org.proteinshader.structure
Class Water

java.lang.Object
  org.proteinshader.structure.Residue
      org.proteinshader.structure.Water

All Implemented Interfaces:

IDTest, Visitable

public class Water
extends Residue

This concrete subclass of the abstract class Residue stores information on a water molecule in a PDB structure entry.

Constructor Summary

Water(String residueID, String chainID, String modelID, String structureID)
Constructs a Water with the requested residueID.

Method Summary

void	accept(Visitor visitor) Accepts a Visitor and does a callback.
Atom	getO() Returns the oxygen Atom (or null if not found).

Methods inherited from class org.proteinshader.structure.Residue

addNewAtom, getAtom, getChainID, getModelID, getResidueID, getStructureID, iteratorAtoms, numberOfAtoms, processID, toString

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

Water

public Water(String residueID,
             String chainID,
             String modelID,
             String structureID)
      throws InvalidIDException

Constructs a Water with the requested residueID. When read from a PDB formatted file, the residueID is normally in a form such as "HOH 50" where "HOH" is the residue name and the integer is the residue sequence number. An leading or trailing whitespace will be trimmed from the residueId before it is stored.

Parameters:

residueID - the ID of the Water.

chainID - the ID of the Chain the Water is associated with.

modelID - the ID of the Model the Water is associated with.

structureID - the ID of the Structure the Water is associated with.

Throws:

InvalidIDException - if residueID is null or does not have at least one non-whitespace character.

Method Detail

accept

public void accept(Visitor visitor)
            throws VisitorException

Accepts a Visitor and does a callback.

Specified by:

accept in interface Visitable

Specified by:

accept in class Residue

Parameters:

visitor - the Visitor to do a callback with.

Throws:

VisitorException - if an error occurs while an object is being visited.

getO

public Atom getO()

Returns the oxygen Atom (or null if not found).

Returns:

The oxygen Atom.