org.openscience.cdk.stereo

Class ExtendedTetrahedral

java.lang.Object

org.openscience.cdk.stereo.ExtendedTetrahedral

All Implemented Interfaces:

Cloneable, ICDKObject, IStereoElement

public final class ExtendedTetrahedral
extends Object
implements IStereoElement

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

Constructor Summary

Constructors

Constructor and Description
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

Methods

Modifier and Type	Method and Description
boolean	contains(IAtom atom) Does the stereo element contain the provided atom.
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.
IStereoElement	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.
IAtom[]	peripherals() The neighbouring peripherals atoms, these are attached to the terminal atoms in the cumulated system.
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

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

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)

contains

public boolean contains(IAtom atom)

Does the stereo element contain the provided atom.

Specified by:

contains in interface IStereoElement

Parameters:

atom - an atom to test membership

Returns:

whether the atom is present

map

public IStereoElement 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 replaced with a null reference. However the provided atom and bonds maps must not be null.

Specified by:

map in interface IStereoElement

Parameters:

atoms - non-null atom mapping, used to convert the original atoms to their mapped counterparts

bonds - non-null 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.

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