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 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, 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
TrigonalBipyramidal(IAtom focus, IAtom[] carriers, int order) Create a new trigonal bipyramidal configuration.

Method Summary

Modifier and Type	Method and Description
boolean	contains(IAtom atom) Does the stereo element contain the provided atom.
protected TrigonalBipyramidal	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.
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)
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) Set the configuration order of the stereochemistry.

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

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 Detail

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 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

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)