Modifier and Type | Method and Description |
---|---|
void |
DirectMoleculeDrawer.addToChiralMap(java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> chirals) |
void |
DirectAtomDrawer.setChirals(java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> chiralMap) |
Modifier and Type | Method and Description |
---|---|
void |
AtomLayout.setChirals(java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> chiralMap) |
Modifier and Type | Method and Description |
---|---|
java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> |
RBlastReaction.getAtomStereoProductMap() |
java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> |
RBlastReaction.getAtomStereoReactantMap() |
Modifier and Type | Method and Description |
---|---|
IStereoAndConformation |
StereoChange.getProductAtomStereo() |
IStereoAndConformation |
StereoChange.getReactantAtomStereo() |
Modifier and Type | Method and Description |
---|---|
boolean |
StereogenicCenterCalculator.isStereogenicChange(IStereoAndConformation a,
IStereoAndConformation b)
Returns type of stereo changes
|
Modifier and Type | Method and Description |
---|---|
java.util.List<StereoChange> |
StereogenicCenterCalculator.compare(org.openscience.cdk.interfaces.IReaction reaction,
java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> chirality2DCDK) |
java.util.List<StereoChange> |
StereogenicCenterCalculator.compare(org.openscience.cdk.interfaces.IReaction reaction,
java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> chirality2DCDK,
java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> chirality2DChemaxon) |
java.util.List<StereoChange> |
StereogenicCenterCalculator.compare(org.openscience.cdk.interfaces.IReaction reaction,
java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> chirality2DCDK,
java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> chirality2DChemaxon) |
java.util.List<StereoChange> |
StereogenicCenterCalculator.compare(org.openscience.cdk.interfaces.IReaction reaction,
java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> chirality2DCDK,
java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> chirality2DChemaxon,
java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> chirality3DChemaxon) |
java.util.List<StereoChange> |
StereogenicCenterCalculator.compare(org.openscience.cdk.interfaces.IReaction reaction,
java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> chirality2DCDK,
java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> chirality2DChemaxon,
java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> chirality3DChemaxon) |
java.util.List<StereoChange> |
StereogenicCenterCalculator.compare(org.openscience.cdk.interfaces.IReaction reaction,
java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> chirality2DCDK,
java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> chirality2DChemaxon,
java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> chirality3DChemaxon) |
Constructor and Description |
---|
StereoChange(IStereoAndConformation rAtomStereo,
IStereoAndConformation pAtomStereo,
org.openscience.cdk.interfaces.IAtom rAtom,
org.openscience.cdk.interfaces.IAtom pAtom) |
Modifier and Type | Method and Description |
---|---|
IStereoAndConformation |
AtomStereoChangeInformation.getProductAtomStereo() |
IStereoAndConformation |
AtomStereoChangeInformation.getReactantAtomStereo() |
Modifier and Type | Method and Description |
---|---|
void |
AtomStereoChangeInformation.setAtomStereo(IStereoAndConformation atomStereoR,
IStereoAndConformation atomStereoP) |
Constructor and Description |
---|
AtomStereoChangeInformation(org.openscience.cdk.interfaces.IAtom atomE,
org.openscience.cdk.interfaces.IAtom atomP,
IStereoAndConformation aStereoR,
IStereoAndConformation aStereoP) |
Modifier and Type | Method and Description |
---|---|
static IStereoAndConformation |
IStereoAndConformation.valueOf(java.lang.String name)
Returns the enum constant of this type with the specified name.
|
static IStereoAndConformation[] |
IStereoAndConformation.values()
Returns an array containing the constants of this enum type, in
the order they are declared.
|
Modifier and Type | Method and Description |
---|---|
java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> |
ChiralityTool.getTetrahedralChiralities(org.openscience.cdk.interfaces.IAtomContainer atomContainer) |
java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> |
ChiralityTool.getTetrahedralChiralities(org.openscience.cdk.interfaces.IAtomContainer atomContainer,
boolean getNoneAssignments) |
Modifier and Type | Method and Description |
---|---|
static java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> |
StereoCenteralityTool.getChirality2D(org.openscience.cdk.interfaces.IAtomContainer ac,
CDKPerceptor perceptor) |
static java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> |
StereoCenteralityTool.getChirality2D(org.openscience.cdk.interfaces.IReaction reaction)
This Chirality is based on the 2D with stereo code written by John May in our collaboration.
|
Modifier and Type | Method and Description |
---|---|
static IStereoAndConformation |
Chirality2DTool.getChirality2D(org.openscience.cdk.interfaces.IStereoElement stereoElement,
org.openscience.cdk.interfaces.IAtomContainer atomContainer) |
static IStereoAndConformation |
Chirality2DTool.getChirality2D(WedgeStereoLifter lifter,
org.openscience.cdk.interfaces.IAtom atom,
org.openscience.cdk.interfaces.IAtomContainer atomContainer) |
Modifier and Type | Method and Description |
---|---|
java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> |
Chirality2DTool.getTetrahedralChiralities(org.openscience.cdk.interfaces.IAtomContainer atomContainer) |
java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> |
Chirality3DTool.getTetrahedralChiralities(org.openscience.cdk.interfaces.IAtomContainer atomContainer)
Get R/S Chirality assignments for an atom container that should have 3D
coordinates as Point3d set in the atoms.
|
java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> |
Chirality2DTool.getTetrahedralChiralities(org.openscience.cdk.interfaces.IAtomContainer atomContainer,
boolean getNoneAssesments) |
java.util.Map<org.openscience.cdk.interfaces.IAtom,IStereoAndConformation> |
Chirality3DTool.getTetrahedralChiralities(org.openscience.cdk.interfaces.IAtomContainer atomContainer,
boolean getNoneAssigments)
Get R/S Chirality assignments for an atom container that should have 3D
coordinates as Point3d set in the atoms.
|