Package org.openscience.cdk.stereo

Class DoubleBondStereochemistry

java.lang.Object

org.openscience.cdk.stereo.DoubleBondStereochemistry

All Implemented Interfaces:

Cloneable, ICDKObject, IDoubleBondStereochemistry, IStereoElement<IBond,IBond>

public class DoubleBondStereochemistry
extends Object
implements IDoubleBondStereochemistry

Stereochemistry specification for double bonds. See IDoubleBondStereochemistry for further details.

See Also:

• IDoubleBondStereochemistry

Nested Class Summary

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

IDoubleBondStereochemistry.Conformation

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
DoubleBondStereochemistry(IBond stereoBond, IBond[] ligandBonds, int config)
DoubleBondStereochemistry(IBond stereoBond, IBond[] ligandBonds, IDoubleBondStereochemistry.Conformation stereo)	Creates a new double bond stereo chemistry.

Method Summary

Modifier and Type	Method	Description
boolean	contains(IAtom atom)	Does the stereo element contain the provided atom.
protected IStereoElement<IBond,IBond>	create(IBond focus, List<IBond> carriers, int cfg)
IBond[]	getBonds()	Returns an array of ligand bonds around the double bond.
IChemObjectBuilder	getBuilder()	Returns a IChemObjectBuilder for the data classes that extend this class.
List<IBond>	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.
IBond	getFocus()	The focus atom or bond at the 'centre' of the stereo-configuration.
int	getGroupInfo()	Access the stereo group information - see class doc.
IDoubleBondStereochemistry.Conformation	getStereo()	Defines the stereochemistry around the double bond.
IBond	getStereoBond()	IBond that is the stereo center.
protected static <T> T[]	invapply(T[] src, int[] perm)
IDoubleBondStereochemistry	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<IBond,IBond>	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.
final IStereoElement<IBond,IBond>	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)
protected IBond[]	processCarriers(IBond focus, IBond[] carriers)	Processes the given carrier bonds to ensure the first carrier is connected to the beginning atom of the focus bond.
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.
IStereoElement<IBond,IBond>	updateCarriers(IBond remove, Iterable<IBond> adds)
IStereoElement<IBond,IBond>	updateCarriers(Set<IBond> remove, IBond rep)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, 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, map, mapStrict, setConfigOrder, setGroupInfo, updateCarriers, updateCarriers, updateCarriers

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

DoubleBondStereochemistry

public DoubleBondStereochemistry(IBond stereoBond,
 IBond[] ligandBonds,
 IDoubleBondStereochemistry.Conformation stereo)

Creates a new double bond stereo chemistry. The path of length three is defined by ligandBonds[0], stereoBonds, and ligandBonds[1].

DoubleBondStereochemistry

public DoubleBondStereochemistry(IBond stereoBond,
 IBond[] ligandBonds,
 int config)

Method Details

processCarriers

protected IBond[] processCarriers(IBond focus,
 IBond[] carriers)

Processes the given carrier bonds to ensure the first carrier is connected to the beginning atom of the focus bond. Swaps the carriers if this condition is not met.

Parameters:

focus - the focus bond whose beginning atom should be connected to the first carrier bond

carriers - an array of two carrier bonds associated with the stereochemistry, where the first bond should connect to the beginning atom of the focus bond

Returns:

an array of carrier bonds where the above constraint is satisfied

setBuilder

public void setBuilder(IChemObjectBuilder builder)

getBonds

public IBond[] getBonds()

Returns an array of ligand bonds around the double bond.

Specified by:

getBonds in interface IDoubleBondStereochemistry

Returns:

an array of two IBonds.

getStereoBond

public IBond getStereoBond()

IBond that is the stereo center.

Specified by:

getStereoBond in interface IDoubleBondStereochemistry

Returns:

the double IBond.

getStereo

public IDoubleBondStereochemistry.Conformation getStereo()

Defines the stereochemistry around the double bond.

Specified by:

getStereo in interface IDoubleBondStereochemistry

Returns:

the IDoubleBondStereochemistry.Conformation for this stereo element.

map

public IDoubleBondStereochemistry 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 IDoubleBondStereochemistry

Specified by:

map in interface IStereoElement<IBond,IBond>

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.

create

protected IStereoElement<IBond,IBond> create(IBond focus,
 List<IBond> carriers,
 int cfg)

numCarriers

protected static int numCarriers(int cfg)

getFocus

public IBond 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<IBond> 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<IBond,IBond> 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<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.

updateCarriers

public IStereoElement<IBond,IBond> updateCarriers(IBond remove,
 Iterable<IBond> adds)

Specified by:

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

updateCarriers

public IStereoElement<IBond,IBond> updateCarriers(Set<IBond> remove,
 IBond rep)

Specified by:

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

mapStrict

public final IStereoElement<IBond,IBond> 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)