org.proteinshader.structure
Class Heterogen

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

All Implemented Interfaces:

IDTest, Visitable

public class Heterogen
extends Residue

This concrete subclass of the abstract class Residue stores information on a heterogen in a PDB structure entry. Because water molecules are a special case of the heterogen concept, their information is stored in a Water object rather than in a Heterogen object.

Field Summary

static String

HETEROGEN_PREFIX 'HET_' will be added to the beginning the residueID for a Heterogen (if it is not already present).

Constructor Summary

Heterogen(String name, String residueID, String chainID, String modelID, String structureID)
Creates a Heterogen with the name and IDs given as arguments (after adding the HETEROGEN_PREFIX ("HET_") to the beginning of residueID).

Method Summary

void	accept(Visitor visitor) Accepts a Visitor and does a callback.
String	getName() Returns the Heterogen's name.
String	processID(String id, String typeOfID) Overrides the processID() method of Residue in order to add guarantee that the residueID of a Heterogen always begins with the HETEROGEN_PREFIX.

Methods inherited from class org.proteinshader.structure.Residue

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

Methods inherited from class java.lang.Object

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

Field Detail

HETEROGEN_PREFIX

public static final String HETEROGEN_PREFIX

'HET_' will be added to the beginning the residueID for a Heterogen (if it is not already present).

See Also:

Constant Field Values

Constructor Detail

Heterogen

public Heterogen(String name,
                 String residueID,
                 String chainID,
                 String modelID,
                 String structureID)
          throws MissingHetNameException,
                 InvalidIDException

Creates a Heterogen with the name and IDs given as arguments (after adding the HETEROGEN_PREFIX ("HET_") to the beginning of residueID). Any leading or trailing whitespace is trimmed from the residueID (before adding "HET_") and from the name.

Parameters:

name - Heterogen's name (preferably the full name).

residueID - ID of the Heterogen.

chainID - ID of the Chain.

modelID - ID of the Model.

structureID - ID of the Structure.

Throws:

MissingHetNameException - if name is null or does not have at least one non-whitespace character before add the HETEROGEN_PREFIX.

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.

getName

public String getName()

Returns the Heterogen's name. The String returned cannot be null or empty, because the constructor checks that this read-only attribute has at least one non-whitespace character.

Returns:

The Heterogen name as a String.

processID

public String processID(String id,
                        String typeOfID)
                 throws InvalidIDException

Overrides the processID() method of Residue in order to add guarantee that the residueID of a Heterogen always begins with the HETEROGEN_PREFIX. If the HETEROGEN_PREFIX is not already present, it will be added. Also, any leading or trailing whitespace will be trimmed off of the residueID.

Specified by:

processID in interface IDTest

Overrides:

processID in class Residue

Parameters:

id - Residue ID to process.

typeOfID - type of ID (for possible use in error message).

Returns:

The trimmed Residue ID beginning with the HETEROGEN_PREFIX.

Throws:

InvalidIDException - if the trimmed Residue ID does not have at least one character before adding the prefix.