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

Methods

Modifier and Type	Method and 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 Detail

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