public class DoubleBondStereochemistry extends Object implements IDoubleBondStereochemistry
IDoubleBondStereochemistry
for
further details.IDoubleBondStereochemistry
IDoubleBondStereochemistry.Conformation
Modifier and Type | Field and Description |
---|---|
protected static int |
A |
protected static int |
B |
protected static int |
C |
protected static int |
D |
protected static int |
E |
protected static int |
F |
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
Constructor and Description |
---|
DoubleBondStereochemistry(IBond stereoBond,
IBond[] ligandBonds,
IDoubleBondStereochemistry.Conformation stereo)
Creates a new double bond stereo chemistry.
|
DoubleBondStereochemistry(IBond stereoBond,
IBond[] ligandBonds,
int config) |
Modifier and Type | Method and Description |
---|---|
boolean |
contains(IAtom atom)
Does the stereo element contain the provided atom.
|
protected IStereoElement<IBond,IBond> |
create(IBond focus,
List<IBond> carriers,
int cfg) |
IBond[] |
getBonds()
Returns an array of ligand bonds around the double bond.
|
IChemObjectBuilder |
getBuilder()
Returns a
IChemObjectBuilder for the data classes that extend
this class. |
List<C> |
getCarriers()
The carriers of the stereochemistry
|
int |
getConfig()
Access the configuration order and class of the stereochemistry.
|
int |
getConfigClass()
The configuration class of the stereochemistry.
|
int |
getConfigOrder()
The configuration order of the stereochemistry.
|
F |
getFocus()
The focus atom or bond at the 'centre' of the stereo-configuration.
|
int |
getGroupInfo()
Access the stereo group information - see class doc.
|
IDoubleBondStereochemistry.Conformation |
getStereo()
Defines the stereochemistry around the double bond.
|
IBond |
getStereoBond()
IBond that is the stereo center. |
protected static <T> T[] |
invapply(T[] src,
int[] perm) |
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.
|
IStereoElement<F,C> |
map(Map<IChemObject,IChemObject> chemobjs) |
protected static int |
numCarriers(int cfg) |
void |
setBuilder(IChemObjectBuilder builder) |
void |
setConfigOrder(int cfg)
Set the configuration order of the stereochemistry.
|
void |
setGroupInfo(int grp)
Set the stereo group information - see class doc.
|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
contains, getCarriers, getConfig, getConfigClass, getConfigOrder, getFocus, getGroupInfo, map, setConfigOrder, setGroupInfo
getBuilder
protected static final int A
protected static final int B
protected static final int C
protected static final int D
protected static final int E
protected static final int F
public DoubleBondStereochemistry(IBond stereoBond, IBond[] ligandBonds, IDoubleBondStereochemistry.Conformation stereo)
ligandBonds[0]
, stereoBonds
, and ligandBonds[1]
.public void setBuilder(IChemObjectBuilder builder)
public IBond[] getBonds()
getBonds
in interface IDoubleBondStereochemistry
IBond
s.public IBond getStereoBond()
IBond
that is the stereo center.getStereoBond
in interface IDoubleBondStereochemistry
IBond
.public IDoubleBondStereochemistry.Conformation getStereo()
getStereo
in interface IDoubleBondStereochemistry
IDoubleBondStereochemistry.Conformation
for this stereo element.public IDoubleBondStereochemistry map(Map<IAtom,IAtom> atoms, Map<IBond,IBond> bonds)
map
in interface IDoubleBondStereochemistry
map
in interface IStereoElement<IBond,IBond>
atoms
- nullable atom mapping, used to convert the original atoms to their mapped
counterpartsbonds
- nullable bond mapping, used to convert the original bonds to their mapped
counterpartsprotected static int numCarriers(int cfg)
public F getFocus()
getFocus
in interface IStereoElement<F extends IChemObject,C extends IChemObject>
public List<C> getCarriers()
getCarriers
in interface IStereoElement<F extends IChemObject,C extends IChemObject>
public int getConfigClass()
getConfigClass
in interface IStereoElement<F extends IChemObject,C extends IChemObject>
public int getConfigOrder()
getConfigOrder
in interface IStereoElement<F extends IChemObject,C extends IChemObject>
public int getConfig()
getConfig
in interface IStereoElement<F extends IChemObject,C extends IChemObject>
public void setConfigOrder(int cfg)
setConfigOrder
in interface IStereoElement<F extends IChemObject,C extends IChemObject>
cfg
- the new configurationpublic int getGroupInfo()
getGroupInfo
in interface IStereoElement<F extends IChemObject,C extends IChemObject>
public void setGroupInfo(int grp)
setGroupInfo
in interface IStereoElement<F extends IChemObject,C extends IChemObject>
grp
- the group infopublic boolean contains(IAtom atom)
contains
in interface IStereoElement<F extends IChemObject,C extends IChemObject>
atom
- an atom to test membershippublic IStereoElement<F,C> map(Map<IChemObject,IChemObject> chemobjs)
map
in interface IStereoElement<F extends IChemObject,C extends IChemObject>
public IChemObjectBuilder getBuilder()
IChemObjectBuilder
for the data classes that extend
this class.getBuilder
in interface ICDKObject
IChemObjectBuilder
matching this ICDKObject
protected static <T> T[] invapply(T[] src, int[] perm)
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