org.biojava.bio.structure
Enum Element

java.lang.Object
  extended by java.lang.Enum<Element>
      extended by org.biojava.bio.structure.Element
All Implemented Interfaces:
Serializable, Comparable<Element>

public enum Element
extends Enum<Element>
implements Serializable

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
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
          Deuterim
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
 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.
 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
Deuterim


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

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: currently Deuterium (D) and Tritium (T) are not considered Hydrogen.

Returns:
true if the Element is Hydrogen.

isHeavyAtom

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

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()