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Chemistry::3DBuilder
Generate 3D coordinates from a connection table

Chemistry::3DBuilder - Generate 3D coordinates from a connection table


NAME

Chemistry::3DBuilder - Generate 3D coordinates from a connection table


SYNOPSIS


    # example: convert SMILES to MDL molfile

    use Chemistry::3DBuilder qw(build_3d);

    use Chemistry::File::SMILES;

    use Chemistry::File::MDLMol;

    my $s = '[O-]C(=O)C(N)C(C)CC';

    my $mol = Chemistry::Mol->parse($s, format => 'smiles');

    build_3d($mol);

    print $mol->print(format => 'mdl');


DESCRIPTION

This module generates a three-dimensional molecular structure from a connection table, such as that obtained by a 2D representation of the molecule or from a SMILES string.

NOTE: this module is still at a very early stage of development so it has important limitations. 1) It doesn't handle rings or stereochemistry yet! 2) The bond lengths and atoms are very approximate as they don't really account for different elements. 3) Only the sp3, sp2, and sp hybridizations are supported.


SUBROUTINES

These subroutines may be exported; to export all, use the ':all' tag.

build_3d($mol)
Add internal and cartesian coordinates to the molecule $mol.


VERSION

0.10


SEE ALSO

the Chemistry::Mol manpage, the Chemistry::InternalCoords manpage.

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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