Uses of Class
com.hfg.bio.AminoAcid

Packages that use AminoAcid

Package	Description
com.hfg.bio
com.hfg.bio.proteinproperty	Classes for calculating physical properties of proteins.
com.hfg.bio.seq

Uses of AminoAcid in com.hfg.bio

Fields in com.hfg.bio declared as AminoAcid

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

Fields in com.hfg.bio with type parameters of type AminoAcid

Modifier and Type	Field and Description
static Comparator<AminoAcid>	AminoAcid.AA_ORDINAL_COMPARATOR

Methods in com.hfg.bio that return AminoAcid

Modifier and Type	Method and Description
AminoAcid	AminoAcid.addAtoms(Element inElement, int inNum)
AminoAcid	AminoAcid.addSidechainKa(IonizableGroup inValue)
AminoAcid	AminoAcid.clone() Returns an unlocked copy of the AminoAcid.
AminoAcid	AminoAcidSet.getAA(char inResidue)
AminoAcid	AminoAcidSet.getAA(Character inResidue)
AminoAcid	DigestSettings.getAlkylatedCys()
AminoAcid	AminoAcid.lock()
AminoAcid	AminoAcidSet.remove(Character inChar)
AminoAcid	AminoAcid.setOneLetterCode(Character inValue)
AminoAcid	AminoAcid.setThreeLetterCode(String inValue)
static AminoAcid	AminoAcid.valueOf(String inString) Returns the AminoAcid whose name or 3-letter code matches the specified String.
static AminoAcid[]	AminoAcid.values()

Methods in com.hfg.bio that return types with arguments of type AminoAcid

Modifier and Type	Method and Description
Set<AminoAcid>	AAGroup.getAminoAcids()
Collection<AminoAcid>	AminoAcidSet.getAminoAcids()
Iterator<AminoAcid>	AminoAcidSet.iterator()
Set<AminoAcid>	AminoAcidFreqTable.keySet()

Methods in com.hfg.bio with parameters of type AminoAcid

Modifier and Type	Method and Description
AAGroup	AAGroup.add(AminoAcid inAA)
boolean	AminoAcidSet.add(AminoAcid inAminoAcid)
KaSet	KaSet.addpKa(AminoAcid inResidue, float inpKa, Charge inProtonatedForm) Adds a pKa value for the specified amino acid to the set.
boolean	AAGroup.contains(AminoAcid inAA)
Float	AminoAcidFreqTable.get(AminoAcid inAA)
AAGroup	AAGroupingScheme.getAAGroup(AminoAcid inAA)
AAGroup	AAGroupingSchemeImpl.getAAGroup(AminoAcid inAA)
IonizableGroup	KaSet.getCTerminalKa(CTerminalGroup inCTerminalGroup, AminoAcid inCTerminalResidue)
IonizableGroup	KaSet.getCTerminalSidechainKa(AminoAcid inResidue)
Set<Character>	AminoAcidSet.getMapping(AminoAcid inAA)
IonizableGroup	KaSet.getNTerminalKa(NTerminalGroup inNTerminalGroup, AminoAcid inNTerminalResidue)
DigestSettings	DigestSettings.setAlkylatedCys(AminoAcid inValue) By specifying a modified cysteine a "virtual reduction" will be performed on the protein before digestion.
KaSet	KaSet.setCTerminalpKa(AminoAcid inResidue, float inpKa, Charge inProtonatedForm)
KaSet	KaSet.setCTerminalSidechainpKa(AminoAcid inResidue, float inpKa, Charge inProtonatedForm)
boolean	AminoAcidSet.setMapping(char inChar, AminoAcid inAA)
KaSet	KaSet.setNTerminalpKa(AminoAcid inResidue, float inpKa, Charge inProtonatedForm)

Method parameters in com.hfg.bio with type arguments of type AminoAcid

Modifier and Type	Method and Description
boolean	AminoAcidSet.addAll(Collection<? extends AminoAcid> inCollection)

Constructor parameters in com.hfg.bio with type arguments of type AminoAcid

Constructor and Description
AAGroup(String inName, Character inLetter, Collection<AminoAcid> inAAs)
AminoAcidFreqTable(Map<AminoAcid,Float> inData)

Uses of AminoAcid in com.hfg.bio.proteinproperty

Methods in com.hfg.bio.proteinproperty that return AminoAcid

Modifier and Type	Method and Description
AminoAcid	ReducedAnalysisMode.getAlkylatedCysteine()

Methods in com.hfg.bio.proteinproperty with parameters of type AminoAcid

Modifier and Type	Method and Description
ReducedAnalysisMode	ReducedAnalysisMode.setAlkylatedCysteine(AminoAcid inAA)

Uses of AminoAcid in com.hfg.bio.seq

Methods in com.hfg.bio.seq that return AminoAcid

Modifier and Type	Method and Description
AminoAcid	Protein.aminoAcidAt(int inPosition)

Methods in com.hfg.bio.seq that return types with arguments of type AminoAcid

Modifier and Type	Method and Description
Set<AminoAcid>	AminoAcidComposition.keySet()

Methods in com.hfg.bio.seq with parameters of type AminoAcid

Modifier and Type	Method and Description
int	AminoAcidComposition.get(AminoAcid inAA)
void	AminoAcidComposition.increment(AminoAcid inAA)
void	AminoAcidComposition.increment(AminoAcid inAA, int inAmount)
boolean	ProteinXLinkType.isAcceptableSite(AminoAcid inDonor, AminoAcid inAcceptor)

Constructor parameters in com.hfg.bio.seq with type arguments of type AminoAcid

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