Modifier and Type | Class and Description |
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class |
Ring
Class representing a ring structure in a molecule.
|
Modifier and Type | Method and Description |
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IRing |
Ring.clone()
Clones this
IChemObject . |
Modifier and Type | Method and Description |
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IRingSet |
RingSet.getConnectedRings(IRing ring)
Returns all the rings in the RingSet that share
one or more atoms with a given ring.
|
Modifier and Type | Method and Description |
---|---|
static boolean |
AromaticityCalculator.isAromatic(IRing ring,
IAtomContainer atomContainer)
Deprecated.
Tests the
ring in the molecule for aromaticity. |
Modifier and Type | Class and Description |
---|---|
class |
DebugRing
Debugging data class.
|
Modifier and Type | Method and Description |
---|---|
IRing |
DebugRing.clone()
Clones this
IChemObject . |
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.
|
Modifier and Type | Method and Description |
---|---|
IRing |
IRing.clone()
Returns a deep clone of this IChemObject.
|
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.
|
Modifier and Type | Method and Description |
---|---|
double |
RingPlacer.getNativeRingRadius(IRing ring,
double bondLength)
Returns the ring radius of a perfect polygons of size ring.getAtomCount()
The ring radius is the distance of each atom to the ringcenter.
|
void |
RingPlacer.partitionNonRingPartners(IAtom atom,
IRing ring,
IAtomContainer ringAtoms,
IAtomContainer nonRingAtoms)
Partition the bonding partners of a given atom into ring atoms and non-ring atoms
|
void |
RingPlacer.placeFusedRing(IRing ring,
IAtomContainer sharedAtoms,
javax.vecmath.Vector2d ringCenterVector,
double bondLength)
Generated coordinates for a given ring, which is fused to another ring.
|
void |
RingPlacer.placeRing(IRing ring,
IAtomContainer sharedAtoms,
javax.vecmath.Point2d sharedAtomsCenter,
javax.vecmath.Vector2d ringCenterVector,
double bondLength)
Generated coordinates for a given ring.
|
void |
RingPlacer.placeRing(IRing ring,
javax.vecmath.Point2d ringCenter,
double bondLength)
Place ring with default start angles, using
RingPlacer.defaultAngles . |
void |
RingPlacer.placeRing(IRing ring,
javax.vecmath.Point2d ringCenter,
double bondLength,
Map<Integer,Double> startAngles)
Place ring with user provided angles.
|
void |
RingPlacer.placeSpiroRing(IRing ring,
IAtomContainer sharedAtoms,
javax.vecmath.Point2d sharedAtomsCenter,
javax.vecmath.Vector2d ringCenterVector,
double bondLength)
Generated coordinates for a given ring, which is connected to a spiro ring.
|
Modifier and Type | Method and Description |
---|---|
LineElement |
BasicBondGenerator.generateInnerElement(IBond bond,
IRing ring,
RendererModel model)
Make the inner ring bond, which is slightly shorter than the outer bond.
|
IRenderingElement |
BasicBondGenerator.generateRingElements(IBond bond,
IRing ring,
RendererModel model)
Generate ring elements, such as inner-ring bonds or ring stereo elements.
|
IRenderingElement |
RingGenerator.generateRingElements(IBond bond,
IRing ring,
RendererModel model)
Generate ring elements, such as inner-ring bonds or ring stereo elements.
|
Modifier and Type | Method and Description |
---|---|
IRing |
Ring.clone()
Clones this
IChemObject . |
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.
|
Modifier and Type | Method and Description |
---|---|
static boolean |
DeAromatizationTool.deAromatize(IRing ring)
Deprecated.
Methods that takes a ring of which all bonds are aromatic, and assigns single
and double bonds.
|
Modifier and Type | Method and Description |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
int |
RingSizeComparator.compare(IRing object1,
IRing object2) |
static void |
RingManipulator.markAromaticRings(IRing ring)
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.
|
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