=head1 NAME

Bio::Tools::ProteinogenicAA - A object list of proteinogenic amino acids.

=head1 SYNOPSIS

Quick summary of what the module does.

    use Bio::Tools::ProteinogenicAA;

    my $p = Bio::Tools::ProteinogenicAA->new();
    
    #recover the amino acids list from the object
    my @aas = @{$p->aminoacids};

    say $aas[0]->short_name
    ...

=head1 DESCRIPTION

This is a simple module that organizes in a single object a list of proteinogenic amino acids and some of its characteristics. Most of the stored information are important for mass spectrometry based proteomics.

This is an example of how the object is organizied:

    internals: {
        abbreviation           "Ala",
        amino_acid             "Alanine",
        avg_mass               71.0788,
        codons                 "GCU GCC GCA GCG",
        formula                "C3H5NO",
        is_hydrophobic         1,
        is_polar               0,
        monoisotopic_mass      71.03711,
        pH                     "-",
        pI                     6.01,
        pK1                    2.35,
        pK2                    9.87,
        short_name             "A",
        side_chain             "-CH3",
        van_der_waals_volume   67
    }

=head1 METHODS


=head2 amino_acid

    The amino acid common name.

    $aa->amino_acid();


=head2 short_name

    The single letter reference.

    $aa->short_name();


=head2 abbreviation

    The amino acid short abbreviation.

    $aa->abbreviation();

=head2 pI

    The amino acid isoelectric point.
    Note: Pyrrolysine have a pI of 0, the true value was not setted yet.

    $aa->pI();


=head2 pK1

    The amino acid Dissociation constant (alpha-COOH).
    Note: Pyrrolysine and Selenocysteine have a pK1 of 0, the true value was not setted yet.

    $aa->pK1();


=head2 pK2

    The amino acid Dissociation constant (alpha-NH3).
    Note: Pyrrolysine and Selenocysteine have a pK2 of 0, the true value was not setted yet.

    $aa->pK2();


=head2 side_chain

    The amino acid side chain.

    $aa->side_chain();


=head2 is_hydrophobic

    Returns true if the amino acid is hydrophobic.

    $aa->is_hydrophobic();


=head2 is_polar

    Returns true if the amino acid is polar.

    $aa->is_polar();


=head2 pH

    Returns the amino acids pH.

    $aa->pH();


=head2 Van der Walls Volume

    Returns the approximate Van der Walls volume.

    $aa->van_der_waals_volume();


=head2 codons

    Returns a string with all codons responsible for the amino acid.

    $aa->codons();


=head2 formula

    The amino acid chemical formula.

    $aa->formula();


=head2 monoisotopic_mass

    The amino acid monoisotopic_mass (Da).

    $aa->monoisotopic_mass();


=head2 avg_mass

    The amino average mass (Da).

    $aa->avg_mass();


=head1 AUTHOR

Felipe da Veiga Leprevost, C<< <leprevost at cpan.org> >>

=head1 BUGS

Please report any bugs or feature requests to C<bug-bio-tools-proteinogenicaa at rt.cpan.org>, or through
the web interface at L<http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Tools-ProteinogenicAA>.  I will be notified, and then you'll
automatically be notified of progress on your bug as I make changes.




=head1 SUPPORT

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

    perldoc Bio::Tools::ProteinogenicAA


You can also look for information at:

=over 4

=item * RT: CPAN's request tracker (report bugs here)

L<http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-Tools-ProteinogenicAA>

=item * AnnoCPAN: Annotated CPAN documentation

L<http://annocpan.org/dist/Bio-Tools-ProteinogenicAA>

=item * CPAN Ratings

L<http://cpanratings.perl.org/d/Bio-Tools-ProteinogenicAA>

=item * Search CPAN

L<http://search.cpan.org/dist/Bio-Tools-ProteinogenicAA/>

=back


=head1 ACKNOWLEDGEMENTS


=head1 LICENSE AND COPYRIGHT

Copyright 2014 Felipe da Veiga Leprevost.

This program is free software; you can redistribute it and/or modify it
under the terms of the the Artistic License (2.0). You may obtain a
copy of the full license at:

L<http://www.perlfoundation.org/artistic_license_2_0>

Any use, modification, and distribution of the Standard or Modified
Versions is governed by this Artistic License. By using, modifying or
distributing the Package, you accept this license. Do not use, modify,
or distribute the Package, if you do not accept this license.

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by someone other than you, you are nevertheless required to ensure that
your Modified Version complies with the requirements of this license.

This license does not grant you the right to use any trademark, service
mark, tradename, or logo of the Copyright Holder.

This license includes the non-exclusive, worldwide, free-of-charge
patent license to make, have made, use, offer to sell, sell, import and
otherwise transfer the Package with respect to any patent claims
licensable by the Copyright Holder that are necessarily infringed by the
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