Package org.biojava.nbio.structure
Enum Class Element
- All Implemented Interfaces:
 Serializable,Comparable<Element>,Constable
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
 
- 
Nested Class Summary
Nested classes/interfaces inherited from class java.lang.Enum
Enum.EnumDesc<E extends Enum<E>> - 
Enum Constant Summary
Enum ConstantsEnum ConstantDescriptionDeuteriumR-group to represent generic groups that are sometimes present in MDL .sdf files.Tritium - 
Method Summary
Modifier and TypeMethodDescriptionint[]Returns a list of all oxidation states the element is found in.floatReturns the atomic mass for this Element.intReturns the atomic number of this Element.intReturns the common valence for this Element.intReturns the number of core electrons for this Element.floatReturns the covalent radius of this Element.static ElementgetElementFromHillIndex(int index) Returns the Element that corresponds to the specified Hill Order.Returns the Element Type for this Element.intReturns the Hill Order of this Element.intReturns the maximum valence for this Element.intReturns the maximum valence for this Element.intReturns the minimum valence for this Element.intReturns a typical oxidation state for this Element.floatReturns the Pauling electronegativity for this Element.intReturns the period in the periodic table of this Element.intReturns the number of valence electrons for this Element.floatReturns the van der Waals radius of this Element.booleanReturnstrueif Element is a chalcogen (O, S, Se, Te, Po).booleanReturnstrueif Element is a halogen (F, Cl, Br, I, At).booleanReturnstrueis the Element is an not Hydrogen (or an isotope of Hydrogen).booleanReturnstrueif Element is not Hydrogen and not Carbon.booleanReturnstrueif this Element is Hydrogen.booleanisMetal()Returnstrueif ElementType is a metal.booleanReturnstrueif ElementType is a metalloid.booleanReturnstrueif ElementType is a non-metal.static ElementReturns the enum constant of this class with the specified name.static ElementvalueOfIgnoreCase(String elementSymbol) Returns the Element that corresponds to the specified element symbol.static Element[]values()Returns an array containing the constants of this enum class, in the order they are declared. 
- 
Enum Constant Details
- 
H
 - 
C
 - 
N
 - 
O
 - 
D
Deuterium - 
T
Tritium - 
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
 - 
Ta
 - 
W
 - 
Re
 - 
Os
 - 
Ir
 - 
Pt
 - 
Au
 - 
Hg
 - 
Tl
 - 
Pb
 - 
Bi
 - 
Po
 - 
At
 - 
Rn
 - 
Fr
 - 
Ra
 - 
Ac
 - 
Th
 - 
Pa
 - 
U
 - 
Np
 - 
Pu
 - 
Am
 - 
Cm
 - 
Bk
 - 
Cf
 - 
Es
 - 
Fm
 - 
Md
 - 
No
 - 
Lr
 - 
R
R-group to represent generic groups that are sometimes present in MDL .sdf files. 
 - 
 - 
Method Details
- 
values
Returns an array containing the constants of this enum class, in the order they are declared.- Returns:
 - an array containing the constants of this enum class, in the order they are declared
 
 - 
valueOf
Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (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 class has no constant with the specified nameNullPointerException- 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.
- 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
Returns the Element Type for this Element.- Returns:
 - the Element Type for this Element.
 
 - 
valueOfIgnoreCase
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()Returnstrueif this Element is Hydrogen.Note: Deuterium (
D) and Tritium (T) will returntrueto this method.- Returns:
 trueif the Element is Hydrogen.
 - 
isHeavyAtom
public boolean isHeavyAtom()Returnstrueis the Element is an not Hydrogen (or an isotope of Hydrogen).This method is the exact opposite of
isHydrogen().- Returns:
 trueis Element is not Hydrogen.
 - 
isHeteroAtom
public boolean isHeteroAtom()Returnstrueif Element is not Hydrogen and not Carbon.- Returns:
 trueif Element is not Hydrogen and not Carbon.
 - 
isMetal
public boolean isMetal()Returnstrueif ElementType is a metal.- Returns:
 trueif ElementType is a metal.
 - 
isMetalloid
public boolean isMetalloid()Returnstrueif ElementType is a metalloid.- Returns:
 trueif ElementType is a metalloid.
 - 
isNonMetal
public boolean isNonMetal()Returnstrueif ElementType is a non-metal.- Returns:
 trueif ElementType is a non-metal.
 - 
isHalogen
public boolean isHalogen()Returnstrueif Element is a halogen (F, Cl, Br, I, At).- Returns:
 trueif Element is a halogen.
 - 
isChalcogen
public boolean isChalcogen()Returnstrueif Element is a chalcogen (O, S, Se, Te, Po).- Returns:
 trueif Element is a chalcogen.
 - 
getElementFromHillIndex
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:
 
 
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