Package org.openscience.cdk.stereo

Class Atropisomeric

java.lang.Object

org.openscience.cdk.stereo.Atropisomeric

All Implemented Interfaces:

Cloneable, ICDKObject, IStereoElement<IBond,IAtom>

public class Atropisomeric
extends Object

Restricted axial rotation around Aryl-Aryl bonds. The atropisomer is stored in a similar manner to ExtendedTetrahedral (and TetrahedralChirality) except instead of storing the central atom we store the sigma bond around which the rotation is restricted and the four carriers are connect to either end atom of the 'focus' bond.

      a     b'
     /       \
    Ar --f-- Ar
     \      /
      a'   b
 f: focus
 Ar: Aryl (carriers connected to either end of 'f')
 a,a',b,b': ortho substituted on the Aryl
 

Typical examples include BiNOL, and BiNAP.

See Also:

• Atropisomer (Wikipedia)

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
Atropisomeric(IBond focus, IAtom[] carriers, int value)	Define a new atropisomer using the focus bond and the carrier atoms.

Method Summary

Modifier and Type	Method	Description
boolean	contains(IAtom atom)
protected IStereoElement<IBond,IAtom>	create(IBond focus, List<IAtom> carriers, int cfg)
IChemObjectBuilder	getBuilder()
List<IAtom>	getCarriers()
int	getConfig()
int	getConfigClass()
int	getConfigOrder()
IBond	getFocus()
int	getGroupInfo()
protected static <T> T[]	invapply(T[] src, int[] perm)
IStereoElement<IBond,IAtom>	map(Map<IAtom,IAtom> atoms, Map<IBond,IBond> bonds)
IStereoElement<IBond,IAtom>	map(Map<IChemObject,IChemObject> chemobjs)
final IStereoElement<IBond,IAtom>	mapStrict(Map<IChemObject,IChemObject> chemobjs)
protected static int	numCarriers(int cfg)
protected 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

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

Atropisomeric

public Atropisomeric(IBond focus,
 IAtom[] carriers,
 int value)

Define a new atropisomer using the focus bond and the carrier atoms.

Parameters:

focus - the focus bond

carriers - the carriers

value - the configuration IStereoElement.LEFT or IStereoElement.RIGHT

Method Details

create

protected IStereoElement<IBond,IAtom> create(IBond focus,
 List<IAtom> 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<IAtom> 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,IAtom> map(Map<IAtom,IAtom> atoms,
 Map<IBond,IBond> bonds)

Specified by:

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

map

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

Specified by:

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

mapStrict

public final IStereoElement<IBond,IAtom> 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

setBuilder

protected void setBuilder(IChemObjectBuilder builder)

invapply

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