ExtendedTetrahedral (cdk 2.2 API)

java.lang.Object
- org.openscience.cdk.stereo.ExtendedTetrahedral

All Implemented Interfaces:

Cloneable, ICDKObject, IStereoElement<IAtom,IAtom>
```
public final class ExtendedTetrahedral
extends Object
```
Extended tetrahedral configuration. Defines the winding configuration in a system with an even number of cumulated pi bonds. Examples include, (R)-laballenic acid (CHEBI:38401) and (S)-laballenic acid (CHEBI:38402). The extended tetrahedral stereochemistry can be represented and handled the same as normal tetrahedral stereochemistry. However the handling of the neighbours is subtly different. To assist in the description here are how atoms are referred to.
```
 p0           p2     p<i>: periphals
  \          /       t<i>: terminals
   t0 = f = t1       f:    focus
  /          \
 p1           p3
 
```
The data structure stores, the central 'focus' atom and the four peripheral atoms. The peripheral atoms are stored in a single array, {p0, p1, p2, p3}, the first two and last two entries should be attached to the same terminal atom (t0 or t1). For convenience the terminal atoms can be found with findTerminalAtoms(IAtomContainer).
```
 p0           p2          p0   p2
  \          /              \ /
   t0 = f = t1       -->     c       c: t0/f/t1
  /          \              / \
 p1           p3           p1  p3
 
```
The configuration treats the focus and terminal atoms as a single atom, the neighbours {p1, p2, p3} then proceeded either clockwise or anti-clockwise when the centre (t0/f/t1) is viewed from the first peripheral atom p0. If any of the peripherals are implicit hydrogen atoms, then the terminal atom to which the hydrogen is attached can be used as a placeholder.
Author:

John May

Keywords:

extended tetrahedral, allene, axial chirality

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
`ExtendedTetrahedral(IAtom focus, IAtom[] peripherals, int config)`
`ExtendedTetrahedral(IAtom focus, IAtom[] peripherals, ITetrahedralChirality.Stereo winding)` Create an extended tetrahedral stereo element for the provided 'focus' and 'peripherals' in the given 'winding'.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`boolean`	`contains(IAtom atom)` Does the stereo element contain the provided atom.
`protected IStereoElement<IAtom,IAtom>`	`create(IAtom focus, List<IAtom> carriers, int cfg)`
`IAtom[]`	`findTerminalAtoms(IAtomContainer container)` Helper method to locate two terminal atoms in a container for this extended tetrahedral element.
`static IAtom[]`	`findTerminalAtoms(IAtomContainer container, IAtom focus)` Helper method to locate two terminal atoms in a container for a given focus.
`IAtom`	`focus()` The central atom in the cumulated system.
`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)`
`protected static int`	`numCarriers(int cfg)`
`IAtom[]`	`peripherals()` The neighbouring peripherals atoms, these are attached to the terminal atoms in the cumulated system.
`protected void`	`setBuilder(IChemObjectBuilder builder)`
`void`	`setConfigOrder(int cfg)` Set the configuration order of the stereochemistry.
`ITetrahedralChirality.Stereo`	`winding()` The winding of the peripherals, when viewed from the first atom.

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
  - ExtendedTetrahedral
```
public ExtendedTetrahedral(IAtom focus,
                           IAtom[] peripherals,
                           ITetrahedralChirality.Stereo winding)
```
    Create an extended tetrahedral stereo element for the provided 'focus' and 'peripherals' in the given 'winding'. See class documentation an annotated storage description.
    
    Parameters:
    
    focus - the central cumulated atom
    
    peripherals - atoms attached to the terminal atoms
    
    winding - the configuration
  - ExtendedTetrahedral
```
public ExtendedTetrahedral(IAtom focus,
                           IAtom[] peripherals,
                           int config)
```
- Method Detail
  - focus
```
public IAtom focus()
```
    The central atom in the cumulated system.
    
    Returns:
    
    the focus
  - peripherals
```
public IAtom[] peripherals()
```
    The neighbouring peripherals atoms, these are attached to the terminal atoms in the cumulated system.
    
    Returns:
    
    the peripheral atoms
  - winding
```
public ITetrahedralChirality.Stereo winding()
```
    The winding of the peripherals, when viewed from the first atom.
    
    Returns:
    
    winding configuration
  - findTerminalAtoms
```
public static IAtom[] findTerminalAtoms(IAtomContainer container,
                                        IAtom focus)
```
    Helper method to locate two terminal atoms in a container for a given focus.
    
    Parameters:
    
    container - structure representation
    
    focus - cumulated atom
    
    Returns:
    
    the terminal atoms (unordered)
  - findTerminalAtoms
```
public IAtom[] findTerminalAtoms(IAtomContainer container)
```
    Helper method to locate two terminal atoms in a container for this extended tetrahedral element. The atoms are ordered such that the first index is attached to the first two peripheral atoms and the second index is attached to the second two peripheral atoms.
    
    Parameters:
    
    container - structure representation
    
    Returns:
    
    the terminal atoms (ordered)
  - create
```
protected IStereoElement<IAtom,IAtom> 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)
```

Class ExtendedTetrahedral

Field Summary

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

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

A

B

C

D

E

F

Constructor Detail

ExtendedTetrahedral

ExtendedTetrahedral

Method Detail

focus

peripherals

winding

findTerminalAtoms

findTerminalAtoms

create

numCarriers

getFocus

getCarriers

getConfigClass

getConfigOrder

getConfig

setConfigOrder

contains

map

map

getBuilder

setBuilder

invapply