Package org.openscience.cdk.stereo

Class 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

    • 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)

      • 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

      • 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

      • setGroupInfo

        public void setGroupInfo​(int grp)
        Set the stereo group information - see class doc.
        Specified by:
        setGroupInfo in interface IStereoElement<F extends IChemObject,​C extends IChemObject>
        Parameters:
        grp - the group info

      • 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 - used to convert the original atoms to their mapped counterparts
        bonds - 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.

      • mapStrict

        public final IStereoElement<F,​C> mapStrict​(Map<IChemObject,​IChemObject> chemobjs)
        Description copied from interface: IStereoElement
        Update the stereo using the remapping of 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 a new element is NOT created.
        Specified by:
        mapStrict in interface IStereoElement<F extends IChemObject,​C extends IChemObject>
        Parameters:
        chemobjs - chem object mapping
        Returns:
        a new stereo element in the same configuration but with atoms/bonds replaced with their mapped equivalence.

      • invapply

        protected static <T> T[] invapply​(T[] src,
                                  int[] perm)