Bio-Tools-ProteinogenicAA
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202122232425262728293031323334353637383940This 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
122123124125126127128129130131132133134135136137138139140141142143144145146
$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
4142434445464748495051525354555657585960
$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
596061626364656667686970717273747576777879has
'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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