Package org.openscience.cdk.stereo

Class ExtendedCisTrans

java.lang.Object

org.openscience.cdk.stereo.ExtendedCisTrans

All Implemented Interfaces:

Cloneable, ICDKObject, IStereoElement<IBond,IBond>

public final class ExtendedCisTrans
extends Object

Extended Cis/Trans double bond configuration. This stereo element is used to represent configurations of odd numbers of double bonds:

                  C
                 /
   C = C = C = C
  /
 C
 

Author:

John Mayfield

See Also:

ExtendedTetrahedral

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
ExtendedCisTrans(IBond focus, IBond[] peripherals, int config)

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)
static IBond	findCentralBond(IAtomContainer mol, IAtom atom)	Locate the central double-bond in a chain of cumulated double bonds.
static IAtom[]	findTerminalAtoms(IAtomContainer container, IBond focus)	Helper method to locate two terminal atoms in a container for this extended Cis/Trans element.
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.
int	getGroupInfo()	Access the stereo group information - see class doc.
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)	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)
protected 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.

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

ExtendedCisTrans

public ExtendedCisTrans(IBond focus,
                        IBond[] peripherals,
                        int config)

Method Detail

findTerminalAtoms

public static IAtom[] findTerminalAtoms(IAtomContainer container,
                                        IBond focus)

Helper method to locate two terminal atoms in a container for this extended Cis/Trans element. The atoms are ordered such that the first atom is closer to first carrier.

Parameters:

container - structure representation

Returns:

the terminal atoms (ordered)

findCentralBond

public static IBond findCentralBond(IAtomContainer mol,
                                    IAtom atom)

Locate the central double-bond in a chain of cumulated double bonds.

 A = C = C = B
       ^
 A = C = C = C = C = B
           ^
 

Parameters:

mol - molecule

atom - at atom from either end of the cumulated chains

Returns:

the central bond, or null if not found

create

protected IStereoElement<IBond,IBond> create(IBond focus,
                                                   List<IBond> 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

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<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 - 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 IStereoElement<F,C> 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.

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

setBuilder

protected void setBuilder(IChemObjectBuilder builder)

invapply

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