Modifier and Type | Class and Description |
---|---|
class |
RingSet
Maintains a set of Ring objects.
|
Modifier and Type | Field and Description |
---|---|
protected IRingSet |
ChemModel.ringSet
A RingSet.
|
Modifier and Type | Method and Description |
---|---|
IRingSet |
RingSet.getConnectedRings(IRing ring)
Returns all the rings in the RingSet that share
one or more atoms with a given ring.
|
IRingSet |
RingSet.getRings(IAtom atom)
Returns a vector of all rings that this atom is part of.
|
IRingSet |
RingSet.getRings(IBond bond)
Returns a vector of all rings that this bond is part of.
|
IRingSet |
ChemModel.getRingSet()
Returns the RingSet of this ChemModel.
|
Modifier and Type | Method and Description |
---|---|
void |
RingSet.add(IRingSet ringSet)
Adds all rings of another RingSet if they are not already part of this ring set.
|
void |
ChemModel.setRingSet(IRingSet ringSet)
Sets the RingSet of this ChemModel.
|
Modifier and Type | Method and Description |
---|---|
static boolean |
EStateAtomTypeMatcher.inSameAromaticRing(IAtomContainer m,
IAtom atom1,
IAtom atom2,
IRingSet rs) |
void |
EStateAtomTypeMatcher.setRingSet(IRingSet rs) |
Modifier and Type | Class and Description |
---|---|
class |
DebugRingSet
Debugging data class.
|
Modifier and Type | Method and Description |
---|---|
IRingSet |
DebugRingSet.getConnectedRings(IRing ring)
Returns all the rings in the RingSet that share
one or more atoms with a given ring.
|
IRingSet |
DebugRingSet.getRings(IAtom atom)
Returns a vector of all rings that this atom is part of.
|
IRingSet |
DebugRingSet.getRings(IBond bond)
Returns a vector of all rings that this bond is part of.
|
IRingSet |
DebugChemModel.getRingSet()
Returns the RingSet of this ChemModel.
|
Modifier and Type | Method and Description |
---|---|
void |
DebugRingSet.add(IRingSet ringSet)
Adds all rings of another RingSet if they are not already part of this ring set.
|
void |
DebugChemModel.setRingSet(IRingSet ringSet)
Sets the RingSet of this ChemModel.
|
Modifier and Type | Method and Description |
---|---|
IBitFingerprint |
ExtendedFingerprinter.getBitFingerprint(IAtomContainer atomContainer,
IRingSet ringSet,
List<IRingSet> rslist)
Generates a fingerprint of the default size for the given
AtomContainer, using path and ring metrics.
|
Modifier and Type | Method and Description |
---|---|
IBitFingerprint |
ExtendedFingerprinter.getBitFingerprint(IAtomContainer atomContainer,
IRingSet ringSet,
List<IRingSet> rslist)
Generates a fingerprint of the default size for the given
AtomContainer, using path and ring metrics.
|
Modifier and Type | Method and Description |
---|---|
static javax.vecmath.Point2d |
GeometryTools.get2DCenter(IRingSet ringSet)
Returns the geometric center of all the rings in this ringset.
|
static javax.vecmath.Point2d |
GeometryUtil.get2DCenter(IRingSet ringSet)
Returns the geometric center of all the rings in this ringset.
|
Modifier and Type | Method and Description |
---|---|
IRingSet |
SpanningTree.getAllRings()
All basic rings and the all pairs of basic rings share at least one edge
combined.
|
IRingSet |
SpanningTree.getBasicRings()
The basic rings of the spanning tree.
|
IRingSet |
Cycles.toRingSet()
|
Modifier and Type | Method and Description |
---|---|
IRingSet |
IRingSet.getConnectedRings(IRing ring)
Returns all the rings in the RingSet that share
one or more atoms with a given ring.
|
IRingSet |
IRingSet.getRings(IAtom atom)
Returns a vector of all rings that this atom is part of.
|
IRingSet |
IRingSet.getRings(IBond bond)
Returns a vector of all rings that this bond is part of.
|
IRingSet |
IChemModel.getRingSet()
Returns the RingSet of this ChemModel.
|
Modifier and Type | Method and Description |
---|---|
void |
IRingSet.add(IRingSet ringSet)
Adds all rings of another RingSet if they are not allready part of this ring set.
|
void |
IChemModel.setRingSet(IRingSet ringSet)
Sets the RingSet of this ChemModel.
|
Modifier and Type | Method and Description |
---|---|
boolean |
RingPlacer.allPlaced(IRingSet rs)
True if coordinates have been assigned to all atoms in all rings.
|
void |
RingPlacer.checkAndMarkPlaced(IRingSet rs)
Walks throught the atoms of each ring in a ring set and marks
a ring as PLACED if all of its atoms have been placed.
|
IAtomContainer |
RingPlacer.placeRingSubstituents(IRingSet rs,
double bondLength)
Positions the aliphatic substituents of a ring system
|
double |
OverlapResolver.resolveOverlap(IAtomContainer ac,
IRingSet sssr)
Deprecated.
Main method to be called to resolve overlap situations.
|
Modifier and Type | Method and Description |
---|---|
IRingSet |
ForceFieldConfigurator.assignAtomTyps(IAtomContainer molecule)
Method assigns atom types to atoms (calculates sssr and aromaticity)
|
IRingSet |
TemplateHandler3D.getLargestRingSet(List<IRingSet> ringSystems)
Returns the largest (number of atoms) ring set in a molecule.
|
Modifier and Type | Method and Description |
---|---|
IRingSet |
TemplateHandler3D.getLargestRingSet(List<IRingSet> ringSystems)
Returns the largest (number of atoms) ring set in a molecule.
|
Modifier and Type | Method and Description |
---|---|
DescriptorValue |
RDFProtonDescriptor_GSR.calculate(IAtom atom,
IAtomContainer atomContainer,
IRingSet precalculatedringset) |
DescriptorValue |
RDFProtonDescriptor_GHR_topol.calculate(IAtom atom,
IAtomContainer atomContainer,
IRingSet precalculatedringset) |
DescriptorValue |
RDFProtonDescriptor_GHR.calculate(IAtom atom,
IAtomContainer atomContainer,
IRingSet precalculatedringset) |
DescriptorValue |
RDFProtonDescriptor_GDR.calculate(IAtom atom,
IAtomContainer atomContainer,
IRingSet precalculatedringset) |
DescriptorValue |
RDFProtonDescriptor_G3R.calculate(IAtom atom,
IAtomContainer atomContainer,
IRingSet precalculatedringset) |
Modifier and Type | Field and Description |
---|---|
protected IRingSet |
BasicBondGenerator.ringSet
Necessary for calculating inner-ring bond elements.
|
Modifier and Type | Method and Description |
---|---|
protected IRingSet |
BasicBondGenerator.getRingSet(IAtomContainer atomContainer)
Determine the ring set for this atom container.
|
Modifier and Type | Method and Description |
---|---|
IRingSet |
AllRingsFinder.findAllRings(IAtomContainer container)
Compute all rings in the given
IAtomContainer . |
IRingSet |
AllRingsFinder.findAllRings(IAtomContainer container,
int maxRingSize)
Compute all rings up to and including the maxRingSize.
|
IRingSet |
AllRingsFinder.findAllRingsInIsolatedRingSystem(IAtomContainer container)
Compute all rings in the given
IAtomContainer . |
IRingSet |
AllRingsFinder.findAllRingsInIsolatedRingSystem(IAtomContainer atomContainer,
int maxRingSize)
Compute all rings up to an including the maxRingSize.
|
IRingSet |
SSSRFinder.findEssentialRings()
Deprecated.
Finds the Set of Essential Rings.
|
IRingSet |
SSSRFinder.findRelevantRings()
Deprecated.
Finds the Set of Relevant Rings.
|
IRingSet |
SSSRFinder.findSSSR()
Deprecated.
Finds a Smallest Set of Smallest Rings.
|
IRingSet |
FiguerasSSSRFinder.findSSSR(IAtomContainer mol)
Deprecated.
Finds the Smallest Set of Smallest Rings.
|
Modifier and Type | Method and Description |
---|---|
static List<IRingSet> |
RingPartitioner.partitionRings(IRingSet ringSet)
Partitions a RingSet into RingSets of connected rings.
|
Modifier and Type | Method and Description |
---|---|
static IAtomContainer |
RingPartitioner.convertToAtomContainer(IRingSet ringSet)
Converts a RingSet to an AtomContainer.
|
static List<IRingSet> |
RingPartitioner.partitionRings(IRingSet ringSet)
Partitions a RingSet into RingSets of connected rings.
|
Modifier and Type | Field and Description |
---|---|
protected IRingSet |
ChemModel.ringSet
A RingSet.
|
Modifier and Type | Method and Description |
---|---|
IRingSet |
RingSet.getConnectedRings(IRing ring)
Returns all the rings in the RingSet that share
one or more atoms with a given ring.
|
IRingSet |
RingSet.getRings(IAtom atom)
Returns a vector of all rings that this atom is part of.
|
IRingSet |
RingSet.getRings(IBond bond)
Returns a vector of all rings that this bond is part of.
|
IRingSet |
ChemModel.getRingSet()
Returns the RingSet of this ChemModel.
|
Modifier and Type | Method and Description |
---|---|
void |
RingSet.add(IRingSet ringSet)
Adds all rings of another RingSet if they are not already part of this ring set.
|
void |
ChemModel.setRingSet(IRingSet ringSet)
Sets the RingSet of this ChemModel.
|
Modifier and Type | Method and Description |
---|---|
IRingSet |
RingFinder.getRingSet(IAtomContainer molecule)
Deprecated.
Returns CDK object Ring set based on Hanser Ring Finding method
|
IRingSet |
HanserRingFinder.getRingSet(IAtomContainer molecule)
Deprecated.
Returns Ring set based on Hanser Ring Finding method
|
Modifier and Type | Method and Description |
---|---|
IRingSet |
AtomTypeTools.assignAtomTypePropertiesToAtom(IAtomContainer molecule) |
IRingSet |
AtomTypeTools.assignAtomTypePropertiesToAtom(IAtomContainer molecule,
boolean aromaticity)
Method assigns certain properties to an atom.
|
Modifier and Type | Method and Description |
---|---|
static boolean |
DeAromatizationTool.Dearomatize566Rings(IRingSet rings)
Deprecated.
|
static boolean |
DeAromatizationTool.Dearomatize56Rings(IRingSet rings)
Deprecated.
|
static boolean |
DeAromatizationTool.Dearomatize5Ring(IRingSet rings)
Deprecated.
|
static boolean |
DeAromatizationTool.Dearomatize666Rings(IRingSet rings)
Deprecated.
|
static boolean |
DeAromatizationTool.Dearomatize66Rings(IRingSet rings)
Deprecated.
|
static boolean |
DeAromatizationTool.Dearomatize6Ring(IRingSet rings)
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
static IRingSet |
RingSetManipulator.getLargestRingSet(List<IRingSet> ringSystems)
Returns the largest (number of atoms) ring set in a molecule
|
Modifier and Type | Method and Description |
---|---|
static List<IAtomContainer> |
RingSetManipulator.getAllAtomContainers(IRingSet set)
Returns all the AtomContainer's in a RingSet.
|
static IAtomContainer |
RingSetManipulator.getAllInOneContainer(IRingSet ringSet)
Puts all rings of a ringSet in a single atomContainer
|
static int |
RingSetManipulator.getAtomCount(IRingSet set)
Return the total number of atoms over all the rings in the colllection.
|
static int |
RingSetManipulator.getBondCount(IRingSet set)
Return the total number of bonds over all the rings in the colllection.
|
static IRing |
RingSetManipulator.getHeaviestRing(IRingSet ringSet,
IBond bond)
We define the heaviest ring as the one with the highest number of double bonds.
|
static IRing |
RingSetManipulator.getMostComplexRing(IRingSet ringSet)
Returns the ring with the highest numbers of other rings attached to it.
|
static boolean |
RingSetManipulator.isSameRing(IRingSet ringSet,
IAtom atom1,
IAtom atom2)
Checks if
atom1 and atom2 share membership in the same ring or ring system. |
static void |
RingSetManipulator.markAromaticRings(IRingSet ringset)
Iterates over the rings in the ring set, and marks the ring
aromatic if all atoms and all bonds are aromatic.
|
static boolean |
RingSetManipulator.ringAlreadyInSet(IRing newRing,
IRingSet ringSet)
Checks - and returns 'true' - if a certain ring is already
stored in the ringset.
|
static void |
RingSetManipulator.sort(IRingSet ringSet)
Sorts the rings in the set by size.
|
Modifier and Type | Method and Description |
---|---|
static IRingSet |
RingSetManipulator.getLargestRingSet(List<IRingSet> ringSystems)
Returns the largest (number of atoms) ring set in a molecule
|
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