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com.hfg xml, html, svg, and bioinformatics utility library
package com.hfg.chem;
import java.util.HashMap;
import java.util.Map;
import java.util.Set;
import java.util.HashSet;
import com.hfg.util.StringUtil;
//------------------------------------------------------------------------------
/**
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.
@author J. Alex Taylor, hairyfatguy.com
*/
//------------------------------------------------------------------------------
// com.hfg XML/HTML Coding Library
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library is distributed in the hope that it will be useful,
// but WITHOUT ANY WARRANTY; without even the implied warranty of
// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
//
// J. Alex Taylor, President, Founder, CEO, COO, CFO, OOPS hairyfatguy.com
// [email protected]
//------------------------------------------------------------------------------
public class Element implements Comparable, OrganicMatter
{
//##########################################################################
// PRIVATE FIELDS
//##########################################################################
private String mName;
private String mSymbol;
private int mAtomicNum;
private Double mMonoisotopicMass;
private Double mAverageMass;
private Double mOrganicAverageMass;
// This declaration has to come before the public constants below.
private static Set sValues = new HashSet<>();
//##########################################################################
// PUBLIC FIELDS
//##########################################################################
public static final Element HYDROGEN = new Element("Hydrogen", "H", 1, 1.007825032, 1.00794, 1.007968);
public static final Element HELIUM = new Element("Helium", "He", 2, 4.00260325413, 4.002602);
public static final Element LITHIUM = new Element("Lithium", "Li", 3, 7.0160034366, 6.941);
public static final Element BERYLLIUM = new Element("Beryllium", "Be", 4, 9.012183065, 9.012182);
public static final Element BORON = new Element("Boron", "B", 5, 11.00930536, 10.811);
public static final Element CARBON = new Element("Carbon", "C", 6, 12, 12.0107, 12.01079);
public static final Element NITROGEN = new Element("Nitrogen", "N", 7, 14.0030740052, 14.0067, 14.00669);
public static final Element OXYGEN = new Element("Oxygen", "O", 8, 15.9949146221, 15.9994, 15.99937);
public static final Element FLUORINE = new Element("Fluorine", "F", 9, 18.99840316273, 18.9984032);
public static final Element NEON = new Element("Neon", "Ne", 10, 19.9924401762, 20.1797);
public static final Element SODIUM = new Element("Sodium", "Na", 11, 22.9897696723, 22.9897702);
public static final Element MAGNESIUM = new Element("Magnesium", "Mg", 12, 23.985041697, 24.3050);
public static final Element ALUMINIUM = new Element("Aluminium", "Al", 13, 26.98153853, 26.9815386);
public static final Element SILICON = new Element("Silicon", "Si", 14, 27.97692653465, 28.0855);
public static final Element PHOSPHOROUS = new Element("Phosphorous", "P", 15, 30.97376151, 30.973761);
public static final Element SULFUR = new Element("Sulfur", "S", 16, 31.97207069, 32.065, 32.0639);
public static final Element CHLORINE = new Element("Chlorine", "Cl", 17, 34.968852682, 35.453);
public static final Element ARGON = new Element("Argon", "Ar", 18, 39.9623831237, 39.948);
public static final Element POTASSIUM = new Element("Potassium", "K", 19, 38.96370693, 39.0983);
public static final Element CALCIUM = new Element("Calcium", "Ca", 20, 39.962590863, 40.078);
public static final Element SCANDIUM = new Element("Scandium", "Sc", 21, 44.95590828, 44.955912);
public static final Element TITANIUM = new Element("Titanium", "Ti", 22, 47.94794198, 47.867);
public static final Element VANADIUM = new Element("Vanadium", "V", 23, 50.94395704, 50.9415);
public static final Element CHROMIUM = new Element("Chromium", "Cr", 24, 51.94050623, 51.9961);
public static final Element MANGANESE = new Element("Manganese", "Mn", 25, 54.93804391, 54.938045);
public static final Element IRON = new Element("Iron", "Fe", 26, 55.93494210, 55.845);
public static final Element COBALT = new Element("Cobalt", "Co", 27, 58.93319429, 58.933195);
public static final Element NICKEL = new Element("Nickel", "Ni", 28, 57.93534241, 58.6934);
public static final Element COPPER = new Element("Copper", "Cu", 29, 62.92959772, 63.546);
public static final Element ZINC = new Element("Zinc", "Zn", 30, 63.92914660, 65.409);
public static final Element GALLIUM = new Element("Gallium", "Ga", 31, 68.9255735, 69.723);
public static final Element GERMANIUM = new Element("Germanium", "Ge", 32, 73.921177761, 72.64);
public static final Element ARSENIC = new Element("Arsenic", "As", 33, 74.92159457, 74.92160);
public static final Element SELENIUM = new Element("Selenium", "Se", 34, 79.9165218, 78.96);
public static final Element BROMINE = new Element("Bromine", "Br", 35, 78.9183376, 79.904);
public static final Element KRYPTON = new Element("Krypton", "Kr", 36, 83.9114977282, 83.798);
public static final Element RUBIDIUM = new Element("Rubidium", "Rb", 37, 84.9117897379, 85.4678);
public static final Element STRONTIUM = new Element("Strontium", "Sr", 38, 87.9056125, 87.62);
public static final Element YTTRIUM = new Element("Yttrium", "Y", 39, 88.9058403, 88.90585);
public static final Element ZIRCONIUM = new Element("Zirconium", "Zr", 40, 89.9046977, 91.224);
public static final Element NIOBIUM = new Element("Niobium", "Nb", 41, 92.9063730, 92.90638);
public static final Element MOLYBDENUM = new Element("Molybdenum", "Mo", 42, 97.90540482, 95.94);
public static final Element TECHNETIUM = new Element("Technetium", "Tc", 43, 96.9063667);
public static final Element RUTHENIUM = new Element("Ruthenium", "Ru", 44, 101.9043441, 101.07);
public static final Element RHODIUM = new Element("Rhodium", "Rh", 45, 102.9054980, 102.90550);
public static final Element PALLADIUM = new Element("Palladium", "Pd", 46, 105.9034804, 106.42);
public static final Element SILVER = new Element("Silver", "Ag", 47, 106.9050916, 107.8682);
public static final Element CADMIUM = new Element("Cadmium", "Cd", 48, 113.90336509, 112.411);
public static final Element INDIUM = new Element("Indium", "In", 49, 114.903878776, 114.818);
public static final Element TIN = new Element("Tin", "Sn", 50, 119.90220163, 118.710);
public static final Element ANTIMONY = new Element("Antimony", "Sb", 51, 120.9038120, 121.760);
public static final Element TELLURIUM = new Element("Tellurium", "Te", 52, 129.906222748, 127.60);
public static final Element IODINE = new Element("Iodine", "I", 53, 126.9044719, 126.90447);
public static final Element XENON = new Element("Xenon", "Xe", 54, 131.9041550856, 131.293);
public static final Element CESIUM = new Element("Cesium", "Cs", 55, 132.9054519610, 132.9054519);
public static final Element BARIUM = new Element("Barium", "Ba", 56, 137.90524700, 137.327);
public static final Element LANTHANUM = new Element("Lanthanum", "La", 57, 138.9063563, 138.90547);
public static final Element CERIUM = new Element("Cerium", "Ce", 58, 139.9054431, 140.116);
public static final Element PRASEODYMIUM = new Element("Praseodymium", "Pr", 59, 140.9076576, 140.90765);
public static final Element NEODYMIUM = new Element("Neodymium", "Nd", 60, 141.9077290, 144.242);
public static final Element PROMETHIUM = new Element("Promethium", "Pm", 61, 144.9127559);
public static final Element SAMARIUM = new Element("Samarium", "Sm", 62, 151.9197397, 150.36);
public static final Element EUROPIUM = new Element("Europium", "Eu", 63, 152.9212380, 151.964);
public static final Element GADOLINIUM = new Element("Gadolinium", "Gd", 64, 157.9241123, 157.25);
public static final Element TERBIUM = new Element("Terbium", "Tb", 65, 158.9253547, 158.92535);
public static final Element DYSPROSIUM = new Element("Dysprosium", "Dy", 66, 163.9291819, 162.500);
public static final Element HOLMIUM = new Element("Holmium", "Ho", 67, 164.9303288, 164.93032);
public static final Element ERBIUM = new Element("Erbium", "Er", 68, 165.9302995, 167.259);
public static final Element THULIUM = new Element("Thulium", "Tm", 69, 168.9342179, 168.93421);
public static final Element YTTERBIUM = new Element("Ytterbium", "Yb", 70, 173.9388664, 173.04);
public static final Element LUTETIUM = new Element("Lutetium", "Lu", 71, 174.9407752, 174.967);
public static final Element HAFNIUM = new Element("Hafnium", "Hf", 72, 179.9465570, 178.49);
public static final Element TANTALUM = new Element("Tantalum", "Ta", 73, 180.9479958, 180.94788);
public static final Element TUNGSTEN = new Element("Tungsten", "W", 74, 183.95093092, 183.84);
public static final Element RHENIUM = new Element("Rhenium", "Re", 75, 186.9557501, 186.207);
public static final Element OSMIUM = new Element("Osmium", "Os", 76, 191.9614770, 190.23);
public static final Element IRIDIUM = new Element("Iridium", "Ir", 77, 192.9629216, 192.217);
public static final Element PLATINUM = new Element("Platinum", "Pt", 78, 194.9647917, 195.084);
public static final Element GOLD = new Element("Gold", "Au", 79, 196.96656879, 196.966569);
public static final Element MERCURY = new Element("Mercury", "Hg", 80, 201.97064340, 200.59);
public static final Element THALLIUM = new Element("Thallium", "Tl", 81, 204.9744278, 204.3833);
public static final Element LEAD = new Element("Lead", "Pb", 82, 207.9766525, 207.2);
public static final Element BISMUTH = new Element("Bismuth", "Bi", 83, 208.9803991, 208.98040);
public static final Element POLONIUM = new Element("Polonium", "Po", 84, 208.9824308);
public static final Element ASTATINE = new Element("Astatine", "At", 85, 209.9871479);
public static final Element RADON = new Element("Radon", "Rn", 86, 222.0175782);
public static final Element FRANCIUM = new Element("Francium", "Fr", 87, 223.0197360);
public static final Element RADIUM = new Element("Radium", "Ra", 88, 226.0254103);
public static final Element ACTINIUM = new Element("Actinium", "Ac", 89, 227.0277523);
public static final Element THORIUM = new Element("Thorium", "Th", 90, 232.0380558);
public static final Element PROACTINIUM = new Element("Proactinium", "Pa", 91, 231.0358842);
public static final Element URANIUM = new Element("Uranium", "U", 92, 238.0507884);
public static final Element NEPTUNIUM = new Element("Neptunium", "Np", 93, 237.0481736);
public static final Element PLUTONIUM = new Element("Plutonium", "Pu", 94, 238.0495601);
public static final Element AMERICIUM = new Element("Americium", "Am", 95, 241.0568293);
public static final Element CURIUM = new Element("Curium", "Cm", 96, 243.0613893);
public static final Element BERKELIUM = new Element("Berkelium", "Bk", 97, 247.0703073);
public static final Element CALIFORNIUM = new Element("Californium", "Cf", 98, 249.0748539);
public static final Element EINSTEINIUM = new Element("Einsteinium", "Es", 99, 252.082980);
public static final Element FERMIUM = new Element("Fermium", "Fm", 100, 257.0951061);
public static final Element MENDELEVIUM = new Element("Mendelevium", "Md", 101, 258.0984315);
public static final Element NOBELIUM = new Element("Nobelium", "No", 102, 259.10103);
public static final Element LAWRENCIUM = new Element("Lawrencium", "Lr", 103, 262.10961);
public static final Element RUTHERFORDIUM = new Element("Rutherfordium", "Rf", 104, 267.12179);
public static final Element DUBNIUM = new Element("Dubnium", "Db", 105, 268.12567);
public static final Element SEABORGIUM = new Element("Seaborgium", "Sg", 106, 271.13393);
public static final Element BOHRIUM = new Element("Bohrium", "Bh", 107, 272.13826);
public static final Element HASSIUM = new Element("Hassium", "Hs", 108, 270.13429);
public static final Element MEITNERIUM = new Element("Meitnerium", "Mt", 109, 276.15159);
public static final Element DARMSTADTIUM = new Element("Darmstadtium", "Ds", 110, 281.16451);
public static final Element ROENTGENIUM = new Element("Roentgenium", "Rg", 111, 280.16514);
public static final Element COPERNICIUM = new Element("Copernicium", "Cn", 112, 285.17712);
public static final Element UNUNTRIUM = new Element("Ununtrium", "Uut", 113, 284.17873);
public static final Element FLEROVIUM = new Element("Flerovium", "Fl", 114, 289.19042);
public static final Element UNUNPENTIUM = new Element("Ununpentium", "Uup", 115, 288.19274);
public static final Element LIVERMORIUM = new Element("Livermorium", "Lv", 116, 293.20449);
public static final Element UNUNSEPTIUM = new Element("Ununseptium", "Uus", 117, 292.20746);
public static final Element UNUNOCTIUM = new Element("Ununoctium", "Uuo", 118, 294.21392);
//##########################################################################
// CONSTRUCTORS
//##########################################################################
//--------------------------------------------------------------------------
private Element(String inName, String inSymbol, int inAtomicNum,
double inMonoMass)
{
mName = inName;
mSymbol = inSymbol;
mAtomicNum = inAtomicNum;
mMonoisotopicMass = inMonoMass;
if (getClass().equals(Element.class)) // We don't want to include isotopes
{
sValues.add(this);
}
}
//--------------------------------------------------------------------------
protected Element(String inName, String inSymbol, int inAtomicNum,
double inMonoMass, double inAvgMass)
{
this(inName, inSymbol, inAtomicNum, inMonoMass);
mAverageMass = inAvgMass;
}
//--------------------------------------------------------------------------
protected Element(String inName, String inSymbol, int inAtomicNum,
double inMonoMass, double inAvgMass, double inOrgainicAvgMass)
{
this(inName, inSymbol, inAtomicNum, inMonoMass, inAvgMass);
mOrganicAverageMass = inOrgainicAvgMass;
}
//##########################################################################
// PUBLIC METHODS
//##########################################################################
//--------------------------------------------------------------------------
public static Element valueOf(String inString)
{
Element value = null;
if (StringUtil.isSet(inString))
{
for (Element element : sValues)
{
if (element.getName().equalsIgnoreCase(inString)
|| element.getSymbol().equals(inString))
{
value = element;
break;
}
}
}
return value;
}
//--------------------------------------------------------------------------
public static Element valueOf(Integer inAtomicNum)
{
Element value = null;
if (inAtomicNum != null)
{
for (Element element : sValues)
{
if (element.getAtomicNum() == inAtomicNum)
{
value = element;
break;
}
}
}
return value;
}
//--------------------------------------------------------------------------
public static Element[] values()
{
return sValues.toArray(new Element[sValues.size()]);
}
//--------------------------------------------------------------------------
public String getName()
{
return mName;
}
//--------------------------------------------------------------------------
public String getSymbol()
{
return mSymbol;
}
//--------------------------------------------------------------------------
public int getAtomicNum()
{
return mAtomicNum;
}
//--------------------------------------------------------------------------
@Override
public String toString()
{
return getSymbol();
}
//--------------------------------------------------------------------------
public int compareTo(Element element)
{
int result = 0;
if (mMonoisotopicMass > element.mMonoisotopicMass)
{
result = 1;
}
else if (mMonoisotopicMass < element.mMonoisotopicMass)
{
result = -1;
}
return result;
}
// OrganicMatter interface methods:
//--------------------------------------------------------------------------
public Map getElementalComposition()
{
Map elemComp = new HashMap<>(1);
elemComp.put(this, 1.0f);
return elemComp;
}
//--------------------------------------------------------------------------
public Double getMonoisotopicMass()
{
return mMonoisotopicMass;
}
//--------------------------------------------------------------------------
public Double getAverageMass()
{
return mAverageMass;
}
//--------------------------------------------------------------------------
/**
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.]
*/
public Double getOrganicAverageMass()
{
return mOrganicAverageMass;
}
}