Package org.openscience.cdk.interfaces
Interface ITetrahedralChirality
- All Superinterfaces:
Cloneable
,ICDKObject
,IStereoElement<IAtom,
IAtom>
- All Known Implementing Classes:
TetrahedralChirality
Stereochemistry specification for quadrivalent atoms. The data model defines the central, chiral
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.- Source code:
- main
- Belongs to CDK module:
- interfaces
-
Nested Class Summary
Nested ClassesModifier and TypeInterfaceDescriptionstatic enum
Enumeration that defines the two possible chiralities for this stereochemistry type. -
Field Summary
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
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Method Summary
Modifier and TypeMethodDescriptionAtom that is the chirality center.IAtom[]
Returns 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.void
Set the stereochemistry of this tetrahedral centre.Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject
getBuilder
Methods inherited from interface org.openscience.cdk.interfaces.IStereoElement
contains, getCarriers, getConfig, getConfigClass, getConfigOrder, getFocus, getGroupInfo, map, mapStrict, setConfigOrder, setGroupInfo
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Method Details
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getLigands
IAtom[] 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 (getChiralAtom()
).- Returns:
- an array of four
IAtom
s.
-
getChiralAtom
IAtom getChiralAtom()Atom that is the chirality center.- Returns:
- the chiral
IAtom
.
-
getStereo
ITetrahedralChirality.Stereo getStereo()Defines the stereochemistry around the chiral atom. The value depends on the order of ligand atoms.- Returns:
- the
ITetrahedralChirality.Stereo
for this stereo element.
-
setStereo
Set the stereochemistry of this tetrahedral centre.- Parameters:
stereo
- the new stereo assignment
-
map
Map 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:
map
in interfaceIStereoElement<IAtom,
IAtom> - Parameters:
atoms
- used to convert the original atoms to their mapped counterpartsbonds
- used to convert the original bonds to their mapped counterparts- Returns:
- a new stereo element in the same configuration but with atoms/bonds replaced with their mapped equivalence.
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