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

Packages that use IChemModel

Package	Description
org.openscience.cdk
org.openscience.cdk.debug
org.openscience.cdk.geometry
org.openscience.cdk.interfaces
org.openscience.cdk.io.cml
org.openscience.cdk.io.iterator
org.openscience.cdk.io.pubchemxml
org.openscience.cdk.libio.cml
org.openscience.cdk.renderer
org.openscience.cdk.renderer.selection
org.openscience.cdk.silent
org.openscience.cdk.tools.manipulator
org.openscience.cdk.validate

Uses of IChemModel in org.openscience.cdk

Classes in org.openscience.cdk that implement IChemModel

Modifier and Type	Class	Description
class	ChemModel	An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.

Fields in org.openscience.cdk declared as IChemModel

Modifier and Type	Field	Description
protected IChemModel[]	ChemSequence.chemModels	Array of ChemModels.

Methods in org.openscience.cdk that return IChemModel

Modifier and Type	Method	Description
IChemModel	ChemSequence.getChemModel(int number)	Returns the ChemModel at position number in the container.

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

Modifier and Type	Method	Description
Iterable<IChemModel>	ChemSequence.chemModels()	Returns an Iterable to ChemModels in this container.

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

Modifier and Type	Method	Description
void	ChemSequence.addChemModel(IChemModel chemModel)	Adds an chemModel to this container.

Uses of IChemModel in org.openscience.cdk.debug

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

Modifier and Type	Class	Description
class	DebugChemModel	Debugging data class.

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

Modifier and Type	Method	Description
IChemModel	DebugChemSequence.getChemModel(int number)	Returns the ChemModel at position number in the container.

Methods in org.openscience.cdk.debug that return types with arguments of type IChemModel

Modifier and Type	Method	Description
Iterable<IChemModel>	DebugChemSequence.chemModels()	Returns an Iterable to ChemModels in this container.

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

Modifier and Type	Method	Description
void	DebugChemSequence.addChemModel(IChemModel chemModel)	Adds an chemModel to this container.

Uses of IChemModel in org.openscience.cdk.geometry

Methods in org.openscience.cdk.geometry with parameters of type IChemModel

Modifier and Type	Method	Description
static boolean	GeometryTools.has3DCoordinates(IChemModel chemModel)	Deprecated. Determines if this model contains 3D coordinates for all atoms.
static boolean	GeometryUtil.has3DCoordinates(IChemModel chemModel)	Determines if this model contains 3D coordinates for all atoms.

Uses of IChemModel in org.openscience.cdk.interfaces

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

Modifier and Type	Method	Description
IChemModel	IChemSequence.getChemModel(int number)	Returns the ChemModel at position number in the container.

Methods in org.openscience.cdk.interfaces that return types with arguments of type IChemModel

Modifier and Type	Method	Description
Iterable<IChemModel>	IChemSequence.chemModels()	Returns an Iterable to ChemModels in this container.

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

Modifier and Type	Method	Description
void	IChemSequence.addChemModel(IChemModel chemModel)	Adds an chemModel to this container.

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

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

Modifier and Type	Field	Description
protected IChemModel	CMLCoreModule.currentChemModel

Uses of IChemModel in org.openscience.cdk.io.iterator

Methods in org.openscience.cdk.io.iterator that return IChemModel

Modifier and Type	Method	Description
IChemModel	IteratingPCSubstancesXMLReader.next()

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

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

Modifier and Type	Method	Description
IChemModel	PubChemXMLHelper.parseSubstance(XMLStreamReader parser)

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

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

Modifier and Type	Method	Description
org.xmlcml.cml.element.CMLList	Convertor.cdkChemModelToCMLList(IChemModel model)

Uses of IChemModel in org.openscience.cdk.renderer

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

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

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

Modifier and Type	Method	Description
static double	AverageBondLengthCalculator.calculateAverageBondLength(IChemModel model)	Calculate the average bond length for the bonds in a chem model.
static Rectangle2D	BoundsCalculator.calculateBounds(IChemModel chemModel)	Calculate the bounding rectangle for a chem model.
Rectangle	ChemModelRenderer.calculateDiagramBounds(IChemModel model)	Given a chem model, calculates the bounding rectangle in screen space.
Rectangle	ChemModelRenderer.paint(IChemModel chemModel, IDrawVisitor drawVisitor)	Paint an IChemModel using the IDrawVisitor at a scale determined by the bond length in RendererModel.
void	ChemModelRenderer.paint(IChemModel chemModel, IDrawVisitor drawVisitor, Rectangle2D bounds, boolean resetCenter)	Paint a ChemModel.
void	ChemModelRenderer.setScale(IChemModel chemModel)	Set the scale for an IChemModel.
void	ChemModelRenderer.setup(IChemModel chemModel, Rectangle screen)	Setup the transformations necessary to draw this Chem Model.

Uses of IChemModel in org.openscience.cdk.renderer.selection

Methods in org.openscience.cdk.renderer.selection with parameters of type IChemModel

Modifier and Type	Method	Description
void	AbstractSelection.select(IChemModel chemModel)	Perform a selection by some method.
void	IChemObjectSelection.select(IChemModel chemModel)	Perform a selection by some method.

Uses of IChemModel in org.openscience.cdk.silent

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

Modifier and Type	Class	Description
class	ChemModel	An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.

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

Modifier and Type	Field	Description
protected IChemModel[]	ChemSequence.chemModels	Array of ChemModels.

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

Modifier and Type	Method	Description
IChemModel	ChemSequence.getChemModel(int number)	Returns the ChemModel at position number in the container.

Methods in org.openscience.cdk.silent that return types with arguments of type IChemModel

Modifier and Type	Method	Description
Iterable<IChemModel>	ChemSequence.chemModels()	Returns an Iterable to ChemModels in this container.

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

Modifier and Type	Method	Description
void	ChemSequence.addChemModel(IChemModel chemModel)	Adds an chemModel to this container.

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

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

Modifier and Type	Method	Description
static IChemModel	ChemModelManipulator.newChemModel(IAtomContainer atomContainer)	Create a new ChemModel containing an IAtomContainer.

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

Modifier and Type	Method	Description
static List<IChemModel>	ChemFileManipulator.getAllChemModels(IChemFile file)	Get a list of all ChemModels inside an IChemFile.

Methods in org.openscience.cdk.tools.manipulator with parameters of type IChemModel

Modifier and Type	Method	Description
static IAtomContainer	ChemModelManipulator.createNewMolecule(IChemModel chemModel)	Adds a new Molecule to the MoleculeSet inside a given ChemModel.
static List<IAtomContainer>	ChemModelManipulator.getAllAtomContainers(IChemModel chemModel)	Returns all the AtomContainer's of a ChemModel.
static List<IChemObject>	ChemModelManipulator.getAllChemObjects(IChemModel chemModel)	Retrieve a List of all ChemObject objects within an IChemModel.
static List<String>	ChemModelManipulator.getAllIDs(IChemModel chemModel)
static int	ChemModelManipulator.getAtomCount(IChemModel chemModel)	Get the total number of atoms inside an IChemModel.
static int	ChemModelManipulator.getBondCount(IChemModel chemModel)	Get the total number of bonds inside an IChemModel.
static IAtomContainer	ChemModelManipulator.getRelevantAtomContainer(IChemModel chemModel, IAtom atom)	This badly named methods tries to determine which AtomContainer in the ChemModel is best suited to contain added Atom's and Bond's.
static IAtomContainer	ChemModelManipulator.getRelevantAtomContainer(IChemModel chemModel, IBond bond)	Retrieves the first IAtomContainer containing a given IBond from an IChemModel.
static IReaction	ChemModelManipulator.getRelevantReaction(IChemModel chemModel, IAtom atom)	Retrieves the first IReaction containing a given IAtom from an IChemModel.
static void	ChemModelManipulator.removeAtomAndConnectedElectronContainers(IChemModel chemModel, IAtom atom)	Remove an Atom and the connected ElectronContainers from all AtomContainers inside an IChemModel.
static void	ChemModelManipulator.removeElectronContainer(IChemModel chemModel, IElectronContainer electrons)	Remove an ElectronContainer from all AtomContainers inside an IChemModel.
static void	ChemModelManipulator.setAtomProperties(IChemModel chemModel, Object propKey, Object propVal)	Sets the AtomProperties of all Atoms inside an IChemModel.

Uses of IChemModel in org.openscience.cdk.validate

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

Modifier and Type	Method	Description
ValidationReport	AbstractValidator.validateChemModel(IChemModel subject)
ValidationReport	IValidator.validateChemModel(IChemModel subject)
ValidationReport	ValidatorEngine.validateChemModel(IChemModel subject)