Package org.helm.notation2.tools

Class PeptideUtils

java.lang.Object

org.helm.notation2.tools.PeptideUtils

public final class PeptideUtils
extends Object

PeptideUtils, class to provide peptide utils

Author:

hecht

Method Summary

Modifier and Type	Method	Description
static String	getNaturalAnalogueSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)	method to produce for a peptide PolymerNotation the natural analogue sequence
static String	getSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer)	method to produce for a peptide PolymerNotation the sequence

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Details

getNaturalAnalogueSequence

public static String getNaturalAnalogueSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) throws HELM2HandledException, PeptideUtilsException, ChemistryException

method to produce for a peptide PolymerNotation the natural analogue sequence

Parameters:

polymer - PolymerNotation

Returns:

natural analogue sequence

Throws:

HELM2HandledException - if the polymer contains HELM2 features

PeptideUtilsException - if the polymer is not a peptide

ChemistryException - if the Chemistry Engine is not initialized

getSequence

public static String getSequence(org.helm.notation2.parser.notation.polymer.PolymerNotation polymer) throws HELM2HandledException, PeptideUtilsException, ChemistryException

method to produce for a peptide PolymerNotation the sequence

Parameters:

polymer - PolymerNotation

Returns:

sequence

Throws:

HELM2HandledException - if the polmyer contains HELM2 features

PeptideUtilsException - is not a peptide

ChemistryException - if the Chemistry Engine is not initialized