org.openscience.cdk.tools.manipulator

Class ReactionSchemeManipulator

java.lang.Object

org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator

public class ReactionSchemeManipulator
extends Object

See Also:

ChemModelManipulator

Source code:

master

Belongs to CDK module:

standard

Constructor Summary

Constructors

Constructor and Description
ReactionSchemeManipulator()

Method Summary

Modifier and Type	Method and Description
static IReactionScheme	createReactionScheme(IReactionSet reactionSet) Create a IReactionScheme give a IReactionSet object.
static IReactionSet	extractTopReactions(IReactionScheme reactionScheme) Extract a set of Reactions which are in top of a IReactionScheme.
static IAtomContainerSet	getAllAtomContainers(IReactionScheme scheme) get all AtomContainers object from a set of Reactions.
static IAtomContainerSet	getAllAtomContainers(IReactionScheme scheme, IAtomContainerSet molSet) Get all molecule objects from a set of Reactions given a IAtomContainerSet to add.
static List<String>	getAllIDs(IReactionScheme scheme) Get all ID of this IReactionSet.
static IReactionSet	getAllReactions(IReactionScheme scheme) Get all IReaction's object from a given IReactionScheme.
static ArrayList<IAtomContainerSet>	getAtomContainerSet(IAtomContainer origenMol, IAtomContainer finalMol, IReactionScheme reactionScheme) Extract the list of AtomContainers taking part in the IReactionScheme to originate a product given a reactant.

Methods inherited from class java.lang.Object

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

Constructor Detail

ReactionSchemeManipulator

public ReactionSchemeManipulator()

Method Detail

getAllAtomContainers

public static IAtomContainerSet getAllAtomContainers(IReactionScheme scheme,
                                                     IAtomContainerSet molSet)

Get all molecule objects from a set of Reactions given a IAtomContainerSet to add.

Parameters:

scheme - The set of reaction to inspect

molSet - The set of molecules to be added

Returns:

The IAtomContainerSet

getAllAtomContainers

public static IAtomContainerSet getAllAtomContainers(IReactionScheme scheme)

get all AtomContainers object from a set of Reactions.

Parameters:

scheme - The scheme of reaction to inspect

Returns:

The IAtomContainerSet

getAllIDs

public static List<String> getAllIDs(IReactionScheme scheme)

Get all ID of this IReactionSet.

Parameters:

scheme - The IReactionScheme to analyze

Returns:

A List with all ID

getAllReactions

public static IReactionSet getAllReactions(IReactionScheme scheme)

Get all IReaction's object from a given IReactionScheme.

Parameters:

scheme - The IReactionScheme to extract

Returns:

The IReactionSet

createReactionScheme

public static IReactionScheme createReactionScheme(IReactionSet reactionSet)

Create a IReactionScheme give a IReactionSet object.

Parameters:

reactionSet - The IReactionSet

Returns:

The IReactionScheme

extractTopReactions

public static IReactionSet extractTopReactions(IReactionScheme reactionScheme)

Extract a set of Reactions which are in top of a IReactionScheme. The top reactions are those which any of their reactants are participating in other reactions as a products.

Parameters:

reactionScheme - The IReactionScheme

Returns:

The set of top reactions

getAtomContainerSet

public static ArrayList<IAtomContainerSet> getAtomContainerSet(IAtomContainer origenMol,
                                                               IAtomContainer finalMol,
                                                               IReactionScheme reactionScheme)

Extract the list of AtomContainers taking part in the IReactionScheme to originate a product given a reactant.

Parameters:

origenMol - The start IAtomContainer

finalMol - The end IAtomContainer

reactionScheme - The IReactionScheme containing the AtomContainers

Returns:

A List of IAtomContainerSet given the path