Package | Description |
---|---|
org.openscience.cdk | |
org.openscience.cdk.debug | |
org.openscience.cdk.interfaces | |
org.openscience.cdk.nonotify | |
org.openscience.cdk.silent | |
org.openscience.cdk.stereo |
Modifier and Type | Class and Description |
---|---|
class |
AtomParity
Represents the concept of an atom parity identifying the stereochemistry
around an atom, given four neighbouring atoms.
|
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) |
Modifier and Type | Class and Description |
---|---|
class |
DebugAtomParity
Debugging data class.
|
Modifier and Type | Method and Description |
---|---|
Iterable<IStereoElement> |
DebugStrand.stereoElements() |
Iterable<IStereoElement> |
DebugRing.stereoElements() |
Iterable<IStereoElement> |
DebugPolymer.stereoElements() |
Iterable<IStereoElement> |
DebugMonomer.stereoElements() |
Iterable<IStereoElement> |
DebugMolecule.stereoElements() |
Iterable<IStereoElement> |
DebugCrystal.stereoElements() |
Iterable<IStereoElement> |
DebugBioPolymer.stereoElements() |
Iterable<IStereoElement> |
DebugAtomContainer.stereoElements() |
Iterable<IStereoElement> |
DebugAminoAcid.stereoElements() |
Modifier and Type | Method and Description |
---|---|
void |
DebugStrand.addStereoElement(IStereoElement parity) |
void |
DebugRing.addStereoElement(IStereoElement parity) |
void |
DebugPolymer.addStereoElement(IStereoElement parity) |
void |
DebugMonomer.addStereoElement(IStereoElement parity) |
void |
DebugMolecule.addStereoElement(IStereoElement parity) |
void |
DebugCrystal.addStereoElement(IStereoElement parity) |
void |
DebugBioPolymer.addStereoElement(IStereoElement parity) |
void |
DebugAtomContainer.addStereoElement(IStereoElement parity) |
void |
DebugAminoAcid.addStereoElement(IStereoElement parity) |
Modifier and Type | Method and Description |
---|---|
void |
DebugAtomContainer.setStereoElements(List<IStereoElement> elements) |
Modifier and Type | Interface and Description |
---|---|
interface |
IAtomParity
Represents the concept of an atom parity identifying the stereochemistry
around an atom, given four neighbouring atoms.
|
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 | Class and Description |
---|---|
class |
NNAtomParity
Deprecated.
Use the
AtomParity instead. |
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) |
Modifier and Type | Class and Description |
---|---|
class |
DoubleBondStereochemistry
Stereochemistry specification for double bonds.
|
class |
TetrahedralChirality
Stereochemistry specification for quadrivalent atoms.
|