org.jscience.biology
Class AminoAcid

java.lang.Object
  extended by org.jscience.chemistry.Molecule
      extended by org.jscience.biology.AminoAcid
All Implemented Interfaces:
java.io.Serializable, java.lang.Cloneable, Named
Direct Known Subclasses:
Alanine, Arginine, Asparagine, AsparticAcid, Cysteine, GlutamicAcid, Glutamine, Glycine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Proline, Serine, Threonine, Tryptophan, Tyrosine, Valine

public abstract class AminoAcid
extends Molecule
implements Named

A class representing an Amino-Acid.

See Also:
Serialized Form

Constructor Summary
AminoAcid(Atom atom, java.lang.String name)
          Creates a new AminoAcid object.
AminoAcid(Atom atom, java.lang.String name, java.lang.String abbreviation, java.lang.String symbol)
          Creates a new AminoAcid object.
 
Method Summary
 java.lang.String getAbbreviation()
          Returns the abbreviation.
 double getHydrophobicity()
          Returns the hydrophobiticy.
 double getIsoelectricPoint()
          Returns the isoelectric point.
 java.lang.String getName()
          Returns the name.
 java.lang.String getSymbol()
          Returns the symbol.
protected  void setAbbreviation(java.lang.String abbreviation)
          Sets the abbreviation.
protected  void setHydrophobicity(double hydrophobicity)
          Sets the hydrophobiticy.
protected  void setIsoelectricPoint(double isoelectricPoint)
          Sets the isoelectric point.
protected  void setName(java.lang.String name)
          Sets the abbreviation.
protected  void setSymbol(java.lang.String symbol)
          Sets the symbol.
 
Methods inherited from class org.jscience.chemistry.Molecule
clone, computeBondingEnergy, computeMolecularWeight, containsAtom, containsBond, getAtoms, getBoilingPoint, getBonds, getCASRegistryNumber, getCharge, getCombustionEnthaply, getDensity, getEnthropy, getFormationEnthalpy, getFormula, getFusionEnthalpy, getFusionEnthropy, getMeltingEnthalpy, getMeltingEnthropy, getMeltingPoint, getMolecularWeight, getSpecificHeat, getVanDerWaalsA, getVanDerWaalsB, isBondingIsomer, isChemicalIsomer, isIon, isValidCASNumber, isValidCASNumber, setBoilingPoint, setCASRegistryNumber, setCombustionEnthaply, setDensity, setEnthropy, setFormationEnthalpy, setFusionEnthalpy, setFusionEnthropy, setMeltingEnthalpy, setMeltingEnthropy, setMeltingPoint, setMolecularWeight, setSpecificHeat, setVanDerWaalsA, setVanDerWaalsB, toString
 
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Constructor Detail

AminoAcid

public AminoAcid(Atom atom,
                 java.lang.String name)
Creates a new AminoAcid object.

Parameters:
atom - DOCUMENT ME!
name - DOCUMENT ME!

AminoAcid

public AminoAcid(Atom atom,
                 java.lang.String name,
                 java.lang.String abbreviation,
                 java.lang.String symbol)
Creates a new AminoAcid object.

Parameters:
atom - DOCUMENT ME!
name - DOCUMENT ME!
abbreviation - DOCUMENT ME!
symbol - DOCUMENT ME!
Throws:
java.lang.IllegalArgumentException - DOCUMENT ME!
Method Detail

getName

public java.lang.String getName()
Returns the name.

Specified by:
getName in interface Named
Returns:
DOCUMENT ME!

setName

protected void setName(java.lang.String name)
Sets the abbreviation.

Parameters:
name - DOCUMENT ME!
Throws:
java.lang.IllegalArgumentException - DOCUMENT ME!

getAbbreviation

public java.lang.String getAbbreviation()
Returns the abbreviation.

Returns:
DOCUMENT ME!

setAbbreviation

protected void setAbbreviation(java.lang.String abbreviation)
Sets the abbreviation.

Parameters:
abbreviation - DOCUMENT ME!

getSymbol

public java.lang.String getSymbol()
Returns the symbol.

Returns:
DOCUMENT ME!

setSymbol

protected void setSymbol(java.lang.String symbol)
Sets the symbol.

Parameters:
symbol - DOCUMENT ME!

getIsoelectricPoint

public double getIsoelectricPoint()
Returns the isoelectric point.

Returns:
DOCUMENT ME!

setIsoelectricPoint

protected void setIsoelectricPoint(double isoelectricPoint)
Sets the isoelectric point.

Parameters:
isoelectricPoint - DOCUMENT ME!

getHydrophobicity

public double getHydrophobicity()
Returns the hydrophobiticy.

Returns:
DOCUMENT ME!

setHydrophobicity

protected void setHydrophobicity(double hydrophobicity)
Sets the hydrophobiticy.

Parameters:
hydrophobicity - DOCUMENT ME!