Docs For Class Protein

Description

Protein

Sequence class for protein sequences

$oProtein = new Protein($sProtein, "Haemoglobin");

author: Mark Brooks <markabrooks@users.sourceforge.net>
version: 0.8.2
copyright: 2004-2008 Mark Brooks <markabrooks@users.sourceforge.net>

PEAR
   |
   --Bio
      |
      --Str
         |
         --Seq
            |
            --Protein

Method Summary

static float ExtCoeff_ (string $sSeq)

static float MolWt_ (string $sSeq, [boolean $bAvgWeights = TRUE])

static string OneToThree_ (string $sSequenceAsOneLetterCode, [string $sCodonStyle = "ThreeLetter"])

static $pI Pi_ ($sSeq $sSeq, [string $sDataSource = "EMBOSS"])

object this __construct ([string $sSeq = ""], [string $sAlphabetName = ""], [string $sName = ""], [boolean $bIsRev = 0])

float abs0pOnePc ()

float extCoeff ()

string oneToThree ([string $sCodonStyle = "ThreeLetter"])

string OneToThreeCodon_ (char $cAminoAsOneLetterCode, [string $sCodonStyle = "ThreeLetter"])

float pI ([string $sDataSource = "EMBOSS"])

Variables

Inherited Variables

Inherited from Bio

Bio::$bWarnings

Methods

static method ExtCoeff_ (line 218)

function ExtCoeff_

Calculates extinction coefficient from a given sequence and returns it

$fExCoeff = Protein::ExtCoeff_("MVRIGLTHNQLLI...");

return: Extinction coefficient
author: Mark Brooks
access: public

static float ExtCoeff_ (string $sSeq)

string $sSeq: Sequence of the string

static method MolWt_ (line 141)

function MolWt_

Calculates the molecular weight of a protein sequence without an instance required

return: Molecular weight of peptide
author: Serge Gregorio
access: public

static float MolWt_ (string $sSeq, [boolean $bAvgWeights = TRUE])

string $sSeq: Sequence to calculate the weight of (required)
boolean $bAvgWeights: Should the mass be for average molecular weights? (optional) (Defaults to TRUE, otherwise will be monoisotopic).

Redefinition of:

Seq::MolWt_(): function MolWt_

static method OneToThree_ (line 447)

function OneToThree_

Converts a protein Str from 1 to 3 letter code

access: public

static string OneToThree_ (string $sSequenceAsOneLetterCode, [string $sCodonStyle = "ThreeLetter"])

string $sSequenceAsOneLetterCode
string $sCodonStyle

static method Pi_ (line 325)

function Pi_ Calculates isoelectric point.

At the isoelectric point, the charge of protein will be 0 To calculate pH where charge is 0 a loop is required The loop will start computing charge of protein at pH=7, and if charge is not 0, new charge value will be computed by using a different pH. Procedure will be repeated until charge is 0 (at isoelectric point)

$fAbsOnePc = Protein::Pi_("MVRIGLTHNQLLI...");

return: float Isoelectric point
author: www.biophp.org
access: public

static $pI Pi_ ($sSeq $sSeq, [string $sDataSource = "EMBOSS"])

string $sDataSource: Source of pKvalues One of: "EMBOSS", "DTASelect", "Solomon"
$sSeq $sSeq: string Amino acids in sequence

Constructor __construct (line 115)

function __construct

Protein constructor, takes the sequence of the protein as a string for the first argument:

$oProtein = new Protein($sProtein);

object this __construct ([string $sSeq = ""], [string $sAlphabetName = ""], [string $sName = ""], [boolean $bIsRev = 0])

string $sName: Name of the sequence. (optional)
boolean $bIsRev: Is it a reversed sequence? (optional)
string $sSeq: sSeq sequence string (optional)
string $sAlphabetName: sAlphabetName Name of the alphabet. (optional)

Redefinition of:

Seq::__construct(): function __construct

abs0pOnePc (line 265)

function abs0pOnePc

Calculates the absorbance of a one percent solution of the protein

$fAbsOnePc = $oProtein->abs0pOnePc();

return: absorbance of a one percent solution of the protein
author: Mark Brooks

float abs0pOnePc ()

extCoeff (line 246)

function extCoeff

Calculates extiction coefficient for the instantiated protein

$fExCoeff = $oProtein->extCoeff();

return: Extinction coefficient
author: Mark Brooks
access: public

float extCoeff ()

oneToThree (line 477)

function oneToThree

Converts a protein Seq object from 1 to 3 letter code

access: public

string oneToThree ([string $sCodonStyle = "ThreeLetter"])

string $sCodonStyle

OneToThreeCodon_ (line 183)

function OneToThreeCodon_

Static function to convert a protein sequence from 1 to 3 letter code

return: Amino acid as three-letter code
author: Iddo Friedberg
access: public

string OneToThreeCodon_ (char $cAminoAsOneLetterCode, [string $sCodonStyle = "ThreeLetter"])

char $cAminoAsOneLetterCode: Amino Acid character (required)
string $sCodonStyle: Codon style (optional). Either "SingleLetterSpaced" or "ThreeLetter"

pI (line 296)

function pI Calculates isoelectric point.

Calls self::Pi_() to do the dirty work

$fPi = $oProtein->pI();

$fPi = $oProtein->pI("EMBOSS");

$fPi = $oProtein->pI("DTASelect");

$fPi = $oProtein->pI("Solomon");

return: Isoelectric point
author: www.biophp.org
access: public

float pI ([string $sDataSource = "EMBOSS"])

string $sDataSource: Source of pKvalues One of: "EMBOSS", "DTASelect", "Solomon"

Inherited Methods

Inherited From Seq

Seq::__construct()
Seq::alphabetFactory()
Seq::cat()
Seq::catStr()
Seq::getAlphabet()
Seq::getAlphabetLetters()
Seq::getAlphabetType()
Seq::getAlphabetWeights()
Seq::getMolWt()
Seq::getName()
Seq::getPrettyView()
Seq::molWt()
Seq::MolWt_()
Seq::PrettyView_()
Seq::setAlphabet()
Seq::setAlphabetByName()
Seq::setMolWt()
Seq::setName()
Seq::stripIMet()
Seq::stripStop()
Seq::ValidateSeqVersusLetters_()
Seq::WriteRuler_()
Seq::__call()
Seq::__toString()

Inherited From Str

Str::__construct()
Str::cat()
Str::catStr()
Str::CatStr_()
Str::errorCallBack()
Str::getData()
Str::getIsRev()
Str::getRev()
Str::inTrim()
Str::InTrim_()
Str::left()
Str::Left_()
Str::len()
Str::Len_()
Str::reMatch()
Str::ReMatch_()
Str::ReReplace_()
Str::ReSplit_()
Str::rev()
Str::Rev_()
Str::right()
Str::Right_()
Str::setData()
Str::setIsRev()
Str::sub()
Str::Sub_()
Str::symFreq()
Str::SymFreq_()
Str::toggleIsRev()
Str::trim()
Str::Trim_()
Str::__toString()

Inherited From Bio

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

Class Constants

Inherited Constants

Inherited from Bio

Bio::NEWLINE