Interface WSmolecule

  • All Superinterfaces:
    Incomplecule, Smolecule

    @PublicAPI
    public interface WSmolecule
    extends Smolecule
    Writable abstract molecule class.

    PLEASE DO NOT IMPLEMENT THIS INTERFACE! It may get more abstract methods in later versions.

    Since:
    Marvin 5.3, 05/21/2009
    • Method Detail

      • newInstance

        WSmolecule newInstance​(int na,
                               int nb,
                               int aflags)
        Creates a new WSmolecule instance with the specified capacity.
        Parameters:
        na - the maximum number of atoms
        nb - the maximum number of bonds
        aflags - arrays to enable, see Smolecule.A_ALL
      • reset

        void reset​(int aflags)
        Clears the molecule and sets the array flags.
        Parameters:
        aflags - the array flags
      • addAtom

        void addAtom​(Smolecule smol,
                     int k)
        Adds an atom from another Smolecule.
        Parameters:
        smol - the other Smolecule
        k - atom index in smol
      • addAtom

        void addAtom​(int atno)
        Adds an atom.
        Parameters:
        atno - the atomic number
      • addBond

        void addBond​(int atom1,
                     int atom2,
                     int type)
        Adds a bond.
        Parameters:
        atom1 - first atom index
        atom2 - second atom index
        type - bond type
      • removeAtom

        void removeAtom​(int k)
        Removes an atom.
        Parameters:
        k - the atom index
      • removeBond

        void removeBond​(int k)
        Removes a bond.
        Parameters:
        k - the bond index
      • setCharge

        void setCharge​(int atom,
                       int chg)
        Sets the charge of an ion.
        Parameters:
        atom - the atom index
        chg - the charge
      • setRadical

        void setRadical​(int atom,
                        int rad)
        Sets the radical value of an atom.
        Parameters:
        atom - the atom index
        rad - the radical value
      • setHybridizationState

        void setHybridizationState​(int atom,
                                   int hs)
        Sets the hybridization state of an atom.
        Parameters:
        atom - the atom index
        hs - the hybridization state
        See Also:
        HybridizationStateConsts
      • setMassno

        void setMassno​(int atom,
                       int m)
        Sets the mass number.
        Parameters:
        atom - the atom index
        m - the mass number or zero to unset
      • setValence

        void setValence​(int atom,
                        int v)
        Sets the valence.
        Parameters:
        atom - the atom index
        v - the valence
      • setImplicitHcount

        void setImplicitHcount​(int atom,
                               int h)
        Sets the number of implicit Hydrogens.
        Parameters:
        atom - the atom index
        h - the number of implicit Hydrogens
      • setRgroupId

        void setRgroupId​(int atom,
                         int rgid)
        Sets the R-group identifier of an atom.
        Parameters:
        atom - the atom index
        rgid - the R-group identifier or 0 to unset
      • setAtomMap

        void setAtomMap​(int atom,
                        int map)
        Sets the atom-atom mapping number.
        Parameters:
        atom - the atom index
        map - the map value (positive integer) or 0