Uses of Interface
org.openscience.cdk.interfaces.IElectronContainer
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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 CDKIBond
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 positionnumber
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 positionnumber
in the container.IElectronContainer
DebugAtomContainer. getElectronContainer(int number)
Returns the ElectronContainer at positionnumber
in the container.IElectronContainer
DebugBioPolymer. getElectronContainer(int number)
Returns the ElectronContainer at positionnumber
in the container.IElectronContainer
DebugCrystal. getElectronContainer(int number)
Returns the ElectronContainer at positionnumber
in the container.IElectronContainer
DebugMonomer. getElectronContainer(int number)
Returns the ElectronContainer at positionnumber
in the container.IElectronContainer
DebugPolymer. getElectronContainer(int number)
Returns the ElectronContainer at positionnumber
in the container.IElectronContainer
DebugRing. getElectronContainer(int number)
Returns the ElectronContainer at positionnumber
in the container.IElectronContainer
DebugStrand. getElectronContainer(int number)
Returns the ElectronContainer at positionnumber
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 positionnumber
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.UseExpr.Type.SINGLE_OR_AROMATIC
etc.class
OrderQueryBond
Deprecated.class
OrderQueryBondOrderOnly
Deprecated.Usenew 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 positionnumber
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 positionnumber
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)
Removes the providedelectrons
from the reaction.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)
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