Bio-Tools-ProteinogenicAA

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README.pod  view on Meta::CPAN

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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

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    $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

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                $aa->abbreviation($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

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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' => (



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