Package org.openscience.cdk.stereo

Class ExtendedTetrahedral

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