Package | Description |
---|---|
org.openscience.cdk | |
org.openscience.cdk.debug | |
org.openscience.cdk.interfaces | |
org.openscience.cdk.isomorphism.matchers | |
org.openscience.cdk.silent |
Modifier and Type | Class and Description |
---|---|
class |
SingleElectron
A Single Electron is an orbital which is occupied by only one electron.
|
Modifier and Type | Field and Description |
---|---|
protected ISingleElectron[] |
AtomContainer.singleElectrons
Internal array of single electrons.
|
Modifier and Type | Method and Description |
---|---|
ISingleElectron |
AtomContainer.getSingleElectron(int idx)
Get the single electron at the specified idx, the index should
be in the range 0 ≤ idx <
IAtomContainer.getSingleElectronCount() . |
ISingleElectron |
AtomContainer.removeSingleElectron(int position)
Removes the single electron at the given position from the AtomContainer.
|
Modifier and Type | Method and Description |
---|---|
List<ISingleElectron> |
AtomContainer.getConnectedSingleElectronsList(IAtom atom)
Returns the single electrons connected connected to the specified atom.
|
Iterable<ISingleElectron> |
AtomContainer.singleElectrons()
Returns an Iterable for looping over all single electrons in this container.
|
Modifier and Type | Method and Description |
---|---|
void |
AtomContainer.addSingleElectron(ISingleElectron singleElectron)
Adds a single electron to this AtomContainer.
|
boolean |
AtomContainer.contains(ISingleElectron singleElectron)
True, if the AtomContainer contains the given SingleElectron object.
|
int |
AtomContainer.getSingleElectronNumber(ISingleElectron singleElectron)
Returns the position of a given single electron in the single electron array.
|
int |
AtomContainer.indexOf(ISingleElectron electron)
Access the storage index of a single electron (radical).
|
void |
AtomContainer.removeSingleElectron(ISingleElectron singleElectron)
Removes the single electron from the AtomContainer.
|
Modifier and Type | Class and Description |
---|---|
class |
DebugSingleElectron
Debugging data class.
|
Modifier and Type | Method and Description |
---|---|
ISingleElectron |
DebugStrand.getSingleElectron(int idx)
Get the single electron at the specified idx, the index should
be in the range 0 ≤ idx <
IAtomContainer.getSingleElectronCount() . |
ISingleElectron |
DebugRing.getSingleElectron(int idx)
Get the single electron at the specified idx, the index should
be in the range 0 ≤ idx <
IAtomContainer.getSingleElectronCount() . |
ISingleElectron |
DebugCrystal.getSingleElectron(int idx)
Get the single electron at the specified idx, the index should
be in the range 0 ≤ idx <
IAtomContainer.getSingleElectronCount() . |
ISingleElectron |
DebugAminoAcid.getSingleElectron(int idx)
Get the single electron at the specified idx, the index should
be in the range 0 ≤ idx <
IAtomContainer.getSingleElectronCount() . |
ISingleElectron |
DebugPolymer.getSingleElectron(int idx)
Get the single electron at the specified idx, the index should
be in the range 0 ≤ idx <
IAtomContainer.getSingleElectronCount() . |
ISingleElectron |
DebugBioPolymer.getSingleElectron(int idx)
Get the single electron at the specified idx, the index should
be in the range 0 ≤ idx <
IAtomContainer.getSingleElectronCount() . |
ISingleElectron |
DebugMonomer.getSingleElectron(int idx)
Get the single electron at the specified idx, the index should
be in the range 0 ≤ idx <
IAtomContainer.getSingleElectronCount() . |
ISingleElectron |
DebugAtomContainer.getSingleElectron(int idx)
Get the single electron at the specified idx, the index should
be in the range 0 ≤ idx <
IAtomContainer.getSingleElectronCount() . |
ISingleElectron |
DebugStrand.removeSingleElectron(int pos)
Removes the single electron at the given position from the AtomContainer.
|
ISingleElectron |
DebugRing.removeSingleElectron(int pos)
Removes the single electron at the given position from the AtomContainer.
|
ISingleElectron |
DebugCrystal.removeSingleElectron(int pos)
Removes the single electron at the given position from the AtomContainer.
|
ISingleElectron |
DebugAminoAcid.removeSingleElectron(int pos)
Removes the single electron at the given position from the AtomContainer.
|
ISingleElectron |
DebugPolymer.removeSingleElectron(int pos)
Removes the single electron at the given position from the AtomContainer.
|
ISingleElectron |
DebugBioPolymer.removeSingleElectron(int pos)
Removes the single electron at the given position from the AtomContainer.
|
ISingleElectron |
DebugMonomer.removeSingleElectron(int pos)
Removes the single electron at the given position from the AtomContainer.
|
ISingleElectron |
DebugAtomContainer.removeSingleElectron(int pos)
Removes the single electron at the given position from the AtomContainer.
|
Modifier and Type | Method and Description |
---|---|
List<ISingleElectron> |
DebugStrand.getConnectedSingleElectronsList(IAtom atom)
Returns the single electrons connected connected to the specified atom.
|
List<ISingleElectron> |
DebugRing.getConnectedSingleElectronsList(IAtom atom)
Returns the single electrons connected connected to the specified atom.
|
List<ISingleElectron> |
DebugCrystal.getConnectedSingleElectronsList(IAtom atom)
Returns the single electrons connected connected to the specified atom.
|
List<ISingleElectron> |
DebugAminoAcid.getConnectedSingleElectronsList(IAtom atom)
Returns the single electrons connected connected to the specified atom.
|
List<ISingleElectron> |
DebugPolymer.getConnectedSingleElectronsList(IAtom atom)
Returns the single electrons connected connected to the specified atom.
|
List<ISingleElectron> |
DebugBioPolymer.getConnectedSingleElectronsList(IAtom atom)
Returns the single electrons connected connected to the specified atom.
|
List<ISingleElectron> |
DebugMonomer.getConnectedSingleElectronsList(IAtom atom)
Returns the single electrons connected connected to the specified atom.
|
List<ISingleElectron> |
DebugAtomContainer.getConnectedSingleElectronsList(IAtom atom)
Returns the single electrons connected connected to the specified atom.
|
Iterable<ISingleElectron> |
DebugStrand.singleElectrons()
Returns an Iterable for looping over all single electrons in this container.
|
Iterable<ISingleElectron> |
DebugRing.singleElectrons()
Returns an Iterable for looping over all single electrons in this container.
|
Iterable<ISingleElectron> |
DebugCrystal.singleElectrons()
Returns an Iterable for looping over all single electrons in this container.
|
Iterable<ISingleElectron> |
DebugAminoAcid.singleElectrons()
Returns an Iterable for looping over all single electrons in this container.
|
Iterable<ISingleElectron> |
DebugPolymer.singleElectrons()
Returns an Iterable for looping over all single electrons in this container.
|
Iterable<ISingleElectron> |
DebugBioPolymer.singleElectrons()
Returns an Iterable for looping over all single electrons in this container.
|
Iterable<ISingleElectron> |
DebugMonomer.singleElectrons()
Returns an Iterable for looping over all single electrons in this container.
|
Iterable<ISingleElectron> |
DebugAtomContainer.singleElectrons()
Returns an Iterable for looping over all single electrons in this container.
|
Modifier and Type | Method and Description |
---|---|
void |
DebugStrand.addSingleElectron(ISingleElectron ec)
Adds a single electron to this AtomContainer.
|
void |
DebugRing.addSingleElectron(ISingleElectron ec)
Adds a single electron to this AtomContainer.
|
void |
DebugCrystal.addSingleElectron(ISingleElectron ec)
Adds a single electron to this AtomContainer.
|
void |
DebugAminoAcid.addSingleElectron(ISingleElectron ec)
Adds a single electron to this AtomContainer.
|
void |
DebugPolymer.addSingleElectron(ISingleElectron ec)
Adds a single electron to this AtomContainer.
|
void |
DebugBioPolymer.addSingleElectron(ISingleElectron ec)
Adds a single electron to this AtomContainer.
|
void |
DebugMonomer.addSingleElectron(ISingleElectron ec)
Adds a single electron to this AtomContainer.
|
void |
DebugAtomContainer.addSingleElectron(ISingleElectron ec)
Adds a single electron to this AtomContainer.
|
boolean |
DebugStrand.contains(ISingleElectron ec)
True, if the AtomContainer contains the given SingleElectron object.
|
boolean |
DebugRing.contains(ISingleElectron ec)
True, if the AtomContainer contains the given SingleElectron object.
|
boolean |
DebugCrystal.contains(ISingleElectron ec)
True, if the AtomContainer contains the given SingleElectron object.
|
boolean |
DebugAminoAcid.contains(ISingleElectron ec)
True, if the AtomContainer contains the given SingleElectron object.
|
boolean |
DebugPolymer.contains(ISingleElectron ec)
True, if the AtomContainer contains the given SingleElectron object.
|
boolean |
DebugBioPolymer.contains(ISingleElectron ec)
True, if the AtomContainer contains the given SingleElectron object.
|
boolean |
DebugMonomer.contains(ISingleElectron ec)
True, if the AtomContainer contains the given SingleElectron object.
|
boolean |
DebugAtomContainer.contains(ISingleElectron ec)
True, if the AtomContainer contains the given SingleElectron object.
|
int |
DebugStrand.getSingleElectronNumber(ISingleElectron bond)
Returns the position of a given single electron in the single electron array.
|
int |
DebugRing.getSingleElectronNumber(ISingleElectron bond)
Returns the position of a given single electron in the single electron array.
|
int |
DebugCrystal.getSingleElectronNumber(ISingleElectron bond)
Returns the position of a given single electron in the single electron array.
|
int |
DebugAminoAcid.getSingleElectronNumber(ISingleElectron bond)
Returns the position of a given single electron in the single electron array.
|
int |
DebugPolymer.getSingleElectronNumber(ISingleElectron bond)
Returns the position of a given single electron in the single electron array.
|
int |
DebugBioPolymer.getSingleElectronNumber(ISingleElectron bond)
Returns the position of a given single electron in the single electron array.
|
int |
DebugMonomer.getSingleElectronNumber(ISingleElectron bond)
Returns the position of a given single electron in the single electron array.
|
int |
DebugAtomContainer.indexOf(ISingleElectron electron)
Access the storage index of a single electron (radical).
|
void |
DebugStrand.removeSingleElectron(ISingleElectron ec)
Removes the single electron from the AtomContainer.
|
void |
DebugRing.removeSingleElectron(ISingleElectron ec)
Removes the single electron from the AtomContainer.
|
void |
DebugCrystal.removeSingleElectron(ISingleElectron ec)
Removes the single electron from the AtomContainer.
|
void |
DebugAminoAcid.removeSingleElectron(ISingleElectron ec)
Removes the single electron from the AtomContainer.
|
void |
DebugPolymer.removeSingleElectron(ISingleElectron ec)
Removes the single electron from the AtomContainer.
|
void |
DebugBioPolymer.removeSingleElectron(ISingleElectron ec)
Removes the single electron from the AtomContainer.
|
void |
DebugMonomer.removeSingleElectron(ISingleElectron ec)
Removes the single electron from the AtomContainer.
|
void |
DebugAtomContainer.removeSingleElectron(ISingleElectron ec)
Removes the single electron from the AtomContainer.
|
Modifier and Type | Method and Description |
---|---|
ISingleElectron |
IAtomContainer.getSingleElectron(int idx)
Get the single electron at the specified idx, the index should
be in the range 0 ≤ idx <
IAtomContainer.getSingleElectronCount() . |
ISingleElectron |
IAtomContainer.removeSingleElectron(int position)
Removes the single electron at the given position from the AtomContainer.
|
Modifier and Type | Method and Description |
---|---|
List<ISingleElectron> |
IAtomContainer.getConnectedSingleElectronsList(IAtom atom)
Returns the single electrons connected connected to the specified atom.
|
Iterable<ISingleElectron> |
IAtomContainer.singleElectrons()
Returns an Iterable for looping over all single electrons in this container.
|
Modifier and Type | Method and Description |
---|---|
void |
IAtomContainer.addSingleElectron(ISingleElectron singleElectron)
Adds a single electron to this AtomContainer.
|
boolean |
IAtomContainer.contains(ISingleElectron singleElectron)
True, if the AtomContainer contains the given SingleElectron object.
|
int |
IAtomContainer.getSingleElectronNumber(ISingleElectron singleElectron)
Deprecated.
|
int |
IAtomContainer.indexOf(ISingleElectron electron)
Access the storage index of a single electron (radical).
|
void |
IAtomContainer.removeSingleElectron(ISingleElectron singleElectron)
Removes the single electron from the AtomContainer.
|
Modifier and Type | Field and Description |
---|---|
protected ISingleElectron[] |
QueryAtomContainer.singleElectrons
Internal array of single electrons.
|
Modifier and Type | Method and Description |
---|---|
ISingleElectron |
QueryAtomContainer.getSingleElectron(int idx)
Get the single electron at the specified idx, the index should
be in the range 0 ≤ idx <
IAtomContainer.getSingleElectronCount() . |
ISingleElectron |
QueryAtomContainer.removeSingleElectron(int position)
Removes the single electron at the given position from the AtomContainer.
|
Modifier and Type | Method and Description |
---|---|
List<ISingleElectron> |
QueryAtomContainer.getConnectedSingleElectronsList(IAtom atom)
Returns an array of all SingleElectron connected to the given atom.
|
Iterable<ISingleElectron> |
QueryAtomContainer.singleElectrons()
Returns an Iterable for looping over all single electrons in this container.
|
Modifier and Type | Method and Description |
---|---|
void |
QueryAtomContainer.addSingleElectron(ISingleElectron singleElectron)
Adds a single electron to this AtomContainer.
|
boolean |
QueryAtomContainer.contains(ISingleElectron singleElectron)
True, if the AtomContainer contains the given SingleElectron object.
|
int |
QueryAtomContainer.getSingleElectronNumber(ISingleElectron singleElectron)
Returns the position of a given single electron in the single electron array.
|
int |
QueryAtomContainer.indexOf(ISingleElectron electron) |
void |
QueryAtomContainer.removeSingleElectron(ISingleElectron singleElectron)
Removes the single electron from the AtomContainer.
|
Modifier and Type | Field and Description |
---|---|
protected ISingleElectron[] |
AtomContainer.singleElectrons
Internal array of single electrons.
|
Modifier and Type | Method and Description |
---|---|
ISingleElectron |
AtomContainer.getSingleElectron(int idx)
Get the single electron at the specified idx, the index should
be in the range 0 ≤ idx <
IAtomContainer.getSingleElectronCount() . |
ISingleElectron |
AtomContainer.removeSingleElectron(int position)
Removes the single electron at the given position from the AtomContainer.
|
Modifier and Type | Method and Description |
---|---|
List<ISingleElectron> |
AtomContainer.getConnectedSingleElectronsList(IAtom atom)
Returns the single electrons connected connected to the specified atom.
|
Iterable<ISingleElectron> |
AtomContainer.singleElectrons()
Returns an Iterable for looping over all single electrons in this container.
|
Modifier and Type | Method and Description |
---|---|
void |
AtomContainer.addSingleElectron(ISingleElectron singleElectron)
Adds a single electron to this AtomContainer.
|
boolean |
AtomContainer.contains(ISingleElectron singleElectron)
True, if the AtomContainer contains the given SingleElectron object.
|
int |
AtomContainer.getSingleElectronNumber(ISingleElectron singleElectron)
Returns the position of a given single electron in the single electron array.
|
int |
AtomContainer.indexOf(ISingleElectron electron)
Access the storage index of a single electron (radical).
|
void |
AtomContainer.removeSingleElectron(ISingleElectron singleElectron)
Removes the single electron from the AtomContainer.
|
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