Package org.openscience.cdk.interfaces
Interface IDoubleBondStereochemistry
- All Superinterfaces:
Cloneable
,ICDKObject
,IStereoElement<IBond,
IBond>
- All Known Implementing Classes:
DoubleBondStereochemistry
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
IBond
s 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:
- main
- Belongs to CDK module:
- interfaces
-
Nested Class Summary
Nested ClassesModifier and TypeInterfaceDescriptionstatic enum
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
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Method Summary
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
-
getBonds
IBond[] getBonds()Returns an array of ligand bonds around the double bond.- Returns:
- an array of two
IBond
s.
-
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
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<IBond,
IBond> - 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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