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 int`	`A`
`protected static int`	`B`
`protected static int`	`C`
`protected static int`	`D`
`protected static int`	`E`
`protected static 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

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`boolean`	`contains(IAtom atom)`	Does the stereo element contain the provided atom.
`protected IStereoElement<IBond,IAtom>`	`create(IBond focus, List<IAtom> carriers, int cfg)`
`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.
`protected static <T> T[]`	`invapply(T[] src, int[] perm)`
`IStereoElement<F,C>`	`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)`	Update the stereo using the remapping of atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.
`IStereoElement<F,C>`	`mapStrict(Map<IChemObject,IChemObject> chemobjs)`	Update the stereo using the remapping of atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.
`protected static int`	`numCarriers(int cfg)`
`protected 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.
`IStereoElement<F,C>`	`updateCarriers(C remove, Iterable<C> adds)`
`IStereoElement<F,C>`	`updateCarriers(Set<C> remove, C rep)`

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.IStereoElement
updateCarriers

- Field Detail
  - 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 Detail
  - 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 Detail
  - create
```
protected IStereoElement<IBond,IAtom> create(IBond focus,
                                                   List<IAtom> carriers,
                                                   int cfg)
```
  - numCarriers
```
protected static int numCarriers(int cfg)
```
  - getFocus
```
public F getFocus()
```
    The focus atom or bond at the 'centre' of the stereo-configuration.
    
    Specified by:
    
    getFocus in interface IStereoElement<F extends IChemObject,C extends IChemObject>
    
    Returns:
    
    the focus
  - getCarriers
```
public List<C> getCarriers()
```
    The carriers of the stereochemistry
    
    Specified by:
    
    getCarriers in interface IStereoElement<F extends IChemObject,C extends IChemObject>
    
    Returns:
    
    the carriers
  - getConfigClass
```
public int getConfigClass()
```
    The configuration class of the stereochemistry.
    
    Specified by:
    
    getConfigClass in interface IStereoElement<F extends IChemObject,C extends IChemObject>
    
    Returns:
    
    configuration class
  - getConfigOrder
```
public int getConfigOrder()
```
    The configuration order of the stereochemistry.
    
    Specified by:
    
    getConfigOrder in interface IStereoElement<F extends IChemObject,C extends IChemObject>
    
    Returns:
    
    configuration
  - getConfig
```
public int getConfig()
```
    Access the configuration order and class of the stereochemistry.
    
    Specified by:
    
    getConfig in interface IStereoElement<F extends IChemObject,C extends IChemObject>
    
    Returns:
    
    the configuration
  - setConfigOrder
```
public void setConfigOrder(int cfg)
```
    Set the configuration order of the stereochemistry.
    
    Specified by:
    
    setConfigOrder in interface IStereoElement<F extends IChemObject,C extends IChemObject>
    
    Parameters:
    
    cfg - the new configuration
  - getGroupInfo
```
public int getGroupInfo()
```
    Access the stereo group information - see class doc.
    
    Specified by:
    
    getGroupInfo in interface IStereoElement<F extends IChemObject,C extends IChemObject>
    
    Returns:
    
    the group info
  - setGroupInfo
```
public void setGroupInfo(int grp)
```
    Set the stereo group information - see class doc.
    
    Specified by:
    
    setGroupInfo in interface IStereoElement<F extends IChemObject,C extends IChemObject>
    
    Parameters:
    
    grp - the group info
  - contains
```
public boolean contains(IAtom atom)
```
    Does the stereo element contain the provided atom.
    
    Specified by:
    
    contains in interface IStereoElement<F extends IChemObject,C extends IChemObject>
    
    Parameters:
    
    atom - an atom to test membership
    
    Returns:
    
    whether the atom is present
  - map
```
public IStereoElement<F,C> 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<F extends IChemObject,C extends IChemObject>
    
    Parameters:
    
    atoms - used to convert the original atoms to their mapped counterparts
    
    bonds - 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.
  - map
```
public IStereoElement<F,C> map(Map<IChemObject,IChemObject> chemobjs)
```
    Description copied from interface: IStereoElement
    
    Update the stereo using the remapping of 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 the existing atom/bond it is left intact. If you want to remove stereo in such cases please use IStereoElement.mapStrict(java.util.Map<org.openscience.cdk.interfaces.IChemObject, org.openscience.cdk.interfaces.IChemObject>).
    
    Specified by:
    
    map in interface IStereoElement<F extends IChemObject,C extends IChemObject>
    
    Parameters:
    
    chemobjs - chem object mapping
    
    Returns:
    
    a new stereo element in the same configuration but with atoms/bonds replaced with their mapped equivalence.
  - updateCarriers
```
public IStereoElement<F,C> updateCarriers(C remove,
                                                Iterable<C> adds)
```
    Specified by:
    
    updateCarriers in interface IStereoElement<F extends IChemObject,C extends IChemObject>
  - updateCarriers
```
public IStereoElement<F,C> updateCarriers(Set<C> remove,
                                                C rep)
```
    Specified by:
    
    updateCarriers in interface IStereoElement<F extends IChemObject,C extends IChemObject>
  - mapStrict
```
public final IStereoElement<F,C> mapStrict(Map<IChemObject,IChemObject> chemobjs)
```
    Description copied from interface: IStereoElement
    
    Update the stereo using the remapping of 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 a new element is NOT created.
    
    Specified by:
    
    mapStrict in interface IStereoElement<F extends IChemObject,C extends IChemObject>
    
    Parameters:
    
    chemobjs - chem object mapping
    
    Returns:
    
    a new stereo element in the same configuration but with atoms/bonds replaced with their mapped equivalence.
  - getBuilder
```
public IChemObjectBuilder getBuilder()
```
    Returns a IChemObjectBuilder for the data classes that extend this class.
    
    Specified by:
    
    getBuilder in interface ICDKObject
    
    Returns:
    
    The IChemObjectBuilder matching this ICDKObject
  - setBuilder
```
protected void setBuilder(IChemObjectBuilder builder)
```
  - invapply
```
protected static <T> T[] invapply(T[] src,
                                  int[] perm)
```

Class Atropisomeric

Field Summary

Fields inherited from interface org.openscience.cdk.interfaces.IStereoElement

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface org.openscience.cdk.interfaces.IStereoElement

Field Detail

A

B

C

D

E

F

Constructor Detail

Atropisomeric

Method Detail

create

numCarriers

getFocus

getCarriers

getConfigClass

getConfigOrder

getConfig

setConfigOrder

getGroupInfo

setGroupInfo

contains

map

map

updateCarriers

updateCarriers

mapStrict

getBuilder

setBuilder

invapply