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=item * $object->size

    Return the number of atoms contained in the molecule.


=item * $object->atom(5)

    Return the atom located at position five (starting from zero).


=item * $object->push(atom)

    Push atom object at the end of the molecule.


=item * $object->proten

    Return a molecule that only contains atoms with type ATOM


=item * $object->hetatoms

    Retruns a molecule that only contains HETATM records


=item * $object->alpha

    Returns a molecule with the alpha carbons


=item * $object->backbone

    Returns a molecule with the backbone of a protein


=item * $object->sidechains

    Returns a molecule with the sidechains of a protein


=item * $object->list_atoms('logical expression')

    Creates a molecule with a custom atom selection. The logical expression must use
    Perl's logical operators and the properties of atoms. For example to select all
    atoms from residue 50 onwards and only belonging to ALA residues on would use
    the logical expression: 'residue_number >= 50 && residue_name eq "ALA"'


=item * $object->center

    Return an atom object that respresents the centroid for the given molecule.


=item * $object->cm

    Return an atom object that sits at the center of mass for the given molecule.


=item * $object->translate(x,y,z)

    Translate the molecule as a rigid object by x,y,z.


=item * $object->rotate(u11,u12,u13,u21,u22,u23,u31,u32,u33)

    Do a rigid rotation of the molecule using matrix u.


=item * $object->rotate_translate(@matrix,@vector)

    Apply a rotation matrix followed by a translation. To facilitate structural
    supperpositions.


=item * $object->superpose($reference)

    Find the transformation that overlaps $object on to $reference. The resulting
    transformation is in the format @transformation= (@matrix,@vector). Molecules
    must have the same number of atoms.


=item * $object->rmsd($reference)

    Compute the RMSD between two molecules. The molecules must have the same number
    of atoms


=back

=head1 SEE ALSO

http://www.pdb.org

=head1 AUTHOR

Raul Alcantara Aragon, E<lt>rulix@hotmail.comE<gt>

=head1 COPYRIGHT AND LICENSE

Copyright (C) 2012 by Raul Alcantara

This library is free software; you can redistribute it and/or modify
it under the same terms as Perl itself, either Perl version 5.12.3 or,
at your option, any later version of Perl 5 you may have available.


=cut