org.openscience.cdk.interfaces

Interface ITetrahedralChirality

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, 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.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:

master

Belongs to CDK module:

interfaces

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	ITetrahedralChirality.Stereo 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

Method Summary

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.

Methods inherited from interface org.openscience.cdk.interfaces.IStereoElement

contains, getCarriers, getConfig, getConfigClass, getConfigOrder, getFocus, getGroupInfo, map, setConfigOrder, setGroupInfo

Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject

getBuilder

Method Detail

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 IAtoms.

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

void setStereo(ITetrahedralChirality.Stereo stereo)

Set the stereochemistry of this tetrahedral centre.

Parameters:

stereo - the new stereo assignment

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 interface IStereoElement<IAtom,IAtom>

Parameters:

atoms - nullable atom mapping, used to convert the original atoms to their mapped counterparts

bonds - nullable bond mapping, 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.