Package org.openscience.cdk.silent

Class ChemModel

java.lang.Object

org.openscience.cdk.silent.ChemObject

org.openscience.cdk.silent.ChemModel

All Implemented Interfaces:

Serializable, Cloneable, ICDKObject, IChemModel, IChemObject, IChemObjectListener

public class ChemModel
extends ChemObject
implements Serializable, IChemModel, IChemObjectListener, Cloneable

An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
protected ICrystal	crystal	A Crystal.
protected IRingSet	ringSet	A RingSet.
protected IAtomContainerSet	setOfMolecules	A MoleculeSet.
protected IReactionSet	setOfReactions	A ReactionSet.

Fields inherited from interface org.openscience.cdk.interfaces.IChemObject

ALIPHATIC, AROMATIC, CONJUGATED, HYDROGEN_BOND_ACCEPTOR, HYDROGEN_BOND_DONOR, IN_RING, MAPPED, MARKUSH, NOT_IN_RING, PLACED, REACTIVE_CENTER, SINGLE_OR_DOUBLE, TYPEABLE, VISITED

Constructor Summary

Constructors

Constructor	Description
ChemModel()	Constructs an new ChemModel with a null setOfMolecules.

Method Summary

Modifier and Type	Method	Description
Object	clone()	Clones this ChemModel and its content.
ICrystal	getCrystal()	Gets the Crystal contained in this ChemModel.
IAtomContainerSet	getMoleculeSet()	Returns the MoleculeSet of this ChemModel.
IReactionSet	getReactionSet()	Gets the ReactionSet contained in this ChemModel.
IRingSet	getRingSet()	Returns the RingSet of this ChemModel.
boolean	isEmpty()	Returns true if this ChemModel is empty.
void	setCrystal(ICrystal crystal)	Sets the Crystal contained in this ChemModel.
void	setMoleculeSet(IAtomContainerSet setOfMolecules)	Sets the MoleculeSet of this ChemModel.
void	setReactionSet(IReactionSet sor)	Sets the ReactionSet contained in this ChemModel.
void	setRingSet(IRingSet ringSet)	Sets the RingSet of this ChemModel.
void	stateChanged(IChemObjectChangeEvent event)	Called by objects to which this object has registered as a listener.
String	toString()	Returns a String representation of the contents of this IChemObject.

Methods inherited from class org.openscience.cdk.silent.ChemObject

addListener, addProperties, clear, compare, flags, getBuilder, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty, shallowCopy

Methods inherited from class java.lang.Object

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

Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject

getBuilder

Methods inherited from interface org.openscience.cdk.interfaces.IChemObject

addListener, addProperties, clear, flags, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, is, notifyChanged, notifyChanged, removeListener, removeProperty, set, setFlag, setFlags, setID, setNotification, setProperties, setProperty

Field Details

setOfMolecules

protected IAtomContainerSet setOfMolecules

A MoleculeSet.

setOfReactions

protected IReactionSet setOfReactions

A ReactionSet.

ringSet

protected IRingSet ringSet

A RingSet.

crystal

protected ICrystal crystal

A Crystal.

Constructor Details

ChemModel

public ChemModel()

Constructs an new ChemModel with a null setOfMolecules.

Method Details

getMoleculeSet

public IAtomContainerSet getMoleculeSet()

Returns the MoleculeSet of this ChemModel.

Specified by:

getMoleculeSet in interface IChemModel

Returns:

The MoleculeSet of this ChemModel

See Also:

• setMoleculeSet(org.openscience.cdk.interfaces.IAtomContainerSet)

setMoleculeSet

public void setMoleculeSet(IAtomContainerSet setOfMolecules)

Sets the MoleculeSet of this ChemModel.

Specified by:

setMoleculeSet in interface IChemModel

Parameters:

setOfMolecules - the content of this model

See Also:

• getMoleculeSet()

getRingSet

public IRingSet getRingSet()

Returns the RingSet of this ChemModel.

Specified by:

getRingSet in interface IChemModel

Returns:

the ringset of this model

See Also:

• setRingSet(org.openscience.cdk.interfaces.IRingSet)

setRingSet

public void setRingSet(IRingSet ringSet)

Sets the RingSet of this ChemModel.

Specified by:

setRingSet in interface IChemModel

Parameters:

ringSet - the content of this model

See Also:

• getRingSet()

getCrystal

public ICrystal getCrystal()

Gets the Crystal contained in this ChemModel.

Specified by:

getCrystal in interface IChemModel

Returns:

The crystal in this model

See Also:

• setCrystal(org.openscience.cdk.interfaces.ICrystal)

setCrystal

public void setCrystal(ICrystal crystal)

Sets the Crystal contained in this ChemModel.

Specified by:

setCrystal in interface IChemModel

Parameters:

crystal - the Crystal to store in this model

See Also:

• getCrystal()

getReactionSet

public IReactionSet getReactionSet()

Gets the ReactionSet contained in this ChemModel.

Specified by:

getReactionSet in interface IChemModel

Returns:

The ReactionSet in this model

See Also:

• setReactionSet(org.openscience.cdk.interfaces.IReactionSet)

setReactionSet

public void setReactionSet(IReactionSet sor)

Sets the ReactionSet contained in this ChemModel.

Specified by:

setReactionSet in interface IChemModel

Parameters:

sor - the ReactionSet to store in this model

See Also:

• getReactionSet()

toString

public String toString()

Returns a String representation of the contents of this IChemObject.

Specified by:

toString in interface IChemObject

Overrides:

toString in class Object

Returns:

String representation of content

clone

public Object clone()
             throws CloneNotSupportedException

Clones this ChemModel and its content.

Specified by:

clone in interface IChemObject

Overrides:

clone in class ChemObject

Returns:

The cloned object

Throws:

CloneNotSupportedException - if the IChemObject cannot be cloned

stateChanged

public void stateChanged(IChemObjectChangeEvent event)

Called by objects to which this object has registered as a listener.

Specified by:

stateChanged in interface IChemObjectListener

Parameters:

event - A change event pointing to the source of the change

isEmpty

public boolean isEmpty()

Returns true if this ChemModel is empty.

Specified by:

isEmpty in interface IChemModel

Returns:

a boolean indicating if this model has no content