com.hfg.bio.seq

Class ProteinXLinkType

java.lang.Object

com.hfg.chem.Molecule

com.hfg.bio.seq.ProteinXLinkType

All Implemented Interfaces:

Matter, HfgXMLSerializable, Cloneable, Comparable

public class ProteinXLinkType
extends Molecule

Biological protein sequence cross-link types.

Field Summary

Fields

Modifier and Type	Field and Description
static ProteinXLinkType	DISULFIDE
static ProteinXLinkType	GLUCOSEPANE Lysine-arginine protein cross-linking product common with aging of collagen and crystallin.

Fields inherited from class com.hfg.chem.Molecule

H2O, mLocked, mName, NaCl, NH3

Constructor Summary

Constructors

Constructor and Description
ProteinXLinkType(String inName, Map<Element,Float> inElementalComposition, Set<AminoAcid> inDonorSpecificity, Set<AminoAcid> inAcceptorSpecificity)
ProteinXLinkType(XMLNode inXML)

Method Summary

Modifier and Type	Method and Description
int	compareTo(Object inObj)
boolean	equals(Object inObj)
boolean	isAcceptableSite(AminoAcid inDonor, AminoAcid inAcceptor)
ProteinXLinkType	lock()
ProteinXLinkType	register() Puts the ProteinXLinkType into the Set of unique ProteinXLinkType returned by ProteinXLinkType.values().
XMLNode	toXMLNode()
static ProteinXLinkType	valueOf(String inString) Returns the ProteinXLinkType whose name matches the specified String.
static ProteinXLinkType[]	values()

Methods inherited from class com.hfg.chem.Molecule

add, add, addAtom, addAtoms, addAtoms, addAtoms, addElementalComposition, addElementalComposition, addElementalComposition, addKa, addKa, calculateMassFromElementalComposition, clearAttributes, clearCalculatedProperties, clearElementalComposition, clone, formatMassString, getAtoms, getAttribute, getAttributeNames, getAverageMass, getChemicalFormula, getChemicalFormulaWithSubscripts, getElementalComposition, getKas, getLastAtom, getMonoisotopicMass, getOrganicAverageMass, getPhysicalProperty, hasAttribute, hasAttributes, hashCode, isLocked, massesAreUserSet, name, remove, remove, removeAttribute, setAttribute, setAverageMass, setChemicalFormula, setElementalComposition, setMonoisotopicMass, setName, setOrganicAverageMass, setPhysicalProperty, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

DISULFIDE

public static final ProteinXLinkType DISULFIDE

GLUCOSEPANE

public static final ProteinXLinkType GLUCOSEPANE

Lysine-arginine protein cross-linking product common with aging of collagen and crystallin. Sjöberg, Johan Svantesson, and Sven Bulterijs. 2009. “Characteristics, Formation, and Pathophysiology of Glucosepane: A Major Protein Cross-Link.” Rejuvenation Research 12 (2) (April): 137–148. doi:10.1089/rej.2009.0846.

Constructor Detail

ProteinXLinkType

public ProteinXLinkType(String inName,
                        Map<Element,Float> inElementalComposition,
                        Set<AminoAcid> inDonorSpecificity,
                        Set<AminoAcid> inAcceptorSpecificity)

ProteinXLinkType

public ProteinXLinkType(XMLNode inXML)

Method Detail

valueOf

public static ProteinXLinkType valueOf(String inString)

Returns the ProteinXLinkType whose name matches the specified String.

Parameters:

inString - the name for the ProteinXLinkType to retrieve

Returns:

the ProteinXLinkType whose name matches the specified String

values

public static ProteinXLinkType[] values()

register

public ProteinXLinkType register()

Puts the ProteinXLinkType into the Set of unique ProteinXLinkType returned by ProteinXLinkType.values().

lock

public ProteinXLinkType lock()

Overrides:

lock in class Molecule

equals

public boolean equals(Object inObj)

Overrides:

equals in class Molecule

compareTo

public int compareTo(Object inObj)

Specified by:

compareTo in interface Comparable

Overrides:

compareTo in class Molecule

isAcceptableSite

public boolean isAcceptableSite(AminoAcid inDonor,
                                AminoAcid inAcceptor)

toXMLNode

public XMLNode toXMLNode()

Specified by:

toXMLNode in interface HfgXMLSerializable

Overrides:

toXMLNode in class Molecule