Classes
class	Element
	An Element represents a chemical element. More...

Functions
def	get_by_symbol
	Get the element with a particular chemical symbol. More...

Variables
string	__author__ = "Christopher M. Bruns"

string	__version__ = "1.0"

tuple	hydrogen = Element( 1, "hydrogen", "H", 1.007947*daltons)

tuple	deuterium = Element( 1, "deuterium", "D", 2.01355321270*daltons)

tuple	helium = Element( 2, "helium", "He", 4.003*daltons)

tuple	lithium = Element( 3, "lithium", "Li", 6.9412*daltons)

tuple	beryllium = Element( 4, "beryllium", "Be", 9.0121823*daltons)

tuple	boron = Element( 5, "boron", "B", 10.8117*daltons)

tuple	carbon = Element( 6, "carbon", "C", 12.01078*daltons)

tuple	nitrogen = Element( 7, "nitrogen", "N", 14.00672*daltons)

tuple	oxygen = Element( 8, "oxygen", "O", 15.99943*daltons)

tuple	fluorine = Element( 9, "fluorine", "F", 18.99840325*daltons)

tuple	neon = Element( 10, "neon", "Ne", 20.17976*daltons)

tuple	sodium = Element( 11, "sodium", "Na", 22.989769282*daltons)

tuple	magnesium = Element( 12, "magnesium", "Mg", 24.30506*daltons)

tuple	aluminum = Element( 13, "aluminum", "Al", 26.98153868*daltons)

tuple	silicon = Element( 14, "silicon", "Si", 28.08553*daltons)

tuple	phosphorus = Element( 15, "phosphorus", "P", 30.9737622*daltons)

tuple	sulfur = Element( 16, "sulfur", "S", 32.0655*daltons)

tuple	chlorine = Element( 17, "chlorine", "Cl", 35.4532*daltons)

tuple	argon = Element( 18, "argon", "Ar", 39.9481*daltons)

tuple	potassium = Element( 19, "potassium", "K", 39.09831*daltons)

tuple	calcium = Element( 20, "calcium", "Ca", 40.0784*daltons)

tuple	scandium = Element( 21, "scandium", "Sc", 44.9559126*daltons)

tuple	titanium = Element( 22, "titanium", "Ti", 47.8671*daltons)

tuple	vanadium = Element( 23, "vanadium", "V", 50.94151*daltons)

tuple	chromium = Element( 24, "chromium", "Cr", 51.99616*daltons)

tuple	manganese = Element( 25, "manganese", "Mn", 54.9380455*daltons)

tuple	iron = Element( 26, "iron", "Fe", 55.8452*daltons)

tuple	cobalt = Element( 27, "cobalt", "Co", 58.9331955*daltons)

tuple	nickel = Element( 28, "nickel", "Ni", 58.69342*daltons)

tuple	copper = Element( 29, "copper", "Cu", 63.5463*daltons)

tuple	zinc = Element( 30, "zinc", "Zn", 65.4094*daltons)

tuple	gallium = Element( 31, "gallium", "Ga", 69.7231*daltons)

tuple	germanium = Element( 32, "germanium", "Ge", 72.641*daltons)

tuple	arsenic = Element( 33, "arsenic", "As", 74.921602*daltons)

tuple	selenium = Element( 34, "selenium", "Se", 78.963*daltons)

tuple	bromine = Element( 35, "bromine", "Br", 79.9041*daltons)

tuple	krypton = Element( 36, "krypton", "Kr", 83.7982*daltons)

tuple	rubidium = Element( 37, "rubidium", "Rb", 85.46783*daltons)

tuple	strontium = Element( 38, "strontium", "Sr", 87.621*daltons)

tuple	yttrium = Element( 39, "yttrium", "Y", 88.905852*daltons)

tuple	zirconium = Element( 40, "zirconium", "Zr", 91.2242*daltons)

tuple	niobium = Element( 41, "niobium", "Nb", 92.906382*daltons)

tuple	molybdenum = Element( 42, "molybdenum", "Mo", 95.942*daltons)

tuple	technetium = Element( 43, "technetium", "Tc", 98*daltons)

tuple	ruthenium = Element( 44, "ruthenium", "Ru", 101.072*daltons)

tuple	rhodium = Element( 45, "rhodium", "Rh", 102.905502*daltons)

tuple	palladium = Element( 46, "palladium", "Pd", 106.421*daltons)

tuple	silver = Element( 47, "silver", "Ag", 107.86822*daltons)

tuple	cadmium = Element( 48, "cadmium", "Cd", 112.4118*daltons)

tuple	indium = Element( 49, "indium", "In", 114.8183*daltons)

tuple	tin = Element( 50, "tin", "Sn", 118.7107*daltons)

tuple	antimony = Element( 51, "antimony", "Sb", 121.7601*daltons)

tuple	tellurium = Element( 52, "tellurium", "Te", 127.603*daltons)

tuple	iodine = Element( 53, "iodine", "I", 126.904473*daltons)

tuple	xenon = Element( 54, "xenon", "Xe", 131.2936*daltons)

tuple	cesium = Element( 55, "cesium", "Cs", 132.90545192*daltons)

tuple	barium = Element( 56, "barium", "Ba", 137.3277*daltons)

tuple	lanthanum = Element( 57, "lanthanum", "La", 138.905477*daltons)

tuple	cerium = Element( 58, "cerium", "Ce", 140.1161*daltons)

tuple	praseodymium = Element( 59, "praseodymium", "Pr", 140.907652*daltons)

tuple	neodymium = Element( 60, "neodymium", "Nd", 144.2423*daltons)

tuple	promethium = Element( 61, "promethium", "Pm", 145*daltons)

tuple	samarium = Element( 62, "samarium", "Sm", 150.362*daltons)

tuple	europium = Element( 63, "europium", "Eu", 151.9641*daltons)

tuple	gadolinium = Element( 64, "gadolinium", "Gd", 157.253*daltons)

tuple	terbium = Element( 65, "terbium", "Tb", 158.925352*daltons)

tuple	dysprosium = Element( 66, "dysprosium", "Dy", 162.5001*daltons)

tuple	holmium = Element( 67, "holmium", "Ho", 164.930322*daltons)

tuple	erbium = Element( 68, "erbium", "Er", 167.2593*daltons)

tuple	thulium = Element( 69, "thulium", "Tm", 168.934212*daltons)

tuple	ytterbium = Element( 70, "ytterbium", "Yb", 173.043*daltons)

tuple	lutetium = Element( 71, "lutetium", "Lu", 174.9671*daltons)

tuple	hafnium = Element( 72, "hafnium", "Hf", 178.492*daltons)

tuple	tantalum = Element( 73, "tantalum", "Ta", 180.947882*daltons)

tuple	tungsten = Element( 74, "tungsten", "W", 183.841*daltons)

tuple	rhenium = Element( 75, "rhenium", "Re", 186.2071*daltons)

tuple	osmium = Element( 76, "osmium", "Os", 190.233*daltons)

tuple	iridium = Element( 77, "iridium", "Ir", 192.2173*daltons)

tuple	platinum = Element( 78, "platinum", "Pt", 195.0849*daltons)

tuple	gold = Element( 79, "gold", "Au", 196.9665694*daltons)

tuple	mercury = Element( 80, "mercury", "Hg", 200.592*daltons)

tuple	thallium = Element( 81, "thallium", "Tl", 204.38332*daltons)

tuple	lead = Element( 82, "lead", "Pb", 207.21*daltons)

tuple	bismuth = Element( 83, "bismuth", "Bi", 208.980401*daltons)

tuple	polonium = Element( 84, "polonium", "Po", 209*daltons)

tuple	astatine = Element( 85, "astatine", "At", 210*daltons)

tuple	radon = Element( 86, "radon", "Rn", 222.018*daltons)

tuple	francium = Element( 87, "francium", "Fr", 223*daltons)

tuple	radium = Element( 88, "radium", "Ra", 226*daltons)

tuple	actinium = Element( 89, "actinium", "Ac", 227*daltons)

tuple	thorium = Element( 90, "thorium", "Th", 232.038062*daltons)

tuple	protactinium = Element( 91, "protactinium", "Pa", 231.035882*daltons)

tuple	uranium = Element( 92, "uranium", "U", 238.028913*daltons)

tuple	neptunium = Element( 93, "neptunium", "Np", 237*daltons)

tuple	plutonium = Element( 94, "plutonium", "Pu", 244*daltons)

tuple	americium = Element( 95, "americium", "Am", 243*daltons)

tuple	curium = Element( 96, "curium", "Cm", 247*daltons)

tuple	berkelium = Element( 97, "berkelium", "Bk", 247*daltons)

tuple	californium = Element( 98, "californium", "Cf", 251*daltons)

tuple	einsteinium = Element( 99, "einsteinium", "Es", 252*daltons)

tuple	fermium = Element(100, "fermium", "Fm", 257*daltons)

tuple	mendelevium = Element(101, "mendelevium", "Md", 258*daltons)

tuple	nobelium = Element(102, "nobelium", "No", 259*daltons)

tuple	lawrencium = Element(103, "lawrencium", "Lr", 262*daltons)

tuple	rutherfordium = Element(104, "rutherfordium", "Rf", 261*daltons)

tuple	dubnium = Element(105, "dubnium", "Db", 262*daltons)

tuple	seaborgium = Element(106, "seaborgium", "Sg", 266*daltons)

tuple	bohrium = Element(107, "bohrium", "Bh", 264*daltons)

tuple	hassium = Element(108, "hassium", "Hs", 269*daltons)

tuple	meitnerium = Element(109, "meitnerium", "Mt", 268*daltons)

tuple	darmstadtium = Element(110, "darmstadtium", "Ds", 281*daltons)

tuple	roentgenium = Element(111, "roentgenium", "Rg", 272*daltons)

tuple	ununbium = Element(112, "ununbium", "Uub", 285*daltons)

tuple	ununtrium = Element(113, "ununtrium", "Uut", 284*daltons)

tuple	ununquadium = Element(114, "ununquadium", "Uuq", 289*daltons)

tuple	ununpentium = Element(115, "ununpentium", "Uup", 288*daltons)

tuple	ununhexium = Element(116, "ununhexium", "Uuh", 292*daltons)

	sulphur = sulfur

	aluminium = aluminum

Detailed Description

element.py: Used for managing elements.



This is part of the OpenMM molecular simulation toolkit originating from

Simbios, the NIH National Center for Physics-Based Simulation of

Biological Structures at Stanford, funded under the NIH Roadmap for

Medical Research, grant U54 GM072970. See https://simtk.org.



Portions copyright (c) 2012 Stanford University and the Authors.

Authors: Christopher M. Bruns

Contributors:



Permission is hereby granted, free of charge, to any person obtaining a

copy of this software and associated documentation files (the "Software"),

to deal in the Software without restriction, including without limitation

the rights to use, copy, modify, merge, publish, distribute, sublicense,

and/or sell copies of the Software, and to permit persons to whom the

Software is furnished to do so, subject to the following conditions:



The above copyright notice and this permission notice shall be included in

all copies or substantial portions of the Software.



THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL

THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,

DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR

OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE

USE OR OTHER DEALINGS IN THE SOFTWARE.

Function Documentation

def simtk.openmm.app.element.get_by_symbol ( symbol )

Get the element with a particular chemical symbol.

Variable Documentation

string __author__ = "Christopher M. Bruns"

string __version__ = "1.0"

tuple actinium = Element( 89, "actinium", "Ac", 227*daltons)

aluminium = aluminum

tuple aluminum = Element( 13, "aluminum", "Al", 26.98153868*daltons)

tuple americium = Element( 95, "americium", "Am", 243*daltons)

tuple antimony = Element( 51, "antimony", "Sb", 121.7601*daltons)

tuple argon = Element( 18, "argon", "Ar", 39.9481*daltons)

tuple arsenic = Element( 33, "arsenic", "As", 74.921602*daltons)

tuple astatine = Element( 85, "astatine", "At", 210*daltons)

tuple barium = Element( 56, "barium", "Ba", 137.3277*daltons)

tuple berkelium = Element( 97, "berkelium", "Bk", 247*daltons)

tuple beryllium = Element( 4, "beryllium", "Be", 9.0121823*daltons)

tuple bismuth = Element( 83, "bismuth", "Bi", 208.980401*daltons)

tuple bohrium = Element(107, "bohrium", "Bh", 264*daltons)

tuple boron = Element( 5, "boron", "B", 10.8117*daltons)

tuple bromine = Element( 35, "bromine", "Br", 79.9041*daltons)

tuple cadmium = Element( 48, "cadmium", "Cd", 112.4118*daltons)

tuple calcium = Element( 20, "calcium", "Ca", 40.0784*daltons)

tuple californium = Element( 98, "californium", "Cf", 251*daltons)

tuple carbon = Element( 6, "carbon", "C", 12.01078*daltons)

tuple cerium = Element( 58, "cerium", "Ce", 140.1161*daltons)

tuple cesium = Element( 55, "cesium", "Cs", 132.90545192*daltons)

tuple chlorine = Element( 17, "chlorine", "Cl", 35.4532*daltons)

tuple chromium = Element( 24, "chromium", "Cr", 51.99616*daltons)

tuple cobalt = Element( 27, "cobalt", "Co", 58.9331955*daltons)

tuple copper = Element( 29, "copper", "Cu", 63.5463*daltons)

tuple curium = Element( 96, "curium", "Cm", 247*daltons)

tuple darmstadtium = Element(110, "darmstadtium", "Ds", 281*daltons)

tuple deuterium = Element( 1, "deuterium", "D", 2.01355321270*daltons)

tuple dubnium = Element(105, "dubnium", "Db", 262*daltons)

tuple dysprosium = Element( 66, "dysprosium", "Dy", 162.5001*daltons)

tuple einsteinium = Element( 99, "einsteinium", "Es", 252*daltons)

tuple erbium = Element( 68, "erbium", "Er", 167.2593*daltons)

tuple europium = Element( 63, "europium", "Eu", 151.9641*daltons)

tuple fermium = Element(100, "fermium", "Fm", 257*daltons)

tuple fluorine = Element( 9, "fluorine", "F", 18.99840325*daltons)

tuple francium = Element( 87, "francium", "Fr", 223*daltons)

tuple gadolinium = Element( 64, "gadolinium", "Gd", 157.253*daltons)

tuple gallium = Element( 31, "gallium", "Ga", 69.7231*daltons)

tuple germanium = Element( 32, "germanium", "Ge", 72.641*daltons)

tuple gold = Element( 79, "gold", "Au", 196.9665694*daltons)

tuple hafnium = Element( 72, "hafnium", "Hf", 178.492*daltons)

tuple hassium = Element(108, "hassium", "Hs", 269*daltons)

tuple helium = Element( 2, "helium", "He", 4.003*daltons)

tuple holmium = Element( 67, "holmium", "Ho", 164.930322*daltons)

tuple hydrogen = Element( 1, "hydrogen", "H", 1.007947*daltons)

tuple indium = Element( 49, "indium", "In", 114.8183*daltons)

tuple iodine = Element( 53, "iodine", "I", 126.904473*daltons)

tuple iridium = Element( 77, "iridium", "Ir", 192.2173*daltons)

tuple iron = Element( 26, "iron", "Fe", 55.8452*daltons)

tuple krypton = Element( 36, "krypton", "Kr", 83.7982*daltons)

tuple lanthanum = Element( 57, "lanthanum", "La", 138.905477*daltons)

tuple lawrencium = Element(103, "lawrencium", "Lr", 262*daltons)

tuple lead = Element( 82, "lead", "Pb", 207.21*daltons)

tuple lithium = Element( 3, "lithium", "Li", 6.9412*daltons)

tuple lutetium = Element( 71, "lutetium", "Lu", 174.9671*daltons)

tuple magnesium = Element( 12, "magnesium", "Mg", 24.30506*daltons)

tuple manganese = Element( 25, "manganese", "Mn", 54.9380455*daltons)

tuple meitnerium = Element(109, "meitnerium", "Mt", 268*daltons)

tuple mendelevium = Element(101, "mendelevium", "Md", 258*daltons)

tuple mercury = Element( 80, "mercury", "Hg", 200.592*daltons)

tuple molybdenum = Element( 42, "molybdenum", "Mo", 95.942*daltons)

tuple neodymium = Element( 60, "neodymium", "Nd", 144.2423*daltons)

tuple neon = Element( 10, "neon", "Ne", 20.17976*daltons)

tuple neptunium = Element( 93, "neptunium", "Np", 237*daltons)

tuple nickel = Element( 28, "nickel", "Ni", 58.69342*daltons)

tuple niobium = Element( 41, "niobium", "Nb", 92.906382*daltons)

tuple nitrogen = Element( 7, "nitrogen", "N", 14.00672*daltons)

tuple nobelium = Element(102, "nobelium", "No", 259*daltons)

tuple osmium = Element( 76, "osmium", "Os", 190.233*daltons)

tuple oxygen = Element( 8, "oxygen", "O", 15.99943*daltons)

tuple palladium = Element( 46, "palladium", "Pd", 106.421*daltons)

tuple phosphorus = Element( 15, "phosphorus", "P", 30.9737622*daltons)

tuple platinum = Element( 78, "platinum", "Pt", 195.0849*daltons)

tuple plutonium = Element( 94, "plutonium", "Pu", 244*daltons)

tuple polonium = Element( 84, "polonium", "Po", 209*daltons)

tuple potassium = Element( 19, "potassium", "K", 39.09831*daltons)

tuple praseodymium = Element( 59, "praseodymium", "Pr", 140.907652*daltons)

tuple promethium = Element( 61, "promethium", "Pm", 145*daltons)

tuple protactinium = Element( 91, "protactinium", "Pa", 231.035882*daltons)

tuple radium = Element( 88, "radium", "Ra", 226*daltons)

tuple radon = Element( 86, "radon", "Rn", 222.018*daltons)

tuple rhenium = Element( 75, "rhenium", "Re", 186.2071*daltons)

tuple rhodium = Element( 45, "rhodium", "Rh", 102.905502*daltons)

tuple roentgenium = Element(111, "roentgenium", "Rg", 272*daltons)

tuple rubidium = Element( 37, "rubidium", "Rb", 85.46783*daltons)

tuple ruthenium = Element( 44, "ruthenium", "Ru", 101.072*daltons)

tuple rutherfordium = Element(104, "rutherfordium", "Rf", 261*daltons)

tuple samarium = Element( 62, "samarium", "Sm", 150.362*daltons)

tuple scandium = Element( 21, "scandium", "Sc", 44.9559126*daltons)

tuple seaborgium = Element(106, "seaborgium", "Sg", 266*daltons)

tuple selenium = Element( 34, "selenium", "Se", 78.963*daltons)

tuple silicon = Element( 14, "silicon", "Si", 28.08553*daltons)

tuple silver = Element( 47, "silver", "Ag", 107.86822*daltons)

tuple sodium = Element( 11, "sodium", "Na", 22.989769282*daltons)

tuple strontium = Element( 38, "strontium", "Sr", 87.621*daltons)

tuple sulfur = Element( 16, "sulfur", "S", 32.0655*daltons)

sulphur = sulfur

tuple tantalum = Element( 73, "tantalum", "Ta", 180.947882*daltons)

tuple technetium = Element( 43, "technetium", "Tc", 98*daltons)

tuple tellurium = Element( 52, "tellurium", "Te", 127.603*daltons)

tuple terbium = Element( 65, "terbium", "Tb", 158.925352*daltons)

tuple thallium = Element( 81, "thallium", "Tl", 204.38332*daltons)

tuple thorium = Element( 90, "thorium", "Th", 232.038062*daltons)

tuple thulium = Element( 69, "thulium", "Tm", 168.934212*daltons)

tuple tin = Element( 50, "tin", "Sn", 118.7107*daltons)

tuple titanium = Element( 22, "titanium", "Ti", 47.8671*daltons)

tuple tungsten = Element( 74, "tungsten", "W", 183.841*daltons)

tuple ununbium = Element(112, "ununbium", "Uub", 285*daltons)

tuple ununhexium = Element(116, "ununhexium", "Uuh", 292*daltons)

tuple ununpentium = Element(115, "ununpentium", "Uup", 288*daltons)

tuple ununquadium = Element(114, "ununquadium", "Uuq", 289*daltons)

tuple ununtrium = Element(113, "ununtrium", "Uut", 284*daltons)

tuple uranium = Element( 92, "uranium", "U", 238.028913*daltons)

tuple vanadium = Element( 23, "vanadium", "V", 50.94151*daltons)

tuple xenon = Element( 54, "xenon", "Xe", 131.2936*daltons)

tuple ytterbium = Element( 70, "ytterbium", "Yb", 173.043*daltons)

tuple yttrium = Element( 39, "yttrium", "Y", 88.905852*daltons)

tuple zinc = Element( 30, "zinc", "Zn", 65.4094*daltons)

tuple zirconium = Element( 40, "zirconium", "Zr", 91.2242*daltons)

Classes

Functions

Variables

Detailed Description

Function Documentation

Variable Documentation