VeaR/JEllipse

pl.krakow.cmuj.bioinformatics.jellipse.chemtoolkit.aminoacids
Interface AminoacidProperties

All Known Implementing Classes:
Alanine, Arginine, Asparagine, Aspartate, Cysteine, Glutamate, Glutamine, Glycine, Histidine, Isoleucine, Leucine, Lysine, Methionine, Phenylalanine, Proline, Serine, Threonine, Tryptophan, Tyrosine, Valine

public interface AminoacidProperties

Reading chemical properties of aminoacids.


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 getHydropathy()
           
 float getMass()
           
 byte getNumOfNonHAtoms()
           
 float getPI()
           
 char getSymbol()
           
 boolean isAcidic()
           
 boolean isAliphatic()
           
 boolean isAromatic()
           
 boolean isBasic()
           
 boolean isBuried()
           
 boolean isCyclic()
           
 boolean isHydrophobic()
           
 

Method Detail

getAtoms

java.util.List getAtoms()
return all atoms in concrete aminoacid molecule


getBonds

java.util.List getBonds()
return all COVALENT non-SS bonds in concrete aminoacid molecule


getSymbol

char getSymbol()
Returns:
one-letter conventional symbol

getAbbrev

java.lang.String getAbbrev()
Returns:
three-letter conventional abbreviation of the name

getNumOfNonHAtoms

byte getNumOfNonHAtoms()
Returns:
number of atoms excluding hydrogens

getPI

float getPI()
Returns:
isoelectric point of the aminoacid

getHydropathy

float getHydropathy()
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

getMass

float getMass()
Returns:
molecular mass of a single aminoacid molecule

isBuried

boolean isBuried()
Returns:
true, if the aminoacid tends to avoid surfacial localization in the peptide

isHydrophobic

boolean isHydrophobic()
Returns:
true, if the aminoacid is rather hydrophobic than polar

isAliphatic

boolean isAliphatic()
Returns:
true, if the amioacid's backbone is purely C- & H-based

isAromatic

boolean isAromatic()
Returns:
true, if the aminoacid comprise the aromatic ring

isCyclic

boolean isCyclic()
Returns:
true, if the aminoacid has a closed ring of atoms

isAcidic

boolean isAcidic()
Returns:
true, if the aminoacid is of rather acidic character

isBasic

boolean isBasic()
Returns:
true, if the aminoacid is of rather basic character

VeaR/JEllipse