Docs For Class IUPACData

Description

IUPACData

Information about the IUPAC alphabets

author: Mark Brooks <markabrooks@users.sourceforge.net>
author: Port from Bio::Python
version: 0.8.2
copyright: 2004-2008 Mark Brooks <markabrooks@users.sourceforge.net>
todo: Debug Accessor functions Notes: B == 5-bromouridine D == 5,6-dihydrouridine S == thiouridine W == wyosine No setters because are not mutable

Located in /Data/IUPACData.php (line 53)

PEAR
   |
   --Bio
      |
      --IUPACData

Direct descendents

Class	Description
Alphabet	Alphabet This is used by sequences which contain a finite number of similar words.

Variable Summary

static mixed $aAvgPeptideWeights

static mixed $aMonoPeptideWeights

Method Summary

static $this->aAmbiguousDnaComplement getAmbiguousDnaComplement (none 0)

static $this->aAmbiguousDnaLetters getAmbiguousDnaLetters (none 0)

static $this->aAmbiguousDnaValues getAmbiguousDnaValues (none 0)

static $this->aAmbiguousRnaLetters getAmbiguousRnaLetters (none 0)

static $this->_rna_values getAmbiguousRnaValues (none 0)

static $this->aExtendedDnaLetters getExtendedDnaLetters (none 0)

static $this->_proteinletters getExtendedProteinLetters (none 0)

static $this->_protein_values getExtendedProteinValues (none 0)

static $this->aExtendedRnaLetters getExtendedRnaLetters (none 0)

static $this->_proteinletters getProteinLetters (none 0)

static $this->aProteinWeights getProteinWeights ([none $bAvgWeights = TRUE])

static $this->sProteinWithStopLetters getProteinWithStopLetters (none 0)

static $this->aUnambiguousDnaLetters getUnambiguousDnaLetters (none 0)

static $this->aUnambiguousDnaWeights getUnambiguousDnaWeights (none 0)

static $this->aUnambiguousRnaLetters getUnambiguousRnaLetters (none 0)

static $this->aUnambiguousRnaWeights getUnambiguousRnaWeights (none 0)

$this __construct (none 0)

Variables

static mixed $aAvgPeptideWeights = array (
"A" => "71.0788",
"C" => "103.1388",
"D" => "115.0886",
"E" => "129.1155",
"F" => "147.1766",
"G" => "57.0519",
"H" => "137.1411",
"I" => "113.08406",
"K" => "128.1741",
"L" => "113.1594",
"M" => "131.1926",
"N" => "114.1038",
"P" => "97.1167",
"Q" => "128.1307",
"R" => "156.1875",
"S" => "87.0782",
"T" => "101.1051",
"V" => "99.1326",
"W" => "186.2132",
"Y" => "163.1760"
) (line 283)

array $aAvgPeptideWeights

access: public
uses: Weights - without water (i.e. in peptide chain)

static mixed $aMonoPeptideWeights = array (
"A" => "71.03711",
"C" => "103.00919",
"D" => "115.02694",
"E" => "129.04259",
"F" => "147.06841",
"G" => "57.02146",
"H" => "137.05891",
"I" => "113.08406",
"K" => "128.09496",
"L" => "113.08406",
"M" => "131.04049",
"N" => "114.04293",
"P" => "97.05276",
"Q" => "128.05858",
"R" => "156.10111",
"S" => "87.03203",
"T" => "101.04768",
"V" => "99.06841",
"W" => "186.07931",
"Y" => "163.06333"
) (line 254)

array $aMonoPeptideWeights

Weights without water (i.e. in peptide chain)

access: public

Inherited Variables

Inherited from Bio

Bio::$bWarnings

Methods

static method getAmbiguousDnaComplement (line 552)

function getAmbiguousDnaComplement

accessor

access: public

static $this->aAmbiguousDnaComplement getAmbiguousDnaComplement (none 0)

none 0

static method getAmbiguousDnaLetters (line 390)

function getAmbiguousDnaLetters

accessor

access: public

static $this->aAmbiguousDnaLetters getAmbiguousDnaLetters (none 0)

none 0

static method getAmbiguousDnaValues (line 498)

function getAmbiguousDnaValues

accessor

access: public

static $this->aAmbiguousDnaValues getAmbiguousDnaValues (none 0)

none 0

static method getAmbiguousRnaLetters (line 444)

function getAmbiguousRnaLetters

accessor

access: public

static $this->aAmbiguousRnaLetters getAmbiguousRnaLetters (none 0)

none 0

static method getAmbiguousRnaValues (line 516)

function getAmbiguousRnaValues

accessor

access: public

static $this->_rna_values getAmbiguousRnaValues (none 0)

none 0

static method getExtendedDnaLetters (line 426)

function getExtendedDnaLetters

accessor

access: public

static $this->aExtendedDnaLetters getExtendedDnaLetters (none 0)

none 0

static method getExtendedProteinLetters (line 372)

function getExtendedProteinLetters

accessor

access: public

static $this->_proteinletters getExtendedProteinLetters (none 0)

none 0

static method getExtendedProteinValues (line 534)

function getExtendedProteinValues

accessor

access: public

static $this->_protein_values getExtendedProteinValues (none 0)

none 0

static method getExtendedRnaLetters (line 480)

function getExtendedRnaLetters

accessor

access: public

static $this->aExtendedRnaLetters getExtendedRnaLetters (none 0)

none 0

static method getProteinLetters (line 336)

function getProteinLetters

accessor

access: public

static $this->_proteinletters getProteinLetters (none 0)

none 0

static method getProteinWeights (line 606)

function getProteinWeights

accessor

access: public

static $this->aProteinWeights getProteinWeights ([none $bAvgWeights = TRUE])

none $bAvgWeights

static method getProteinWithStopLetters (line 354)

function getProteinWithStopLetters

accessor

access: public

static $this->sProteinWithStopLetters getProteinWithStopLetters (none 0)

none 0

static method getUnambiguousDnaLetters (line 408)

function getUnambiguousDnaLetters

accessor

access: public

static $this->aUnambiguousDnaLetters getUnambiguousDnaLetters (none 0)

none 0

static method getUnambiguousDnaWeights (line 570)

function getUnambiguousDnaWeights

accessor

access: public

static $this->aUnambiguousDnaWeights getUnambiguousDnaWeights (none 0)

none 0

static method getUnambiguousRnaLetters (line 462)

function getUnambiguousRnaLetters

accessor

access: public

static $this->aUnambiguousRnaLetters getUnambiguousRnaLetters (none 0)

none 0

static method getUnambiguousRnaWeights (line 588)

function getUnambiguousRnaWeights

accessor

access: public

static $this->aUnambiguousRnaWeights getUnambiguousRnaWeights (none 0)

none 0

Constructor __construct (line 318)

function __construct

Constructor

access: public

$this __construct (none 0)

none 0

Redefinition of:

Bio::__construct(): function Bio ()

Redefined in descendants as:

Alphabet::__construct() : function Alphabet
SingleLetterAlphabet::__construct() : function __construct
ProteinAlphabet::__construct() : function __construct
IUPACProtein::__construct() : function __construct
ExtendedIUPACProtein::__construct() : function __construct
NucleotideAlphabet::__construct() : function __construct
DnaAlphabet::__construct() : function __construct
IUPACAmbiguousDna::__construct() : function __construct
IUPACUnambiguousDna::__construct() : function __construct
ExtendedIUPACDna::__construct() : function __construct
RnaAlphabet::__construct() : function __construct
IUPACAmbiguousRna::__construct() : function __construct
IUPACUnambiguousRna::__construct() : function __construct
ExtendedIUPACRna::__construct() : function __construct
SecondaryStructure::__construct() : function __construct
ThreeLetterProtein::__construct() : function __construct

Inherited Methods

Inherited From Bio

Bio::__construct()
Bio::printWithNl()

Class Constants

Inherited Constants

Inherited from Bio

Bio::NEWLINE