Package org.openscience.cdk.tools.manipulator

Class ReactionManipulator

java.lang.Object

org.openscience.cdk.tools.manipulator.ReactionManipulator

public class ReactionManipulator
extends Object

Provides a variety of methods to manipulate and convert from/to IReaction.

Author:

uli-f

See Also:

ChemModelManipulator

Source code:

main

Belongs to CDK module:

standard

Constructor Summary

Constructors

Constructor	Description
ReactionManipulator()

Method Summary

Modifier and Type	Method	Description
static void	clearAtomConfigurations(IReaction reaction)	This method will reset all atom properties related to atom configuration to the value CDKConstants.UNSET.
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)	Returns all agents of an IReaction.
static List<IAtomContainer>	getAllAtomContainers(IReaction reaction)	Returns all IAtomContainers of the given reaction.
static List<IChemObject>	getAllChemObjects(IReaction reaction)
static List<String>	getAllIDs(IReaction reaction)
static IAtomContainerSet	getAllMolecules(IReaction reaction)	Returns all components of an IReaction, that is, reactants, agents and products.
static IAtomContainerSet	getAllProducts(IReaction reaction)	Returns all products of an IReaction.
static IAtomContainerSet	getAllReactants(IReaction reaction)	Returns all reactants of an IReaction.
static int	getAtomCount(IReaction reaction)	Returns the total number of atoms for all components of the given reaction.
static int	getBondCount(IReaction reaction)	Returns the total number of atoms for all components of the given reaction.
static IChemObject	getMappedChemObject(IReaction reaction, IChemObject chemObject)	Returns the IAtom that is mapped.
static IAtomContainer	getRelevantAtomContainer(IReaction reaction, IAtom atom)
static IAtomContainer	getRelevantAtomContainer(IReaction reaction, IBond bond)
static void	perceiveAtomTypesAndConfigureAtoms(IReaction reaction)	Convenience method to perceive atom types for all IAtoms of all components of the provided IReaction.
static void	perceiveAtomTypesAndConfigureUnsetProperties(IReaction reaction)	Convenience method to perceive atom types for all IAtoms of all components of the provided IReaction.
static void	removeAtomAndConnectedElectronContainers(IReaction reaction, IAtom atom)	Removes the provided atom and its connected electron containers from the reaction.
static void	removeElectronContainer(IReaction reaction, IElectronContainer electrons)	Removes the provided electrons from the reaction.
static IReaction	reverse(IReaction reaction)	Returns a new IReaction 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)

Returns the total number of atoms for all components of the given reaction.

Parameters:

reaction - the number of atoms is summed up for all components of this reaction

Returns:

total number of atoms for all IAtomContainer that are part of this reaction

getBondCount

public static int getBondCount(IReaction reaction)

Returns the total number of atoms for all components of the given reaction.

Parameters:

reaction - the number of atoms is summed up for all components of this reaction

Returns:

total number of atoms for all IAtomContainer that are part of this reaction

removeAtomAndConnectedElectronContainers

public static void removeAtomAndConnectedElectronContainers(IReaction reaction,
                                                            IAtom atom)

Removes the provided atom and its connected electron containers from the reaction.

Parameters:

reaction - reaction the atom is removed from

atom - atom that is removed

removeElectronContainer

public static void removeElectronContainer(IReaction reaction,
                                           IElectronContainer electrons)

Removes the provided electrons from the reaction.

Parameters:

reaction - reaction the electron container is removed from

electrons - electron container that is removed

getAllMolecules

public static IAtomContainerSet getAllMolecules(IReaction reaction)

Returns all components of an IReaction, that is, reactants, agents and products.

Parameters:

reaction - all components of this reaction are returned

Returns:

IAtomContainerSet containing all components of the reaction provided as an argument

getAllProducts

public static IAtomContainerSet getAllProducts(IReaction reaction)

Returns all products of an IReaction.

Parameters:

reaction - all products of this reaction are returned

Returns:

IAtomContainerSet containing all products of the reaction provided as an argument

getAllReactants

public static IAtomContainerSet getAllReactants(IReaction reaction)

Returns all reactants of an IReaction.

Parameters:

reaction - all reactants of this reaction are returned

Returns:

IAtomContainerSet containing all reactants of the reaction provided as an argument

getAllAgents

public static IAtomContainerSet getAllAgents(IReaction reaction)

Returns all agents of an IReaction.

Parameters:

reaction - all agents of this reaction are returned

Returns:

IAtomContainerSet containing all agents of the reaction provided as an argument

reverse

public static IReaction reverse(IReaction reaction)

Returns a new IReaction which is the reverse of the given reaction. The IAtomContainers of the reversed reaction that is returned are the same that are part of the reaction provided as an argument.

Parameters:

reaction - the reaction being considered

Returns:

the reverse reaction

getAllAtomContainers

public static List<IAtomContainer> getAllAtomContainers(IReaction reaction)

Returns all IAtomContainers of the given reaction.

Parameters:

reaction - the reaction whose IAtomContainers are returned

Returns:

list of IAtomContainers 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)

Returns the IAtom that is mapped.

Parameters:

reaction - reaction that contains the mapping

chemObject - IChemObject which will be searched for the mapped IChemObject

Returns:

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

perceiveAtomTypesAndConfigureAtoms

public static void perceiveAtomTypesAndConfigureAtoms(IReaction reaction)
                                               throws CDKException

Convenience method to perceive atom types for all IAtoms of all components of the provided IReaction. This method uses the CDKAtomTypeMatcher. If the matcher finds a matching atom type, the IAtom will be configured to have the same properties as the IAtomType. If no matching atom type is found, no configuration is performed.
This method overwrites existing values.

Parameters:

reaction - the reaction whose atom types are to be perceived

Throws:

CDKException - thrown if an error is encountered when finding matching atom types

See Also:

AtomTypeManipulator.configure(IAtom, IAtomType)

perceiveAtomTypesAndConfigureUnsetProperties

public static void perceiveAtomTypesAndConfigureUnsetProperties(IReaction reaction)
                                                         throws CDKException

Convenience method to perceive atom types for all IAtoms of all components of the provided IReaction. This method uses the CDKAtomTypeMatcher. If the matcher finds a matching atom type, the IAtom will be configured to have the same properties as the IAtomType. If no matching atom type is found, no configuration is performed.
This method only sets null values.

Parameters:

reaction - the reaction whose atom types are to be perceived

Throws:

CDKException - thrown if an error is encountered when finding matching atom types

See Also:

AtomTypeManipulator.configureUnsetProperties(IAtom, IAtomType)

clearAtomConfigurations

public static void clearAtomConfigurations(IReaction reaction)

This method will reset all atom properties related to atom configuration to the value CDKConstants.UNSET.
This method reverses most of the effects of perceiveAtomTypesAndConfigureAtoms(org.openscience.cdk.interfaces.IReaction) and after a call to this method all atoms will be "unconfigured".
Note that this method is not a complete reversal of perceiveAtomTypesAndConfigureAtoms(org.openscience.cdk.interfaces.IReaction) since the atomic symbol of the atoms remain unchanged. Also, all flags that were set by the configuration method (such as IChemObject.HYDROGEN_BOND_ACCEPTOR or IChemObject.AROMATIC) will be set to False.

Parameters:

reaction - the reaction whose atoms confiuration properties are to be cleared

See Also:

perceiveAtomTypesAndConfigureAtoms(org.openscience.cdk.interfaces.IReaction)