Modifier and Type | Class and Description |
---|---|
class |
AtomContainerSet
A set of AtomContainers.
|
class |
MoleculeSet
A set of molecules, for example those taking part in a reaction.
|
class |
RingSet
Maintains a set of Ring objects.
|
Modifier and Type | Method and Description |
---|---|
void |
AtomContainerSet.add(IAtomContainerSet atomContainerSet)
Adds all atomContainers in the AtomContainerSet to this container.
|
Modifier and Type | Method and Description |
---|---|
double[][] |
GasteigerPEPEPartialCharges.assignrPiMarsilliFactors(IAtomContainerSet setAc)
Method which stores and assigns the factors a,b,c and CHI+
|
Modifier and Type | Class and Description |
---|---|
class |
DebugAtomContainerSet
Debugging data class.
|
class |
DebugMoleculeSet
Debugging data class.
|
class |
DebugRingSet
Debugging data class.
|
Modifier and Type | Method and Description |
---|---|
void |
DebugMoleculeSet.add(IAtomContainerSet atomContainerSet) |
void |
DebugAtomContainerSet.add(IAtomContainerSet atomContainerSet) |
Modifier and Type | Method and Description |
---|---|
static IAtomContainerSet |
ConjugatedPiSystemsDetector.detect(IAtomContainer ac)
Detect all conjugated pi systems in an AtomContainer.
|
Modifier and Type | Interface and Description |
---|---|
interface |
IMoleculeSet
Represents a set of Molecules.
|
interface |
IRingSet
Maintains a set of Ring objects.
|
Modifier and Type | Method and Description |
---|---|
void |
IAtomContainerSet.add(IAtomContainerSet atomContainerSet)
Adds all atomContainers in the AtomContainerSet to this container.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainerSet |
TemplateHandler.getMappedSubstructures(IAtomContainer molecule)
Checks if one of the loaded templates is a substructure in the given
Molecule and returns all matched substructures in a IAtomContainerSet.
|
Modifier and Type | Class and Description |
---|---|
class |
NNAtomContainerSet
Deprecated.
Use the
AtomContainerSet instead. |
class |
NNMoleculeSet
Deprecated.
Use the
MoleculeSet instead. |
class |
NNRingSet
Deprecated.
Use the
RingSet instead. |
Modifier and Type | Method and Description |
---|---|
void |
AtomContainerSet.add(IAtomContainerSet atomContainerSet)
Adds all atomContainers in the AtomContainerSet to this container.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
PartialFilledStructureMerger.generate(IAtomContainerSet atomContainers)
Randomly generates a single, connected, correctly bonded structure from
a number of fragments.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainerSet |
StructureResonanceGenerator.getContainers(IMolecule molecule)
Get the container which is found resonance from a IMolecule.
|
Modifier and Type | Method and Description |
---|---|
static boolean |
AtomContainerSetManipulator.containsByID(IAtomContainerSet atomContainerSet,
String id)
Tells if an AtomContainerSet contains at least one AtomContainer with the
same ID as atomContainer.
|
static List<IAtomContainer> |
AtomContainerSetManipulator.getAllAtomContainers(IAtomContainerSet set)
Returns all the AtomContainer's of a MoleculeSet.
|
static List<IChemObject> |
AtomContainerSetManipulator.getAllChemObjects(IAtomContainerSet set)
Does not recursively return the contents of the AtomContainer.
|
static List<String> |
AtomContainerSetManipulator.getAllIDs(IAtomContainerSet set) |
static int |
MoleculeSetManipulator.getAtomCount(IAtomContainerSet set) |
static int |
AtomContainerSetManipulator.getAtomCount(IAtomContainerSet set) |
static int |
MoleculeSetManipulator.getBondCount(IAtomContainerSet set) |
static int |
AtomContainerSetManipulator.getBondCount(IAtomContainerSet set) |
static IAtomContainer |
AtomContainerSetManipulator.getRelevantAtomContainer(IAtomContainerSet containerSet,
IAtom atom) |
static IAtomContainer |
AtomContainerSetManipulator.getRelevantAtomContainer(IAtomContainerSet containerSet,
IBond bond) |
static double |
AtomContainerSetManipulator.getTotalCharge(IAtomContainerSet set) |
static double |
AtomContainerSetManipulator.getTotalFormalCharge(IAtomContainerSet set) |
static int |
AtomContainerSetManipulator.getTotalHydrogenCount(IAtomContainerSet set) |
static void |
AtomContainerSetManipulator.removeAtomAndConnectedElectronContainers(IAtomContainerSet set,
IAtom atom) |
static void |
AtomContainerSetManipulator.removeElectronContainer(IAtomContainerSet set,
IElectronContainer electrons) |
static void |
AtomContainerSetManipulator.setAtomProperties(IAtomContainerSet set,
Object propKey,
Object propVal) |
static void |
AtomContainerSetManipulator.sort(IAtomContainerSet atomContainerSet)
Sorts the IAtomContainers in the given IAtomContainerSet by the following
criteria with decreasing priority:
|