Package org.openscience.cdk.libio.cml

Class MDMoleculeCustomizer

java.lang.Object

org.openscience.cdk.libio.cml.MDMoleculeCustomizer

All Implemented Interfaces:

ICMLCustomizer

public class MDMoleculeCustomizer
extends Object
implements ICMLCustomizer

Customize persistence of MDMolecule by adding support for residues and charge groups.

Author:

ola

Source code:

main

Belongs to CDK module:

libiomd

Belongs to the set:

libio-cml-customizers

Constructor Summary

Constructors

Constructor	Description
MDMoleculeCustomizer()

Method Summary

Modifier and Type	Method	Description
void	customize(IAtomContainer molecule, Object nodeToAdd)	Customize Molecule.
void	customize(IAtom atom, Object nodeToAdd)	Customize Atom.
void	customize(IBond bond, Object nodeToAdd)	No customization for bonds.

Methods inherited from class java.lang.Object

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

Constructor Details

MDMoleculeCustomizer

public MDMoleculeCustomizer()

Method Details

customize

public void customize(IBond bond,
 Object nodeToAdd)
               throws Exception

No customization for bonds.

Specified by:

customize in interface ICMLCustomizer

Parameters:

bond - Bond to base the customization on

nodeToAdd - XOM Element to customize

Throws:

Exception - thrown if nodeToAdd is not an instance of nu.xom.Element

customize

public void customize(IAtom atom,
 Object nodeToAdd)
               throws Exception

Customize Atom.

Specified by:

customize in interface ICMLCustomizer

Parameters:

atom - Atom to base the customization on

nodeToAdd - XOM Element to customize

Throws:

Exception - thrown if nodeToAdd is not an instance of nu.xom.Element

customize

public void customize(IAtomContainer molecule,
 Object nodeToAdd)
               throws Exception

Customize Molecule.

Specified by:

customize in interface ICMLCustomizer

Parameters:

molecule - Molecule to base the customization on

nodeToAdd - XOM Element to customize

Throws:

Exception - thrown if nodeToAdd is not an instance of nu.xom.Element