org.openscience.cdk.interfaces

Interface IDoubleBondStereochemistry

All Superinterfaces:

Cloneable, ICDKObject, IStereoElement<IBond,IBond>

All Known Implementing Classes:

DoubleBondStereochemistry

public interface IDoubleBondStereochemistry
extends IStereoElement<IBond,IBond>

Stereochemistry specification for double bond stereochemistry. The data model defines the double atoms and two ligands attached to those two atoms, linearly connected with the double bond in the middle. The IBonds that define the stereo element are defined as an array where the bonds are sorted according to the linear connectivity. Thus, the first and third bonds are the two bonds attached on either side of the double bond, and the second bond is the double bond. The stereo annotation then indicates if the ligand atoms are in the cis position (IDoubleBondStereochemistry.Conformation.TOGETHER) or in the trans position (IDoubleBondStereochemistry.Conformation.OPPOSITE), matching the orientation of the methyls in but-2-ene respectively as Z and E.

Source code:

master

Belongs to CDK module:

interfaces

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	IDoubleBondStereochemistry.Conformation Enumeration that defines the two possible values 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
IBond[]	getBonds() Returns an array of ligand bonds around the double bond.
IDoubleBondStereochemistry.Conformation	getStereo() Defines the stereochemistry around the double bond.
IBond	getStereoBond() IBond that is the stereo center.
IDoubleBondStereochemistry	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.

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

getBonds

IBond[] getBonds()

Returns an array of ligand bonds around the double bond.

Returns:

an array of two IBonds.

getStereoBond

IBond getStereoBond()

IBond that is the stereo center.

Returns:

the double IBond.

getStereo

IDoubleBondStereochemistry.Conformation getStereo()

Defines the stereochemistry around the double bond.

Returns:

the IDoubleBondStereochemistry.Conformation for this stereo element.

map

IDoubleBondStereochemistry 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<IBond,IBond>

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.