Package org.openscience.cdk.interfaces
Interface ITetrahedralChirality
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- All Superinterfaces:
Cloneable
,ICDKObject
,IStereoElement<IAtom,IAtom>
- All Known Implementing Classes:
TetrahedralChirality
public interface ITetrahedralChirality extends IStereoElement<IAtom,IAtom>
Stereochemistry specification for quadrivalent atoms. The data model defines the central, chiralIAtom
, and its four ligandIAtom
s, directly bonded to the chiral atom via anIBond
. The ordering of the four ligands is important, and defines together with theITetrahedralChirality.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; theITetrahedralChirality.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
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Nested Class Summary
Nested Classes Modifier and Type Interface Description static class
ITetrahedralChirality.Stereo
Enumeration that defines the two possible chiralities for this stereochemistry type.
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Field Summary
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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
All Methods Instance Methods Abstract Methods Modifier and Type Method 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.-
Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject
getBuilder
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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 Detail
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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.
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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.
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setStereo
void setStereo(ITetrahedralChirality.Stereo stereo)
Set the stereochemistry of this tetrahedral centre.- Parameters:
stereo
- the new stereo assignment
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map
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. 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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