Uses of Interface
org.openscience.cdk.interfaces.IRingSet
-
-
Uses of IRingSet in org.openscience.cdk
Classes in org.openscience.cdk that implement IRingSet Modifier and Type Class Description class
RingSet
Maintains a set of Ring objects.Fields in org.openscience.cdk declared as IRingSet Modifier and Type Field Description protected IRingSet
ChemModel. ringSet
A RingSet.Methods in org.openscience.cdk that return IRingSet Modifier and Type Method 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.Methods in org.openscience.cdk with parameters of type IRingSet Modifier and Type Method 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. -
Uses of IRingSet in org.openscience.cdk.atomtype
Methods in org.openscience.cdk.atomtype with parameters of type IRingSet Modifier and Type Method Description static boolean
EStateAtomTypeMatcher. inSameAromaticRing(IAtomContainer m, IAtom atom1, IAtom atom2, IRingSet rs)
void
EStateAtomTypeMatcher. setRingSet(IRingSet rs)
-
Uses of IRingSet in org.openscience.cdk.debug
Classes in org.openscience.cdk.debug that implement IRingSet Modifier and Type Class Description class
DebugRingSet
Debugging data class.Methods in org.openscience.cdk.debug that return IRingSet Modifier and Type Method 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.Methods in org.openscience.cdk.debug with parameters of type IRingSet Modifier and Type Method 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. -
Uses of IRingSet in org.openscience.cdk.fingerprint
Methods in org.openscience.cdk.fingerprint with parameters of type IRingSet Modifier and Type Method 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.Method parameters in org.openscience.cdk.fingerprint with type arguments of type IRingSet Modifier and Type Method 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. -
Uses of IRingSet in org.openscience.cdk.geometry
Methods in org.openscience.cdk.geometry with parameters of type IRingSet Modifier and Type Method Description static javax.vecmath.Point2d
GeometryTools. get2DCenter(IRingSet ringSet)
Deprecated.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. -
Uses of IRingSet in org.openscience.cdk.graph
Methods in org.openscience.cdk.graph that return IRingSet Modifier and Type Method 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()
-
Uses of IRingSet in org.openscience.cdk.interfaces
Methods in org.openscience.cdk.interfaces that return IRingSet Modifier and Type Method 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.Methods in org.openscience.cdk.interfaces with parameters of type IRingSet Modifier and Type Method 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. -
Uses of IRingSet in org.openscience.cdk.layout
Methods in org.openscience.cdk.layout with parameters of type IRingSet Modifier and Type Method 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 systemdouble
OverlapResolver. resolveOverlap(IAtomContainer ac, IRingSet sssr)
Deprecated.Main method to be called to resolve overlap situations. -
Uses of IRingSet in org.openscience.cdk.modeling.builder3d
Methods in org.openscience.cdk.modeling.builder3d that return IRingSet Modifier and Type Method 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.Method parameters in org.openscience.cdk.modeling.builder3d with type arguments of type IRingSet Modifier and Type Method Description IRingSet
TemplateHandler3D. getLargestRingSet(List<IRingSet> ringSystems)
Returns the largest (number of atoms) ring set in a molecule. -
Uses of IRingSet in org.openscience.cdk.qsar.descriptors.atomic
Methods in org.openscience.cdk.qsar.descriptors.atomic with parameters of type IRingSet Modifier and Type Method Description DescriptorValue
RDFProtonDescriptor_G3R. calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)
DescriptorValue
RDFProtonDescriptor_GDR. 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_GSR. calculate(IAtom atom, IAtomContainer atomContainer, IRingSet precalculatedringset)
-
Uses of IRingSet in org.openscience.cdk.renderer.generators
Fields in org.openscience.cdk.renderer.generators declared as IRingSet Modifier and Type Field Description protected IRingSet
BasicBondGenerator. ringSet
Necessary for calculating inner-ring bond elements.Methods in org.openscience.cdk.renderer.generators that return IRingSet Modifier and Type Method Description protected IRingSet
BasicBondGenerator. getRingSet(IAtomContainer atomContainer)
Determine the ring set for this atom container. -
Uses of IRingSet in org.openscience.cdk.ringsearch
Methods in org.openscience.cdk.ringsearch that return IRingSet Modifier and Type Method Description IRingSet
AllRingsFinder. findAllRings(IAtomContainer container)
Compute all rings in the givenIAtomContainer
.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 givenIAtomContainer
.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
FiguerasSSSRFinder. findSSSR(IAtomContainer mol)
Deprecated.Finds the Smallest Set of Smallest Rings.IRingSet
SSSRFinder. findSSSR()
Deprecated.Finds a Smallest Set of Smallest Rings.Methods in org.openscience.cdk.ringsearch that return types with arguments of type IRingSet Modifier and Type Method Description static List<IRingSet>
RingPartitioner. partitionRings(IRingSet ringSet)
Partitions a RingSet into RingSets of connected rings.Methods in org.openscience.cdk.ringsearch with parameters of type IRingSet Modifier and Type Method 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. -
Uses of IRingSet in org.openscience.cdk.silent
Classes in org.openscience.cdk.silent that implement IRingSet Modifier and Type Class Description class
RingSet
Maintains a set of Ring objects.Fields in org.openscience.cdk.silent declared as IRingSet Modifier and Type Field Description protected IRingSet
ChemModel. ringSet
A RingSet.Methods in org.openscience.cdk.silent that return IRingSet Modifier and Type Method 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.Methods in org.openscience.cdk.silent with parameters of type IRingSet Modifier and Type Method 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. -
Uses of IRingSet in org.openscience.cdk.smsd.ring
Methods in org.openscience.cdk.smsd.ring that return IRingSet Modifier and Type Method Description IRingSet
HanserRingFinder. getRingSet(IAtomContainer molecule)
Deprecated.Returns Ring set based on Hanser Ring Finding methodIRingSet
RingFinder. getRingSet(IAtomContainer molecule)
Deprecated.Returns CDK object Ring set based on Hanser Ring Finding method -
Uses of IRingSet in org.openscience.cdk.tools
Methods in org.openscience.cdk.tools that return IRingSet Modifier and Type Method Description IRingSet
AtomTypeTools. assignAtomTypePropertiesToAtom(IAtomContainer molecule)
IRingSet
AtomTypeTools. assignAtomTypePropertiesToAtom(IAtomContainer molecule, boolean aromaticity)
Method assigns certain properties to an atom.Methods in org.openscience.cdk.tools with parameters of type IRingSet Modifier and Type Method 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. -
Uses of IRingSet in org.openscience.cdk.tools.manipulator
Methods in org.openscience.cdk.tools.manipulator that return IRingSet Modifier and Type Method Description static IRingSet
RingSetManipulator. getLargestRingSet(List<IRingSet> ringSystems)
Returns the largest (number of atoms) ring set in a moleculeMethods in org.openscience.cdk.tools.manipulator with parameters of type IRingSet Modifier and Type Method 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 atomContainerstatic 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 ifatom1
andatom2
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.Method parameters in org.openscience.cdk.tools.manipulator with type arguments of type IRingSet Modifier and Type Method Description static IRingSet
RingSetManipulator. getLargestRingSet(List<IRingSet> ringSystems)
Returns the largest (number of atoms) ring set in a molecule
-