public class ReactionManipulator extends Object
ChemModelManipulator
Constructor and Description |
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ReactionManipulator() |
Modifier and Type | Method and Description |
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static Set<IBond> |
findMappedBonds(IReaction reaction)
Collect the set of bonds that mapped in both a reactant and a product.
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static IAtomContainerSet |
getAllAgents(IReaction reaction) |
static List<IAtomContainer> |
getAllAtomContainers(IReaction reaction)
Returns all the AtomContainer's of a Reaction.
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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
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static int |
getAtomCount(IReaction reaction) |
static int |
getBondCount(IReaction reaction) |
static IChemObject |
getMappedChemObject(IReaction reaction,
IChemObject chemObject)
get the IAtom which is mapped
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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.
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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.
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static IReaction |
toReaction(IAtomContainer mol)
Converts an 'inlined' reaction stored in a molecule back to a reaction.
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public static int getAtomCount(IReaction reaction)
public static int getBondCount(IReaction reaction)
public static void removeAtomAndConnectedElectronContainers(IReaction reaction, IAtom atom)
public static void removeElectronContainer(IReaction reaction, IElectronContainer electrons)
public static IAtomContainerSet getAllMolecules(IReaction reaction)
IReaction
: reactants + products.reaction
- The IReactionpublic static IAtomContainerSet getAllProducts(IReaction reaction)
reaction
- The IReactionpublic static IAtomContainerSet getAllReactants(IReaction reaction)
reaction
- The IReactionpublic static IAtomContainerSet getAllAgents(IReaction reaction)
public static IReaction reverse(IReaction reaction)
reaction
- the reaction being consideredpublic static List<IAtomContainer> getAllAtomContainers(IReaction reaction)
reaction
- The reaction being consideredpublic static IAtomContainer getRelevantAtomContainer(IReaction reaction, IAtom atom)
public static IAtomContainer getRelevantAtomContainer(IReaction reaction, IBond bond)
public static void setAtomProperties(IReaction reaction, Object propKey, Object propVal)
public static List<IChemObject> getAllChemObjects(IReaction reaction)
public static IChemObject getMappedChemObject(IReaction reaction, IChemObject chemObject)
reaction
- The IReaction which contains the mappingchemObject
- The IChemObject which will be searched its mapped IChemObjectpublic 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).
rxn
- reaction to converttoReaction(org.openscience.cdk.interfaces.IAtomContainer)
public static IReaction toReaction(IAtomContainer mol)
Converts an 'inlined' reaction stored in a molecule back to a reaction.
mol
- molecule to converttoMolecule(IReaction)
public static Set<IBond> findMappedBonds(IReaction reaction)
CDKConstants.ATOM_ATOM_MAPPING
property of atoms.reaction
- reactionCopyright © 2021. All rights reserved.