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 |
LonePair
A LonePair is an orbital primarily located with one Atom, containing
two electrons.
|
Modifier and Type | Field and Description |
---|---|
protected ILonePair[] |
AtomContainer.lonePairs
Internal array of lone pairs.
|
Modifier and Type | Method and Description |
---|---|
ILonePair |
AtomContainer.getLonePair(int idx)
Get the lone pair at the specified idx, the index should be in the
range 0 ≤ idx <
IAtomContainer.getLonePairCount() . |
ILonePair |
AtomContainer.removeLonePair(int position)
Removes the lone pair at the given position from the AtomContainer.
|
Modifier and Type | Method and Description |
---|---|
List<ILonePair> |
AtomContainer.getConnectedLonePairsList(IAtom atom)
Returns the lone pairs connected connected to the specified atom.
|
Iterable<ILonePair> |
AtomContainer.lonePairs()
Returns an Iterable for looping over all lone pairs in this container.
|
Modifier and Type | Method and Description |
---|---|
void |
AtomContainer.addLonePair(ILonePair lonePair)
Adds a lone pair to this AtomContainer.
|
boolean |
AtomContainer.contains(ILonePair lonePair)
True, if the AtomContainer contains the given LonePair object.
|
int |
AtomContainer.getLonePairNumber(ILonePair lonePair)
Returns the position of a given lone pair in the lone pair array.
|
int |
AtomContainer.indexOf(ILonePair pair)
Access the storage index of a long pair.
|
void |
AtomContainer.removeLonePair(ILonePair lonePair)
Removes the lone pair from the AtomContainer.
|
Modifier and Type | Class and Description |
---|---|
class |
DebugLonePair
Debugging data class.
|
Modifier and Type | Method and Description |
---|---|
ILonePair |
DebugStrand.getLonePair(int idx)
Get the lone pair at the specified idx, the index should be in the
range 0 ≤ idx <
IAtomContainer.getLonePairCount() . |
ILonePair |
DebugRing.getLonePair(int idx)
Get the lone pair at the specified idx, the index should be in the
range 0 ≤ idx <
IAtomContainer.getLonePairCount() . |
ILonePair |
DebugCrystal.getLonePair(int idx)
Get the lone pair at the specified idx, the index should be in the
range 0 ≤ idx <
IAtomContainer.getLonePairCount() . |
ILonePair |
DebugAminoAcid.getLonePair(int idx)
Get the lone pair at the specified idx, the index should be in the
range 0 ≤ idx <
IAtomContainer.getLonePairCount() . |
ILonePair |
DebugPolymer.getLonePair(int idx)
Get the lone pair at the specified idx, the index should be in the
range 0 ≤ idx <
IAtomContainer.getLonePairCount() . |
ILonePair |
DebugBioPolymer.getLonePair(int idx)
Get the lone pair at the specified idx, the index should be in the
range 0 ≤ idx <
IAtomContainer.getLonePairCount() . |
ILonePair |
DebugMonomer.getLonePair(int idx)
Get the lone pair at the specified idx, the index should be in the
range 0 ≤ idx <
IAtomContainer.getLonePairCount() . |
ILonePair |
DebugAtomContainer.getLonePair(int idx)
Get the lone pair at the specified idx, the index should be in the
range 0 ≤ idx <
IAtomContainer.getLonePairCount() . |
ILonePair |
DebugStrand.removeLonePair(int pos)
Removes the lone pair at the given position from the AtomContainer.
|
ILonePair |
DebugRing.removeLonePair(int pos)
Removes the lone pair at the given position from the AtomContainer.
|
ILonePair |
DebugCrystal.removeLonePair(int pos)
Removes the lone pair at the given position from the AtomContainer.
|
ILonePair |
DebugAminoAcid.removeLonePair(int pos)
Removes the lone pair at the given position from the AtomContainer.
|
ILonePair |
DebugPolymer.removeLonePair(int pos)
Removes the lone pair at the given position from the AtomContainer.
|
ILonePair |
DebugBioPolymer.removeLonePair(int pos)
Removes the lone pair at the given position from the AtomContainer.
|
ILonePair |
DebugMonomer.removeLonePair(int pos)
Removes the lone pair at the given position from the AtomContainer.
|
ILonePair |
DebugAtomContainer.removeLonePair(int pos)
Removes the lone pair at the given position from the AtomContainer.
|
Modifier and Type | Method and Description |
---|---|
List<ILonePair> |
DebugStrand.getConnectedLonePairsList(IAtom atom)
Returns the lone pairs connected connected to the specified atom.
|
List<ILonePair> |
DebugRing.getConnectedLonePairsList(IAtom atom)
Returns the lone pairs connected connected to the specified atom.
|
List<ILonePair> |
DebugCrystal.getConnectedLonePairsList(IAtom atom)
Returns the lone pairs connected connected to the specified atom.
|
List<ILonePair> |
DebugAminoAcid.getConnectedLonePairsList(IAtom atom)
Returns the lone pairs connected connected to the specified atom.
|
List<ILonePair> |
DebugPolymer.getConnectedLonePairsList(IAtom atom)
Returns the lone pairs connected connected to the specified atom.
|
List<ILonePair> |
DebugBioPolymer.getConnectedLonePairsList(IAtom atom)
Returns the lone pairs connected connected to the specified atom.
|
List<ILonePair> |
DebugMonomer.getConnectedLonePairsList(IAtom atom)
Returns the lone pairs connected connected to the specified atom.
|
List<ILonePair> |
DebugAtomContainer.getConnectedLonePairsList(IAtom atom)
Returns the lone pairs connected connected to the specified atom.
|
Iterable<ILonePair> |
DebugStrand.lonePairs()
Returns an Iterable for looping over all lone pairs in this container.
|
Iterable<ILonePair> |
DebugRing.lonePairs()
Returns an Iterable for looping over all lone pairs in this container.
|
Iterable<ILonePair> |
DebugCrystal.lonePairs()
Returns an Iterable for looping over all lone pairs in this container.
|
Iterable<ILonePair> |
DebugAminoAcid.lonePairs()
Returns an Iterable for looping over all lone pairs in this container.
|
Iterable<ILonePair> |
DebugPolymer.lonePairs()
Returns an Iterable for looping over all lone pairs in this container.
|
Iterable<ILonePair> |
DebugBioPolymer.lonePairs()
Returns an Iterable for looping over all lone pairs in this container.
|
Iterable<ILonePair> |
DebugMonomer.lonePairs()
Returns an Iterable for looping over all lone pairs in this container.
|
Iterable<ILonePair> |
DebugAtomContainer.lonePairs()
Returns an Iterable for looping over all lone pairs in this container.
|
Modifier and Type | Method and Description |
---|---|
void |
DebugStrand.addLonePair(ILonePair ec)
Adds a lone pair to this AtomContainer.
|
void |
DebugRing.addLonePair(ILonePair ec)
Adds a lone pair to this AtomContainer.
|
void |
DebugCrystal.addLonePair(ILonePair ec)
Adds a lone pair to this AtomContainer.
|
void |
DebugAminoAcid.addLonePair(ILonePair ec)
Adds a lone pair to this AtomContainer.
|
void |
DebugPolymer.addLonePair(ILonePair ec)
Adds a lone pair to this AtomContainer.
|
void |
DebugBioPolymer.addLonePair(ILonePair ec)
Adds a lone pair to this AtomContainer.
|
void |
DebugMonomer.addLonePair(ILonePair ec)
Adds a lone pair to this AtomContainer.
|
void |
DebugAtomContainer.addLonePair(ILonePair ec)
Adds a lone pair to this AtomContainer.
|
boolean |
DebugStrand.contains(ILonePair ec)
True, if the AtomContainer contains the given LonePair object.
|
boolean |
DebugRing.contains(ILonePair ec)
True, if the AtomContainer contains the given LonePair object.
|
boolean |
DebugCrystal.contains(ILonePair ec)
True, if the AtomContainer contains the given LonePair object.
|
boolean |
DebugAminoAcid.contains(ILonePair ec)
True, if the AtomContainer contains the given LonePair object.
|
boolean |
DebugPolymer.contains(ILonePair ec)
True, if the AtomContainer contains the given LonePair object.
|
boolean |
DebugBioPolymer.contains(ILonePair ec)
True, if the AtomContainer contains the given LonePair object.
|
boolean |
DebugMonomer.contains(ILonePair ec)
True, if the AtomContainer contains the given LonePair object.
|
boolean |
DebugAtomContainer.contains(ILonePair ec)
True, if the AtomContainer contains the given LonePair object.
|
int |
DebugStrand.getLonePairNumber(ILonePair bond)
Returns the position of a given lone pair in the lone pair array.
|
int |
DebugRing.getLonePairNumber(ILonePair bond)
Returns the position of a given lone pair in the lone pair array.
|
int |
DebugCrystal.getLonePairNumber(ILonePair bond)
Returns the position of a given lone pair in the lone pair array.
|
int |
DebugAminoAcid.getLonePairNumber(ILonePair bond)
Returns the position of a given lone pair in the lone pair array.
|
int |
DebugPolymer.getLonePairNumber(ILonePair bond)
Returns the position of a given lone pair in the lone pair array.
|
int |
DebugBioPolymer.getLonePairNumber(ILonePair bond)
Returns the position of a given lone pair in the lone pair array.
|
int |
DebugMonomer.getLonePairNumber(ILonePair bond)
Returns the position of a given lone pair in the lone pair array.
|
int |
DebugAtomContainer.indexOf(ILonePair pair)
Access the storage index of a long pair.
|
void |
DebugStrand.removeLonePair(ILonePair ec)
Removes the lone pair from the AtomContainer.
|
void |
DebugRing.removeLonePair(ILonePair ec)
Removes the lone pair from the AtomContainer.
|
void |
DebugCrystal.removeLonePair(ILonePair ec)
Removes the lone pair from the AtomContainer.
|
void |
DebugAminoAcid.removeLonePair(ILonePair ec)
Removes the lone pair from the AtomContainer.
|
void |
DebugPolymer.removeLonePair(ILonePair ec)
Removes the lone pair from the AtomContainer.
|
void |
DebugBioPolymer.removeLonePair(ILonePair ec)
Removes the lone pair from the AtomContainer.
|
void |
DebugMonomer.removeLonePair(ILonePair ec)
Removes the lone pair from the AtomContainer.
|
void |
DebugAtomContainer.removeLonePair(ILonePair ec)
Removes the lone pair from the AtomContainer.
|
Modifier and Type | Method and Description |
---|---|
ILonePair |
IAtomContainer.getLonePair(int idx)
Get the lone pair at the specified idx, the index should be in the
range 0 ≤ idx <
IAtomContainer.getLonePairCount() . |
ILonePair |
IAtomContainer.removeLonePair(int position)
Removes the lone pair at the given position from the AtomContainer.
|
Modifier and Type | Method and Description |
---|---|
List<ILonePair> |
IAtomContainer.getConnectedLonePairsList(IAtom atom)
Returns the lone pairs connected connected to the specified atom.
|
Iterable<ILonePair> |
IAtomContainer.lonePairs()
Returns an Iterable for looping over all lone pairs in this container.
|
Modifier and Type | Method and Description |
---|---|
void |
IAtomContainer.addLonePair(ILonePair lonePair)
Adds a lone pair to this AtomContainer.
|
boolean |
IAtomContainer.contains(ILonePair lonePair)
True, if the AtomContainer contains the given LonePair object.
|
int |
IAtomContainer.getLonePairNumber(ILonePair lonePair)
Deprecated.
|
int |
IAtomContainer.indexOf(ILonePair pair)
Access the storage index of a long pair.
|
void |
IAtomContainer.removeLonePair(ILonePair lonePair)
Removes the lone pair from the AtomContainer.
|
Modifier and Type | Field and Description |
---|---|
protected ILonePair[] |
QueryAtomContainer.lonePairs
Internal array of lone pairs.
|
Modifier and Type | Method and Description |
---|---|
ILonePair |
QueryAtomContainer.getLonePair(int idx)
Get the lone pair at the specified idx, the index should be in the
range 0 ≤ idx <
IAtomContainer.getLonePairCount() . |
ILonePair |
QueryAtomContainer.removeLonePair(int position)
Removes the lone pair at the given position from the AtomContainer.
|
Modifier and Type | Method and Description |
---|---|
List<ILonePair> |
QueryAtomContainer.getConnectedLonePairsList(IAtom atom)
Returns the array of lone pairs connected to an atom.
|
Iterable<ILonePair> |
QueryAtomContainer.lonePairs()
Returns an Iterable for looping over all lone pairs in this container.
|
Modifier and Type | Method and Description |
---|---|
void |
QueryAtomContainer.addLonePair(ILonePair lonePair)
Adds a lone pair to this AtomContainer.
|
boolean |
QueryAtomContainer.contains(ILonePair lonePair)
True, if the AtomContainer contains the given LonePair object.
|
int |
QueryAtomContainer.getLonePairNumber(ILonePair lonePair)
Returns the position of a given lone pair in the lone pair array.
|
int |
QueryAtomContainer.indexOf(ILonePair pair) |
void |
QueryAtomContainer.removeLonePair(ILonePair lonePair)
Removes the lone pair from the AtomContainer.
|
Modifier and Type | Field and Description |
---|---|
protected ILonePair[] |
AtomContainer.lonePairs
Internal array of lone pairs.
|
Modifier and Type | Method and Description |
---|---|
ILonePair |
AtomContainer.getLonePair(int idx)
Get the lone pair at the specified idx, the index should be in the
range 0 ≤ idx <
IAtomContainer.getLonePairCount() . |
ILonePair |
AtomContainer.removeLonePair(int position)
Removes the lone pair at the given position from the AtomContainer.
|
Modifier and Type | Method and Description |
---|---|
List<ILonePair> |
AtomContainer.getConnectedLonePairsList(IAtom atom)
Returns the lone pairs connected connected to the specified atom.
|
Iterable<ILonePair> |
AtomContainer.lonePairs()
Returns an Iterable for looping over all lone pairs in this container.
|
Modifier and Type | Method and Description |
---|---|
void |
AtomContainer.addLonePair(ILonePair lonePair)
Adds a lone pair to this AtomContainer.
|
boolean |
AtomContainer.contains(ILonePair lonePair)
True, if the AtomContainer contains the given LonePair object.
|
int |
AtomContainer.getLonePairNumber(ILonePair lonePair)
Returns the position of a given lone pair in the lone pair array.
|
int |
AtomContainer.indexOf(ILonePair pair)
Access the storage index of a long pair.
|
void |
AtomContainer.removeLonePair(ILonePair lonePair)
Removes the lone pair from the AtomContainer.
|
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