org.openscience.cdk.tools.manipulator

Class ChemModelManipulator

java.lang.Object

org.openscience.cdk.tools.manipulator.ChemModelManipulator

public class ChemModelManipulator
extends Object

Class with convenience methods that provide methods from methods from ChemObjects within the ChemModel. For example:

 ChemModelManipulator.removeAtom(chemModel, atom);
 

will find the Atom in the model by traversing the ChemModel's MoleculeSet, Crystal and ReactionSet fields and remove it with the removeAtom(Atom) method.

See Also:

AtomContainer.removeAtomAndConnectedElectronContainers(IAtom)

Source code:

master

Belongs to CDK module:

standard

Constructor Summary

Constructors

Constructor and Description
ChemModelManipulator()

Method Summary

Modifier and Type	Method and Description
static IAtomContainer	createNewMolecule(IChemModel chemModel) Adds a new Molecule to the MoleculeSet inside a given ChemModel.
static List<IAtomContainer>	getAllAtomContainers(IChemModel chemModel) Returns all the AtomContainer's of a ChemModel.
static List<IChemObject>	getAllChemObjects(IChemModel chemModel) Retrieve a List of all ChemObject objects within an IChemModel.
static List<String>	getAllIDs(IChemModel chemModel)
static int	getAtomCount(IChemModel chemModel) Get the total number of atoms inside an IChemModel.
static int	getBondCount(IChemModel chemModel) Get the total number of bonds inside an IChemModel.
static IAtomContainer	getRelevantAtomContainer(IChemModel chemModel, IAtom atom) This badly named methods tries to determine which AtomContainer in the ChemModel is best suited to contain added Atom's and Bond's.
static IAtomContainer	getRelevantAtomContainer(IChemModel chemModel, IBond bond) Retrieves the first IAtomContainer containing a given IBond from an IChemModel.
static IReaction	getRelevantReaction(IChemModel chemModel, IAtom atom) Retrieves the first IReaction containing a given IAtom from an IChemModel.
static IChemModel	newChemModel(IAtomContainer atomContainer) Create a new ChemModel containing an IAtomContainer.
static void	removeAtomAndConnectedElectronContainers(IChemModel chemModel, IAtom atom) Remove an Atom and the connected ElectronContainers from all AtomContainers inside an IChemModel.
static void	removeElectronContainer(IChemModel chemModel, IElectronContainer electrons) Remove an ElectronContainer from all AtomContainers inside an IChemModel.
static void	setAtomProperties(IChemModel chemModel, Object propKey, Object propVal) Sets the AtomProperties of all Atoms inside an IChemModel.

Methods inherited from class java.lang.Object

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

Constructor Detail

ChemModelManipulator

public ChemModelManipulator()

Method Detail

getAtomCount

public static int getAtomCount(IChemModel chemModel)

Get the total number of atoms inside an IChemModel.

Parameters:

chemModel - The IChemModel object.

Returns:

The number of Atom object inside.

getBondCount

public static int getBondCount(IChemModel chemModel)

Get the total number of bonds inside an IChemModel.

Parameters:

chemModel - The IChemModel object.

Returns:

The number of Bond object inside.

removeAtomAndConnectedElectronContainers

public static void removeAtomAndConnectedElectronContainers(IChemModel chemModel,
                                                            IAtom atom)

Remove an Atom and the connected ElectronContainers from all AtomContainers inside an IChemModel.

Parameters:

chemModel - The IChemModel object.

atom - The Atom object to remove.

removeElectronContainer

public static void removeElectronContainer(IChemModel chemModel,
                                           IElectronContainer electrons)

Remove an ElectronContainer from all AtomContainers inside an IChemModel.

Parameters:

chemModel - The IChemModel object.

electrons - The ElectronContainer to remove.

createNewMolecule

public static IAtomContainer createNewMolecule(IChemModel chemModel)

Adds a new Molecule to the MoleculeSet inside a given ChemModel. Creates a MoleculeSet if none is contained.

Parameters:

chemModel - The ChemModel object.

Returns:

The created Molecule object.

newChemModel

public static IChemModel newChemModel(IAtomContainer atomContainer)

Create a new ChemModel containing an IAtomContainer. It will create an IAtomContainer from the passed IAtomContainer when needed, which may cause information loss.

Parameters:

atomContainer - The AtomContainer to have inside the ChemModel.

Returns:

The new IChemModel object.

getRelevantAtomContainer

public static IAtomContainer getRelevantAtomContainer(IChemModel chemModel,
                                                      IAtom atom)

This badly named methods tries to determine which AtomContainer in the ChemModel is best suited to contain added Atom's and Bond's.

getRelevantAtomContainer

public static IAtomContainer getRelevantAtomContainer(IChemModel chemModel,
                                                      IBond bond)

Retrieves the first IAtomContainer containing a given IBond from an IChemModel.

Parameters:

chemModel - The IChemModel object.

bond - The IBond object to search.

Returns:

The IAtomContainer object found, null if none is found.

getRelevantReaction

public static IReaction getRelevantReaction(IChemModel chemModel,
                                            IAtom atom)

Retrieves the first IReaction containing a given IAtom from an IChemModel.

Parameters:

chemModel - The IChemModel object.

atom - The IAtom object to search.

Returns:

The IAtomContainer object found, null if none is found.

getAllAtomContainers

public static List<IAtomContainer> getAllAtomContainers(IChemModel chemModel)

Returns all the AtomContainer's of a ChemModel.

setAtomProperties

public static void setAtomProperties(IChemModel chemModel,
                                     Object propKey,
                                     Object propVal)

Sets the AtomProperties of all Atoms inside an IChemModel.

Parameters:

chemModel - The IChemModel object.

propKey - The key of the property.

propVal - The value of the property.

getAllChemObjects

public static List<IChemObject> getAllChemObjects(IChemModel chemModel)

Retrieve a List of all ChemObject objects within an IChemModel.

Parameters:

chemModel - The IChemModel object.

Returns:

A List of all ChemObjects inside.

getAllIDs

public static List<String> getAllIDs(IChemModel chemModel)