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

Packages that use IElectronContainer

Package	Description
org.openscience.cdk
org.openscience.cdk.debug
org.openscience.cdk.interfaces
org.openscience.cdk.isomorphism.matchers
org.openscience.cdk.isomorphism.matchers.smarts
org.openscience.cdk.pharmacophore
org.openscience.cdk.silent
org.openscience.cdk.tools.manipulator
org.openscience.cdk.validate

Uses of IElectronContainer in org.openscience.cdk

Classes in org.openscience.cdk that implement IElectronContainer

Modifier and Type	Class	Description
class	Association	Base class for storing interactions like hydrogen bonds and ionic interactions.
class	Bond	Implements the concept of a covalent bond between two or more atoms.
class	BondRef	A bond ref, references a CDK IBond indirectly.
class	ElectronContainer	Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
class	LonePair	A LonePair is an orbital primarily located with one Atom, containing two electrons.
class	SingleElectron	A Single Electron is an orbital which is occupied by only one electron.

Methods in org.openscience.cdk that return IElectronContainer

Modifier and Type	Method	Description
IElectronContainer	AtomContainer.getElectronContainer(int number)	Returns the ElectronContainer at position number in the container.
IElectronContainer	AtomContainer.removeElectronContainer(int number)	Removes the bond at the given position from this container.

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

Modifier and Type	Method	Description
Iterable<IElectronContainer>	AtomContainer.electronContainers()	Returns an Iterable for looping over all electron containers in this container.
List<IElectronContainer>	AtomContainer.getConnectedElectronContainersList(IAtom atom)	Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.

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

Modifier and Type	Method	Description
void	AtomContainer.addElectronContainer(IElectronContainer electronContainer)	Adds a ElectronContainer to this AtomContainer.
boolean	AtomContainer.contains(IElectronContainer electronContainer)	True, if the AtomContainer contains the given ElectronContainer object.
void	AtomContainer.removeElectronContainer(IElectronContainer electronContainer)	Removes this ElectronContainer from this container.

Uses of IElectronContainer in org.openscience.cdk.debug

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

Modifier and Type	Class	Description
class	DebugBond	Debugging data class.
class	DebugElectronContainer	Debugging data class.
class	DebugLonePair	Debugging data class.
class	DebugSingleElectron	Debugging data class.

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

Modifier and Type	Method	Description
IElectronContainer	DebugAminoAcid.getElectronContainer(int number)	Returns the ElectronContainer at position number in the container.
IElectronContainer	DebugAtomContainer.getElectronContainer(int number)	Returns the ElectronContainer at position number in the container.
IElectronContainer	DebugBioPolymer.getElectronContainer(int number)	Returns the ElectronContainer at position number in the container.
IElectronContainer	DebugCrystal.getElectronContainer(int number)	Returns the ElectronContainer at position number in the container.
IElectronContainer	DebugMonomer.getElectronContainer(int number)	Returns the ElectronContainer at position number in the container.
IElectronContainer	DebugPolymer.getElectronContainer(int number)	Returns the ElectronContainer at position number in the container.
IElectronContainer	DebugRing.getElectronContainer(int number)	Returns the ElectronContainer at position number in the container.
IElectronContainer	DebugStrand.getElectronContainer(int number)	Returns the ElectronContainer at position number in the container.
IElectronContainer	DebugAminoAcid.removeElectronContainer(int position)	Removes the bond at the given position from this container.
IElectronContainer	DebugAtomContainer.removeElectronContainer(int position)	Removes the bond at the given position from this container.
IElectronContainer	DebugBioPolymer.removeElectronContainer(int position)	Removes the bond at the given position from this container.
IElectronContainer	DebugCrystal.removeElectronContainer(int position)	Removes the bond at the given position from this container.
IElectronContainer	DebugMonomer.removeElectronContainer(int position)	Removes the bond at the given position from this container.
IElectronContainer	DebugPolymer.removeElectronContainer(int position)	Removes the bond at the given position from this container.
IElectronContainer	DebugRing.removeElectronContainer(int position)	Removes the bond at the given position from this container.
IElectronContainer	DebugStrand.removeElectronContainer(int position)	Removes the bond at the given position from this container.

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

Modifier and Type	Method	Description
Iterable<IElectronContainer>	DebugAminoAcid.electronContainers()	Returns an Iterable for looping over all electron containers in this container.
Iterable<IElectronContainer>	DebugAtomContainer.electronContainers()	Returns an Iterable for looping over all electron containers in this container.
Iterable<IElectronContainer>	DebugBioPolymer.electronContainers()	Returns an Iterable for looping over all electron containers in this container.
Iterable<IElectronContainer>	DebugCrystal.electronContainers()	Returns an Iterable for looping over all electron containers in this container.
Iterable<IElectronContainer>	DebugMonomer.electronContainers()	Returns an Iterable for looping over all electron containers in this container.
Iterable<IElectronContainer>	DebugPolymer.electronContainers()	Returns an Iterable for looping over all electron containers in this container.
Iterable<IElectronContainer>	DebugRing.electronContainers()	Returns an Iterable for looping over all electron containers in this container.
Iterable<IElectronContainer>	DebugStrand.electronContainers()	Returns an Iterable for looping over all electron containers in this container.
List<IElectronContainer>	DebugAminoAcid.getConnectedElectronContainersList(IAtom atom)	Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
List<IElectronContainer>	DebugAtomContainer.getConnectedElectronContainersList(IAtom atom)	Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
List<IElectronContainer>	DebugBioPolymer.getConnectedElectronContainersList(IAtom atom)	Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
List<IElectronContainer>	DebugCrystal.getConnectedElectronContainersList(IAtom atom)	Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
List<IElectronContainer>	DebugMonomer.getConnectedElectronContainersList(IAtom atom)	Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
List<IElectronContainer>	DebugPolymer.getConnectedElectronContainersList(IAtom atom)	Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
List<IElectronContainer>	DebugRing.getConnectedElectronContainersList(IAtom atom)	Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.
List<IElectronContainer>	DebugStrand.getConnectedElectronContainersList(IAtom atom)	Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.

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

Modifier and Type	Method	Description
void	DebugAminoAcid.addElectronContainer(IElectronContainer electronContainer)	Adds a ElectronContainer to this AtomContainer.
void	DebugAtomContainer.addElectronContainer(IElectronContainer electronContainer)	Adds a ElectronContainer to this AtomContainer.
void	DebugBioPolymer.addElectronContainer(IElectronContainer electronContainer)	Adds a ElectronContainer to this AtomContainer.
void	DebugCrystal.addElectronContainer(IElectronContainer electronContainer)	Adds a ElectronContainer to this AtomContainer.
void	DebugMonomer.addElectronContainer(IElectronContainer electronContainer)	Adds a ElectronContainer to this AtomContainer.
void	DebugPolymer.addElectronContainer(IElectronContainer electronContainer)	Adds a ElectronContainer to this AtomContainer.
void	DebugRing.addElectronContainer(IElectronContainer electronContainer)	Adds a ElectronContainer to this AtomContainer.
void	DebugStrand.addElectronContainer(IElectronContainer electronContainer)	Adds a ElectronContainer to this AtomContainer.
boolean	DebugAminoAcid.contains(IElectronContainer electronContainer)	True, if the AtomContainer contains the given ElectronContainer object.
boolean	DebugAtomContainer.contains(IElectronContainer electronContainer)	True, if the AtomContainer contains the given ElectronContainer object.
boolean	DebugBioPolymer.contains(IElectronContainer electronContainer)	True, if the AtomContainer contains the given ElectronContainer object.
boolean	DebugCrystal.contains(IElectronContainer electronContainer)	True, if the AtomContainer contains the given ElectronContainer object.
boolean	DebugMonomer.contains(IElectronContainer electronContainer)	True, if the AtomContainer contains the given ElectronContainer object.
boolean	DebugPolymer.contains(IElectronContainer electronContainer)	True, if the AtomContainer contains the given ElectronContainer object.
boolean	DebugRing.contains(IElectronContainer electronContainer)	True, if the AtomContainer contains the given ElectronContainer object.
boolean	DebugStrand.contains(IElectronContainer electronContainer)	True, if the AtomContainer contains the given ElectronContainer object.
void	DebugAminoAcid.removeElectronContainer(IElectronContainer electronContainer)	Removes this ElectronContainer from this container.
void	DebugAtomContainer.removeElectronContainer(IElectronContainer electronContainer)	Removes this ElectronContainer from this container.
void	DebugBioPolymer.removeElectronContainer(IElectronContainer electronContainer)	Removes this ElectronContainer from this container.
void	DebugCrystal.removeElectronContainer(IElectronContainer electronContainer)	Removes this ElectronContainer from this container.
void	DebugMonomer.removeElectronContainer(IElectronContainer electronContainer)	Removes this ElectronContainer from this container.
void	DebugPolymer.removeElectronContainer(IElectronContainer electronContainer)	Removes this ElectronContainer from this container.
void	DebugRing.removeElectronContainer(IElectronContainer electronContainer)	Removes this ElectronContainer from this container.
void	DebugStrand.removeElectronContainer(IElectronContainer electronContainer)	Removes this ElectronContainer from this container.

Uses of IElectronContainer in org.openscience.cdk.interfaces

Subinterfaces of IElectronContainer in org.openscience.cdk.interfaces

Modifier and Type	Interface	Description
interface	IBond	Implements the concept of a covalent bond between two or more atoms.
interface	ILonePair	A LonePair is an orbital primarily located with one Atom, containing two electrons.
interface	ISingleElectron	A Single Electron is an orbital which is occupied by only one electron.

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

Modifier and Type	Method	Description
IElectronContainer	IAtomContainer.getElectronContainer(int number)	Returns the ElectronContainer at position number in the container.
IElectronContainer	IAtomContainer.removeElectronContainer(int position)	Removes the bond at the given position from this container.

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

Modifier and Type	Method	Description
Iterable<IElectronContainer>	IAtomContainer.electronContainers()	Returns an Iterable for looping over all electron containers in this container.
List<IElectronContainer>	IAtomContainer.getConnectedElectronContainersList(IAtom atom)	Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.

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

Modifier and Type	Method	Description
void	IAtomContainer.addElectronContainer(IElectronContainer electronContainer)	Adds a ElectronContainer to this AtomContainer.
boolean	IAtomContainer.contains(IElectronContainer electronContainer)	True, if the AtomContainer contains the given ElectronContainer object.
void	IAtomContainer.removeElectronContainer(IElectronContainer electronContainer)	Removes this ElectronContainer from this container.

Uses of IElectronContainer in org.openscience.cdk.isomorphism.matchers

Subinterfaces of IElectronContainer in org.openscience.cdk.isomorphism.matchers

Modifier and Type	Interface	Description
interface	IQueryBond	Defines the abililty to be matched against IBond's.

Classes in org.openscience.cdk.isomorphism.matchers that implement IElectronContainer

Modifier and Type	Class	Description
class	CTFileQueryBond	Deprecated. Use Expr.Type.SINGLE_OR_AROMATIC etc.
class	OrderQueryBond	Deprecated.
class	OrderQueryBondOrderOnly	Deprecated. Use new QueryBond(beg, end, ORDER, bord)
class	QueryBond	Implements the concept of a "query bond" between two or more atoms.

Methods in org.openscience.cdk.isomorphism.matchers that return IElectronContainer

Modifier and Type	Method	Description
IElectronContainer	QueryAtomContainer.getElectronContainer(int number)	Returns the ElectronContainer at position number in the container.
IElectronContainer	QueryAtomContainer.removeElectronContainer(int number)	Removes the bond at the given position from this container.

Methods in org.openscience.cdk.isomorphism.matchers that return types with arguments of type IElectronContainer

Modifier and Type	Method	Description
Iterable<IElectronContainer>	QueryAtomContainer.electronContainers()	Returns an Iterable for looping over all electron containers in this container.
List<IElectronContainer>	QueryAtomContainer.getConnectedElectronContainersList(IAtom atom)	Returns an ArrayList of all electronContainers connected to the given atom.

Methods in org.openscience.cdk.isomorphism.matchers with parameters of type IElectronContainer

Modifier and Type	Method	Description
void	QueryAtomContainer.addElectronContainer(IElectronContainer electronContainer)	Adds a ElectronContainer to this AtomContainer.
boolean	QueryAtomContainer.contains(IElectronContainer electronContainer)	True, if the AtomContainer contains the given ElectronContainer object.
void	QueryAtomContainer.removeElectronContainer(IElectronContainer electronContainer)	Removes this ElectronContainer from this container.

Uses of IElectronContainer in org.openscience.cdk.isomorphism.matchers.smarts

Classes in org.openscience.cdk.isomorphism.matchers.smarts that implement IElectronContainer

Modifier and Type	Class	Description
class	AnyOrderQueryBond	Deprecated.
class	AromaticOrSingleQueryBond	Deprecated.
class	AromaticQueryBond	Deprecated.
class	LogicalOperatorBond	Deprecated.
class	OrderQueryBond	Deprecated.
class	RingBond	Deprecated.
class	SMARTSBond	Deprecated.
class	StereoBond	Deprecated.

Uses of IElectronContainer in org.openscience.cdk.pharmacophore

Classes in org.openscience.cdk.pharmacophore that implement IElectronContainer

Modifier and Type	Class	Description
class	PharmacophoreAngleBond	Represents an angle relationship between three pharmacophore groups.
class	PharmacophoreBond	Represents a distance relationship between two pharmacophore groups.
class	PharmacophoreQueryAngleBond	Represents a pharmacophore query angle constraint.
class	PharmacophoreQueryBond	Represents a pharmacophore query distance constraint.

Uses of IElectronContainer in org.openscience.cdk.silent

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

Modifier and Type	Class	Description
class	Bond	Implements the concept of a covalent bond between two or more atoms.
class	ElectronContainer	Base class for entities containing electrons, like bonds, orbitals, lone-pairs.
class	LonePair	A LonePair is an orbital primarily located with one Atom, containing two electrons.
class	SingleElectron	A Single Electron is an orbital which is occupied by only one electron.

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

Modifier and Type	Method	Description
IElectronContainer	AtomContainer.getElectronContainer(int number)	Returns the ElectronContainer at position number in the container.
IElectronContainer	AtomContainer.removeElectronContainer(int number)	Removes the bond at the given position from this container.

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

Modifier and Type	Method	Description
Iterable<IElectronContainer>	AtomContainer.electronContainers()	Returns an Iterable for looping over all electron containers in this container.
List<IElectronContainer>	AtomContainer.getConnectedElectronContainersList(IAtom atom)	Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.

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

Modifier and Type	Method	Description
void	AtomContainer.addElectronContainer(IElectronContainer electronContainer)	Adds a ElectronContainer to this AtomContainer.
boolean	AtomContainer.contains(IElectronContainer electronContainer)	True, if the AtomContainer contains the given ElectronContainer object.
void	AtomContainer.removeElectronContainer(IElectronContainer electronContainer)	Removes this ElectronContainer from this container.

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

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

Modifier and Type	Method	Description
static IElectronContainer[]	AtomContainerManipulator.getElectronContainerArray(List<IElectronContainer> list)	Constructs an array of Atom objects from a List of Atom objects.
static IElectronContainer[]	AtomContainerManipulator.getElectronContainerArray(IAtomContainer container)	Constructs an array of Bond objects from an AtomContainer.

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

Modifier and Type	Method	Description
static void	AtomContainerSetManipulator.removeElectronContainer(IAtomContainerSet set, IElectronContainer electrons)
static void	ChemModelManipulator.removeElectronContainer(IChemModel chemModel, IElectronContainer electrons)	Remove an ElectronContainer from all AtomContainers inside an IChemModel.
static void	MoleculeSetManipulator.removeElectronContainer(IAtomContainerSet set, IElectronContainer electrons)
static void	ReactionManipulator.removeElectronContainer(IReaction reaction, IElectronContainer electrons)
static void	ReactionSetManipulator.removeElectronContainer(IReactionSet set, IElectronContainer electrons)

Method parameters in org.openscience.cdk.tools.manipulator with type arguments of type IElectronContainer

Modifier and Type	Method	Description
static IElectronContainer[]	AtomContainerManipulator.getElectronContainerArray(List<IElectronContainer> list)	Constructs an array of Atom objects from a List of Atom objects.

Uses of IElectronContainer in org.openscience.cdk.validate

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

Modifier and Type	Method	Description
ValidationReport	AbstractValidator.validateElectronContainer(IElectronContainer subject)
ValidationReport	IValidator.validateElectronContainer(IElectronContainer subject)
ValidationReport	ValidatorEngine.validateElectronContainer(IElectronContainer subject)