Class AtomType

    • Field Detail

      • formalCharge

        protected Integer formalCharge
        The formal charge of the atom with CDKConstants.UNSET as default. Implements RFC #6. Note that some constructors (AtomType(String) and AtomType(String, String) ) will explicitly set this field to 0
      • hybridization

        protected IAtomType.Hybridization hybridization
        The hybridization state of this atom with CDKConstants.HYBRIDIZATION_UNSET as default.
      • electronValency

        protected Integer electronValency
        The electron Valency of this atom with CDKConstants.UNSET as default.
      • formalNeighbourCount

        protected Integer formalNeighbourCount
        The formal number of neighbours this atom type can have with CDKConstants_UNSET as default. This includes explicitely and implicitely connected atoms, including implicit hydrogens.
    • Constructor Detail

      • AtomType

        public AtomType​(String elementSymbol)
        Constructor for the AtomType object. Defaults to a zero formal charge. All other fields are set to CDKConstants.UNSET.
        elementSymbol - Symbol of the atom
      • AtomType

        public AtomType​(String identifier,
                        String elementSymbol)
        Constructor for the AtomType object. Defaults to a zero formal charge.
        identifier - An id for this atom type, like C3 for sp3 carbon
        elementSymbol - The element symbol identifying the element to which this atom type applies
      • AtomType

        public AtomType​(IElement element)
        Constructs an isotope by copying the symbol, atomic number, flags, identifier, exact mass, natural abundance and mass number from the given IIsotope. It does not copy the listeners and properties. If the element is an instanceof IAtomType, then the maximum bond order, bond order sum, van der Waals and covalent radii, formal charge, hybridization, electron valency, formal neighbour count and atom type name are copied too.
        element - IIsotope to copy information from