Package org.openscience.cdk.stereo

Class Octahedral

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

Method Summary

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

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 Details

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 IAtom 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<IAtom,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<IAtom,IAtom> map(Map<IChemObject,IChemObject> chemobjs)

Specified by:

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

mapStrict

public final IStereoElement<IAtom,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)