Uses of Interface
org.openscience.cdk.interfaces.IChemModel
Packages that use IChemModel
Package
Description
-
Uses of IChemModel in org.openscience.cdk
Classes in org.openscience.cdk that implement IChemModelModifier and TypeClassDescriptionclass
An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.Fields in org.openscience.cdk declared as IChemModelModifier and TypeFieldDescriptionprotected IChemModel[]
ChemSequence.chemModels
Array of ChemModels.Methods in org.openscience.cdk that return IChemModelModifier and TypeMethodDescriptionChemSequence.getChemModel
(int number) Returns the ChemModel at positionnumber
in the container.Methods in org.openscience.cdk that return types with arguments of type IChemModelModifier and TypeMethodDescriptionChemSequence.chemModels()
Returns an Iterable to ChemModels in this container.Methods in org.openscience.cdk with parameters of type IChemModelModifier and TypeMethodDescriptionvoid
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 IChemModelMethods in org.openscience.cdk.debug that return IChemModelModifier and TypeMethodDescriptionDebugChemSequence.getChemModel
(int number) Returns the ChemModel at positionnumber
in the container.Methods in org.openscience.cdk.debug that return types with arguments of type IChemModelModifier and TypeMethodDescriptionDebugChemSequence.chemModels()
Returns an Iterable to ChemModels in this container.Methods in org.openscience.cdk.debug with parameters of type IChemModelModifier and TypeMethodDescriptionvoid
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 IChemModelModifier and TypeMethodDescriptionstatic 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 IChemModelModifier and TypeMethodDescriptionIChemSequence.getChemModel
(int number) Returns the ChemModel at positionnumber
in the container.Methods in org.openscience.cdk.interfaces that return types with arguments of type IChemModelModifier and TypeMethodDescriptionIChemSequence.chemModels()
Returns an Iterable to ChemModels in this container.Methods in org.openscience.cdk.interfaces with parameters of type IChemModelModifier and TypeMethodDescriptionvoid
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 -
Uses of IChemModel in org.openscience.cdk.io.iterator
Methods in org.openscience.cdk.io.iterator that return IChemModel -
Uses of IChemModel in org.openscience.cdk.io.pubchemxml
Methods in org.openscience.cdk.io.pubchemxml that return IChemModel -
Uses of IChemModel in org.openscience.cdk.libio.cml
Methods in org.openscience.cdk.libio.cml with parameters of type IChemModelModifier and TypeMethodDescriptionorg.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 IChemModelModifier and TypeMethodDescriptionChemModelRenderer.getGenerators()
Returns aList
ofIGenerator
s for this renderer.Methods in org.openscience.cdk.renderer with parameters of type IChemModelModifier and TypeMethodDescriptionstatic 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.ChemModelRenderer.calculateDiagramBounds
(IChemModel model) Given a chem model, calculates the bounding rectangle in screen space.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 IChemModelModifier and TypeMethodDescriptionvoid
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 IChemModelModifier and TypeClassDescriptionclass
An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.Fields in org.openscience.cdk.silent declared as IChemModelModifier and TypeFieldDescriptionprotected IChemModel[]
ChemSequence.chemModels
Array of ChemModels.Methods in org.openscience.cdk.silent that return IChemModelModifier and TypeMethodDescriptionChemSequence.getChemModel
(int number) Returns the ChemModel at positionnumber
in the container.Methods in org.openscience.cdk.silent that return types with arguments of type IChemModelModifier and TypeMethodDescriptionChemSequence.chemModels()
Returns an Iterable to ChemModels in this container.Methods in org.openscience.cdk.silent with parameters of type IChemModelModifier and TypeMethodDescriptionvoid
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 IChemModelModifier and TypeMethodDescriptionstatic 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 IChemModelModifier and TypeMethodDescriptionstatic 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 IChemModelModifier and TypeMethodDescriptionstatic 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.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 IChemModelModifier and TypeMethodDescriptionAbstractValidator.validateChemModel
(IChemModel subject) IValidator.validateChemModel
(IChemModel subject) ValidatorEngine.validateChemModel
(IChemModel subject)