org.jscience.biology
Class Protein

java.lang.Object
  extended by org.jscience.biology.Protein
All Implemented Interfaces:
java.lang.Cloneable
Direct Known Subclasses:
Enzyme, Hemoglobin, Insulin

public class Protein
extends java.lang.Object
implements java.lang.Cloneable

A class representing Protein. This class accounts for peptides (small proteins) and enzyms (catalyst proteins). Proteins are also known as protides. Please note we do not represent these molecules as we should: we do not develop the formula beyond the amino acids level, therefore there are extraneous H20 molecules (as many as aminoacids minus one). Correct terminations NH2 and COOH are however included (as normal aminoacids terminations). For the same reason there is no internal binding such as dissfulfur bridges.


Constructor Summary
Protein(AminoAcid[] aminoacids)
          Creates a new Protein object.
Protein(mRNA mrna, Alphabet coding)
          Constructs a Protein molecule.
Protein(java.lang.String acids)
          Creates a new Protein object.
 
Method Summary
 Protein clone()
          DOCUMENT ME!
 AminoAcid[] getAminoAcids()
          DOCUMENT ME!
 
Methods inherited from class java.lang.Object
equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Protein

public Protein(mRNA mrna,
               Alphabet coding)
Constructs a Protein molecule. The length of the mRNA array must be a multiple of 3. Moreover, only the last codon (the last three elements of the array) should contain the stop sequence (sequence TGA, TAG, TAA or UGA, UAG, UAA, for the universal codons). This is a "pass all coding" as arrays if length not dividable by 3 are also coded as well as sequence that contain no or many stop codons (that are simply ignored).

Parameters:
mrna - DOCUMENT ME!
coding - DOCUMENT ME!
Throws:
java.lang.IllegalArgumentException - DOCUMENT ME!

Protein

public Protein(AminoAcid[] aminoacids)
Creates a new Protein object.

Parameters:
aminoacids - DOCUMENT ME!

Protein

public Protein(java.lang.String acids)
Creates a new Protein object.

Parameters:
acids - DOCUMENT ME!
Method Detail

getAminoAcids

public AminoAcid[] getAminoAcids()
DOCUMENT ME!

Returns:
DOCUMENT ME!

clone

public Protein clone()
DOCUMENT ME!

Overrides:
clone in class java.lang.Object
Returns:
DOCUMENT ME!