Element (biojava 5.3.0 API)

java.lang.Object
- java.lang.Enum<Element>
- - org.biojava.nbio.structure.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

Enum Constant Summary

Enum Constants
Enum Constant and Description
`Ac`
`Ag`
`Al`
`Am`
`Ar`
`As`
`At`
`Au`
`B`
`Ba`
`Be`
`Bi`
`Bk`
`Br`
`C`
`Ca`
`Cd`
`Ce`
`Cf`
`Cl`
`Cm`
`Co`
`Cr`
`Cs`
`Cu`
`D` Deuterium
`Dy`
`Er`
`Es`
`Eu`
`F`
`Fe`
`Fm`
`Fr`
`Ga`
`Gd`
`Ge`
`H`
`He`
`Hf`
`Hg`
`Ho`
`I`
`In`
`Ir`
`K`
`Kr`
`La`
`Li`
`Lr`
`Lu`
`Md`
`Mg`
`Mn`
`Mo`
`N`
`Na`
`Nb`
`Nd`
`Ne`
`Ni`
`No`
`Np`
`O`
`Os`
`P`
`Pa`
`Pb`
`Pd`
`Pm`
`Po`
`Pr`
`Pt`
`Pu`
`R` R-group to represent generic groups that are sometimes present in MDL .sdf files.
`Ra`
`Rb`
`Re`
`Rh`
`Rn`
`Ru`
`S`
`Sb`
`Sc`
`Se`
`Si`
`Sm`
`Sn`
`Sr`
`T` Tritium
`Ta`
`Tb`
`Tc`
`Te`
`Th`
`Ti`
`Tl`
`Tm`
`U`
`V`
`W`
`Xe`
`Y`
`Yb`
`Zn`
`Zr`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int[]`	`getAllOxidationStates()` Returns a list of all oxidation states the element is found in.
`float`	`getAtomicMass()` Returns the atomic mass for this Element.
`int`	`getAtomicNumber()` Returns the atomic number of this Element.
`int`	`getCommonValence()` Returns the common valence for this Element.
`int`	`getCoreElectronCount()` Returns the number of core electrons for this Element.
`float`	`getCovalentRadius()` Returns the covalent radius of this Element.
`static Element`	`getElementFromHillIndex(int index)` Returns the Element that corresponds to the specified Hill Order.
`ElementType`	`getElementType()` Returns the Element Type for this Element.
`int`	`getHillOrder()` Returns the Hill Order of this Element.
`int`	`getMaximumCovalentValence()` Returns the maximum valence for this Element.
`int`	`getMaximumValence()` Returns the maximum valence for this Element.
`int`	`getMinimumValence()` Returns the minimum valence for this Element.
`int`	`getOxidationState()` Returns a typical oxidation state for this Element.
`float`	`getPaulingElectronegativity()` Returns the Pauling electronegativity for this Element.
`int`	`getPeriod()` Returns the period in the periodic table of this Element.
`int`	`getValenceElectronCount()` Returns the number of valence electrons for this Element.
`float`	`getVDWRadius()` Returns the van der Waals radius of this Element.
`boolean`	`isChalcogen()` Returns `true` if Element is a chalcogen (O, S, Se, Te, Po).
`boolean`	`isHalogen()` Returns `true` if Element is a halogen (F, Cl, Br, I, At).
`boolean`	`isHeavyAtom()` Returns `true` is the Element is an not Hydrogen (or an isotope of Hydrogen).
`boolean`	`isHeteroAtom()` Returns `true` if Element is not Hydrogen and not Carbon.
`boolean`	`isHydrogen()` Returns `true` if this Element is Hydrogen.
`boolean`	`isMetal()` Returns `true` if ElementType is a metal.
`boolean`	`isMetalloid()` Returns `true` if ElementType is a metalloid.
`boolean`	`isNonMetal()` Returns `true` if ElementType is a non-metal.
`static Element`	`valueOf(String name)` Returns the enum constant of this type with the specified name.
`static Element`	`valueOfIgnoreCase(String elementSymbol)` Returns the Element that corresponds to the specified element symbol.
`static Element[]`	`values()` Returns an array containing the constants of this enum type, in the order they are declared.

Methods inherited from class java.lang.Enum
clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object
getClass, notify, notifyAll, wait, wait, wait

- Enum Constant Detail
  - H
```
public static final Element H
```
  - C
```
public static final Element C
```
  - N
```
public static final Element N
```
  - O
```
public static final Element O
```
  - D
```
public static final Element D
```
    Deuterium
  - T
```
public static final Element T
```
    Tritium
  - He
```
public static final Element He
```
  - Li
```
public static final Element Li
```
  - Be
```
public static final Element Be
```
  - B
```
public static final Element B
```
  - F
```
public static final Element F
```
  - Ne
```
public static final Element Ne
```
  - Na
```
public static final Element Na
```
  - Mg
```
public static final Element Mg
```
  - Al
```
public static final Element Al
```
  - Si
```
public static final Element Si
```
  - P
```
public static final Element P
```
  - S
```
public static final Element S
```
  - Cl
```
public static final Element Cl
```
  - Ar
```
public static final Element Ar
```
  - K
```
public static final Element K
```
  - Ca
```
public static final Element Ca
```
  - Sc
```
public static final Element Sc
```
  - Ti
```
public static final Element Ti
```
  - V
```
public static final Element V
```
  - Cr
```
public static final Element Cr
```
  - Mn
```
public static final Element Mn
```
  - Fe
```
public static final Element Fe
```
  - Co
```
public static final Element Co
```
  - Ni
```
public static final Element Ni
```
  - Cu
```
public static final Element Cu
```
  - Zn
```
public static final Element Zn
```
  - Ga
```
public static final Element Ga
```
  - Ge
```
public static final Element Ge
```
  - As
```
public static final Element As
```
  - Se
```
public static final Element Se
```
  - Br
```
public static final Element Br
```
  - Kr
```
public static final Element Kr
```
  - Rb
```
public static final Element Rb
```
  - Sr
```
public static final Element Sr
```
  - Y
```
public static final Element Y
```
  - Zr
```
public static final Element Zr
```
  - Nb
```
public static final Element Nb
```
  - Mo
```
public static final Element Mo
```
  - Tc
```
public static final Element Tc
```
  - Ru
```
public static final Element Ru
```
  - Rh
```
public static final Element Rh
```
  - Pd
```
public static final Element Pd
```
  - Ag
```
public static final Element Ag
```
  - Cd
```
public static final Element Cd
```
  - In
```
public static final Element In
```
  - Sn
```
public static final Element Sn
```
  - Sb
```
public static final Element Sb
```
  - Te
```
public static final Element Te
```
  - I
```
public static final Element I
```
  - Xe
```
public static final Element Xe
```
  - Cs
```
public static final Element Cs
```
  - Ba
```
public static final Element Ba
```
  - La
```
public static final Element La
```
  - Ce
```
public static final Element Ce
```
  - Pr
```
public static final Element Pr
```
  - Nd
```
public static final Element Nd
```
  - Pm
```
public static final Element Pm
```
  - Sm
```
public static final Element Sm
```
  - Eu
```
public static final Element Eu
```
  - Gd
```
public static final Element Gd
```
  - Tb
```
public static final Element Tb
```
  - Dy
```
public static final Element Dy
```
  - Ho
```
public static final Element Ho
```
  - Er
```
public static final Element Er
```
  - Tm
```
public static final Element Tm
```
  - Yb
```
public static final Element Yb
```
  - Lu
```
public static final Element Lu
```
  - Hf
```
public static final Element Hf
```
  - Ta
```
public static final Element Ta
```
  - W
```
public static final Element W
```
  - Re
```
public static final Element Re
```
  - Os
```
public static final Element Os
```
  - Ir
```
public static final Element Ir
```
  - Pt
```
public static final Element Pt
```
  - Au
```
public static final Element Au
```
  - Hg
```
public static final Element Hg
```
  - Tl
```
public static final Element Tl
```
  - Pb
```
public static final Element Pb
```
  - Bi
```
public static final Element Bi
```
  - Po
```
public static final Element Po
```
  - At
```
public static final Element At
```
  - Rn
```
public static final Element Rn
```
  - Fr
```
public static final Element Fr
```
  - Ra
```
public static final Element Ra
```
  - Ac
```
public static final Element Ac
```
  - Th
```
public static final Element Th
```
  - Pa
```
public static final Element Pa
```
  - U
```
public static final Element U
```
  - Np
```
public static final Element Np
```
  - Pu
```
public static final Element Pu
```
  - Am
```
public static final Element Am
```
  - Cm
```
public static final Element Cm
```
  - Bk
```
public static final Element Bk
```
  - Cf
```
public static final Element Cf
```
  - Es
```
public static final Element Es
```
  - Fm
```
public static final Element Fm
```
  - Md
```
public static final Element Md
```
  - No
```
public static final Element No
```
  - Lr
```
public static final Element Lr
```
  - R
```
public static final Element R
```
    R-group to represent generic groups that are sometimes present in MDL .sdf files.
- 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()

Enum Element

Enum Constant Summary

Method Summary

Methods inherited from class java.lang.Enum

Methods inherited from class java.lang.Object

Enum Constant Detail

H

C

N

O

D

T

He

Li

Be

B

F

Ne

Na

Mg

Al

Si

P

S

Cl

Ar

K

Ca

Sc

Ti

V

Cr

Mn

Fe

Co

Ni

Cu

Zn

Ga

Ge

As

Se

Br

Kr

Rb

Sr

Y

Zr

Nb

Mo

Tc

Ru

Rh

Pd

Ag

Cd

In

Sn

Sb

Te

I

Xe

Cs

Ba

La

Ce

Pr

Nd

Pm

Sm

Eu

Gd

Tb

Dy

Ho

Er

Tm

Yb

Lu

Hf