VeaR/JEllipse

pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids
Class Phenylalanine

java.lang.Object
  extended by pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Aminoacid
      extended by pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Phenylalanine
All Implemented Interfaces:
AminoacidProperties

public class Phenylalanine
extends Aminoacid
implements AminoacidProperties

A phenylalanine molecule.

See Also:
Aminoacid, AminoacidProperties

Field Summary
private  Atom Cb
           
private  Atom Cd1
           
private  Atom Cd2
           
private  Atom Ce1
           
private  Atom Ce2
           
private  Atom Cg
           
private  Atom Cz
           
 
Fields inherited from class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Aminoacid
absdeviation, avgdihedralangle, C, Ca, deviation, lnradiusofcurvature, N, O, pdbindex, phi, psi
 
Constructor Summary
Phenylalanine(java.lang.String residuenum, java.util.Map AtomCoords)
          Creates a new instance of the Methionine aminoacid.
 
Method Summary
 java.lang.String getAbbrev()
           
 java.util.List getAtoms()
          return all atoms in concrete aminoacid molecule
 java.util.List getBonds()
          return all COVALENT non-SS bonds in concrete aminoacid molecule
 float[] getCoordsOfCbeta()
           
 float[] getCoordsOfCdelta1()
           
 float[] getCoordsOfCdelta2()
           
 float[] getCoordsOfCepsilon()
           
 float[] getCoordsOfCepsilon1()
           
 float[] getCoordsOfCepsilon2()
           
 float[] getCoordsOfCgamma()
           
 float getHydropathy()
           
 float getMass()
           
 byte getNumOfNonHAtoms()
           
 float getPI()
           
 char getSymbol()
           
 boolean isAcidic()
           
 boolean isAliphatic()
           
 boolean isAromatic()
           
 boolean isBasic()
           
 boolean isBuried()
           
 boolean isCyclic()
           
 boolean isHydrophobic()
           
 
Methods inherited from class pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids.Aminoacid
getAbsDeviation, getAvgDihedralAngle, getBackboneAtoms, getBackboneAtomsWithoutOcarbonyl, getBackboneBonds, getCcarbonyl, getCoordsOfCalpha, getCoordsOfCcarbonyl, getCoordsOfNamid, getCoordsOfOcarbonyl, getDeviation, getLnRadiusOfCurvature, getNamid, getPhiAngle, getPsiAngle, getResiduePdbIndex, setAbsDeviation, setAvgDihedralAngle, setDeviation, setLnRadiusOfCurvature, setPhiAngle, setPsiAngle
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

Cb

private Atom Cb

Cg

private Atom Cg

Cd1

private Atom Cd1

Cd2

private Atom Cd2

Ce1

private Atom Ce1

Ce2

private Atom Ce2

Cz

private Atom Cz
Constructor Detail

Phenylalanine

public Phenylalanine(java.lang.String residuenum,
                     java.util.Map AtomCoords)
Creates a new instance of the Methionine aminoacid.

Parameters:
residuenum - sequential residue number - due to the PdbFile index
AtomCoords - a HashMap with atoms' coordinates
Method Detail

getAtoms

public java.util.List getAtoms()
Description copied from interface: AminoacidProperties
return all atoms in concrete aminoacid molecule

Specified by:
getAtoms in interface AminoacidProperties

getBonds

public java.util.List getBonds()
Description copied from interface: AminoacidProperties
return all COVALENT non-SS bonds in concrete aminoacid molecule

Specified by:
getBonds in interface AminoacidProperties

getSymbol

public char getSymbol()
Specified by:
getSymbol in interface AminoacidProperties
Returns:
one-letter conventional symbol

getAbbrev

public java.lang.String getAbbrev()
Specified by:
getAbbrev in interface AminoacidProperties
Specified by:
getAbbrev in class Aminoacid
Returns:
three-letter abbreviation for the kind of aminoacid

getNumOfNonHAtoms

public byte getNumOfNonHAtoms()
Specified by:
getNumOfNonHAtoms in interface AminoacidProperties
Returns:
number of atoms excluding hydrogens

getPI

public float getPI()
Specified by:
getPI in interface AminoacidProperties
Returns:
isoelectric point of the aminoacid

getMass

public float getMass()
Specified by:
getMass in interface AminoacidProperties
Returns:
molecular mass of a single aminoacid molecule

getHydropathy

public float getHydropathy()
Specified by:
getHydropathy in interface AminoacidProperties
Returns:
hydropathy index
hydropathy index - a scale combining hydrophobicity and hyrophilicity of R groups; used to estimate general "polarity" of aminoacid:
when < 0, aacid is rather hydrophobic;
when > 0, aacid is rather polar.
Kyte J, Doolitle RF (1982) A Simple Method For Displaying the hydropahitic character of a protein, J Mol Biol, 157, 105-132

isBuried

public boolean isBuried()
Specified by:
isBuried in interface AminoacidProperties
Returns:
true, if the aminoacid tends to avoid surfacial localization in the peptide

isHydrophobic

public boolean isHydrophobic()
Specified by:
isHydrophobic in interface AminoacidProperties
Returns:
true, if the aminoacid is rather hydrophobic than polar

isAliphatic

public boolean isAliphatic()
Specified by:
isAliphatic in interface AminoacidProperties
Returns:
true, if the amioacid's backbone is purely C- & H-based

isAromatic

public boolean isAromatic()
Specified by:
isAromatic in interface AminoacidProperties
Returns:
true, if the aminoacid comprise the aromatic ring

isCyclic

public boolean isCyclic()
Specified by:
isCyclic in interface AminoacidProperties
Returns:
true, if the aminoacid has a closed ring of atoms

isAcidic

public boolean isAcidic()
Specified by:
isAcidic in interface AminoacidProperties
Returns:
true, if the aminoacid is of rather acidic character

isBasic

public boolean isBasic()
Specified by:
isBasic in interface AminoacidProperties
Returns:
true, if the aminoacid is of rather basic character

getCoordsOfCbeta

public float[] getCoordsOfCbeta()
Returns:
coordinates of Cbeta

getCoordsOfCgamma

public float[] getCoordsOfCgamma()
Returns:
coordinates of Cgamma

getCoordsOfCdelta1

public float[] getCoordsOfCdelta1()
Returns:
coordinates of Cdelta1

getCoordsOfCdelta2

public float[] getCoordsOfCdelta2()
Returns:
coordinates of Cdelta2

getCoordsOfCepsilon1

public float[] getCoordsOfCepsilon1()
Returns:
coordinates of Cepsilon1

getCoordsOfCepsilon2

public float[] getCoordsOfCepsilon2()
Returns:
coordinates of Cepsilon2

getCoordsOfCepsilon

public float[] getCoordsOfCepsilon()
Returns:
coordinates of Czeta

VeaR/JEllipse