NAME

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

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
...

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
}

METHODS

amino_acid

The amino acid common name.

$aa->amino_acid();

short_name

The single letter reference.

$aa->short_name();

abbreviation

The amino acid short abbreviation.

$aa->abbreviation();

pI

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

$aa->pI();

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();

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();

side_chain

The amino acid side chain.

$aa->side_chain();

is_hydrophobic

Returns true if the amino acid is hydrophobic.

$aa->is_hydrophobic();

is_polar

Returns true if the amino acid is polar.

$aa->is_polar();

pH

Returns the amino acids pH.

$aa->pH();

Van der Walls Volume

Returns the approximate Van der Walls volume.

$aa->van_der_waals_volume();

codons

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

$aa->codons();

formula

The amino acid chemical formula.

$aa->formula();

monoisotopic_mass

The amino acid monoisotopic_mass (Da).

$aa->monoisotopic_mass();

avg_mass

The amino average mass (Da).

$aa->avg_mass();

AUTHOR

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

BUGS

Please report any bugs or feature requests to bug-bio-tools-proteinogenicaa at rt.cpan.org, or through the web interface at 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.

SUPPORT

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

perldoc Bio::Tools::ProteinogenicAA

You can also look for information at:

• RT: CPAN's request tracker (report bugs here)

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

• AnnoCPAN: Annotated CPAN documentation

  http://annocpan.org/dist/Bio-Tools-ProteinogenicAA

• CPAN Ratings

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

• Search CPAN

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

ACKNOWLEDGEMENTS

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:

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.

If your Modified Version has been derived from a Modified Version made 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 Package. If you institute patent litigation (including a cross-claim or counterclaim) against any party alleging that the Package constitutes direct or contributory patent infringement, then this Artistic License to you shall terminate on the date that such litigation is filed.

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