Package org.openscience.cdk.silent

Class AtomContainerSet

java.lang.Object

org.openscience.cdk.silent.ChemObject

org.openscience.cdk.silent.AtomContainerSet

All Implemented Interfaces:

Serializable, Cloneable, Iterable<IAtomContainer>, IAtomContainerSet, ICDKObject, IChemObject, IChemObjectListener

Direct Known Subclasses:

RingSet, Substance

public class AtomContainerSet
extends ChemObject
implements Serializable, IAtomContainerSet, IChemObjectListener, Cloneable

A set of AtomContainers.

Author:

hel

See Also:

Serialized Form

Source code:

main

Belongs to CDK module:

silent

Field Summary

Fields

Modifier and Type	Field	Description
protected int	atomContainerCount	Number of AtomContainers contained by this container.
protected IAtomContainer[]	atomContainers	Array of AtomContainers.
protected int	growArraySize	Amount by which the AtomContainers array grows when elements are added and the array is not large enough for that.
protected Double[]	multipliers	Defines the number of instances of a certain molecule in the set.

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

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

Constructor Summary

Constructors

Constructor	Description
AtomContainerSet()	Constructs an empty AtomContainerSet.

Method Summary

Modifier and Type	Method	Description
void	add(IAtomContainerSet atomContainerSet)	Adds all atomContainers in the AtomContainerSet to this container.
void	addAtomContainer(IAtomContainer atomContainer)	Adds an atomContainer to this container.
void	addAtomContainer(IAtomContainer atomContainer, double multiplier)	Adds an atomContainer to this container with the given multiplier.
Iterable<IAtomContainer>	atomContainers()	Get an iterator for this AtomContainerSet.
Object	clone()	Clones this AtomContainerSet and its content.
IAtomContainer	getAtomContainer(int number)	Returns the AtomContainer at position number in the container.
int	getAtomContainerCount()	Returns the number of AtomContainers in this Container.
Double	getMultiplier(int number)	Returns the multiplier for the AtomContainer at position number in the container.
Double	getMultiplier(IAtomContainer container)	Returns the multiplier of the given AtomContainer.
Double[]	getMultipliers()	Returns an array of double with the stoichiometric coefficients of the products.
protected void	growAtomContainerArray()	Grows the atomContainer array by a given size.
boolean	isEmpty()	Returns true if this IAtomContainerSet is empty.
void	removeAllAtomContainers()	Removes all AtomContainer from this container.
void	removeAtomContainer(int pos)	Removes an AtomContainer from this container.
void	removeAtomContainer(IAtomContainer atomContainer)	Removes an AtomContainer from this container.
void	replaceAtomContainer(int position, IAtomContainer container)	Replace the AtomContainer at a specific position (array has to be large enough).
void	setMultiplier(int position, Double multiplier)	Sets the coefficient of a AtomContainer to a given value.
boolean	setMultiplier(IAtomContainer container, Double multiplier)	Sets the coefficient of a AtomContainer to a given value.
boolean	setMultipliers(Double[] newMultipliers)	Sets the multipliers of the AtomContainers.
void	sortAtomContainers(Comparator<IAtomContainer> comparator)	Sort the AtomContainers and multipliers using a provided Comparator
void	stateChanged(IChemObjectChangeEvent event)	Called by objects to which this object has registered as a listener.
String	toString()	Returns the String representation of this AtomContainerSet.

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.IAtomContainerSet

iterator

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Field Detail

atomContainers

protected IAtomContainer[] atomContainers

Array of AtomContainers.

atomContainerCount

protected int atomContainerCount

Number of AtomContainers contained by this container.

multipliers

protected Double[] multipliers

Defines the number of instances of a certain molecule in the set. It is 1 by default.

growArraySize

protected int growArraySize

Amount by which the AtomContainers array grows when elements are added and the array is not large enough for that.

Constructor Detail

AtomContainerSet

public AtomContainerSet()

Constructs an empty AtomContainerSet.

Method Detail

addAtomContainer

public void addAtomContainer(IAtomContainer atomContainer)

Adds an atomContainer to this container.

Specified by:

addAtomContainer in interface IAtomContainerSet

Parameters:

atomContainer - The atomContainer to be added to this container

removeAtomContainer

public void removeAtomContainer(IAtomContainer atomContainer)

Removes an AtomContainer from this container.

Specified by:

removeAtomContainer in interface IAtomContainerSet

Parameters:

atomContainer - The atomContainer to be removed from this container

removeAllAtomContainers

public void removeAllAtomContainers()

Removes all AtomContainer from this container.

Specified by:

removeAllAtomContainers in interface IAtomContainerSet

removeAtomContainer

public void removeAtomContainer(int pos)

Removes an AtomContainer from this container.

Specified by:

removeAtomContainer in interface IAtomContainerSet

Parameters:

pos - The position of the AtomContainer to be removed from this container

replaceAtomContainer

public void replaceAtomContainer(int position,
                                 IAtomContainer container)

Replace the AtomContainer at a specific position (array has to be large enough).

Specified by:

replaceAtomContainer in interface IAtomContainerSet

Parameters:

position - position in array for AtomContainer

container - the replacement AtomContainer

setMultiplier

public boolean setMultiplier(IAtomContainer container,
                             Double multiplier)

Sets the coefficient of a AtomContainer to a given value.

Specified by:

setMultiplier in interface IAtomContainerSet

Parameters:

container - The AtomContainer for which the multiplier is set

multiplier - The new multiplier for the AtomContatiner

Returns:

true if multiplier has been set

See Also:

getMultiplier(IAtomContainer)

setMultiplier

public void setMultiplier(int position,
                          Double multiplier)

Sets the coefficient of a AtomContainer to a given value.

Specified by:

setMultiplier in interface IAtomContainerSet

Parameters:

position - The position of the AtomContainer for which the multiplier is set in [0,..]

multiplier - The new multiplier for the AtomContatiner at position

See Also:

getMultiplier(int)

getMultipliers

public Double[] getMultipliers()

Returns an array of double with the stoichiometric coefficients of the products.

Specified by:

getMultipliers in interface IAtomContainerSet

Returns:

The multipliers for the AtomContainer's in this set

See Also:

setMultipliers(java.lang.Double[])

setMultipliers

public boolean setMultipliers(Double[] newMultipliers)

Sets the multipliers of the AtomContainers.

Specified by:

setMultipliers in interface IAtomContainerSet

Parameters:

newMultipliers - The new multipliers for the AtomContainers in this set

Returns:

true if multipliers have been set.

See Also:

getMultipliers()

addAtomContainer

public void addAtomContainer(IAtomContainer atomContainer,
                             double multiplier)

Adds an atomContainer to this container with the given multiplier.

Specified by:

addAtomContainer in interface IAtomContainerSet

Parameters:

atomContainer - The atomContainer to be added to this container

multiplier - The multiplier of this atomContainer

add

public void add(IAtomContainerSet atomContainerSet)

Adds all atomContainers in the AtomContainerSet to this container.

Specified by:

add in interface IAtomContainerSet

Parameters:

atomContainerSet - The AtomContainerSet

atomContainers

public Iterable<IAtomContainer> atomContainers()

Get an iterator for this AtomContainerSet.

Specified by:

atomContainers in interface IAtomContainerSet

Returns:

A new Iterator for this AtomContainerSet.

getAtomContainer

public IAtomContainer getAtomContainer(int number)

Returns the AtomContainer at position number in the container.

Specified by:

getAtomContainer in interface IAtomContainerSet

Parameters:

number - The position of the AtomContainer to be returned.

Returns:

The AtomContainer at position number .

getMultiplier

public Double getMultiplier(int number)

Returns the multiplier for the AtomContainer at position number in the container.

Specified by:

getMultiplier in interface IAtomContainerSet

Parameters:

number - The position of the multiplier of the AtomContainer to be returned.

Returns:

The multiplier for the AtomContainer at position number .

See Also:

setMultiplier(int, Double)

getMultiplier

public Double getMultiplier(IAtomContainer container)

Returns the multiplier of the given AtomContainer.

Specified by:

getMultiplier in interface IAtomContainerSet

Parameters:

container - The AtomContainer for which the multiplier is given

Returns:

-1, if the given molecule is not a container in this set

See Also:

setMultiplier(IAtomContainer, Double)

growAtomContainerArray

protected void growAtomContainerArray()

Grows the atomContainer array by a given size.

See Also:

growArraySize

getAtomContainerCount

public int getAtomContainerCount()

Returns the number of AtomContainers in this Container.

Specified by:

getAtomContainerCount in interface IAtomContainerSet

Returns:

The number of AtomContainers in this Container

toString

public String toString()

Returns the String representation of this AtomContainerSet.

Specified by:

toString in interface IChemObject

Overrides:

toString in class Object

Returns:

The String representation of this AtomContainerSet

clone

public Object clone()
             throws CloneNotSupportedException

Clones this AtomContainerSet 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

sortAtomContainers

public void sortAtomContainers(Comparator<IAtomContainer> comparator)

Sort the AtomContainers and multipliers using a provided Comparator

Specified by:

sortAtomContainers in interface IAtomContainerSet

Parameters:

comparator - defines the sorting method

isEmpty

public boolean isEmpty()

Returns true if this IAtomContainerSet is empty.

Specified by:

isEmpty in interface IAtomContainerSet

Returns:

a boolean indicating if this ring set no atom containers