Class Water

  extended by org.proteinshader.structure.Residue
      extended by 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


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.

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


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
visitor - the Visitor to do a callback with.
VisitorException - if an error occurs while an object is being visited.


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

The oxygen Atom.

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