org.openscience.cdk.tools.manipulator

Class ReactionSetManipulator

java.lang.Object

org.openscience.cdk.tools.manipulator.ReactionSetManipulator

public class ReactionSetManipulator
extends Object

See Also:

ChemModelManipulator

Source code:

master

Belongs to CDK module:

standard

Constructor Summary

Constructors

Constructor and Description
ReactionSetManipulator()

Method Summary

Modifier and Type	Method and Description
static List<IAtomContainer>	getAllAtomContainers(IReactionSet set) Returns all the AtomContainer's of a Reaction.
static List<IChemObject>	getAllChemObjects(IReactionSet set)
static List<String>	getAllIDs(IReactionSet set)
static IAtomContainerSet	getAllMolecules(IReactionSet set) get all Molecules object from a set of Reactions.
static int	getAtomCount(IReactionSet set)
static int	getBondCount(IReactionSet set)
static IReaction	getReactionByAtomContainerID(IReactionSet reactionSet, String id) Gets a reaction from a ReactionSet by ID of any product or reactant.
static IReaction	getReactionByReactionID(IReactionSet reactionSet, String id) Gets a reaction from a ReactionSet by ID.
static IAtomContainer	getRelevantAtomContainer(IReactionSet set, IAtom atom)
static IAtomContainer	getRelevantAtomContainer(IReactionSet set, IBond bond)
static IReaction	getRelevantReaction(IReactionSet set, IAtom atom)
static IReaction	getRelevantReaction(IReactionSet set, IBond bond)
static IReactionSet	getRelevantReactions(IReactionSet reactSet, IAtomContainer molecule) Get all Reactions object containing a Molecule from a set of Reactions.
static IReactionSet	getRelevantReactionsAsProduct(IReactionSet reactSet, IAtomContainer molecule) Get all Reactions object containing a Molecule as a Product from a set of Reactions.
static IReactionSet	getRelevantReactionsAsReactant(IReactionSet reactSet, IAtomContainer molecule) Get all Reactions object containing a Molecule as a Reactant from a set of Reactions.
static void	removeAtomAndConnectedElectronContainers(IReactionSet set, IAtom atom)
static void	removeElectronContainer(IReactionSet set, IElectronContainer electrons)
static void	setAtomProperties(IReactionSet set, Object propKey, Object propVal)

Methods inherited from class java.lang.Object

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

Constructor Detail

ReactionSetManipulator

public ReactionSetManipulator()

Method Detail

getAtomCount

public static int getAtomCount(IReactionSet set)

getBondCount

public static int getBondCount(IReactionSet set)

removeAtomAndConnectedElectronContainers

public static void removeAtomAndConnectedElectronContainers(IReactionSet set,
                                                            IAtom atom)

removeElectronContainer

public static void removeElectronContainer(IReactionSet set,
                                           IElectronContainer electrons)

getAllMolecules

public static IAtomContainerSet getAllMolecules(IReactionSet set)

get all Molecules object from a set of Reactions.

Parameters:

set - The set of reaction to inspect

Returns:

The IAtomContanerSet

getAllIDs

public static List<String> getAllIDs(IReactionSet set)

getAllAtomContainers

public static List<IAtomContainer> getAllAtomContainers(IReactionSet set)

Returns all the AtomContainer's of a Reaction.

Parameters:

set - the reaction set to get the molecules from

Returns:

a List containing the IAtomContainer objects in the IReactionSet

getRelevantReaction

public static IReaction getRelevantReaction(IReactionSet set,
                                            IAtom atom)

getRelevantReaction

public static IReaction getRelevantReaction(IReactionSet set,
                                            IBond bond)

getRelevantReactions

public static IReactionSet getRelevantReactions(IReactionSet reactSet,
                                                IAtomContainer molecule)

Get all Reactions object containing a Molecule from a set of Reactions.

Parameters:

reactSet - The set of reaction to inspect

molecule - The molecule to find

Returns:

The IReactionSet

getRelevantReactionsAsReactant

public static IReactionSet getRelevantReactionsAsReactant(IReactionSet reactSet,
                                                          IAtomContainer molecule)

Get all Reactions object containing a Molecule as a Reactant from a set of Reactions.

Parameters:

reactSet - The set of reaction to inspect

molecule - The molecule to find as a reactant

Returns:

The IReactionSet

getRelevantReactionsAsProduct

public static IReactionSet getRelevantReactionsAsProduct(IReactionSet reactSet,
                                                         IAtomContainer molecule)

Get all Reactions object containing a Molecule as a Product from a set of Reactions.

Parameters:

reactSet - The set of reaction to inspect

molecule - The molecule to find as a product

Returns:

The IReactionSet

getRelevantAtomContainer

public static IAtomContainer getRelevantAtomContainer(IReactionSet set,
                                                      IAtom atom)

getRelevantAtomContainer

public static IAtomContainer getRelevantAtomContainer(IReactionSet set,
                                                      IBond bond)

setAtomProperties

public static void setAtomProperties(IReactionSet set,
                                     Object propKey,
                                     Object propVal)

getAllChemObjects

public static List<IChemObject> getAllChemObjects(IReactionSet set)

getReactionByAtomContainerID

public static IReaction getReactionByAtomContainerID(IReactionSet reactionSet,
                                                     String id)

Gets a reaction from a ReactionSet by ID of any product or reactant. If several exist, only the first one will be returned.

Parameters:

reactionSet - The reactionSet to search in

id - The id to search for.

Returns:

The Reaction or null;

getReactionByReactionID

public static IReaction getReactionByReactionID(IReactionSet reactionSet,
                                                String id)

Gets a reaction from a ReactionSet by ID. If several exist, only the first one will be returned.

Parameters:

reactionSet - The reactionSet to search in

id - The id to search for.

Returns:

The Reaction or null;