Chemistry::File::InternalCoords - Internal coordinates molecule format reader/writer

NAME

Chemistry::File::InternalCoords - Internal coordinates (z-matrix) molecule format reader/writer

VERSION

Version 0.03

SYNOPSIS

This module is not intended for direct use -- it is intended for use via the Chemistry::Mol manpage.

  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');

DESCRIPTION

This is a subclass of the Chemistry::File manpage for reading and writing the zmatriz (aka Z-matrix aka InternalCoords) molecule data format. It registers the 'zmat' file extension with the Chemistry::Mol manpage.

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

METHODS

This class inherits from the Chemistry::File manpage. The following methods are overloaded:

name_is

Checks if the filename extension is 'zmat'.

file_is

Checks if the filename extension is 'zmat'.

parse_string

Expects a plain zmatrix format. Variables are support. No special options.

write_string

Creates a plain zmatrix formatted string. Any options are also passed to the Chemistry::InternalCoords::Builder manpage's build_zmat function (defaults to bfs off and sort on). Also recognizes these options that affect the output:

symbol

If on (default) uses the element instead of the atomic number

vars

if on (default) uses variables for the bond lengths & angles) options, which affect the output.

vars_sep

if on (defaults to off) with put an '=' between variable names and values. only used when vars option is enabled.

skip_build

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.

PREREQUISITES

SEE ALSO

http://www.perlmol.org/

AUTHOR

David Westbrook (davidrw), <dwestbrook at gmail.com>

BUGS

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. 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.

SUPPORT

You can find documentation for this module with the perldoc command.

    perldoc Chemistry::File::InternalCoords

You can also look for information at:

ACKNOWLEDGEMENTS

COPYRIGHT & LICENSE

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.