Modifier and Type | Class and 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 |
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.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
Iterable<IElectronContainer> |
AtomContainer.electronContainers()
Returns an Iterable for looping over all electron containers in this container.
|
List<IElectronContainer> |
AtomContainer.getConnectedElectronContainersList(IAtom atom)
Returns an ArrayList of all electronContainers connected to the given atom.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Class and Description |
---|---|
class |
DebugBond
Debugging data class.
|
class |
DebugElectronContainer
Debugging data class.
|
class |
DebugLonePair
Debugging data class.
|
class |
DebugSingleElectron
Debugging data class.
|
Modifier and Type | Method and Description |
---|---|
IElectronContainer |
DebugStrand.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 |
DebugPolymer.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 |
DebugCrystal.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 |
DebugAtomContainer.getElectronContainer(int number)
Returns the ElectronContainer at position
number in the
container. |
IElectronContainer |
DebugAminoAcid.getElectronContainer(int number)
Returns the ElectronContainer at position
number in the
container. |
IElectronContainer |
DebugStrand.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 |
DebugPolymer.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 |
DebugCrystal.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 |
DebugAtomContainer.removeElectronContainer(int position)
Removes the bond at the given position from this container.
|
IElectronContainer |
DebugAminoAcid.removeElectronContainer(int position)
Removes the bond at the given position from this container.
|
Modifier and Type | Method and Description |
---|---|
Iterable<IElectronContainer> |
DebugStrand.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> |
DebugPolymer.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> |
DebugCrystal.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> |
DebugAtomContainer.electronContainers()
Returns an Iterable for looping over all electron containers in this container.
|
Iterable<IElectronContainer> |
DebugAminoAcid.electronContainers()
Returns an Iterable for looping over all electron containers in this container.
|
List<IElectronContainer> |
DebugStrand.getConnectedElectronContainersList(IAtom atom)
Returns an ArrayList of all electronContainers connected to the given atom.
|
List<IElectronContainer> |
DebugRing.getConnectedElectronContainersList(IAtom atom)
Returns an ArrayList of all electronContainers connected to the given atom.
|
List<IElectronContainer> |
DebugPolymer.getConnectedElectronContainersList(IAtom atom)
Returns an ArrayList of all electronContainers connected to the given atom.
|
List<IElectronContainer> |
DebugMonomer.getConnectedElectronContainersList(IAtom atom)
Returns an ArrayList of all electronContainers connected to the given atom.
|
List<IElectronContainer> |
DebugCrystal.getConnectedElectronContainersList(IAtom atom)
Returns an ArrayList of all electronContainers connected to the given atom.
|
List<IElectronContainer> |
DebugBioPolymer.getConnectedElectronContainersList(IAtom atom)
Returns an ArrayList of all electronContainers connected to the given atom.
|
List<IElectronContainer> |
DebugAtomContainer.getConnectedElectronContainersList(IAtom atom)
Returns an ArrayList of all electronContainers connected to the given atom.
|
List<IElectronContainer> |
DebugAminoAcid.getConnectedElectronContainersList(IAtom atom)
Returns an ArrayList of all electronContainers connected to the given atom.
|
Modifier and Type | Method and Description |
---|---|
void |
DebugStrand.addElectronContainer(IElectronContainer electronContainer)
Adds a ElectronContainer to this AtomContainer.
|
void |
DebugRing.addElectronContainer(IElectronContainer electronContainer)
Adds a ElectronContainer to this AtomContainer.
|
void |
DebugPolymer.addElectronContainer(IElectronContainer electronContainer)
Adds a ElectronContainer to this AtomContainer.
|
void |
DebugMonomer.addElectronContainer(IElectronContainer electronContainer)
Adds a ElectronContainer to this AtomContainer.
|
void |
DebugCrystal.addElectronContainer(IElectronContainer electronContainer)
Adds a ElectronContainer to this AtomContainer.
|
void |
DebugBioPolymer.addElectronContainer(IElectronContainer electronContainer)
Adds a ElectronContainer to this AtomContainer.
|
void |
DebugAtomContainer.addElectronContainer(IElectronContainer electronContainer)
Adds a ElectronContainer to this AtomContainer.
|
void |
DebugAminoAcid.addElectronContainer(IElectronContainer electronContainer)
Adds a ElectronContainer to this AtomContainer.
|
boolean |
DebugStrand.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 |
DebugPolymer.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 |
DebugCrystal.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 |
DebugAtomContainer.contains(IElectronContainer electronContainer)
True, if the AtomContainer contains the given ElectronContainer object.
|
boolean |
DebugAminoAcid.contains(IElectronContainer electronContainer)
True, if the AtomContainer contains the given ElectronContainer object.
|
void |
DebugStrand.removeElectronContainer(IElectronContainer electronContainer)
Removes this ElectronContainer from this container.
|
void |
DebugRing.removeElectronContainer(IElectronContainer electronContainer)
Removes this ElectronContainer from this container.
|
void |
DebugPolymer.removeElectronContainer(IElectronContainer electronContainer)
Removes this ElectronContainer from this container.
|
void |
DebugMonomer.removeElectronContainer(IElectronContainer electronContainer)
Removes this ElectronContainer from this container.
|
void |
DebugCrystal.removeElectronContainer(IElectronContainer electronContainer)
Removes this ElectronContainer from this container.
|
void |
DebugBioPolymer.removeElectronContainer(IElectronContainer electronContainer)
Removes this ElectronContainer from this container.
|
void |
DebugAtomContainer.removeElectronContainer(IElectronContainer electronContainer)
Removes this ElectronContainer from this container.
|
void |
DebugAminoAcid.removeElectronContainer(IElectronContainer electronContainer)
Removes this ElectronContainer from this container.
|
Modifier and Type | Interface and 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.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
Iterable<IElectronContainer> |
IAtomContainer.electronContainers()
Returns an Iterable for looping over all electron containers in this container.
|
List<IElectronContainer> |
IAtomContainer.getConnectedElectronContainersList(IAtom atom)
Returns an ArrayList of all electronContainers connected to the given atom.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Interface and Description |
---|---|
interface |
IQueryBond
Defines the abililty to be matched against IBond's.
|
Modifier and Type | Class and Description |
---|---|
class |
CTFileQueryBond
Captures query bond types defined in the CTFile.
|
class |
OrderQueryBond |
class |
OrderQueryBondOrderOnly
IQueryBond that matches IBond object only based on bond order, and
disregarding any aromaticity flag. |
class |
QueryBond
Implements the concept of a "query bond" between two or more atoms.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Class and Description |
---|---|
class |
AnyOrderQueryBond
This matches a bond of any order.
|
class |
AromaticOrSingleQueryBond
This matches an aromatic or a single bond, used when no bond is specified between an atom.
|
class |
AromaticQueryBond
This matches an aromatic bond.
|
class |
LogicalOperatorBond
This class matches a logical operator that connects two query bonds.
|
class |
RingBond
This smarts bond matches any bond that is in a ring.
|
class |
SMARTSBond
Abstract smarts bond.
|
class |
StereoBond
This query bond indicates a particular geometric stereo configuration.
|
Modifier and Type | Class and 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.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
Iterable<IElectronContainer> |
AtomContainer.electronContainers()
Returns an Iterable for looping over all electron containers in this container.
|
List<IElectronContainer> |
AtomContainer.getConnectedElectronContainersList(IAtom atom)
Returns an ArrayList of all electronContainers connected to the given atom.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
static IElectronContainer[] |
AtomContainerManipulator.getElectronContainerArray(IAtomContainer container)
Constructs an array of Bond objects from an AtomContainer.
|
static IElectronContainer[] |
AtomContainerManipulator.getElectronContainerArray(List<IElectronContainer> list)
Constructs an array of Atom objects from a List of Atom objects.
|
Modifier and Type | Method and Description |
---|---|
static void |
MoleculeSetManipulator.removeElectronContainer(IAtomContainerSet set,
IElectronContainer electrons) |
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 |
ReactionManipulator.removeElectronContainer(IReaction reaction,
IElectronContainer electrons) |
static void |
ReactionSetManipulator.removeElectronContainer(IReactionSet set,
IElectronContainer electrons) |
Modifier and Type | Method and Description |
---|---|
static IElectronContainer[] |
AtomContainerManipulator.getElectronContainerArray(List<IElectronContainer> list)
Constructs an array of Atom objects from a List of Atom objects.
|
Modifier and Type | Method and Description |
---|---|
ValidationReport |
ValidatorEngine.validateElectronContainer(IElectronContainer subject) |
ValidationReport |
IValidator.validateElectronContainer(IElectronContainer subject) |
ValidationReport |
AbstractValidator.validateElectronContainer(IElectronContainer subject) |
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