org.openscience.cdk.tools.manipulator

Class ReactionManipulator

java.lang.Object

org.openscience.cdk.tools.manipulator.ReactionManipulator

public class ReactionManipulator
extends Object

See Also:

ChemModelManipulator

Source code:

master

Belongs to CDK module:

standard

Constructor Summary

Constructors

Constructor and Description
ReactionManipulator()

Method Summary

Modifier and Type	Method and Description
static Set<IBond>	findMappedBonds(IReaction reaction) Collect the set of bonds that mapped in both a reactant and a product.
static IAtomContainerSet	getAllAgents(IReaction reaction)
static List<IAtomContainer>	getAllAtomContainers(IReaction reaction) Returns all the AtomContainer's of a Reaction.
static List<IChemObject>	getAllChemObjects(IReaction reaction)
static List<String>	getAllIDs(IReaction reaction)
static IAtomContainerSet	getAllMolecules(IReaction reaction) Get all molecule of a IReaction: reactants + products.
static IAtomContainerSet	getAllProducts(IReaction reaction) get all products of a IReaction
static IAtomContainerSet	getAllReactants(IReaction reaction) get all reactants of a IReaction
static int	getAtomCount(IReaction reaction)
static int	getBondCount(IReaction reaction)
static IChemObject	getMappedChemObject(IReaction reaction, IChemObject chemObject) get the IAtom which is mapped
static IAtomContainer	getRelevantAtomContainer(IReaction reaction, IAtom atom)
static IAtomContainer	getRelevantAtomContainer(IReaction reaction, IBond bond)
static void	removeAtomAndConnectedElectronContainers(IReaction reaction, IAtom atom)
static void	removeElectronContainer(IReaction reaction, IElectronContainer electrons)
static IReaction	reverse(IReaction reaction) Returns a new Reaction object which is the reverse of the given Reaction.
static void	setAtomProperties(IReaction reaction, Object propKey, Object propVal)
static IAtomContainer	toMolecule(IReaction rxn) Converts a reaction to an 'inlined' reaction stored as a molecule.
static IReaction	toReaction(IAtomContainer mol) Converts an 'inlined' reaction stored in a molecule back to a reaction.

Methods inherited from class java.lang.Object

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

Constructor Detail

ReactionManipulator

public ReactionManipulator()

Method Detail

getAtomCount

public static int getAtomCount(IReaction reaction)

getBondCount

public static int getBondCount(IReaction reaction)

removeAtomAndConnectedElectronContainers

public static void removeAtomAndConnectedElectronContainers(IReaction reaction,
                                                            IAtom atom)

removeElectronContainer

public static void removeElectronContainer(IReaction reaction,
                                           IElectronContainer electrons)

getAllMolecules

public static IAtomContainerSet getAllMolecules(IReaction reaction)

Get all molecule of a IReaction: reactants + products.

Parameters:

reaction - The IReaction

Returns:

The IAtomContainerSet

getAllProducts

public static IAtomContainerSet getAllProducts(IReaction reaction)

get all products of a IReaction

Parameters:

reaction - The IReaction

Returns:

The IAtomContainerSet

getAllReactants

public static IAtomContainerSet getAllReactants(IReaction reaction)

get all reactants of a IReaction

Parameters:

reaction - The IReaction

Returns:

The IAtomContainerSet

getAllAgents

public static IAtomContainerSet getAllAgents(IReaction reaction)

reverse

public static IReaction reverse(IReaction reaction)

Returns a new Reaction object which is the reverse of the given Reaction.

Parameters:

reaction - the reaction being considered

Returns:

the reverse reaction

getAllAtomContainers

public static List<IAtomContainer> getAllAtomContainers(IReaction reaction)

Returns all the AtomContainer's of a Reaction.

Parameters:

reaction - The reaction being considered

Returns:

a list of the IAtomContainer objects comprising the reaction

getAllIDs

public static List<String> getAllIDs(IReaction reaction)

getRelevantAtomContainer

public static IAtomContainer getRelevantAtomContainer(IReaction reaction,
                                                      IAtom atom)

getRelevantAtomContainer

public static IAtomContainer getRelevantAtomContainer(IReaction reaction,
                                                      IBond bond)

setAtomProperties

public static void setAtomProperties(IReaction reaction,
                                     Object propKey,
                                     Object propVal)

getAllChemObjects

public static List<IChemObject> getAllChemObjects(IReaction reaction)

getMappedChemObject

public static IChemObject getMappedChemObject(IReaction reaction,
                                              IChemObject chemObject)

get the IAtom which is mapped

Parameters:

reaction - The IReaction which contains the mapping

chemObject - The IChemObject which will be searched its mapped IChemObject

Returns:

The mapped IChemObject

toMolecule

public static IAtomContainer toMolecule(IReaction rxn)

Converts a reaction to an 'inlined' reaction stored as a molecule. All reactants, agents, products are added to the molecule as disconnected components with atoms flagged as to their role ReactionRole and component group.

The inlined reaction, stored in a molecule can be converted back to an explicit reaction with toReaction(org.openscience.cdk.interfaces.IAtomContainer). Data stored on the individual components (e.g. titles is lost in the conversion).

Parameters:

rxn - reaction to convert

Returns:

inlined reaction stored in a molecule

See Also:

toReaction(org.openscience.cdk.interfaces.IAtomContainer)

toReaction

public static IReaction toReaction(IAtomContainer mol)

Converts an 'inlined' reaction stored in a molecule back to a reaction.

Parameters:

mol - molecule to convert

Returns:

reaction

See Also:

toMolecule(IReaction)

findMappedBonds

public static Set<IBond> findMappedBonds(IReaction reaction)

Collect the set of bonds that mapped in both a reactant and a product. The method uses the CDKConstants.ATOM_ATOM_MAPPING property of atoms.

Parameters:

reaction - reaction

Returns:

mapped bonds