Package org.openscience.cdk.stereo

Class TetrahedralChirality

java.lang.Object

org.openscience.cdk.stereo.TetrahedralChirality

All Implemented Interfaces:

Cloneable, ICDKObject, IStereoElement<IAtom,IAtom>, ITetrahedralChirality

public class TetrahedralChirality
extends Object
implements ITetrahedralChirality

Stereochemistry specification for tetravalent atoms. See ITetrahedralChirality for further details.

See Also:

ITetrahedralChirality

Source code:

main

Belongs to CDK module:

core

Nested Class Summary

Nested classes/interfaces inherited from interface org.openscience.cdk.interfaces.ITetrahedralChirality

ITetrahedralChirality.Stereo

Field Summary

Fields

Modifier and Type	Field	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	Description
TetrahedralChirality(IAtom chiralAtom, IAtom[] ligands, int config)
TetrahedralChirality(IAtom chiralAtom, IAtom[] ligands, ITetrahedralChirality.Stereo stereo)

Method Summary

Modifier and Type	Method	Description
boolean	contains(IAtom atom)	Does the stereo element contain the provided atom.
protected IStereoElement<IAtom,IAtom>	create(IAtom focus, List<IAtom> carriers, int config)
IChemObjectBuilder	getBuilder()	Returns a IChemObjectBuilder for the data classes that extend this class.
List<C>	getCarriers()	The carriers of the stereochemistry
IAtom	getChiralAtom()	Atom that is the chirality center.
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.
IAtom[]	getLigands()	Returns an array of ligand atoms around the chiral atom.
ITetrahedralChirality.Stereo	getStereo()	Defines the stereochemistry around the chiral atom.
protected static <T> T[]	invapply(T[] src, int[] perm)
ITetrahedralChirality	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.
ITetrahedralChirality	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.
IStereoElement<F,C>	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)
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.
void	setStereo(ITetrahedralChirality.Stereo stereo)	Set the stereochemistry of this tetrahedral centre.
String	toString()	Returns a String representation of this chiral element.
IStereoElement<F,C>	updateCarriers(C remove, Iterable<C> adds)
IStereoElement<F,C>	updateCarriers(Set<C> remove, C rep)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Methods inherited from interface org.openscience.cdk.interfaces.ICDKObject

getBuilder

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

contains, getCarriers, getConfig, getConfigClass, getConfigOrder, getFocus, getGroupInfo, mapStrict, setConfigOrder, setGroupInfo, updateCarriers, updateCarriers, updateCarriers

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

TetrahedralChirality

public TetrahedralChirality(IAtom chiralAtom,
                            IAtom[] ligands,
                            ITetrahedralChirality.Stereo stereo)

TetrahedralChirality

public TetrahedralChirality(IAtom chiralAtom,
                            IAtom[] ligands,
                            int config)

Method Detail

getLigands

public IAtom[] getLigands()

Description copied from interface: ITetrahedralChirality

Returns an array of ligand atoms around the chiral atom. If the chiral centre has an implicit hydrogen or lone pair one of the ligands will be the chiral atom (ITetrahedralChirality.getChiralAtom()).

Specified by:

getLigands in interface ITetrahedralChirality

Returns:

an array of four IAtoms.

getChiralAtom

public IAtom getChiralAtom()

Description copied from interface: ITetrahedralChirality

Atom that is the chirality center.

Specified by:

getChiralAtom in interface ITetrahedralChirality

Returns:

the chiral IAtom.

getStereo

public ITetrahedralChirality.Stereo getStereo()

Description copied from interface: ITetrahedralChirality

Defines the stereochemistry around the chiral atom. The value depends on the order of ligand atoms.

Specified by:

getStereo in interface ITetrahedralChirality

Returns:

the ITetrahedralChirality.Stereo for this stereo element.

setStereo

public void setStereo(ITetrahedralChirality.Stereo stereo)

Description copied from interface: ITetrahedralChirality

Set the stereochemistry of this tetrahedral centre.

Specified by:

setStereo in interface ITetrahedralChirality

Parameters:

stereo - the new stereo assignment

create

protected IStereoElement<IAtom,IAtom> create(IAtom focus,
                                                   List<IAtom> carriers,
                                                   int config)

map

public ITetrahedralChirality 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<IAtom,IAtom>

Specified by:

map in interface ITetrahedralChirality

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 ITetrahedralChirality 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<IAtom,IAtom>

Parameters:

chemobjs - chem object mapping

Returns:

a new stereo element in the same configuration but with atoms/bonds replaced with their mapped equivalence.

setBuilder

public void setBuilder(IChemObjectBuilder builder)

toString

public String toString()

Returns a String representation of this chiral element.

Overrides:

toString in class Object

Returns:

the String representation

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

updateCarriers

public IStereoElement<F,C> updateCarriers(C remove,
                                                Iterable<C> adds)

Specified by:

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

updateCarriers

public IStereoElement<F,C> updateCarriers(Set<C> remove,
                                                C rep)

Specified by:

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

mapStrict

public final IStereoElement<F,C> 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

invapply

protected static <T> T[] invapply(T[] src,
                                  int[] perm)