Package org.openscience.cdk.stereo

Class DoubleBondStereochemistry

java.lang.Object

org.openscience.cdk.stereo.DoubleBondStereochemistry

All Implemented Interfaces:

Cloneable, ICDKObject, IDoubleBondStereochemistry, IStereoElement<IBond,IBond>

public class DoubleBondStereochemistry
extends Object
implements IDoubleBondStereochemistry

Stereochemistry specification for double bonds. See IDoubleBondStereochemistry for further details.

See Also:

• IDoubleBondStereochemistry

Source code:

main

Belongs to CDK module:

core

Nested Class Summary

Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.IDoubleBondStereochemistry

IDoubleBondStereochemistry.Conformation

Field Summary

Fields

Modifier and Type	Field	Description
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

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

Constructor Summary

Constructors

Constructor	Description
DoubleBondStereochemistry(IBond stereoBond, IBond[] ligandBonds, int config)
DoubleBondStereochemistry(IBond stereoBond, IBond[] ligandBonds, IDoubleBondStereochemistry.Conformation stereo)	Creates a new double bond stereo chemistry.

Method Summary

Modifier and Type	Method	Description
boolean	contains(IAtom atom)
protected IStereoElement<IBond,IBond>	create(IBond focus, List<IBond> carriers, int cfg)
IBond[]	getBonds()
IChemObjectBuilder	getBuilder()
List<IBond>	getCarriers()
int	getConfig()
int	getConfigClass()
int	getConfigOrder()
IBond	getFocus()
int	getGroupInfo()
IDoubleBondStereochemistry.Conformation	getStereo()
IBond	getStereoBond()
protected static <T> T[]	invapply(T[] src, int[] perm)
IDoubleBondStereochemistry	map(Map<IAtom,IAtom> atoms, Map<IBond,IBond> bonds)
IStereoElement<IBond,IBond>	map(Map<IChemObject,IChemObject> chemobjs)
final IStereoElement<IBond,IBond>	mapStrict(Map<IChemObject,IChemObject> chemobjs)
protected static int	numCarriers(int cfg)
void	setBuilder(IChemObjectBuilder builder)
void	setConfigOrder(int cfg)
void	setGroupInfo(int grp)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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

Field Details

A

protected static final int A

See Also:

• Constant Field Values

B

protected static final int B

See Also:

• Constant Field Values

C

protected static final int C

See Also:

• Constant Field Values

D

protected static final int D

See Also:

• Constant Field Values

E

protected static final int E

See Also:

• Constant Field Values

F

protected static final int F

See Also:

• Constant Field Values

Constructor Details

DoubleBondStereochemistry

public DoubleBondStereochemistry(IBond stereoBond,
 IBond[] ligandBonds,
 IDoubleBondStereochemistry.Conformation stereo)

Creates a new double bond stereo chemistry. The path of length three is defined by ligandBonds[0], stereoBonds, and ligandBonds[1].

DoubleBondStereochemistry

public DoubleBondStereochemistry(IBond stereoBond,
 IBond[] ligandBonds,
 int config)

Method Details

setBuilder

public void setBuilder(IChemObjectBuilder builder)

getBonds

public IBond[] getBonds()

Specified by:

getBonds in interface IDoubleBondStereochemistry

getStereoBond

public IBond getStereoBond()

Specified by:

getStereoBond in interface IDoubleBondStereochemistry

getStereo

public IDoubleBondStereochemistry.Conformation getStereo()

Specified by:

getStereo in interface IDoubleBondStereochemistry

map

public IDoubleBondStereochemistry map(Map<IAtom,IAtom> atoms,
 Map<IBond,IBond> bonds)

Specified by:

map in interface IDoubleBondStereochemistry

Specified by:

map in interface IStereoElement<IBond,IBond>

create

protected IStereoElement<IBond,IBond> create(IBond focus,
 List<IBond> carriers,
 int cfg)

numCarriers

protected static int numCarriers(int cfg)

getFocus

public IBond getFocus()

Specified by:

getFocus in interface IStereoElement<F extends IChemObject,C extends IChemObject>

getCarriers

public List<IBond> getCarriers()

Specified by:

getCarriers in interface IStereoElement<F extends IChemObject,C extends IChemObject>

getConfigClass

public int getConfigClass()

Specified by:

getConfigClass in interface IStereoElement<F extends IChemObject,C extends IChemObject>

getConfigOrder

public int getConfigOrder()

Specified by:

getConfigOrder in interface IStereoElement<F extends IChemObject,C extends IChemObject>

getConfig

public int getConfig()

Specified by:

getConfig in interface IStereoElement<F extends IChemObject,C extends IChemObject>

setConfigOrder

public void setConfigOrder(int cfg)

Specified by:

setConfigOrder in interface IStereoElement<F extends IChemObject,C extends IChemObject>

getGroupInfo

public int getGroupInfo()

Specified by:

getGroupInfo in interface IStereoElement<F extends IChemObject,C extends IChemObject>

setGroupInfo

public void setGroupInfo(int grp)

Specified by:

setGroupInfo in interface IStereoElement<F extends IChemObject,C extends IChemObject>

contains

public boolean contains(IAtom atom)

Specified by:

contains in interface IStereoElement<F extends IChemObject,C extends IChemObject>

map

public IStereoElement<IBond,IBond> map(Map<IChemObject,IChemObject> chemobjs)

Specified by:

map in interface IStereoElement<F extends IChemObject,C extends IChemObject>

mapStrict

public final IStereoElement<IBond,IBond> mapStrict(Map<IChemObject,IChemObject> chemobjs)

Specified by:

mapStrict in interface IStereoElement<F extends IChemObject,C extends IChemObject>

getBuilder

public IChemObjectBuilder getBuilder()

Specified by:

getBuilder in interface ICDKObject

invapply

protected static <T> T[] invapply(T[] src,
 int[] perm)