Octahedral (cdk 2.5 API)

java.lang.Object
- org.openscience.cdk.stereo.Octahedral

All Implemented Interfaces:

Cloneable, ICDKObject, IStereoElement<IAtom,IAtom>
```
public final class Octahedral
extends Object
```
Represents an octahedral configuration of an atom six neighbors. The configuration order is defined as between 1 and 30 using the same permutation tables as SMILES (e.g. @OH1 .. @OH30). This allows the 720 permutations of atom ordering to be described.
Normalizing the representation (with normalize() returns a configuration reordered such that the configuration order is 1. For example
```
C[Co@OH8](F)(Br)(Cl)(I)S
```
is the same as
```
C[Co@OH1](F)(Cl)(Br)(I)S
```
. The normalised form is easy to work with as the first and last carriers form an axis, the middle four equatorial carriers are arranged anti-clockwise looking from the first carrier.
```
      c
      | a
      |/
  d---x---b = OH1
     /|       where a: first carrier, b: second carried, etc
    f |             x: focus
      e             'a' is in front of the focus 'x', 'f' is behind
 
```
See Also:

Octahedral Centers, OpenSMILES, TrigonalBipyramidal, SquarePlanar

Field Summary

Fields
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`

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 and Description

Octahedral(IAtom focus, IAtom[] carriers, int order)
Create a new octahedral configuration.

Constructors
Constructor and Description
`Octahedral(IAtom focus, IAtom[] carriers, int order)` Create a new octahedral configuration.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`contains(IAtom atom)` Does the stereo element contain the provided atom.
`protected Octahedral`	`create(IAtom 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)`
`Octahedral`	`normalize()` Normalize the configuration to the lowest order (1).
`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 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
  - Octahedral
```
public Octahedral(IAtom focus,
                  IAtom[] carriers,
                  int order)
```
    Create a new octahedral configuration.
    
    Parameters:
    
    focus - the focus
    
    carriers - the carriers
    
    order - the order of the configuration 0-30.
- Method Detail
  - normalize
```
public Octahedral normalize()
```
    Normalize the configuration to the lowest order (1). For example
```
C[Co@OH8](F)(Br)(Cl)(I)S
```
    is the same as
```
C[Co@OH1](F)(Cl)(Br)(I)S
```
    . The normalised form is easy to work with as the first and last carriers form an axis, the middle four equatorial carriers are arranged anti-clockwise looking from the first carrier.
    Returns:
    
    the normalized form
  - create
```
protected Octahedral create(IAtom 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 - nullable atom mapping, used to convert the original atoms to their mapped counterparts
    
    bonds - nullable bond mapping, 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)
```
    Specified by:
    
    map in interface IStereoElement<F extends IChemObject,C extends IChemObject>
  - 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 Octahedral

Field Summary

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

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

A

B

C

D

E

F

Constructor Detail

Octahedral

Method Detail

normalize

create

numCarriers

getFocus

getCarriers

getConfigClass

getConfigOrder

getConfig

setConfigOrder

getGroupInfo

setGroupInfo

contains

map

map

getBuilder

setBuilder

invapply