Class AminoAcid

java.lang.Object

org.episteme.natural.chemistry.Molecule

org.episteme.natural.chemistry.biochemistry.AminoAcid

All Implemented Interfaces:

Serializable, Commented, ComprehensiveIdentification, Identified<Identification>, Named

public class AminoAcid
extends Molecule

Standard amino acid data. Extends Molecule to allow chemical operations.

Since:

1.0

Author:

Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static final AminoAcid	ALANINE
static final AminoAcid	ARGININE
static final AminoAcid	ASPARAGINE
static final AminoAcid	ASPARTATE
static final AminoAcid	CYSTEINE
static final AminoAcid	GLUTAMATE
static final AminoAcid	GLUTAMINE
static final AminoAcid	GLYCINE
static final AminoAcid	HISTIDINE
static final AminoAcid	ISOLEUCINE
static final AminoAcid	LEUCINE
static final AminoAcid	LYSINE
static final AminoAcid	METHIONINE
static final AminoAcid	PHENYLALANINE
static final AminoAcid	PROLINE
static final AminoAcid	SERINE
static final AminoAcid	THREONINE
static final AminoAcid	TRYPTOPHAN
static final AminoAcid	TYROSINE
static final AminoAcid	VALINE

Fields inherited from class Molecule

traits

Method Summary

Modifier and Type	Method	Description
static AminoAcid	fromCode(char code)	Looks up amino acid by one-letter code.
String	getClassification()
Real	getIsoelectricPoint()
Real	getMolarMass()	Gets the molar mass in g/mol.
Quantity<Mass>	getMolecularWeight()	Returns the molecular weight.
String	getOneLetterCode()
String	getThreeLetterCode()
boolean	isCharged()	Checks if amino acid is charged at pH 7.
boolean	isHydrophobic()	Checks if amino acid is hydrophobic.
static Real	peptideWeight(String sequence)	Calculates molecular weight of a peptide sequence.
static AminoAcid	valueOf(String name)	Mimics Enum.valueOf().
static AminoAcid[]	values()	Mimics Enum.values().

Methods inherited from class Molecule

addAtom, addBond, getAtomCount, getAtoms, getBondCount, getBonds, getBondsFor, getFormula, getId, getName, getNeighbors, getTraits, setName, toString

Methods inherited from class Object

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

Methods inherited from interface Commented

getComments, getTrait, setComments

Methods inherited from interface ComprehensiveIdentification

getTrait, setTrait

Field Details

GLYCINE

public static final AminoAcid GLYCINE

ALANINE

public static final AminoAcid ALANINE

VALINE

public static final AminoAcid VALINE

LEUCINE

public static final AminoAcid LEUCINE

ISOLEUCINE

public static final AminoAcid ISOLEUCINE

PROLINE

public static final AminoAcid PROLINE

METHIONINE

public static final AminoAcid METHIONINE

PHENYLALANINE

public static final AminoAcid PHENYLALANINE

TYROSINE

public static final AminoAcid TYROSINE

TRYPTOPHAN

public static final AminoAcid TRYPTOPHAN

SERINE

public static final AminoAcid SERINE

THREONINE

public static final AminoAcid THREONINE

CYSTEINE

public static final AminoAcid CYSTEINE

ASPARAGINE

public static final AminoAcid ASPARAGINE

GLUTAMINE

public static final AminoAcid GLUTAMINE

LYSINE

public static final AminoAcid LYSINE

ARGININE

public static final AminoAcid ARGININE

HISTIDINE

public static final AminoAcid HISTIDINE

ASPARTATE

public static final AminoAcid ASPARTATE

GLUTAMATE

public static final AminoAcid GLUTAMATE

Method Details

getThreeLetterCode

public String getThreeLetterCode()

getOneLetterCode

public String getOneLetterCode()

getMolecularWeight

public Quantity<Mass> getMolecularWeight()

Returns the molecular weight. Overrides Molecule implementation to return the standard stored weight since we aren't populating atoms yet.

Overrides:

getMolecularWeight in class Molecule

getMolarMass

public Real getMolarMass()

Gets the molar mass in g/mol.

getIsoelectricPoint

public Real getIsoelectricPoint()

getClassification

public String getClassification()

values

public static AminoAcid[] values()

Mimics Enum.values().

valueOf

public static AminoAcid valueOf(String name)

Mimics Enum.valueOf().

fromCode

public static AminoAcid fromCode(char code)

Looks up amino acid by one-letter code.

peptideWeight

public static Real peptideWeight(String sequence)

Calculates molecular weight of a peptide sequence. Subtracts water for peptide bond formation. Returns value in g/mol.

isHydrophobic

public boolean isHydrophobic()

Checks if amino acid is hydrophobic.

isCharged

public boolean isCharged()

Checks if amino acid is charged at pH 7.