public interface ITetrahedralChirality extends IStereoElement<IAtom,IAtom>
IAtom
,
and its four ligand IAtom
s, directly bonded to the chiral atom via an IBond
. The ordering of the
four ligands is important, and defines together with the ITetrahedralChirality.Stereo
to spatial geometry around the chiral atom.
The first ligand points towards to observer, and the three other ligands point away from the observer; the
ITetrahedralChirality.Stereo
then defines the order of the second, third, and fourth ligand to be clockwise or anti-clockwise.
If the tetrahedral centre has an implicit hydrogen or lone pair then the
chiral atom is also stored as one of the ligands. This serves as a
placeholder to indicate where the implicit hydrogen or lone pair would be.Modifier and Type | Interface and Description |
---|---|
static class |
ITetrahedralChirality.Stereo
Enumeration that defines the two possible chiralities for this stereochemistry type.
|
AL, Allenal, AT, Atropisomeric, CFG_MASK, CisTrans, CLS_MASK, CT, CU, Cumulene, GRP_ABS, GRP_MASK, GRP_NUM_MASK, GRP_NUM_SHIFT, GRP_RAC, GRP_RAC1, GRP_RAC2, GRP_RAC3, GRP_RAC4, GRP_RAC5, GRP_REL, GRP_REL1, GRP_REL2, GRP_REL3, GRP_REL4, GRP_REL5, GRP_TYPE_MASK, HBPY8, HBPY9, HeptagonalBipyramidal, HexagonalBipyramidal, LEFT, OC, Octahedral, OPPOSITE, PBPY, PentagonalBipyramidal, RIGHT, SP, SP4, SPU, SPY, SPZ, SquarePlanar, SquarePyramidal, TBPY, Tetrahedral, TH, TOGETHER, TrigonalBipyramidal
Modifier and Type | Method and Description |
---|---|
IAtom |
getChiralAtom()
Atom that is the chirality center.
|
IAtom[] |
getLigands()
Returns an array of ligand atoms around the chiral atom.
|
ITetrahedralChirality.Stereo |
getStereo()
Defines the stereochemistry around the chiral atom.
|
ITetrahedralChirality |
map(Map<IAtom,IAtom> atoms,
Map<IBond,IBond> bonds)
Map the atoms/bonds in this instance to a new stereo element using the
provided atom/bond mapping.
|
void |
setStereo(ITetrahedralChirality.Stereo stereo)
Set the stereochemistry of this tetrahedral centre.
|
contains, getCarriers, getConfig, getConfigClass, getConfigOrder, getFocus, getGroupInfo, map, setConfigOrder, setGroupInfo
getBuilder
IAtom[] getLigands()
getChiralAtom()
).IAtom
s.ITetrahedralChirality.Stereo getStereo()
ITetrahedralChirality.Stereo
for this stereo element.void setStereo(ITetrahedralChirality.Stereo stereo)
stereo
- the new stereo assignmentITetrahedralChirality map(Map<IAtom,IAtom> atoms, Map<IBond,IBond> bonds)
map
in interface IStereoElement<IAtom,IAtom>
atoms
- nullable atom mapping, used to convert the original atoms to their mapped
counterpartsbonds
- nullable bond mapping, used to convert the original bonds to their mapped
counterpartsCopyright © 2021. All rights reserved.