Element (com.hfg API Documentation)

java.lang.Object
- com.hfg.chem.Element

All Implemented Interfaces:: Matter, Comparable<Element>

Direct Known Subclasses:: Isotope

public class Element
extends Object
implements Comparable<Element>, Matter

Atomic element. Elemental mass reference:

Coursey JS, Schwab DJ, and Dragoset RA. 2005. Atomic Weights and Isotopic Compositions (version 2.4.1).
   [Online] Available: http://physics.nist.gov/PhysRefData/Compositions/ [2006, August 18].
   National Institute of Standards and Technology, Gaithersburg, MD.
   (Note that the value in parenthesis is the
   standard uncertainty.)

Organic mass values used are from:

   Zhang Z, Pan H, Chen X. 2009. Mass spectrometry for structural characterization
   of therapeutic antibodies. Mass Spectrom Rev 28:147-176.

Field Summary

Fields
Modifier and Type	Field and Description
`static Element`	`ACTINIUM`
`static Element`	`ALUMINIUM`
`static Element`	`AMERICIUM`
`static Element`	`ANTIMONY`
`static Element`	`ARGON`
`static Element`	`ARSENIC`
`static Element`	`ASTATINE`
`static Element`	`BARIUM`
`static Element`	`BERKELIUM`
`static Element`	`BERYLLIUM`
`static Element`	`BISMUTH`
`static Element`	`BOHRIUM`
`static Element`	`BORON`
`static Element`	`BROMINE`
`static Element`	`CADMIUM`
`static Element`	`CALCIUM`
`static Element`	`CALIFORNIUM`
`static Element`	`CARBON`
`static Element`	`CERIUM`
`static Element`	`CESIUM`
`static Element`	`CHLORINE`
`static Element`	`CHROMIUM`
`static Element`	`COBALT`
`static Element`	`COPERNICIUM`
`static Element`	`COPPER`
`static Element`	`CURIUM`
`static Element`	`DARMSTADTIUM`
`static Element`	`DUBNIUM`
`static Element`	`DYSPROSIUM`
`static Element`	`EINSTEINIUM`
`static Element`	`ERBIUM`
`static Element`	`EUROPIUM`
`static Element`	`FERMIUM`
`static Element`	`FLEROVIUM`
`static Element`	`FLUORINE`
`static Element`	`FRANCIUM`
`static Element`	`GADOLINIUM`
`static Element`	`GALLIUM`
`static Element`	`GERMANIUM`
`static Element`	`GOLD`
`static Element`	`HAFNIUM`
`static Element`	`HASSIUM`
`static Element`	`HELIUM`
`static Element`	`HOLMIUM`
`static Element`	`HYDROGEN`
`static Element`	`INDIUM`
`static Element`	`IODINE`
`static Element`	`IRIDIUM`
`static Element`	`IRON`
`static Element`	`KRYPTON`
`static Element`	`LANTHANUM`
`static Element`	`LAWRENCIUM`
`static Element`	`LEAD`
`static Element`	`LITHIUM`
`static Element`	`LIVERMORIUM`
`static Element`	`LUTETIUM`
`static Element`	`MAGNESIUM`
`static Element`	`MANGANESE`
`static Element`	`MEITNERIUM`
`static Element`	`MENDELEVIUM`
`static Element`	`MERCURY`
`static Element`	`MOLYBDENUM`
`static Element`	`NEODYMIUM`
`static Element`	`NEON`
`static Element`	`NEPTUNIUM`
`static Element`	`NICKEL`
`static Element`	`NIOBIUM`
`static Element`	`NITROGEN`
`static Element`	`NOBELIUM`
`static Element`	`OSMIUM`
`static Element`	`OXYGEN`
`static Element`	`PALLADIUM`
`static Element`	`PHOSPHOROUS`
`static Element`	`PLATINUM`
`static Element`	`PLUTONIUM`
`static Element`	`POLONIUM`
`static Element`	`POTASSIUM`
`static Element`	`PRASEODYMIUM`
`static Element`	`PROACTINIUM`
`static Element`	`PROMETHIUM`
`static Element`	`RADIUM`
`static Element`	`RADON`
`static Element`	`RHENIUM`
`static Element`	`RHODIUM`
`static Element`	`ROENTGENIUM`
`static Element`	`RUBIDIUM`
`static Element`	`RUTHENIUM`
`static Element`	`RUTHERFORDIUM`
`static Element`	`SAMARIUM`
`static Element`	`SCANDIUM`
`static Element`	`SEABORGIUM`
`static Element`	`SELENIUM`
`static Element`	`SILICON`
`static Element`	`SILVER`
`static Element`	`SODIUM`
`static Element`	`STRONTIUM`
`static Element`	`SULFUR`
`static Element`	`TANTALUM`
`static Element`	`TECHNETIUM`
`static Element`	`TELLURIUM`
`static Element`	`TERBIUM`
`static Element`	`THALLIUM`
`static Element`	`THORIUM`
`static Element`	`THULIUM`
`static Element`	`TIN`
`static Element`	`TITANIUM`
`static Element`	`TUNGSTEN`
`static Element`	`UNUNOCTIUM`
`static Element`	`UNUNPENTIUM`
`static Element`	`UNUNSEPTIUM`
`static Element`	`UNUNTRIUM`
`static Element`	`URANIUM`
`static Element`	`VANADIUM`
`static Element`	`XENON`
`static Element`	`YTTERBIUM`
`static Element`	`YTTRIUM`
`static Element`	`ZINC`
`static Element`	`ZIRCONIUM`

Constructor Summary

Constructors
Modifier	Constructor and Description
`protected`	`Element(String inName, String inSymbol, int inAtomicNum, double inMonoMass, double inAvgMass)`
`protected`	`Element(String inName, String inSymbol, int inAtomicNum, double inMonoMass, double inAvgMass, double inOrgainicAvgMass)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`compareTo(Element element)`
`int`	`getAtomicNum()`
`Double`	`getAverageMass()`
`String`	`getChemicalFormula()` Returns a chemical formula String.
`Length`	`getCovalentRadius()` Returns the covalent radius.
`int[]`	`getDefaultValences()` Returns the default values for the number of valence electrons for the element.
`Map<Element,Float>`	`getElementalComposition()` Returns an unmodifiable copy of the elemental composition Map.
`Double`	`getMonoisotopicMass()`
`String`	`getName()`
`Double`	`getOrganicAverageMass()` Returns the average mass as estimated from organic sources.
`String`	`getSymbol()`
`Length`	`getVanderWaalsRadius()` Returns the Van der Waals radius.
`String`	`toString()`
`static Element`	`valueOf(Integer inAtomicNum)`
`static Element`	`valueOf(String inString)`
`static Element`	`valueOf(String inString, Case inCaseSensetive)`
`static Element[]`	`values()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

HYDROGEN
```
public static final Element HYDROGEN
```

HELIUM
```
public static final Element HELIUM
```

LITHIUM
```
public static final Element LITHIUM
```

BERYLLIUM
```
public static final Element BERYLLIUM
```

BORON
```
public static final Element BORON
```

CARBON
```
public static final Element CARBON
```

NITROGEN
```
public static final Element NITROGEN
```

OXYGEN
```
public static final Element OXYGEN
```

FLUORINE
```
public static final Element FLUORINE
```

NEON
```
public static final Element NEON
```

SODIUM
```
public static final Element SODIUM
```

MAGNESIUM
```
public static final Element MAGNESIUM
```

ALUMINIUM
```
public static final Element ALUMINIUM
```

SILICON
```
public static final Element SILICON
```

PHOSPHOROUS

public static final Element PHOSPHOROUS

SULFUR
```
public static final Element SULFUR
```

CHLORINE
```
public static final Element CHLORINE
```

ARGON
```
public static final Element ARGON
```

POTASSIUM
```
public static final Element POTASSIUM
```

CALCIUM
```
public static final Element CALCIUM
```

SCANDIUM
```
public static final Element SCANDIUM
```

TITANIUM
```
public static final Element TITANIUM
```

VANADIUM
```
public static final Element VANADIUM
```

CHROMIUM
```
public static final Element CHROMIUM
```

MANGANESE
```
public static final Element MANGANESE
```

IRON
```
public static final Element IRON
```

COBALT
```
public static final Element COBALT
```

NICKEL
```
public static final Element NICKEL
```

COPPER
```
public static final Element COPPER
```

ZINC
```
public static final Element ZINC
```

GALLIUM
```
public static final Element GALLIUM
```

GERMANIUM
```
public static final Element GERMANIUM
```

ARSENIC
```
public static final Element ARSENIC
```

SELENIUM
```
public static final Element SELENIUM
```

BROMINE
```
public static final Element BROMINE
```

KRYPTON
```
public static final Element KRYPTON
```

RUBIDIUM
```
public static final Element RUBIDIUM
```

STRONTIUM
```
public static final Element STRONTIUM
```

YTTRIUM
```
public static final Element YTTRIUM
```

ZIRCONIUM
```
public static final Element ZIRCONIUM
```

NIOBIUM
```
public static final Element NIOBIUM
```

MOLYBDENUM
```
public static final Element MOLYBDENUM
```

TECHNETIUM
```
public static final Element TECHNETIUM
```

RUTHENIUM
```
public static final Element RUTHENIUM
```

RHODIUM
```
public static final Element RHODIUM
```

PALLADIUM
```
public static final Element PALLADIUM
```

SILVER
```
public static final Element SILVER
```

CADMIUM
```
public static final Element CADMIUM
```

INDIUM
```
public static final Element INDIUM
```

TIN
```
public static final Element TIN
```

ANTIMONY
```
public static final Element ANTIMONY
```

TELLURIUM
```
public static final Element TELLURIUM
```

IODINE
```
public static final Element IODINE
```

XENON
```
public static final Element XENON
```

CESIUM
```
public static final Element CESIUM
```

BARIUM
```
public static final Element BARIUM
```

LANTHANUM
```
public static final Element LANTHANUM
```

CERIUM
```
public static final Element CERIUM
```

PRASEODYMIUM

public static final Element PRASEODYMIUM

NEODYMIUM
```
public static final Element NEODYMIUM
```

PROMETHIUM
```
public static final Element PROMETHIUM
```

SAMARIUM
```
public static final Element SAMARIUM
```

EUROPIUM
```
public static final Element EUROPIUM
```

GADOLINIUM
```
public static final Element GADOLINIUM
```

TERBIUM
```
public static final Element TERBIUM
```

DYSPROSIUM
```
public static final Element DYSPROSIUM
```

HOLMIUM
```
public static final Element HOLMIUM
```

ERBIUM
```
public static final Element ERBIUM
```

THULIUM
```
public static final Element THULIUM
```

YTTERBIUM
```
public static final Element YTTERBIUM
```

LUTETIUM
```
public static final Element LUTETIUM
```

HAFNIUM
```
public static final Element HAFNIUM
```

TANTALUM
```
public static final Element TANTALUM
```

TUNGSTEN
```
public static final Element TUNGSTEN
```

RHENIUM
```
public static final Element RHENIUM
```

OSMIUM
```
public static final Element OSMIUM
```

IRIDIUM
```
public static final Element IRIDIUM
```

PLATINUM
```
public static final Element PLATINUM
```

GOLD
```
public static final Element GOLD
```

MERCURY
```
public static final Element MERCURY
```

THALLIUM
```
public static final Element THALLIUM
```

LEAD
```
public static final Element LEAD
```

BISMUTH
```
public static final Element BISMUTH
```

POLONIUM
```
public static final Element POLONIUM
```

ASTATINE
```
public static final Element ASTATINE
```

RADON
```
public static final Element RADON
```

FRANCIUM
```
public static final Element FRANCIUM
```

RADIUM
```
public static final Element RADIUM
```

ACTINIUM
```
public static final Element ACTINIUM
```

THORIUM
```
public static final Element THORIUM
```

PROACTINIUM

public static final Element PROACTINIUM

URANIUM
```
public static final Element URANIUM
```

NEPTUNIUM
```
public static final Element NEPTUNIUM
```

PLUTONIUM
```
public static final Element PLUTONIUM
```

AMERICIUM
```
public static final Element AMERICIUM
```

CURIUM
```
public static final Element CURIUM
```

BERKELIUM
```
public static final Element BERKELIUM
```

CALIFORNIUM

public static final Element CALIFORNIUM

EINSTEINIUM

public static final Element EINSTEINIUM

FERMIUM
```
public static final Element FERMIUM
```

MENDELEVIUM

public static final Element MENDELEVIUM

NOBELIUM
```
public static final Element NOBELIUM
```

LAWRENCIUM
```
public static final Element LAWRENCIUM
```

RUTHERFORDIUM

public static final Element RUTHERFORDIUM

DUBNIUM
```
public static final Element DUBNIUM
```

SEABORGIUM
```
public static final Element SEABORGIUM
```

BOHRIUM
```
public static final Element BOHRIUM
```

HASSIUM
```
public static final Element HASSIUM
```

MEITNERIUM
```
public static final Element MEITNERIUM
```

DARMSTADTIUM

public static final Element DARMSTADTIUM

ROENTGENIUM

public static final Element ROENTGENIUM

COPERNICIUM

public static final Element COPERNICIUM

UNUNTRIUM
```
public static final Element UNUNTRIUM
```

FLEROVIUM
```
public static final Element FLEROVIUM
```

UNUNPENTIUM

public static final Element UNUNPENTIUM

LIVERMORIUM

public static final Element LIVERMORIUM

UNUNSEPTIUM

public static final Element UNUNSEPTIUM

UNUNOCTIUM
```
public static final Element UNUNOCTIUM
```

Constructor Detail

Element

protected Element(String inName,
                  String inSymbol,
                  int inAtomicNum,
                  double inMonoMass,
                  double inAvgMass)

Element

protected Element(String inName,
                  String inSymbol,
                  int inAtomicNum,
                  double inMonoMass,
                  double inAvgMass,
                  double inOrgainicAvgMass)

Method Detail
- valueOf
```
public static Element valueOf(String inString)
```
- valueOf
```
public static Element valueOf(String inString,
                              Case inCaseSensetive)
```
- valueOf
```
public static Element valueOf(Integer inAtomicNum)
```
- values
```
public static Element[] values()
```
- getName
```
public String getName()
```
- getSymbol
```
public String getSymbol()
```
- getAtomicNum
```
public int getAtomicNum()
```
- toString
```
public String toString()
```
  Overrides:
  
  toString in class Object
- compareTo
```
public int compareTo(Element element)
```
  Specified by:
  
  compareTo in interface Comparable<Element>
- getElementalComposition
```
public Map<Element,Float> getElementalComposition()
```
  Description copied from interface: Matter
  
  Returns an unmodifiable copy of the elemental composition Map. The keys are Element objects and the values are Floats. Why Floats instead of Integers you ask? Because some amino acid codes such as B and Z are ambiguous averages.
  
  Specified by:
  
  getElementalComposition in interface Matter
  
  Returns:
  
  Map containing the elemental composition
- getChemicalFormula
```
public String getChemicalFormula()
```
  Returns a chemical formula String. For Elements this returns the symbol.
  
  Specified by:
  
  getChemicalFormula in interface Matter
  
  Returns:
  
  the chemical formula string
- getMonoisotopicMass
```
public Double getMonoisotopicMass()
```
  Specified by:
  
  getMonoisotopicMass in interface Matter
- getAverageMass
```
public Double getAverageMass()
```
  Specified by:
  
  getAverageMass in interface Matter
- getOrganicAverageMass
```
public Double getOrganicAverageMass()
```
  Returns the average mass as estimated from organic sources. [Zhang Z, Pan H, Chen X. 2009. Mass spectrometry for structural characterization of therapeutic antibodies. Mass Spectrom Rev 28:147-176.]
  
  Specified by:
  
  getOrganicAverageMass in interface Matter
- getVanderWaalsRadius
```
public Length getVanderWaalsRadius()
```
  Returns the Van der Waals radius. [From Table 1 in Alvarez, Santiago. 2013. “A Cartography of the van Der Waals Territories.” Dalton Transactions 42 (24): 8617–36. https://doi.org/10.1039/c3dt50599e.
  
  Returns:
  
  the Van der Waals radius
- getCovalentRadius
```
public Length getCovalentRadius()
```
  Returns the covalent radius. [From Table 2 in Cordero, Beatriz, Verónica Gómez, Ana E. Platero-Prats, Marc Revés, Jorge Echeverría, Eduard Cremades, Flavia Barragán, and Santiago Alvarez. 2008. “Covalent Radii Revisited.” Journal of the Chemical Society. Dalton Transactions, no. 21: 2832–38. https://doi.org/10.1039/b801115j.
  
  Returns:
  
  the Van der Waals radius
- getDefaultValences
```
public int[] getDefaultValences()
```
  Returns the default values for the number of valence electrons for the element. Used when calculating implicit hydrogens for a compound.

Class Element

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

HYDROGEN

HELIUM

LITHIUM

BERYLLIUM

BORON

CARBON

NITROGEN

OXYGEN

FLUORINE

NEON

SODIUM

MAGNESIUM

ALUMINIUM

SILICON

PHOSPHOROUS

SULFUR

CHLORINE

ARGON

POTASSIUM

CALCIUM

SCANDIUM

TITANIUM

VANADIUM

CHROMIUM

MANGANESE

IRON

COBALT

NICKEL

COPPER

ZINC

GALLIUM

GERMANIUM

ARSENIC

SELENIUM

BROMINE

KRYPTON

RUBIDIUM

STRONTIUM

YTTRIUM

ZIRCONIUM

NIOBIUM

MOLYBDENUM

TECHNETIUM

RUTHENIUM

RHODIUM

PALLADIUM

SILVER

CADMIUM

INDIUM

TIN

ANTIMONY

TELLURIUM

IODINE

XENON

CESIUM

BARIUM

LANTHANUM

CERIUM

PRASEODYMIUM

NEODYMIUM

PROMETHIUM

SAMARIUM

EUROPIUM

GADOLINIUM

TERBIUM

DYSPROSIUM

HOLMIUM

ERBIUM

THULIUM

YTTERBIUM

LUTETIUM

HAFNIUM

TANTALUM

TUNGSTEN