ProteinManager
in package
implements
ProteinInterface
We can have manipulation with proteins
Tags
Table of Contents
Interfaces
- ProteinInterface
- Defines protein-specific sequence operations.
Properties
- $aminoApi : AminoApiAdapter
- $aminos : array<string|int, mixed>
- $protein : Protein
Methods
- __construct() : mixed
- Constructor
- molwt() : bool|array<string|int, mixed>
- Computes the molecular weight of a protein sequence. Every residue the amino acid weight table holds is weighed, selenocysteine (U) and pyrrolysine (O) included, whatever its case ; the stop a translated ORF ends with ("*") is no residue and is left out.
- seqlen() : int
- Returns the length of a protein sequence().
- setProtein() : mixed
- Sets the protein sequence to operate on.
Properties
$aminoApi
private
AminoApiAdapter
$aminoApi
$aminos
private
array<string|int, mixed>
$aminos
= null
$protein
private
Protein
$protein
= null
Methods
__construct()
Constructor
public
__construct(AminoApiAdapter $aminoApi) : mixed
Parameters
- $aminoApi : AminoApiAdapter
molwt()
Computes the molecular weight of a protein sequence. Every residue the amino acid weight table holds is weighed, selenocysteine (U) and pyrrolysine (O) included, whatever its case ; the stop a translated ORF ends with ("*") is no residue and is left out.
public
molwt() : bool|array<string|int, mixed>
The reference is Biopython's Bio.SeqUtils.molecular_weight (average masses) : the sum of the free amino acids less one water (18.0153) per peptide bond. On a sequence without ambiguity code the result equals it, and the tests pin values it computed ; B, Z and X span the lightest to the heaviest amino acid they stand for.
Return values
bool|array<string|int, mixed> —An array of the form: ( lower_molwt, upper_molwt ), FALSE when the sequence holds a symbol the table does not (an internal stop among them)
seqlen()
Returns the length of a protein sequence().
public
seqlen() : int
Return values
int —An integer representing the number of amino acids in the protein.
setProtein()
Sets the protein sequence to operate on.
public
setProtein(mixed $oProtein) : mixed
Parameters
- $oProtein : mixed