org.openscience.cdk.interfaces

Interface IAtomContainerSet

All Superinterfaces:

Cloneable, ICDKObject, IChemObject

All Known Subinterfaces:

IRingSet, ISubstance

All Known Implementing Classes:

AtomContainerSet, AtomContainerSet, DebugAtomContainerSet, DebugRingSet, DebugSubstance, RingSet, RingSet, Substance, Substance

public interface IAtomContainerSet
extends IChemObject

A set of AtomContainers.

Author:

egonw

Source code:

master

Belongs to CDK module:

interfaces

Method Summary

Modifier and Type	Method and 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 Iterable for this AtomContainerSet.
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(IAtomContainer container) Returns the multiplier of the given AtomContainer.
Double	getMultiplier(int number) Returns the multiplier for the AtomContainer at position number in the container.
Double[]	getMultipliers() Returns an array of double with the stoichiometric coefficients of the products.
boolean	isEmpty() Returns true if this IAtomContainerSet is empty.
void	removeAllAtomContainers() Removes all AtomContainer from this container.
void	removeAtomContainer(IAtomContainer atomContainer) Removes an AtomContainer from this container.
void	removeAtomContainer(int pos) 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).
boolean	setMultiplier(IAtomContainer container, Double multiplier) Sets the coefficient of a AtomContainer to a given value.
void	setMultiplier(int position, 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 using a provided Comparator.

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

addListener, addProperties, clone, getFlag, getFlags, getFlagValue, getID, getListenerCount, getNotification, getProperties, getProperty, getProperty, notifyChanged, notifyChanged, removeListener, removeProperty, setFlag, setFlags, setID, setNotification, setProperties, setProperty, toString

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

getBuilder

Method Detail

addAtomContainer

void addAtomContainer(IAtomContainer atomContainer)

Adds an atomContainer to this container.

Parameters:

atomContainer - The atomContainer to be added to this container

removeAtomContainer

void removeAtomContainer(IAtomContainer atomContainer)

Removes an AtomContainer from this container.

Parameters:

atomContainer - The atomContainer to be removed from this container

removeAllAtomContainers

void removeAllAtomContainers()

Removes all AtomContainer from this container.

removeAtomContainer

void removeAtomContainer(int pos)

Removes an AtomContainer from this container.

Parameters:

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

replaceAtomContainer

void replaceAtomContainer(int position,
                          IAtomContainer container)

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

Parameters:

position - position in array for AtomContainer

container - the replacement AtomContainer

setMultiplier

boolean setMultiplier(IAtomContainer container,
                      Double multiplier)

Sets the coefficient of a AtomContainer to a given value.

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

void setMultiplier(int position,
                   Double multiplier)

Sets the coefficient of a AtomContainer to a given value.

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

Double[] getMultipliers()

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

Returns:

The multipliers for the AtomContainer's in this set

See Also:

setMultipliers(java.lang.Double[])

setMultipliers

boolean setMultipliers(Double[] newMultipliers)

Sets the multipliers of the AtomContainers.

Parameters:

newMultipliers - The new multipliers for the AtomContainers in this set

Returns:

true if multipliers have been set.

See Also:

getMultipliers()

addAtomContainer

void addAtomContainer(IAtomContainer atomContainer,
                      double multiplier)

Adds an atomContainer to this container with the given multiplier.

Parameters:

atomContainer - The atomContainer to be added to this container

multiplier - The multiplier of this atomContainer

add

void add(IAtomContainerSet atomContainerSet)

Adds all atomContainers in the AtomContainerSet to this container.

Parameters:

atomContainerSet - The AtomContainerSet

atomContainers

Iterable<IAtomContainer> atomContainers()

Get an Iterable for this AtomContainerSet.

Returns:

A new Iterable for this AtomContainerSet.

getAtomContainer

IAtomContainer getAtomContainer(int number)

Returns the AtomContainer at position number in the container.

Parameters:

number - The position of the AtomContainer to be returned.

Returns:

The AtomContainer at position number .

getMultiplier

Double getMultiplier(int number)

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

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

Double getMultiplier(IAtomContainer container)

Returns the multiplier of the given AtomContainer.

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)

getAtomContainerCount

int getAtomContainerCount()

Returns the number of AtomContainers in this Container.

Returns:

The number of AtomContainers in this Container

sortAtomContainers

void sortAtomContainers(Comparator<IAtomContainer> comparator)

Sort the AtomContainers using a provided Comparator.

Parameters:

comparator - defines the sorting method

isEmpty

boolean isEmpty()

Returns true if this IAtomContainerSet is empty.

Returns:

a boolean indicating if this ring set no atom containers