Class ReactionSetManipulator
- java.lang.Object
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- org.openscience.cdk.tools.manipulator.ReactionSetManipulator
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public class ReactionSetManipulator extends Object
- See Also:
ChemModelManipulator
- Source code:
- main
- Belongs to CDK module:
- standard
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Constructor Summary
Constructors Constructor Description ReactionSetManipulator()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method 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)
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Method Detail
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getAtomCount
public static int getAtomCount(IReactionSet set)
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getBondCount
public static int getBondCount(IReactionSet set)
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removeAtomAndConnectedElectronContainers
public static void removeAtomAndConnectedElectronContainers(IReactionSet set, IAtom atom)
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removeElectronContainer
public static void removeElectronContainer(IReactionSet set, IElectronContainer electrons)
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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
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getAllIDs
public static List<String> getAllIDs(IReactionSet set)
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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
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getRelevantReaction
public static IReaction getRelevantReaction(IReactionSet set, IAtom atom)
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getRelevantReaction
public static IReaction getRelevantReaction(IReactionSet set, IBond bond)
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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 inspectmolecule
- The molecule to find- Returns:
- The IReactionSet
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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 inspectmolecule
- The molecule to find as a reactant- Returns:
- The IReactionSet
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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 inspectmolecule
- The molecule to find as a product- Returns:
- The IReactionSet
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getRelevantAtomContainer
public static IAtomContainer getRelevantAtomContainer(IReactionSet set, IAtom atom)
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getRelevantAtomContainer
public static IAtomContainer getRelevantAtomContainer(IReactionSet set, IBond bond)
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setAtomProperties
public static void setAtomProperties(IReactionSet set, Object propKey, Object propVal)
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getAllChemObjects
public static List<IChemObject> getAllChemObjects(IReactionSet set)
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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 inid
- The id to search for.- Returns:
- The Reaction or null;
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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 inid
- The id to search for.- Returns:
- The Reaction or null;
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