Modifier and Type | Field and Description |
---|---|
protected Set<IStereoElement> |
AtomContainer.stereoElements
Internal list of atom parities.
|
Modifier and Type | Method and Description |
---|---|
Iterable<IStereoElement> |
AtomContainer.stereoElements()
Returns the stereo elements defined for this atom container.
|
Modifier and Type | Method and Description |
---|---|
void |
AtomContainer.addStereoElement(IStereoElement element)
Adds a stereo element to this container.
|
Modifier and Type | Method and Description |
---|---|
void |
AtomContainer.setStereoElements(List<IStereoElement> elements)
Set the stereo elements - this will replace the existing instance
with a new instance.
|
Modifier and Type | Method and Description |
---|---|
Iterable<IStereoElement> |
DebugStrand.stereoElements()
Returns the stereo elements defined for this atom container.
|
Iterable<IStereoElement> |
DebugRing.stereoElements()
Returns the stereo elements defined for this atom container.
|
Iterable<IStereoElement> |
DebugPolymer.stereoElements()
Returns the stereo elements defined for this atom container.
|
Iterable<IStereoElement> |
DebugMonomer.stereoElements()
Returns the stereo elements defined for this atom container.
|
Iterable<IStereoElement> |
DebugCrystal.stereoElements()
Returns the stereo elements defined for this atom container.
|
Iterable<IStereoElement> |
DebugBioPolymer.stereoElements()
Returns the stereo elements defined for this atom container.
|
Iterable<IStereoElement> |
DebugAtomContainer.stereoElements()
Returns the stereo elements defined for this atom container.
|
Iterable<IStereoElement> |
DebugAminoAcid.stereoElements()
Returns the stereo elements defined for this atom container.
|
Modifier and Type | Method and Description |
---|---|
void |
DebugStrand.addStereoElement(IStereoElement parity)
Adds a stereo element to this container.
|
void |
DebugRing.addStereoElement(IStereoElement parity)
Adds a stereo element to this container.
|
void |
DebugPolymer.addStereoElement(IStereoElement parity)
Adds a stereo element to this container.
|
void |
DebugMonomer.addStereoElement(IStereoElement parity)
Adds a stereo element to this container.
|
void |
DebugCrystal.addStereoElement(IStereoElement parity)
Adds a stereo element to this container.
|
void |
DebugBioPolymer.addStereoElement(IStereoElement parity)
Adds a stereo element to this container.
|
void |
DebugAtomContainer.addStereoElement(IStereoElement parity)
Adds a stereo element to this container.
|
void |
DebugAminoAcid.addStereoElement(IStereoElement parity)
Adds a stereo element to this container.
|
Modifier and Type | Method and Description |
---|---|
void |
DebugAtomContainer.setStereoElements(List<IStereoElement> elements)
Set the stereo elements - this will replace the existing instance
with a new instance.
|
Modifier and Type | Interface and Description |
---|---|
interface |
IDoubleBondStereochemistry
Stereochemistry specification for double bond stereochemistry.
|
interface |
ITetrahedralChirality
Stereochemistry specification for quadrivalent atoms.
|
Modifier and Type | Method and Description |
---|---|
IStereoElement |
IStereoElement.map(Map<IAtom,IAtom> atoms,
Map<IBond,IBond> bonds)
Map the atoms/bonds in this instance to a new stereo element using the
provided atom/bond mapping.
|
Modifier and Type | Method and Description |
---|---|
Iterable<IStereoElement> |
IAtomContainer.stereoElements()
Returns the stereo elements defined for this atom container.
|
Modifier and Type | Method and Description |
---|---|
void |
IAtomContainer.addStereoElement(IStereoElement element)
Adds a stereo element to this container.
|
Modifier and Type | Method and Description |
---|---|
void |
IAtomContainer.setStereoElements(List<IStereoElement> elements)
Set the stereo elements - this will replace the existing instance
with a new instance.
|
Modifier and Type | Field and Description |
---|---|
protected List<IStereoElement> |
QueryAtomContainer.stereoElements
Internal list of atom parities.
|
Modifier and Type | Method and Description |
---|---|
Iterable<IStereoElement> |
QueryAtomContainer.stereoElements()
Returns the stereo elements defined for this atom container.
|
Modifier and Type | Method and Description |
---|---|
void |
QueryAtomContainer.addStereoElement(IStereoElement element)
Adds a stereo element to this container.
|
Modifier and Type | Method and Description |
---|---|
void |
QueryAtomContainer.setStereoElements(List<IStereoElement> elements) |
Modifier and Type | Field and Description |
---|---|
protected Set<IStereoElement> |
AtomContainer.stereoElements
Internal list of atom parities.
|
Modifier and Type | Method and Description |
---|---|
Iterable<IStereoElement> |
AtomContainer.stereoElements()
Returns the stereo elements defined for this atom container.
|
Modifier and Type | Method and Description |
---|---|
void |
AtomContainer.addStereoElement(IStereoElement element)
Adds a stereo element to this container.
|
Modifier and Type | Method and Description |
---|---|
void |
AtomContainer.setStereoElements(List<IStereoElement> elements)
Set the stereo elements - this will replace the existing instance
with a new instance.
|
Modifier and Type | Class and Description |
---|---|
class |
DoubleBondStereochemistry
Stereochemistry specification for double bonds.
|
class |
ExtendedTetrahedral
Extended tetrahedral configuration.
|
class |
TetrahedralChirality
Stereochemistry specification for quadrivalent atoms.
|
Modifier and Type | Method and Description |
---|---|
IStereoElement |
ExtendedTetrahedral.map(Map<IAtom,IAtom> atoms,
Map<IBond,IBond> bonds)
Map the atoms/bonds in this instance to a new stereo element using the
provided atom/bond mapping.
|
Modifier and Type | Method and Description |
---|---|
List<IStereoElement> |
StereoElementFactory.createAll()
Creates all stereo elements found by
Stereocenters using the or
2D/3D coordinates to specify the configuration (clockwise/anticlockwise). |
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