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simtk.openmm.app.element Namespace Reference

## 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)