordinates (z-matrix) molecule format reader/writer
Version 0.03
This module is not intended for direct use -- it is intended for use via Chemistry::Mol.
use Chemistry::File qw/ InternalCoords XYZ /;
my $mol = Chemistry::Mol->read("foo.zmat");
warn $mol->print;
$mol->write(\*STDOUT, format => 'zmat');
$mol->write('foo.xyz', format => 'xyz');
This is a subclass of Chemistry::File for reading and writing the zmatriz (aka Z-matrix aka InternalCoords) molecule data format. It registers the 'zmat' file extension with Chemistry::Mol.
For example, here is hydrogen:
H H 1 B1 B1 0.70000000
and water:
O H 1 B1 H 1 B2 2 A1 B1 0.96659987 B2 0.96659987 A1 107.67114171
This class inherits from Chemistry::File. The following methods are overloaded:
Checks if the filename extension is 'zmat'.
Checks if the filename extension is 'zmat'.
Expects a plain zmatrix format. Variables are support. No special options.
Creates a plain zmatrix formatted string. Any options are also passed to Chemistry::InternalCoords::Builder's build_zmat function (defaults to bfs off and sort on). Also recognizes these options that affect the output:
If on (default) uses the element instead of the atomic number
if on (default) uses variables for the bond lengths & angles) options, which affect the output.
if on (defaults to off) with put an '=' between variable names and values. only used when vars option is enabled.
if on (defaults to off) it will assume that the internal_coords for all the atoms are already set, and will NOT call build_zmat to generate everything.
David Westbrook (davidrw), <dwestbrook at gmail.com>
Please report any bugs or feature requests to bug-chemistry-file-internalcoords at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Chemistry-File-InternalCoords. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.
I'm also available by email or via '/msg davidrw' on http://perlmonks.org.
You can find documentation for this module with the perldoc command.
perldoc Chemistry::File::InternalCoords
You can also look for information at:
http://rt.cpan.org/NoAuth/Bugs.html?Dist=Chemistry-File-InternalCoords
Copyright 2006 David Westbrook, all rights reserved.
This program is free software; you can redistribute it and/or modify it under the same terms as Perl itself.
