Package org.openscience.cdk.stereo

Class TrigonalBipyramidal

java.lang.Object

org.openscience.cdk.stereo.TrigonalBipyramidal

All Implemented Interfaces:

Cloneable, ICDKObject, IStereoElement<IAtom,IAtom>

public final class TrigonalBipyramidal
extends Object

Describes a trigonal-bipyramidal configuration. The configuration carriers are arranged with two co-linear on an axis and three equatorial. The configuration order is between 1 and 20 and follows the same meaning as SMILES.

    d   c     TB1
     \ /
  a---x---e   where a: first carrier, b: second carrier, ... *
      |             x: focus
      b             'c' is in front of 'x', 'd' is behind
 

The configuration can be normalized to the lowest order (1) using the normalize() function.

See Also:

• Trigonal Bipyramidal, OpenSMILES
• Octahedral
• 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
TrigonalBipyramidal(IAtom focus, IAtom[] carriers, int order)	Create a new trigonal bipyramidal configuration.

Method Summary

Modifier and Type	Method	Description
boolean	contains(IAtom atom)
protected TrigonalBipyramidal	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)
TrigonalBipyramidal	normalize()	Normalize the configuration to the lowest configuration order (1) - the axis goes from the first to last carrier, the three middle carriers are anti-clockwise looking from the first carrier.
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

TrigonalBipyramidal

public TrigonalBipyramidal(IAtom focus,
 IAtom[] carriers,
 int order)

Create a new trigonal bipyramidal configuration.

Parameters:

focus - the focus

carriers - the carriers

order - the order (1-20)

Method Details

normalize

public TrigonalBipyramidal normalize()

Normalize the configuration to the lowest configuration order (1) - the axis goes from the first to last carrier, the three middle carriers are anti-clockwise looking from the first carrier.

Returns:

the normalized configuration

create

protected TrigonalBipyramidal 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)