|
OpenMM
|
|
OpenMM
|
Classes | |
| class | Element |
| An Element represents a chemical element. More... | |
Functions | |
| def | get_by_symbol |
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 | |
| def simtk.openmm.app.element.get_by_symbol | ( | symbol | ) |
| 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) |
1.8.5 
