Class ReactionSchemeManipulator
- java.lang.Object
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- org.openscience.cdk.tools.manipulator.ReactionSchemeManipulator
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public class ReactionSchemeManipulator extends Object
- See Also:
ChemModelManipulator
- Source code:
- main
- Belongs to CDK module:
- standard
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Constructor Summary
Constructors Constructor Description ReactionSchemeManipulator()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method 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 aIAtomContainerSet
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.
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Method Detail
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getAllAtomContainers
public static IAtomContainerSet getAllAtomContainers(IReactionScheme scheme, IAtomContainerSet molSet)
Get all molecule objects from a set of Reactions given aIAtomContainerSet
to add.- Parameters:
scheme
- The set of reaction to inspectmolSet
- The set of molecules to be added- Returns:
- The IAtomContainerSet
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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
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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
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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
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createReactionScheme
public static IReactionScheme createReactionScheme(IReactionSet reactionSet)
Create a IReactionScheme give a IReactionSet object.- Parameters:
reactionSet
- The IReactionSet- Returns:
- The IReactionScheme
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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
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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 IAtomContainerfinalMol
- The end IAtomContainerreactionScheme
- The IReactionScheme containing the AtomContainers- Returns:
- A List of IAtomContainerSet given the path
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