com.hfg.bio

Class AminoAcid

java.lang.Object

com.hfg.chem.Molecule

com.hfg.bio.AminoAcid

All Implemented Interfaces:

Matter, HfgXMLSerializable, Cloneable, Comparable

public class AminoAcid
extends Molecule

Amino Acid. Estimated pKa values are from: Jack Kyte, "Structure in Protein Chemistry" (1995), Garland Publishing, Inc. See Nomenclature and Symbolism for Amino Acids and Peptides.

Field Summary

Fields

Modifier and Type	Field and Description
static Comparator<AminoAcid>	AA_ORDINAL_COMPARATOR
static AminoAcid	ALANINE
static AminoAcid	ALPHA_AMINOBUTYRIC_ACID
static AminoAcid	ALPHA_AMINOISOBUTYRIC_ACID
static AminoAcid	AMINO_MERCAPTO_BUTYRIC_ACID
static AminoAcid	ARG_N_METHYL
static AminoAcid	ARGININE
static AminoAcid	ASN_N_METHYL
static AminoAcid	ASP_ASN_AVG
static AminoAcid	ASP_HYDROXY
static AminoAcid	ASPARAGINE
static AminoAcid	ASPARTIC_ACID
static AminoAcid	CITRULLINE
static AminoAcid	CYS_2_HYDROXYETHYL_THIOCYSTEINE
static AminoAcid	CYS_ACETAMIDOMETHYL
static AminoAcid	CYS_AMINOETHYL
static AminoAcid	CYS_CARBAMIDOMETHYL
static AminoAcid	CYS_CARBOXYMETHYL
static AminoAcid	CYS_PYRIDYLETHYL
static AminoAcid	CYS_S_DIOXIDE
static AminoAcid	CYS_S_FARNESYL
static AminoAcid	CYS_S_HYDROXY
static AminoAcid	CYS_S_PALMITYL
static AminoAcid	CYS_S_PHOSPHO
static AminoAcid	CYS_SULFONIC_ACID
static AminoAcid	CYSTEINE
static AminoAcid	D_ALANINE
static AminoAcid	D_ARGININE
static AminoAcid	D_ASPARAGINE
static AminoAcid	D_ASPARTIC_ACID
static AminoAcid	D_CYSTEINE
static AminoAcid	D_GLUTAMIC_ACID
static AminoAcid	D_GLUTAMINE
static AminoAcid	D_HISTIDINE
static AminoAcid	D_ISOLEUCINE
static AminoAcid	D_ISOVALINE
static AminoAcid	D_LEUCINE
static AminoAcid	D_LYSINE
static AminoAcid	D_METHIONINE
static AminoAcid	D_PHENYLALANINE
static AminoAcid	D_PROLINE
static AminoAcid	D_SERINE
static AminoAcid	D_THREONIE
static AminoAcid	D_TRYPTOPHAN
static AminoAcid	D_TYROSINE
static AminoAcid	D_VALINE
static AminoAcid	DEHYDROALANINE
static AminoAcid	GLU_GLN_AVG
static AminoAcid	GLUTAMIC_ACID
static AminoAcid	GLUTAMINE
static AminoAcid	GLYCINE
static AminoAcid	HIS_4_METHYL
static AminoAcid	HISTIDINE
static AminoAcid	HISTIDINE_HID
static AminoAcid	HISTIDINE_HIE
static AminoAcid	HISTIDINE_HIP
static AminoAcid	HOMOSERINE
static AminoAcid	ILE_LEU_AVG The NCBI has starting using 'J' to represent Ile/Leu ambiguity
static AminoAcid	ISOLEUCINE
static AminoAcid	LEUCINE
static AminoAcid	LLP
static AminoAcid	LYS_ACETYLATED
static AminoAcid	LYS_HYDROXY
static AminoAcid	LYS_N_DIMETHYL
static AminoAcid	LYS_N_METHYL
static AminoAcid	LYS_N_TRIMETHYL
static AminoAcid	LYS_NZ_CARBOXYLIC_ACID
static AminoAcid	LYSINE
static AminoAcid	MET_S_DIXOY
static AminoAcid	MET_SULFONE
static AminoAcid	MET_SULFOXIDE
static AminoAcid	METHIONINE
static AminoAcid	NORLEUCINE
static AminoAcid	NORVALINE
static AminoAcid	ORNITHINE
static AminoAcid	PHENYLALANINE
static AminoAcid	PRO_HYDROXY
static AminoAcid	PROLINE
static AminoAcid	PYRROLYSINE Zhang Y, Baranov PV, Atkins JF, Gladyshev VN (May 2005).
static AminoAcid	SARCOSINE
static AminoAcid	SELENOCYSTEINE http://www.albany.edu/faculty/cs812/bio366/selenocysteine_ppt.pdf
static AminoAcid	SELENOMETHIONINE
static AminoAcid	SER_PHOSPHO
static AminoAcid	SERINE
static AminoAcid	STOP
static AminoAcid	THR_PHOSPHO
static AminoAcid	THREE_SULFINOALANINE
static AminoAcid	THREONIE
static AminoAcid	TRYPTOPHAN
static AminoAcid	TYR_O_SULFO
static AminoAcid	TYR_PHOSPHO
static AminoAcid	TYROSINE
static AminoAcid	UNDEFINED
static AminoAcid	VALINE

Fields inherited from class com.hfg.chem.Molecule

H2O, mLocked, mName, NaCl, NH3

Constructor Summary

Constructors

Constructor and Description
AminoAcid(String inName)
AminoAcid(String inName, Map<Element,Float> inElementalComposition)
AminoAcid(String inName, String in3LetterCode)
AminoAcid(String inName, String in3LetterCode, char in1LetterCode)
AminoAcid(XMLNode inXML)

Method Summary

Modifier and Type	Method and Description
AminoAcid	addAtoms(Element inElement, int inNum)
AminoAcid	addSidechainKa(IonizableGroup inValue)
AminoAcid	clone() Returns an unlocked copy of the AminoAcid.
int	compareTo(Object inObj)
boolean	equals(Object inObj)
Character	getOneLetterCode()
Collection<IonizableGroup>	getSidechainKas() Returns any defined sidechain Ka's.
String	getThreeLetterCode()
boolean	isApproximation() Some of the defined amino acids are an average of other amino acids.
AminoAcid	lock()
void	register() Puts the AminoAcid into the Set of unique AminoAcids returned by AminoAcid.values().
AminoAcid	setOneLetterCode(Character inValue)
void	setSidechainKas(Collection<IonizableGroup> inKas) Sets the sidechain Ka's.
AminoAcid	setThreeLetterCode(String inValue)
String	toString()
XMLNode	toXMLNode()
static AminoAcid	valueOf(String inString) Returns the AminoAcid whose name or 3-letter code matches the specified String.
static AminoAcid[]	values()

Methods inherited from class com.hfg.chem.Molecule

add, add, addAtom, addAtoms, addAtoms, addElementalComposition, addElementalComposition, addElementalComposition, addKa, addKa, calculateMassFromElementalComposition, clearAttributes, clearCalculatedProperties, clearElementalComposition, 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

Methods inherited from class java.lang.Object

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

Field Detail

ALANINE

public static final AminoAcid ALANINE

ARGININE

public static final AminoAcid ARGININE

ASPARAGINE

public static final AminoAcid ASPARAGINE

ASPARTIC_ACID

public static final AminoAcid ASPARTIC_ACID

CYSTEINE

public static final AminoAcid CYSTEINE

GLUTAMIC_ACID

public static final AminoAcid GLUTAMIC_ACID

GLUTAMINE

public static final AminoAcid GLUTAMINE

GLYCINE

public static final AminoAcid GLYCINE

HISTIDINE

public static final AminoAcid HISTIDINE

ISOLEUCINE

public static final AminoAcid ISOLEUCINE

LEUCINE

public static final AminoAcid LEUCINE

LYSINE

public static final AminoAcid LYSINE

METHIONINE

public static final AminoAcid METHIONINE

PHENYLALANINE

public static final AminoAcid PHENYLALANINE

PROLINE

public static final AminoAcid PROLINE

SERINE

public static final AminoAcid SERINE

THREONIE

public static final AminoAcid THREONIE

TRYPTOPHAN

public static final AminoAcid TRYPTOPHAN

TYROSINE

public static final AminoAcid TYROSINE

VALINE

public static final AminoAcid VALINE

SELENOCYSTEINE

public static final AminoAcid SELENOCYSTEINE

http://www.albany.edu/faculty/cs812/bio366/selenocysteine_ppt.pdf

PYRROLYSINE

public static final AminoAcid PYRROLYSINE

Zhang Y, Baranov PV, Atkins JF, Gladyshev VN (May 2005). "Pyrrolysine and selenocysteine use dissimilar decoding strategies". The Journal of Biological Chemistry. 280 (21): 20740–51. doi:10.1074/jbc.M501458200. PMID 15788401.

ASP_ASN_AVG

public static final AminoAcid ASP_ASN_AVG

GLU_GLN_AVG

public static final AminoAcid GLU_GLN_AVG

ILE_LEU_AVG

public static final AminoAcid ILE_LEU_AVG

The NCBI has starting using 'J' to represent Ile/Leu ambiguity

UNDEFINED

public static final AminoAcid UNDEFINED

STOP

public static final AminoAcid STOP

D_ALANINE

public static final AminoAcid D_ALANINE

D_ARGININE

public static final AminoAcid D_ARGININE

D_ASPARAGINE

public static final AminoAcid D_ASPARAGINE

D_ASPARTIC_ACID

public static final AminoAcid D_ASPARTIC_ACID

D_CYSTEINE

public static final AminoAcid D_CYSTEINE

D_GLUTAMIC_ACID

public static final AminoAcid D_GLUTAMIC_ACID

D_GLUTAMINE

public static final AminoAcid D_GLUTAMINE

D_HISTIDINE

public static final AminoAcid D_HISTIDINE

D_ISOLEUCINE

public static final AminoAcid D_ISOLEUCINE

D_LEUCINE

public static final AminoAcid D_LEUCINE

D_LYSINE

public static final AminoAcid D_LYSINE

D_METHIONINE

public static final AminoAcid D_METHIONINE

D_PHENYLALANINE

public static final AminoAcid D_PHENYLALANINE

D_PROLINE

public static final AminoAcid D_PROLINE

D_SERINE

public static final AminoAcid D_SERINE

D_THREONIE

public static final AminoAcid D_THREONIE

D_TRYPTOPHAN

public static final AminoAcid D_TRYPTOPHAN

D_TYROSINE

public static final AminoAcid D_TYROSINE

D_VALINE

public static final AminoAcid D_VALINE

D_ISOVALINE

public static final AminoAcid D_ISOVALINE

ARG_N_METHYL

public static final AminoAcid ARG_N_METHYL

ASP_HYDROXY

public static final AminoAcid ASP_HYDROXY

CITRULLINE

public static final AminoAcid CITRULLINE

CYS_ACETAMIDOMETHYL

public static final AminoAcid CYS_ACETAMIDOMETHYL

CYS_AMINOETHYL

public static final AminoAcid CYS_AMINOETHYL

CYS_CARBAMIDOMETHYL

public static final AminoAcid CYS_CARBAMIDOMETHYL

CYS_CARBOXYMETHYL

public static final AminoAcid CYS_CARBOXYMETHYL

CYS_PYRIDYLETHYL

public static final AminoAcid CYS_PYRIDYLETHYL

CYS_S_FARNESYL

public static final AminoAcid CYS_S_FARNESYL

CYS_S_PALMITYL

public static final AminoAcid CYS_S_PALMITYL

CYS_S_HYDROXY

public static final AminoAcid CYS_S_HYDROXY

CYS_S_DIOXIDE

public static final AminoAcid CYS_S_DIOXIDE

CYS_S_PHOSPHO

public static final AminoAcid CYS_S_PHOSPHO

CYS_2_HYDROXYETHYL_THIOCYSTEINE

public static final AminoAcid CYS_2_HYDROXYETHYL_THIOCYSTEINE

CYS_SULFONIC_ACID

public static final AminoAcid CYS_SULFONIC_ACID

DEHYDROALANINE

public static final AminoAcid DEHYDROALANINE

THREE_SULFINOALANINE

public static final AminoAcid THREE_SULFINOALANINE

HOMOSERINE

public static final AminoAcid HOMOSERINE

LYS_ACETYLATED

public static final AminoAcid LYS_ACETYLATED

LYS_HYDROXY

public static final AminoAcid LYS_HYDROXY

LYS_N_METHYL

public static final AminoAcid LYS_N_METHYL

LYS_N_DIMETHYL

public static final AminoAcid LYS_N_DIMETHYL

LYS_N_TRIMETHYL

public static final AminoAcid LYS_N_TRIMETHYL

LYS_NZ_CARBOXYLIC_ACID

public static final AminoAcid LYS_NZ_CARBOXYLIC_ACID

MET_SULFONE

public static final AminoAcid MET_SULFONE

MET_SULFOXIDE

public static final AminoAcid MET_SULFOXIDE

MET_S_DIXOY

public static final AminoAcid MET_S_DIXOY

SELENOMETHIONINE

public static final AminoAcid SELENOMETHIONINE

NORVALINE

public static final AminoAcid NORVALINE

NORLEUCINE

public static final AminoAcid NORLEUCINE

ORNITHINE

public static final AminoAcid ORNITHINE

PRO_HYDROXY

public static final AminoAcid PRO_HYDROXY

SARCOSINE

public static final AminoAcid SARCOSINE

SER_PHOSPHO

public static final AminoAcid SER_PHOSPHO

THR_PHOSPHO

public static final AminoAcid THR_PHOSPHO

TYR_PHOSPHO

public static final AminoAcid TYR_PHOSPHO

TYR_O_SULFO

public static final AminoAcid TYR_O_SULFO

ALPHA_AMINOBUTYRIC_ACID

public static final AminoAcid ALPHA_AMINOBUTYRIC_ACID

AMINO_MERCAPTO_BUTYRIC_ACID

public static final AminoAcid AMINO_MERCAPTO_BUTYRIC_ACID

ALPHA_AMINOISOBUTYRIC_ACID

public static final AminoAcid ALPHA_AMINOISOBUTYRIC_ACID

HIS_4_METHYL

public static final AminoAcid HIS_4_METHYL

LLP

public static final AminoAcid LLP

ASN_N_METHYL

public static final AminoAcid ASN_N_METHYL

HISTIDINE_HID

public static final AminoAcid HISTIDINE_HID

HISTIDINE_HIE

public static final AminoAcid HISTIDINE_HIE

HISTIDINE_HIP

public static final AminoAcid HISTIDINE_HIP

AA_ORDINAL_COMPARATOR

public static final Comparator<AminoAcid> AA_ORDINAL_COMPARATOR

Constructor Detail

AminoAcid

public AminoAcid(String inName)

AminoAcid

public AminoAcid(String inName,
                 String in3LetterCode)

AminoAcid

public AminoAcid(String inName,
                 String in3LetterCode,
                 char in1LetterCode)

AminoAcid

public AminoAcid(String inName,
                 Map<Element,Float> inElementalComposition)

AminoAcid

public AminoAcid(XMLNode inXML)

Method Detail

register

public void register()

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

addAtoms

public AminoAcid addAtoms(Element inElement,
                          int inNum)

Overrides:

addAtoms in class Molecule

lock

public AminoAcid lock()

Overrides:

lock in class Molecule

toString

public String toString()

Overrides:

toString in class Molecule

clone

public AminoAcid clone()

Returns an unlocked copy of the AminoAcid.

Overrides:

clone in class Molecule

Returns:

an unlocked copy of this AminoAcid

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

valueOf

public static AminoAcid valueOf(String inString)

Returns the AminoAcid whose name or 3-letter code matches the specified String. (1-letter codes aren't specific enough.)

Parameters:

inString - the name or 3-letter code for the AminoAcid to retrieve

Returns:

the AminoAcid whose name or 3-letter code matches the specified String

values

public static AminoAcid[] values()

addSidechainKa

public AminoAcid addSidechainKa(IonizableGroup inValue)

setSidechainKas

public void setSidechainKas(Collection<IonizableGroup> inKas)

Sets the sidechain K_a's.

Parameters:

inKas - IonizableGroups present on the AminoAcid's sidechain

getSidechainKas

public Collection<IonizableGroup> getSidechainKas()

Returns any defined sidechain K_a's.

Returns:

sidechain IonizableGroups

setThreeLetterCode

public AminoAcid setThreeLetterCode(String inValue)

getThreeLetterCode

public String getThreeLetterCode()

setOneLetterCode

public AminoAcid setOneLetterCode(Character inValue)

getOneLetterCode

public Character getOneLetterCode()

isApproximation

public boolean isApproximation()

Some of the defined amino acids are an average of other amino acids. Use of these renders the calculated properties as approximations.

Returns:

whether or not the AminoAcid is an average of other amino acids

toXMLNode

public XMLNode toXMLNode()

Specified by:

toXMLNode in interface HfgXMLSerializable

Overrides:

toXMLNode in class Molecule