Bio-Tools-ProteinogenicAA

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README.pod  view on Meta::CPAN

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

README.pod  view on Meta::CPAN

    $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

lib/Bio/Tools/ProteinogenicAA.pm  view on Meta::CPAN

		$aa->abbreviation($info[2]);
		$aa->pI($info[3]);
		$aa->pK1($info[4]);
		$aa->pK2($info[5]);
		$aa->side_chain($info[6]);
		$info[7] eq 'X' ? $aa->is_hydrophobic(1) : $aa->is_hydrophobic(0);
		$info[8] eq 'X' ? $aa->is_polar(1) : $aa->is_polar(0);
		$aa->pH($info[9]);
		$aa->van_der_waals_volume($info[10]);
		$aa->codons($info[11]);
		$aa->formula($info[12]);
		$aa->monoisotopic_mass($info[13]);
		$aa->avg_mass($info[14]);
		
		push(@list, $aa);

	}
	
	return @list;	
};

lib/Bio/Tools/ProteinogenicAA/AAInfo.pm  view on Meta::CPAN

has	'van_der_waals_volume' => (
	is	=>	'rw',
	isa	=>	'Int',
	);

has	'codons' => (
	is	=>	'rw',
	isa	=>	'Str',
	);

has	'formula' => (
	is	=>	'rw',
	isa	=>	'Str',
	);

has	'monoisotopic_mass' => (
	is	=>	'rw',
	isa	=>	'Num',
	);

has 'avg_mass' => (