- All Known Implementing Classes:
Stereochemistry specification for quadrivalent atoms. The data model defines the central, chiral
IAtom, and its four ligand
IAtoms, directly bonded to the chiral atom via an
IBond. The ordering of the four ligands is important, and defines together with the
ITetrahedralChirality.Stereoto 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.Stereothen 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.
- Source code:
- Belongs to CDK module:
Nested Class SummaryModifier and TypeInterfaceDescription
static enumEnumeration that defines the two possible chiralities for this stereochemistry type.
Fields inherited from interface org.openscience.cdk.interfaces.IStereoElement
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
Method SummaryModifier and TypeMethodDescriptionAtom that is the chirality center.
IAtomReturns an array of ligand atoms around the chiral atom.Defines the stereochemistry around the chiral atom.Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.
voidSet the stereochemistry of this tetrahedral centre.
getLigandsIAtom getLigands()Returns an array of ligand atoms around the chiral atom. If the chiral centre has an implicit hydrogen or lone pair one of the ligands will be the chiral atom (
- an array of four
getChiralAtomIAtom getChiralAtom()Atom that is the chirality center.
- the chiral
getStereoITetrahedralChirality.Stereo getStereo()Defines the stereochemistry around the chiral atom. The value depends on the order of ligand atoms.
ITetrahedralChirality.Stereofor this stereo element.
(ITetrahedralChirality.Stereo stereo)Set the stereochemistry of this tetrahedral centre.
stereo- the new stereo assignment
mapMap the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping. This allows the stereo element to be transferred between a cloned or aligned (i.e. isomorphic) chemical graph. If no mapping is found for a given atom or bond it is left intact. However the provided atom and bonds maps must not be null.
- Specified by:
atoms- used to convert the original atoms to their mapped counterparts
bonds- used to convert the original bonds to their mapped counterparts
- a new stereo element in the same configuration but with atoms/bonds replaced with their mapped equivalence.