Uses of Interface
org.openscience.cdk.interfaces.IAtomContainerSet

Packages that use IAtomContainerSet

Package	Description
org.openscience.cdk
org.openscience.cdk.charges
org.openscience.cdk.debug
org.openscience.cdk.graph
org.openscience.cdk.graph.invariant
org.openscience.cdk.interfaces
org.openscience.cdk.io
org.openscience.cdk.io.cml
org.openscience.cdk.io.pubchemxml
org.openscience.cdk.layout
org.openscience.cdk.libio.cml
org.openscience.cdk.modeling.builder3d
org.openscience.cdk.reaction
org.openscience.cdk.reaction.mechanism
org.openscience.cdk.reaction.type
org.openscience.cdk.renderer
org.openscience.cdk.silent
org.openscience.cdk.smsd.algorithm.rgraph
org.openscience.cdk.structgen.stochastic
org.openscience.cdk.tools
org.openscience.cdk.tools.manipulator
org.openscience.cdk.validate

Uses of IAtomContainerSet in org.openscience.cdk

Classes in org.openscience.cdk that implement IAtomContainerSet

Modifier and Type	Class	Description
class	AtomContainerSet	A set of AtomContainers.
class	RingSet	Maintains a set of Ring objects.
class	Substance	An implementation of the ISubstance interface.

Fields in org.openscience.cdk declared as IAtomContainerSet

Modifier and Type	Field	Description
protected IAtomContainerSet	Reaction.agents	These are the used solvent, catalysts etc that normally appear above the reaction arrow
protected IAtomContainerSet	Reaction.products
protected IAtomContainerSet	Reaction.reactants
protected IAtomContainerSet	ChemModel.setOfMolecules	A MoleculeSet.

Methods in org.openscience.cdk that return IAtomContainerSet

Modifier and Type	Method	Description
IAtomContainerSet	Reaction.getAgents()	Returns a MoleculeSet containing the agents in this reaction.
IAtomContainerSet	ChemModel.getMoleculeSet()	Returns the MoleculeSet of this ChemModel.
IAtomContainerSet	Reaction.getProducts()	Returns a MoleculeSet containing the products of this reaction.
IAtomContainerSet	Reaction.getReactants()	Returns a MoleculeSet containing the reactants in this reaction.

Methods in org.openscience.cdk with parameters of type IAtomContainerSet

Modifier and Type	Method	Description
void	AtomContainerSet.add(IAtomContainerSet atomContainerSet)	Adds all atomContainers in the AtomContainerSet to this container.
void	ChemModel.setMoleculeSet(IAtomContainerSet setOfMolecules)	Sets the MoleculeSet of this ChemModel.
void	Reaction.setProducts(IAtomContainerSet setOfMolecules)	Assigns a MoleculeSet to the products of this reaction.
void	Reaction.setReactants(IAtomContainerSet setOfMolecules)	Assigns a MoleculeSet to the reactants in this reaction.

Uses of IAtomContainerSet in org.openscience.cdk.charges

Methods in org.openscience.cdk.charges with parameters of type IAtomContainerSet

Modifier and Type	Method	Description
double[][]	GasteigerPEPEPartialCharges.assignrPiMarsilliFactors(IAtomContainerSet setAc)	Method which stores and assigns the factors a,b,c and CHI+.

Uses of IAtomContainerSet in org.openscience.cdk.debug

Classes in org.openscience.cdk.debug that implement IAtomContainerSet

Modifier and Type	Class	Description
class	DebugAtomContainerSet	Debugging data class.
class	DebugRingSet	Debugging data class.
class	DebugSubstance	Debugging data class.

Methods in org.openscience.cdk.debug that return IAtomContainerSet

Modifier and Type	Method	Description
IAtomContainerSet	DebugReaction.getAgents()	Returns a MoleculeSet containing the agents in this reaction.
IAtomContainerSet	DebugChemModel.getMoleculeSet()	Returns the MoleculeSet of this ChemModel.
IAtomContainerSet	DebugReaction.getProducts()	Returns a MoleculeSet containing the products of this reaction.
IAtomContainerSet	DebugReaction.getReactants()	Returns a MoleculeSet containing the reactants in this reaction.

Methods in org.openscience.cdk.debug with parameters of type IAtomContainerSet

Modifier and Type	Method	Description
void	DebugAtomContainerSet.add(IAtomContainerSet atomContainerSet)	Adds all atomContainers in the AtomContainerSet to this container.
void	DebugSubstance.add(IAtomContainerSet atomContainerSet)	Adds all atomContainers in the AtomContainerSet to this container.
void	DebugChemModel.setMoleculeSet(IAtomContainerSet setOfMolecules)	Sets the MoleculeSet of this ChemModel.
void	DebugReaction.setProducts(IAtomContainerSet products)	Assigns a MoleculeSet to the products of this reaction.
void	DebugReaction.setReactants(IAtomContainerSet reactants)	Assigns a MoleculeSet to the reactants in this reaction.

Uses of IAtomContainerSet in org.openscience.cdk.graph

Methods in org.openscience.cdk.graph that return IAtomContainerSet

Modifier and Type	Method	Description
static IAtomContainerSet	ConnectivityChecker.partitionIntoMolecules(IAtomContainer container)	Partitions the atoms in an AtomContainer into covalently connected components.
static IAtomContainerSet	ConnectivityChecker.partitionIntoMolecules(IAtomContainer container, int[] components)	Split a molecule based on the provided component array.

Uses of IAtomContainerSet in org.openscience.cdk.graph.invariant

Methods in org.openscience.cdk.graph.invariant that return IAtomContainerSet

Modifier and Type	Method	Description
static IAtomContainerSet	ConjugatedPiSystemsDetector.detect(IAtomContainer ac)	Detect all conjugated pi systems in an AtomContainer.

Uses of IAtomContainerSet in org.openscience.cdk.interfaces

Subinterfaces of IAtomContainerSet in org.openscience.cdk.interfaces

Modifier and Type	Interface	Description
interface	IRingSet	Maintains a set of Ring objects.
interface	ISubstance	A chemical substance that consists of one or more chemical structures.

Methods in org.openscience.cdk.interfaces that return IAtomContainerSet

Modifier and Type	Method	Description
IAtomContainerSet	IReaction.getAgents()	Returns a IAtomContaineSet containing the agents in this reaction.
IAtomContainerSet	IChemModel.getMoleculeSet()	Returns the IAtomContainerSet of this ChemModel.
IAtomContainerSet	IReaction.getProducts()	Returns a IAtomContaineSet containing the products of this reaction.
IAtomContainerSet	IReaction.getReactants()	Returns a IAtomContaineSet containing the reactants in this reaction.

Methods in org.openscience.cdk.interfaces with parameters of type IAtomContainerSet

Modifier and Type	Method	Description
void	IAtomContainerSet.add(IAtomContainerSet atomContainerSet)	Adds all atomContainers in the AtomContainerSet to this container.
void	IChemModel.setMoleculeSet(IAtomContainerSet setOfMolecules)	Sets the IAtomContainerSet of this ChemModel.
void	IReaction.setProducts(IAtomContainerSet products)	Assigns a IAtomContaineSet to the products of this reaction.
void	IReaction.setReactants(IAtomContainerSet reactants)	Assigns a IAtomContaineSet to the reactants in this reaction.

Uses of IAtomContainerSet in org.openscience.cdk.io

Methods in org.openscience.cdk.io with parameters of type IAtomContainerSet

Modifier and Type	Method	Description
void	SMILESWriter.writeAtomContainerSet(IAtomContainerSet som)	Writes a list of molecules to an OutputStream.

Uses of IAtomContainerSet in org.openscience.cdk.io.cml

Fields in org.openscience.cdk.io.cml declared as IAtomContainerSet

Modifier and Type	Field	Description
protected IAtomContainerSet	CMLCoreModule.currentMoleculeSet

Uses of IAtomContainerSet in org.openscience.cdk.io.pubchemxml

Methods in org.openscience.cdk.io.pubchemxml that return IAtomContainerSet

Modifier and Type	Method	Description
IAtomContainerSet	PubChemXMLHelper.parseCompoundsBlock(XMLStreamReader parser)

Uses of IAtomContainerSet in org.openscience.cdk.layout

Methods in org.openscience.cdk.layout that return IAtomContainerSet

Modifier and Type	Method	Description
IAtomContainerSet	TemplateHandler.getMappedSubstructures(IAtomContainer molecule)	Checks if one of the loaded templates is a substructure in the given Molecule and returns all matched substructures in a IAtomContainerSet.

Uses of IAtomContainerSet in org.openscience.cdk.libio.cml

Methods in org.openscience.cdk.libio.cml with parameters of type IAtomContainerSet

Modifier and Type	Method	Description
org.xmlcml.cml.element.CMLMoleculeList	Convertor.cdkAtomContainerSetToCMLList(IAtomContainerSet moleculeSet)

Uses of IAtomContainerSet in org.openscience.cdk.modeling.builder3d

Methods in org.openscience.cdk.modeling.builder3d with parameters of type IAtomContainerSet

Modifier and Type	Method	Description
void	TemplateExtractor.writeChemModel(IAtomContainerSet som, String file, String endFix)

Uses of IAtomContainerSet in org.openscience.cdk.reaction

Methods in org.openscience.cdk.reaction with parameters of type IAtomContainerSet

Modifier and Type	Method	Description
IReaction	IReactionMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)	Initiates the process for the given mechanism.
IReactionSet	IReactionProcess.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiates the process for the given Reaction.

Uses of IAtomContainerSet in org.openscience.cdk.reaction.mechanism

Methods in org.openscience.cdk.reaction.mechanism with parameters of type IAtomContainerSet

Modifier and Type	Method	Description
IReaction	AdductionLPMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)	Initiates the process for the given mechanism.
IReaction	AdductionPBMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)	Initiates the process for the given mechanism.
IReaction	HeterolyticCleavageMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)	Initiates the process for the given mechanism.
IReaction	HomolyticCleavageMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)	Initiates the process for the given mechanism.
IReaction	RadicalSiteIonizationMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)	Initiates the process for the given mechanism.
IReaction	RadicalSiteRearrangementMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)	Initiates the process for the given mechanism.
IReaction	RearrangementChargeMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)	Initiates the process for the given mechanism.
IReaction	RemovingSEofBMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)	Initiates the process for the given mechanism.
IReaction	RemovingSEofNBMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)	Initiates the process for the given mechanism.
IReaction	SharingElectronMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)	Initiates the process for the given mechanism.
IReaction	TautomerizationMechanism.initiate(IAtomContainerSet atomContainerSet, ArrayList<IAtom> atomList, ArrayList<IBond> bondList)	Initiates the process for the given mechanism.

Uses of IAtomContainerSet in org.openscience.cdk.reaction.type

Methods in org.openscience.cdk.reaction.type with parameters of type IAtomContainerSet

Modifier and Type	Method	Description
IReactionSet	AdductionProtonLPReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	AdductionProtonPBReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	AdductionSodiumLPReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	CarbonylEliminationReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	ElectronImpactNBEReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	ElectronImpactPDBReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	ElectronImpactSDBReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	HeterolyticCleavagePBReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	HeterolyticCleavageSBReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	HomolyticCleavageReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	HyperconjugationReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	PiBondingMovementReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalChargeSiteInitiationHReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalChargeSiteInitiationReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalSiteHrAlphaReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalSiteHrBetaReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalSiteHrDeltaReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalSiteHrGammaReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalSiteInitiationHReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalSiteInitiationReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalSiteRrAlphaReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalSiteRrBetaReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalSiteRrDeltaReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RadicalSiteRrGammaReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RearrangementAnionReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RearrangementCationReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RearrangementLonePairReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	RearrangementRadicalReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	SharingAnionReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	SharingChargeDBReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	SharingChargeSBReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	SharingLonePairReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.
IReactionSet	TautomerizationReaction.initiate(IAtomContainerSet reactants, IAtomContainerSet agents)	Initiate process.

Uses of IAtomContainerSet in org.openscience.cdk.renderer

Methods in org.openscience.cdk.renderer that return types with arguments of type IAtomContainerSet

Modifier and Type	Method	Description
List<IGenerator<IAtomContainerSet>>	MoleculeSetRenderer.getGenerators()	Returns a List of IGenerators for this renderer.

Methods in org.openscience.cdk.renderer with parameters of type IAtomContainerSet

Modifier and Type	Method	Description
static double	AverageBondLengthCalculator.calculateAverageBondLength(IAtomContainerSet moleculeSet)	Calculate the average bond length for the bonds in a molecule set.
static Rectangle2D	BoundsCalculator.calculateBounds(IAtomContainerSet moleculeSet)	Calculate the bounding rectangle for a molecule set.
Rectangle	MoleculeSetRenderer.calculateDiagramBounds(IAtomContainerSet moleculeSet)	Given a IChemObject, calculates the bounding rectangle in screen space.
IRenderingElement	MoleculeSetRenderer.generateDiagram(IAtomContainerSet molecules)	The main method of the renderer, that uses each of the generators to create a different set of IRenderingElements grouped together into a tree.
Rectangle	MoleculeSetRenderer.paint(IAtomContainerSet moleculeSet, IDrawVisitor drawVisitor)	Paint an IChemObject.
void	MoleculeSetRenderer.paint(IAtomContainerSet molecules, IDrawVisitor drawVisitor, Rectangle2D bounds, boolean resetCenter)	Paint a set of molecules.
void	MoleculeSetRenderer.setScale(IAtomContainerSet moleculeSet)	Set the scale for an IAtomContainerSet.
void	MoleculeSetRenderer.setup(IAtomContainerSet moleculeSet, Rectangle screen)	Setup the transformations necessary to draw this IAtomContainerSet.

Uses of IAtomContainerSet in org.openscience.cdk.silent

Classes in org.openscience.cdk.silent that implement IAtomContainerSet

Modifier and Type	Class	Description
class	AtomContainerSet	A set of AtomContainers.
class	RingSet	Maintains a set of Ring objects.
class	Substance	An implementation of the ISubstance interface.

Fields in org.openscience.cdk.silent declared as IAtomContainerSet

Modifier and Type	Field	Description
protected IAtomContainerSet	Reaction.agents	These are the used solvent, catalysts etc that normally appear above the reaction arrow
protected IAtomContainerSet	Reaction.products
protected IAtomContainerSet	Reaction.reactants
protected IAtomContainerSet	ChemModel.setOfMolecules	A MoleculeSet.

Methods in org.openscience.cdk.silent that return IAtomContainerSet

Modifier and Type	Method	Description
IAtomContainerSet	Reaction.getAgents()	Returns a MoleculeSet containing the agents in this reaction.
IAtomContainerSet	ChemModel.getMoleculeSet()	Returns the MoleculeSet of this ChemModel.
IAtomContainerSet	Reaction.getProducts()	Returns a MoleculeSet containing the products of this reaction.
IAtomContainerSet	Reaction.getReactants()	Returns a MoleculeSet containing the reactants in this reaction.

Methods in org.openscience.cdk.silent with parameters of type IAtomContainerSet

Modifier and Type	Method	Description
void	AtomContainerSet.add(IAtomContainerSet atomContainerSet)	Adds all atomContainers in the AtomContainerSet to this container.
void	ChemModel.setMoleculeSet(IAtomContainerSet setOfMolecules)	Sets the MoleculeSet of this ChemModel.
void	Reaction.setProducts(IAtomContainerSet setOfMolecules)	Assigns a MoleculeSet to the products of this reaction.
void	Reaction.setReactants(IAtomContainerSet setOfMolecules)	Assigns a MoleculeSet to the reactants in this reaction.

Uses of IAtomContainerSet in org.openscience.cdk.smsd.algorithm.rgraph

Methods in org.openscience.cdk.smsd.algorithm.rgraph that return IAtomContainerSet

Modifier and Type	Method	Description
protected IAtomContainerSet	CDKMCSHandler.getUncommon(IAtomContainer mol, IAtomContainer mcss, boolean shouldMatchBonds)	Deprecated.
protected IAtomContainerSet	CDKSubGraphHandler.getUncommon(IAtomContainer mol, IAtomContainer mcss, boolean shouldMatchBonds)	Deprecated.

Uses of IAtomContainerSet in org.openscience.cdk.structgen.stochastic

Methods in org.openscience.cdk.structgen.stochastic with parameters of type IAtomContainerSet

Modifier and Type	Method	Description
IAtomContainer	PartialFilledStructureMerger.generate(IAtomContainerSet atomContainers)	Randomly generates a single, connected, correctly bonded structure from a number of fragments.

Uses of IAtomContainerSet in org.openscience.cdk.tools

Methods in org.openscience.cdk.tools that return IAtomContainerSet

Modifier and Type	Method	Description
IAtomContainerSet	StructureResonanceGenerator.getContainers(IAtomContainer molecule)	Get the container which is found resonance from a IAtomContainer.
IAtomContainerSet	StructureResonanceGenerator.getStructures(IAtomContainer molecule)	Get the resonance structures from an IAtomContainer.

Uses of IAtomContainerSet in org.openscience.cdk.tools.manipulator

Methods in org.openscience.cdk.tools.manipulator that return IAtomContainerSet

Modifier and Type	Method	Description
static IAtomContainerSet	ReactionManipulator.getAllAgents(IReaction reaction)	Returns all agents of an IReaction.
static IAtomContainerSet	ReactionSchemeManipulator.getAllAtomContainers(IReactionScheme scheme)	get all AtomContainers object from a set of Reactions.
static IAtomContainerSet	ReactionSchemeManipulator.getAllAtomContainers(IReactionScheme scheme, IAtomContainerSet molSet)	Get all molecule objects from a set of Reactions given a IAtomContainerSet to add.
static IAtomContainerSet	ReactionManipulator.getAllMolecules(IReaction reaction)	Returns all components of an IReaction, that is, reactants, agents and products.
static IAtomContainerSet	ReactionSetManipulator.getAllMolecules(IReactionSet set)	get all Molecules object from a set of Reactions.
static IAtomContainerSet	ReactionManipulator.getAllProducts(IReaction reaction)	Returns all products of an IReaction.
static IAtomContainerSet	ReactionManipulator.getAllReactants(IReaction reaction)	Returns all reactants of an IReaction.

Methods in org.openscience.cdk.tools.manipulator that return types with arguments of type IAtomContainerSet

Modifier and Type	Method	Description
static ArrayList<IAtomContainerSet>	ReactionSchemeManipulator.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 in org.openscience.cdk.tools.manipulator with parameters of type IAtomContainerSet

Modifier and Type	Method	Description
static boolean	AtomContainerSetManipulator.containsByID(IAtomContainerSet atomContainerSet, String id)	Tells if an AtomContainerSet contains at least one AtomContainer with the same ID as atomContainer.
static List<IAtomContainer>	AtomContainerSetManipulator.getAllAtomContainers(IAtomContainerSet set)	Returns all the AtomContainer's of a MoleculeSet.
static List<IAtomContainer>	MoleculeSetManipulator.getAllAtomContainers(IAtomContainerSet set)	Returns all the AtomContainer's of a MoleculeSet.
static IAtomContainerSet	ReactionSchemeManipulator.getAllAtomContainers(IReactionScheme scheme, IAtomContainerSet molSet)	Get all molecule objects from a set of Reactions given a IAtomContainerSet to add.
static List<IChemObject>	AtomContainerSetManipulator.getAllChemObjects(IAtomContainerSet set)	Does not recursively return the contents of the AtomContainer.
static List<IChemObject>	MoleculeSetManipulator.getAllChemObjects(IAtomContainerSet set)
static List<String>	AtomContainerSetManipulator.getAllIDs(IAtomContainerSet set)
static List<String>	MoleculeSetManipulator.getAllIDs(IAtomContainerSet set)
static int	AtomContainerSetManipulator.getAtomCount(IAtomContainerSet set)
static int	MoleculeSetManipulator.getAtomCount(IAtomContainerSet set)
static int	AtomContainerSetManipulator.getBondCount(IAtomContainerSet set)
static int	MoleculeSetManipulator.getBondCount(IAtomContainerSet set)
static IAtomContainer	AtomContainerSetManipulator.getRelevantAtomContainer(IAtomContainerSet containerSet, IAtom atom)
static IAtomContainer	AtomContainerSetManipulator.getRelevantAtomContainer(IAtomContainerSet containerSet, IBond bond)
static IAtomContainer	MoleculeSetManipulator.getRelevantAtomContainer(IAtomContainerSet moleculeSet, IAtom atom)
static IAtomContainer	MoleculeSetManipulator.getRelevantAtomContainer(IAtomContainerSet moleculeSet, IBond bond)
static double	AtomContainerSetManipulator.getTotalCharge(IAtomContainerSet set)
static double	MoleculeSetManipulator.getTotalCharge(IAtomContainerSet set)
static double	AtomContainerSetManipulator.getTotalFormalCharge(IAtomContainerSet set)
static double	MoleculeSetManipulator.getTotalFormalCharge(IAtomContainerSet set)
static int	AtomContainerSetManipulator.getTotalHydrogenCount(IAtomContainerSet set)
static int	MoleculeSetManipulator.getTotalHydrogenCount(IAtomContainerSet set)
static void	AtomContainerSetManipulator.removeAtomAndConnectedElectronContainers(IAtomContainerSet set, IAtom atom)
static void	MoleculeSetManipulator.removeAtomAndConnectedElectronContainers(IAtomContainerSet set, IAtom atom)
static void	AtomContainerSetManipulator.removeElectronContainer(IAtomContainerSet set, IElectronContainer electrons)
static void	MoleculeSetManipulator.removeElectronContainer(IAtomContainerSet set, IElectronContainer electrons)
static void	AtomContainerSetManipulator.setAtomProperties(IAtomContainerSet set, Object propKey, Object propVal)
static void	MoleculeSetManipulator.setAtomProperties(IAtomContainerSet set, Object propKey, Object propVal)
static void	AtomContainerSetManipulator.sort(IAtomContainerSet atomContainerSet)	Sorts the IAtomContainers in the given IAtomContainerSet by the following criteria with decreasing priority:

Uses of IAtomContainerSet in org.openscience.cdk.validate

Methods in org.openscience.cdk.validate with parameters of type IAtomContainerSet

Modifier and Type	Method	Description
ValidationReport	AbstractValidator.validateMoleculeSet(IAtomContainerSet subject)
ValidationReport	IValidator.validateMoleculeSet(IAtomContainerSet subject)
ValidationReport	ValidatorEngine.validateMoleculeSet(IAtomContainerSet subject)