ProGAL.proteins.structure
Class AminoAcidChain

java.lang.Object
  ProGAL.proteins.structure.AminoAcidChain

Direct Known Subclasses:

SheetLoopStructure

public class AminoAcidChain
extends java.lang.Object

A chain of amino acids. This class together with AminoAcid, Atom and CBond are meant as convenient methods to maintain and traverse a protein structure. There are no methods for changing a protein structure (such classes could appropriately extend AminoAcidChain). Furthermore the pointers between amino acids and atoms are not meant to be changed. The types of atoms and covalent bonds are defined by an AtomGenerator. In a Model-View-Control framework this class together with AminoAcid, Atom and CBond are meant as the model.

Author:

R.Fonseca

Constructor Summary

AminoAcidChain(java.lang.String sequence)

AminoAcidChain(java.lang.String sequence, AtomGenerator ag)

Method Summary

AminoAcid	aminoAcid(int res)
AminoAcid[]	aminoAcids()
Atom	atom(int res, int atomNumber)
Atom	atom(int res, java.lang.String name)
Atom[]	atoms()
CBond[]	covalentBonds()

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AminoAcidChain

public AminoAcidChain(java.lang.String sequence)

AminoAcidChain

public AminoAcidChain(java.lang.String sequence,
                      AtomGenerator ag)

Method Detail

aminoAcids

public AminoAcid[] aminoAcids()

aminoAcid

public AminoAcid aminoAcid(int res)

atom

public Atom atom(int res,
                 java.lang.String name)

atom

public Atom atom(int res,
                 int atomNumber)

atoms

public Atom[] atoms()

covalentBonds

public CBond[] covalentBonds()