Package org.biojava.nbio.structure

Enum Element

  • All Implemented Interfaces:
    Serializable, Comparable<Element>
    public enum Element
extends Enum<Element>
    Element is an enumeration of the elements of the periodic table. In addition, several attributes of each element are accessible. Note: Deuterium and Tritium are treated as separate elements D and T, respectively. Sometimes part of a molecule is represented as an R-group, which is represented as the element R.
    Since:
    3.0
    Version:
    %I% %G%
    Author:
    Peter Rose

    • Method Detail

      • values

        public static Element[] values()
        Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows: 
        for (Element c : Element.values())
    System.out.println(c);
        Returns:
        an array containing the constants of this enum type, in the order they are declared

      • valueOf

        public static Element valueOf​(String name)
        Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)
        Parameters:
        name - the name of the enum constant to be returned.
        Returns:
        the enum constant with the specified name
        Throws:
        IllegalArgumentException - if this enum type has no constant with the specified name
        NullPointerException - if the argument is null

      • getAllOxidationStates

        public int[] getAllOxidationStates()
        Returns a list of all oxidation states the element is found in. The set is by Greenwood and Norman in "Chemistry of the Elements (ISBN:0080379419).
        Returns:
        An array of oxidation states sorted from most negative to most positive.

      • getAtomicNumber

        public int getAtomicNumber()
        Returns the atomic number of this Element.
        Returns:
        the atomic number of this Element.

      • getPeriod

        public int getPeriod()
        Returns the period in the periodic table of this Element.
        Returns:
        the period in the periodic table of this Element.

      • getHillOrder

        public int getHillOrder()
        Returns the Hill Order of this Element. The Hill Order represents the priority by which elements are sorted in molecular formulas. The Hill system is a system of writing chemical formulas such that the number of carbon atoms in a molecule is indicated first, the number of hydrogen atoms next, and then the number of all other chemical elements subsequently, in alphabetical order. When the formula contains no carbon, all the elements, including hydrogen, are listed alphabetically.

        Edwin A. Hill, "On A System Of Indexing Chemical Literature; Adopted By The Classification Division Of The U. S. Patent Office". J. Am. Chem. Soc. 1900, 22(8), 478-494.

        http://en.wikipedia.org/wiki/Hill_system

        Returns:
        the Hill Order of this Element.

      • getVDWRadius

        public float getVDWRadius()
        Returns the van der Waals radius of this Element.
        Returns:
        the van der Waals radius of this Element, measured in Angstroms.

      • getCovalentRadius

        public float getCovalentRadius()
        Returns the covalent radius of this Element.
        Returns:
        covalent radius, measured in Angstroms.

      • getValenceElectronCount

        public int getValenceElectronCount()
        Returns the number of valence electrons for this Element.
        Returns:
        the number of valence electrons for this Element.

      • getMinimumValence

        public int getMinimumValence()
        Returns the minimum valence for this Element.
        Returns:
        the minimum valence of this atom.

      • getMaximumValence

        public int getMaximumValence()
        Returns the maximum valence for this Element.
        Returns:
        the maximum valence for this Element.

      • getCommonValence

        public int getCommonValence()
        Returns the common valence for this Element.
        Returns:
        the common valence for this Element.

      • getMaximumCovalentValence

        public int getMaximumCovalentValence()
        Returns the maximum valence for this Element.
        Returns:
        the maximum valence of this element.

      • getAtomicMass

        public float getAtomicMass()
        Returns the atomic mass for this Element.
        Returns:
        the atomic mass for this Element, measured in g/mol.

      • getCoreElectronCount

        public int getCoreElectronCount()
        Returns the number of core electrons for this Element.
        Returns:
        number of core electrons for this Element.

      • getOxidationState

        public int getOxidationState()
        Returns a typical oxidation state for this Element. This information is mostly useful for metals.
        Returns:
        a typical oxidation state for this Element.

      • getPaulingElectronegativity

        public float getPaulingElectronegativity()
        Returns the Pauling electronegativity for this Element.
        Returns:
        the Pauling electronegativity for this Element.

      • getElementType

        public ElementType getElementType()
        Returns the Element Type for this Element.
        Returns:
        the Element Type for this Element.

      • valueOfIgnoreCase

        public static Element valueOfIgnoreCase​(String elementSymbol)
                                 throws IllegalArgumentException
        Returns the Element that corresponds to the specified element symbol. The case of the element symbol is ignored. Example: FE, fe, Fe represent iron.
        Parameters:
        elementSymbol - element symbol to specify Element.
        Returns:
        the Element specified by the element symbol.
        Throws:
        IllegalArgumentException

      • isHydrogen

        public boolean isHydrogen()
        Returns true if this Element is Hydrogen.

        Note: Deuterium (D) and Tritium (T) will return true to this method.

        Returns:
        true if the Element is Hydrogen.

      • isHeavyAtom

        public boolean isHeavyAtom()
        Returns true is the Element is an not Hydrogen (or an isotope of Hydrogen).

        This method is the exact opposite of isHydrogen().

        Returns:
        true is Element is not Hydrogen.

      • isHeteroAtom

        public boolean isHeteroAtom()
        Returns true if Element is not Hydrogen and not Carbon.
        Returns:
        true if Element is not Hydrogen and not Carbon.

      • isMetal

        public boolean isMetal()
        Returns true if ElementType is a metal.
        Returns:
        true if ElementType is a metal.

      • isMetalloid

        public boolean isMetalloid()
        Returns true if ElementType is a metalloid.
        Returns:
        true if ElementType is a metalloid.

      • isNonMetal

        public boolean isNonMetal()
        Returns true if ElementType is a non-metal.
        Returns:
        true if ElementType is a non-metal.

      • isHalogen

        public boolean isHalogen()
        Returns true if Element is a halogen (F, Cl, Br, I, At).
        Returns:
        true if Element is a halogen.

      • isChalcogen

        public boolean isChalcogen()
        Returns true if Element is a chalcogen (O, S, Se, Te, Po).
        Returns:
        true if Element is a chalcogen.

      • getElementFromHillIndex

        public static Element getElementFromHillIndex​(int index)
        Returns the Element that corresponds to the specified Hill Order.
        Parameters:
        index - the Hill Order.
        Returns:
        the Element that corresponds to the specified Hill Order.
        See Also:
        getHillOrder()