Package org.openscience.cdk.stereo

Class SquarePlanar

  • All Implemented Interfaces:
    Cloneable, ICDKObject, IStereoElement<IAtom,​IAtom>
    public final class SquarePlanar
extends Object
    Describes square planar configuration. The configuration around a square planar is described by 3 possible values (1:U, 2:4, or 3:Z) based on the ordering of the planar carries around the focus: 
    
 Configurations:

     a                a                a
     |                |                |
  d--f--b = U      c--f--d = 4      b--f--c = Z
     |                |                |
     c                b                d

    SP1              SP2              SP3
    cis-platin can be represented as any of the following: 
     [NH3][Pt@SP1]([NH3])(Cl)Cl
 [NH3][Pt@SP3]([NH3])(Cl)Cl
 [NH3][Pt@SP2](Cl)([NH3])Cl
 [NH3][Pt@SP1](Cl)(Cl)[NH3]
    trans-platin can be represented as any of the following: 
     [NH3][Pt@SP2]([NH3])(Cl)Cl
 [NH3][Pt@SP1](Cl)([NH3])Cl
 [NH3][Pt@SP1](Cl)([NH3])Cl
 [NH3][Pt@SP3](Cl)(Cl)[NH3]
    The normalize function (normalize()) create a new 
    IStereoElement
    where the carriers have been reorder such that the configuration is in a U shape (order=1).
    See Also:
    Square Planar Centers, OpenSMILES, TrigonalBipyramidal, Octahedral

    • Constructor Detail

      • SquarePlanar

        public SquarePlanar​(IAtom focus,
                    IAtom[] carriers,
                    int order)
        Create a square-planar configuration around a provided focus atom. The carriers are flat in the plane and their arrangement is either, U-shape, 4-shape, or Z-shape.
        Parameters:
        focus - the focus
        carriers - the carriers
        order - the configuration order, 1-3