Class MulticenterSgroup

    • Constructor Detail

      • MulticenterSgroup

        public MulticenterSgroup​(Molecule parent)
        Constructs a Multicenter S-group. Please note the S-group is not added automatically to the parent molecule.
        Parameters:
        parent - the parent molecule
        Since:
        Marvin 5.0
        See Also:
        Molecule.addSgroup(Sgroup, boolean)
      • MulticenterSgroup

        protected MulticenterSgroup​(MulticenterSgroup sg,
                                    Molecule m,
                                    Sgroup psg)
        Copy constructor.
        Parameters:
        sg - the S-group to copy
        m - the new parent molecule
        psg - the new parent S-group or null
        Since:
        Marvin 5.0
      • MulticenterSgroup

        protected MulticenterSgroup​(MulticenterSgroup sg,
                                    Molecule m,
                                    Sgroup psg,
                                    int[] atomIndexMap)
        Copy constructor.
        Parameters:
        sg - the S-group to copy
        m - the new parent molecule
        psg - the new parent S-group or null
        atomIndexMap - indices of cloned atoms in the original molecule or null
        Since:
        Marvin 5.0
    • Method Detail

      • cloneSgroup

        protected Sgroup cloneSgroup​(Molecule m,
                                     Sgroup psg,
                                     int[] atomIndexMap)
        Gets a new Sgroup instance.
        Overrides:
        cloneSgroup in class Sgroup
        Parameters:
        m - the new parent molecule
        psg - the new parent S-group
        atomIndexMap - indices of cloned atoms in the original molecule or null
        Returns:
        the new object
        Since:
        Marvin 5.0.2
      • addCentralAtom

        public void addCentralAtom()
        Adds a central atom to this sgroup.
      • recalcCentralAtom

        public DPoint3 recalcCentralAtom()
        Recalculates and sets the coordinates of the central atom of this sgroup.
        Returns:
        the recalculated coordinates of the central atom
      • hasBrackets

        public boolean hasBrackets()
        Does a bracket belong to this sgroup?
        Overrides:
        hasBrackets in class Sgroup
        Returns:
        returns false
      • hasNonCoordinateBond

        public boolean hasNonCoordinateBond()
        Decides whether the central atom of the sgroup has a non-coordinate bond.
        Returns:
        returns true if the central atom of the sgroup has at least one non-coordinate bond, false otherwise.
      • getCentralAtom

        public MolAtom getCentralAtom()
        Gets the central atom of this sgroup.
        Returns:
        the central atom
      • setCentralAtom

        public void setCentralAtom​(MolAtom atom)
        Sets the central atom of this sgroup.
        Parameters:
        atom - the central atom
      • replaceMulticenterAtom

        @Deprecated
        public void replaceMulticenterAtom​(MolAtom atom,
                                           MolAtom atom2)
        Deprecated.
        as of Marvin 2014.08.25.0, use setCentralAtom(chemaxon.struc.MolAtom) instead
        Replace an existing central atom by a new one in this S-group and its parent (recursively).
        Parameters:
        atom - the original atom
        atom2 - the new atom