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)	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<IAtom>	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.
IBond	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<IBond,IAtom>	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<IBond,IAtom>	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.
final IStereoElement<IBond,IAtom>	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.

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()

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<IAtom> 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<IBond,IAtom> 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<IBond,IAtom> 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.

mapStrict

public final IStereoElement<IBond,IAtom> 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)