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

Method Summary

Modifier and Type	Method	Description
boolean	contains(IAtom 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()
List<IBond>	getCarriers()
int	getConfig()
int	getConfigClass()
int	getConfigOrder()
IBond	getFocus()
int	getGroupInfo()
protected static <T> T[]	invapply(T[] src, int[] perm)
IStereoElement<IBond,IBond>	map(Map<IAtom,IAtom> atoms, Map<IBond,IBond> bonds)
IStereoElement<IBond,IBond>	map(Map<IChemObject,IChemObject> chemobjs)
final IStereoElement<IBond,IBond>	mapStrict(Map<IChemObject,IChemObject> chemobjs)
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

ExtendedCisTrans

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

Method Details

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 IBond getFocus()

Specified by:

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

getCarriers

public List<IBond> 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<IBond,IBond> map(Map<IAtom,IAtom> atoms,
 Map<IBond,IBond> bonds)

Specified by:

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

map

public IStereoElement<IBond,IBond> map(Map<IChemObject,IChemObject> chemobjs)

Specified by:

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

mapStrict

public final IStereoElement<IBond,IBond> 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)