How to use the mdtraj.core.element.Element function in mdtraj

To help you get started, we’ve selected a few mdtraj examples, based on popular ways it is used in public projects.

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mdtraj / mdtraj / mdtraj / core / element.py View on Github

lutetium =       Element( 71,"lutetium","Lu", 174.9671, 0.2)
hafnium =        Element( 72,"hafnium","Hf", 178.492, 0.2)
tantalum =       Element( 73,"tantalum","Ta", 180.947882, 0.2)
tungsten =       Element( 74,"tungsten","W", 183.841, 0.2)
rhenium =        Element( 75,"rhenium","Re", 186.2071, 0.2)
osmium =         Element( 76,"osmium","Os", 190.233, 0.2)
iridium =        Element( 77,"iridium","Ir", 192.2173, 0.2)
platinum =       Element( 78,"platinum","Pt", 195.0849, 0.172)
gold =           Element( 79,"gold","Au", 196.9665694, 0.166)
mercury =        Element( 80,"mercury","Hg", 200.592, 0.155)
thallium =       Element( 81,"thallium","Tl", 204.38332, 0.196)
lead =           Element( 82,"lead","Pb", 207.21, 0.202)
bismuth =        Element( 83,"bismuth","Bi", 208.980401, 0.2)
polonium =       Element( 84,"polonium","Po", 209, 0.2)
astatine =       Element( 85,"astatine","At", 210, 0.2)
radon =          Element( 86,"radon","Rn", 222.018, 0.2)
francium =       Element( 87,"francium","Fr", 223, 0.2)
radium =         Element( 88,"radium","Ra", 226, 0.2)
actinium =       Element( 89,"actinium","Ac", 227, 0.2)
thorium =        Element( 90,"thorium","Th", 232.038062, 0.2)
protactinium =   Element( 91,"protactinium","Pa", 231.035882, 0.2)
uranium =        Element( 92,"uranium","U", 238.028913, 0.186)
neptunium =      Element( 93,"neptunium","Np", 237, 0.2)
plutonium =      Element( 94,"plutonium","Pu", 244, 0.2)
americium =      Element( 95,"americium","Am", 243, 0.2)
curium =         Element( 96,"curium","Cm", 247, 0.2)
berkelium =      Element( 97,"berkelium","Bk", 247, 0.2)
californium =    Element( 98,"californium","Cf", 251, 0.2)
einsteinium =    Element( 99,"einsteinium","Es", 252, 0.2)
fermium =        Element(100,"fermium","Fm", 257, 0.2)
mendelevium =    Element(101,"mendelevium","Md", 258, 0.2)
nobelium =       Element(102,"nobelium","No", 259, 0.2)

mdtraj / mdtraj / mdtraj / core / element.py View on Github

hydrogen =       Element(  1,"hydrogen","H", 1.007947, 0.12)
deuterium =      Element(  1,"deuterium","D", 2.0135532127, 0.12)
helium =         Element(  2,"helium","He", 4.003, 0.14)
lithium =        Element(  3,"lithium","Li", 6.9412, 0.182)
beryllium =      Element(  4,"beryllium","Be", 9.0121823, 0.2)
boron =          Element(  5,"boron","B", 10.8117, 0.2)
carbon =         Element(  6,"carbon","C", 12.01078, 0.17)
nitrogen =       Element(  7,"nitrogen","N", 14.00672, 0.155)
oxygen =         Element(  8,"oxygen","O", 15.99943, 0.152)
fluorine =       Element(  9,"fluorine","F", 18.99840325, 0.147)
neon =           Element( 10,"neon","Ne", 20.17976, 0.154)
sodium =         Element( 11,"sodium","Na", 22.989769282, 0.136)
magnesium =      Element( 12,"magnesium","Mg", 24.30506, 0.118)
aluminum =       Element( 13,"aluminum","Al", 26.98153868, 0.2)
silicon =        Element( 14,"silicon","Si", 28.08553, 0.21)
phosphorus =     Element( 15,"phosphorus","P", 30.9737622, 0.18)
sulfur =         Element( 16,"sulfur","S", 32.0655, 0.18)
chlorine =       Element( 17,"chlorine","Cl", 35.4532, 0.227)
argon =          Element( 18,"argon","Ar", 39.9481, 0.188)
potassium =      Element( 19,"potassium","K", 39.09831, 0.176)
calcium =        Element( 20,"calcium","Ca", 40.0784, 0.137)
scandium =       Element( 21,"scandium","Sc", 44.9559126, 0.2)
titanium =       Element( 22,"titanium","Ti", 47.8671, 0.2)
vanadium =       Element( 23,"vanadium","V", 50.94151, 0.2)
chromium =       Element( 24,"chromium","Cr", 51.99616, 0.2)
manganese =      Element( 25,"manganese","Mn", 54.9380455, 0.2)
iron =           Element( 26,"iron","Fe", 55.8452, 0.2)
cobalt =         Element( 27,"cobalt","Co", 58.9331955, 0.2)
nickel =         Element( 28,"nickel","Ni", 58.69342, 0.163)
copper =         Element( 29,"copper","Cu", 63.5463, 0.14)
zinc =           Element( 30,"zinc","Zn", 65.4094, 0.139)
gallium =        Element( 31,"gallium","Ga", 69.7231, 0.107)

mdtraj / mdtraj / mdtraj / core / element.py View on Github

hafnium =        Element( 72,"hafnium","Hf", 178.492, 0.2)
tantalum =       Element( 73,"tantalum","Ta", 180.947882, 0.2)
tungsten =       Element( 74,"tungsten","W", 183.841, 0.2)
rhenium =        Element( 75,"rhenium","Re", 186.2071, 0.2)
osmium =         Element( 76,"osmium","Os", 190.233, 0.2)
iridium =        Element( 77,"iridium","Ir", 192.2173, 0.2)
platinum =       Element( 78,"platinum","Pt", 195.0849, 0.172)
gold =           Element( 79,"gold","Au", 196.9665694, 0.166)
mercury =        Element( 80,"mercury","Hg", 200.592, 0.155)
thallium =       Element( 81,"thallium","Tl", 204.38332, 0.196)
lead =           Element( 82,"lead","Pb", 207.21, 0.202)
bismuth =        Element( 83,"bismuth","Bi", 208.980401, 0.2)
polonium =       Element( 84,"polonium","Po", 209, 0.2)
astatine =       Element( 85,"astatine","At", 210, 0.2)
radon =          Element( 86,"radon","Rn", 222.018, 0.2)
francium =       Element( 87,"francium","Fr", 223, 0.2)
radium =         Element( 88,"radium","Ra", 226, 0.2)
actinium =       Element( 89,"actinium","Ac", 227, 0.2)
thorium =        Element( 90,"thorium","Th", 232.038062, 0.2)
protactinium =   Element( 91,"protactinium","Pa", 231.035882, 0.2)
uranium =        Element( 92,"uranium","U", 238.028913, 0.186)
neptunium =      Element( 93,"neptunium","Np", 237, 0.2)
plutonium =      Element( 94,"plutonium","Pu", 244, 0.2)
americium =      Element( 95,"americium","Am", 243, 0.2)
curium =         Element( 96,"curium","Cm", 247, 0.2)
berkelium =      Element( 97,"berkelium","Bk", 247, 0.2)
californium =    Element( 98,"californium","Cf", 251, 0.2)
einsteinium =    Element( 99,"einsteinium","Es", 252, 0.2)
fermium =        Element(100,"fermium","Fm", 257, 0.2)
mendelevium =    Element(101,"mendelevium","Md", 258, 0.2)
nobelium =       Element(102,"nobelium","No", 259, 0.2)
lawrencium =     Element(103,"lawrencium","Lr", 262, 0.2)

mdtraj / mdtraj / mdtraj / core / element.py View on Github

thorium =        Element( 90,"thorium","Th", 232.038062, 0.2)
protactinium =   Element( 91,"protactinium","Pa", 231.035882, 0.2)
uranium =        Element( 92,"uranium","U", 238.028913, 0.186)
neptunium =      Element( 93,"neptunium","Np", 237, 0.2)
plutonium =      Element( 94,"plutonium","Pu", 244, 0.2)
americium =      Element( 95,"americium","Am", 243, 0.2)
curium =         Element( 96,"curium","Cm", 247, 0.2)
berkelium =      Element( 97,"berkelium","Bk", 247, 0.2)
californium =    Element( 98,"californium","Cf", 251, 0.2)
einsteinium =    Element( 99,"einsteinium","Es", 252, 0.2)
fermium =        Element(100,"fermium","Fm", 257, 0.2)
mendelevium =    Element(101,"mendelevium","Md", 258, 0.2)
nobelium =       Element(102,"nobelium","No", 259, 0.2)
lawrencium =     Element(103,"lawrencium","Lr", 262, 0.2)
rutherfordium =  Element(104,"rutherfordium","Rf", 261, 0.2)
dubnium =        Element(105,"dubnium","Db", 262, 0.2)
seaborgium =     Element(106,"seaborgium","Sg", 266, 0.2)
bohrium =        Element(107,"bohrium","Bh", 264, 0.2)
hassium =        Element(108,"hassium","Hs", 269, 0.2)
meitnerium =     Element(109,"meitnerium","Mt", 268, 0.2)
darmstadtium =   Element(110,"darmstadtium","Ds", 281, 0.2)
roentgenium =    Element(111,"roentgenium","Rg", 272, 0.2)
ununbium =       Element(112,"ununbium","Uub", 285, 0.2)
ununtrium =      Element(113,"ununtrium","Uut", 284, 0.2)
ununquadium =    Element(114,"ununquadium","Uuq", 289, 0.2)
ununpentium =    Element(115,"ununpentium","Uup", 288, 0.2)
ununhexium =     Element(116,"ununhexium","Uuh", 292, 0.2)

# Aliases to recognize common alternative spellings. Both the '==' and 'is'
# relational operators will work with any chosen name
sulphur = sulfur
aluminium = aluminum

mdtraj / mdtraj / mdtraj / core / element.py View on Github

argon =          Element( 18,"argon","Ar", 39.9481, 0.188)
potassium =      Element( 19,"potassium","K", 39.09831, 0.176)
calcium =        Element( 20,"calcium","Ca", 40.0784, 0.137)
scandium =       Element( 21,"scandium","Sc", 44.9559126, 0.2)
titanium =       Element( 22,"titanium","Ti", 47.8671, 0.2)
vanadium =       Element( 23,"vanadium","V", 50.94151, 0.2)
chromium =       Element( 24,"chromium","Cr", 51.99616, 0.2)
manganese =      Element( 25,"manganese","Mn", 54.9380455, 0.2)
iron =           Element( 26,"iron","Fe", 55.8452, 0.2)
cobalt =         Element( 27,"cobalt","Co", 58.9331955, 0.2)
nickel =         Element( 28,"nickel","Ni", 58.69342, 0.163)
copper =         Element( 29,"copper","Cu", 63.5463, 0.14)
zinc =           Element( 30,"zinc","Zn", 65.4094, 0.139)
gallium =        Element( 31,"gallium","Ga", 69.7231, 0.107)
germanium =      Element( 32,"germanium","Ge", 72.641, 0.2)
arsenic =        Element( 33,"arsenic","As", 74.921602, 0.185)
selenium =       Element( 34,"selenium","Se", 78.963, 0.19)
bromine =        Element( 35,"bromine","Br", 79.9041, 0.185)
krypton =        Element( 36,"krypton","Kr", 83.7982, 0.202)
rubidium =       Element( 37,"rubidium","Rb", 85.46783, 0.2)
strontium =      Element( 38,"strontium","Sr", 87.621, 0.2)
yttrium =        Element( 39,"yttrium","Y", 88.905852, 0.2)
zirconium =      Element( 40,"zirconium","Zr", 91.2242, 0.2)
niobium =        Element( 41,"niobium","Nb", 92.906382, 0.2)
molybdenum =     Element( 42,"molybdenum","Mo", 95.942, 0.2)
technetium =     Element( 43,"technetium","Tc", 98, 0.2)
ruthenium =      Element( 44,"ruthenium","Ru", 101.072, 0.2)
rhodium =        Element( 45,"rhodium","Rh", 102.905502, 0.2)
palladium =      Element( 46,"palladium","Pd", 106.421, 0.163)
silver =         Element( 47,"silver","Ag", 107.86822, 0.172)
cadmium =        Element( 48,"cadmium","Cd", 112.4118, 0.158)
indium =         Element( 49,"indium","In", 114.8183, 0.193)

mdtraj / mdtraj / mdtraj / core / element.py View on Github

nitrogen =       Element(  7,"nitrogen","N", 14.00672, 0.155)
oxygen =         Element(  8,"oxygen","O", 15.99943, 0.152)
fluorine =       Element(  9,"fluorine","F", 18.99840325, 0.147)
neon =           Element( 10,"neon","Ne", 20.17976, 0.154)
sodium =         Element( 11,"sodium","Na", 22.989769282, 0.136)
magnesium =      Element( 12,"magnesium","Mg", 24.30506, 0.118)
aluminum =       Element( 13,"aluminum","Al", 26.98153868, 0.2)
silicon =        Element( 14,"silicon","Si", 28.08553, 0.21)
phosphorus =     Element( 15,"phosphorus","P", 30.9737622, 0.18)
sulfur =         Element( 16,"sulfur","S", 32.0655, 0.18)
chlorine =       Element( 17,"chlorine","Cl", 35.4532, 0.227)
argon =          Element( 18,"argon","Ar", 39.9481, 0.188)
potassium =      Element( 19,"potassium","K", 39.09831, 0.176)
calcium =        Element( 20,"calcium","Ca", 40.0784, 0.137)
scandium =       Element( 21,"scandium","Sc", 44.9559126, 0.2)
titanium =       Element( 22,"titanium","Ti", 47.8671, 0.2)
vanadium =       Element( 23,"vanadium","V", 50.94151, 0.2)
chromium =       Element( 24,"chromium","Cr", 51.99616, 0.2)
manganese =      Element( 25,"manganese","Mn", 54.9380455, 0.2)
iron =           Element( 26,"iron","Fe", 55.8452, 0.2)
cobalt =         Element( 27,"cobalt","Co", 58.9331955, 0.2)
nickel =         Element( 28,"nickel","Ni", 58.69342, 0.163)
copper =         Element( 29,"copper","Cu", 63.5463, 0.14)
zinc =           Element( 30,"zinc","Zn", 65.4094, 0.139)
gallium =        Element( 31,"gallium","Ga", 69.7231, 0.107)
germanium =      Element( 32,"germanium","Ge", 72.641, 0.2)
arsenic =        Element( 33,"arsenic","As", 74.921602, 0.185)
selenium =       Element( 34,"selenium","Se", 78.963, 0.19)
bromine =        Element( 35,"bromine","Br", 79.9041, 0.185)
krypton =        Element( 36,"krypton","Kr", 83.7982, 0.202)
rubidium =       Element( 37,"rubidium","Rb", 85.46783, 0.2)
strontium =      Element( 38,"strontium","Sr", 87.621, 0.2)

mdtraj / mdtraj / mdtraj / core / element.py View on Github

nickel =         Element( 28,"nickel","Ni", 58.69342, 0.163)
copper =         Element( 29,"copper","Cu", 63.5463, 0.14)
zinc =           Element( 30,"zinc","Zn", 65.4094, 0.139)
gallium =        Element( 31,"gallium","Ga", 69.7231, 0.107)
germanium =      Element( 32,"germanium","Ge", 72.641, 0.2)
arsenic =        Element( 33,"arsenic","As", 74.921602, 0.185)
selenium =       Element( 34,"selenium","Se", 78.963, 0.19)
bromine =        Element( 35,"bromine","Br", 79.9041, 0.185)
krypton =        Element( 36,"krypton","Kr", 83.7982, 0.202)
rubidium =       Element( 37,"rubidium","Rb", 85.46783, 0.2)
strontium =      Element( 38,"strontium","Sr", 87.621, 0.2)
yttrium =        Element( 39,"yttrium","Y", 88.905852, 0.2)
zirconium =      Element( 40,"zirconium","Zr", 91.2242, 0.2)
niobium =        Element( 41,"niobium","Nb", 92.906382, 0.2)
molybdenum =     Element( 42,"molybdenum","Mo", 95.942, 0.2)
technetium =     Element( 43,"technetium","Tc", 98, 0.2)
ruthenium =      Element( 44,"ruthenium","Ru", 101.072, 0.2)
rhodium =        Element( 45,"rhodium","Rh", 102.905502, 0.2)
palladium =      Element( 46,"palladium","Pd", 106.421, 0.163)
silver =         Element( 47,"silver","Ag", 107.86822, 0.172)
cadmium =        Element( 48,"cadmium","Cd", 112.4118, 0.158)
indium =         Element( 49,"indium","In", 114.8183, 0.193)
tin =            Element( 50,"tin","Sn", 118.7107, 0.217)
antimony =       Element( 51,"antimony","Sb", 121.7601, 0.2)
tellurium =      Element( 52,"tellurium","Te", 127.603, 0.206)
iodine =         Element( 53,"iodine","I", 126.904473, 0.198)
xenon =          Element( 54,"xenon","Xe", 131.2936, 0.216)
cesium =         Element( 55,"cesium","Cs", 132.90545192, 0.21)
barium =         Element( 56,"barium","Ba", 137.3277, 0.2)
lanthanum =      Element( 57,"lanthanum","La", 138.905477, 0.2)
cerium =         Element( 58,"cerium","Ce", 140.1161, 0.2)
praseodymium =   Element( 59,"praseodymium","Pr", 140.907652, 0.2)

mdtraj / mdtraj / mdtraj / formats / arc.py View on Github

atom_names[i] = s[1]
        bond_partners[i] = [int(x) for x in s[6:]]
        coords[i,:] = [float(s[pos]) for pos in [2, 3, 4]]
        # Now see if we have to build a topology
        if self.topology is None:
            self.topology = top = Topology()
            chain = top.add_chain()                # only 1 chain
            res = top.add_residue('RES', chain, 1) # only 1 residue
            for at in atom_names:
                # First get the element. Try for common 2-letter elements, then
                # use the first letter only (default to None if I can't find it)
                if at[:2].upper() in ('NA', 'CL', 'MG'):
                    elem = Element.getBySymbol(at[:2])
                else:
                    try:
                        elem = Element.getBySymbol(at[0])
                    except KeyError:
                        elem = virtual
                top.add_atom(at, elem, res)
            # Now add the bonds
            atoms = list(top.atoms)
            for i, bonds in enumerate(bond_partners):
                me = atoms[i]
                for b in bonds:
                    b -= 1
                    if b &lt; i: continue
                    it = atoms[b]
                    top.add_bond(me, it)

        self._frame_index += 1
        return coords, cell_lengths, cell_angles

mdtraj / mdtraj / mdtraj / core / element.py View on Github

phosphorus =     Element( 15,"phosphorus","P", 30.9737622, 0.18)
sulfur =         Element( 16,"sulfur","S", 32.0655, 0.18)
chlorine =       Element( 17,"chlorine","Cl", 35.4532, 0.227)
argon =          Element( 18,"argon","Ar", 39.9481, 0.188)
potassium =      Element( 19,"potassium","K", 39.09831, 0.176)
calcium =        Element( 20,"calcium","Ca", 40.0784, 0.137)
scandium =       Element( 21,"scandium","Sc", 44.9559126, 0.2)
titanium =       Element( 22,"titanium","Ti", 47.8671, 0.2)
vanadium =       Element( 23,"vanadium","V", 50.94151, 0.2)
chromium =       Element( 24,"chromium","Cr", 51.99616, 0.2)
manganese =      Element( 25,"manganese","Mn", 54.9380455, 0.2)
iron =           Element( 26,"iron","Fe", 55.8452, 0.2)
cobalt =         Element( 27,"cobalt","Co", 58.9331955, 0.2)
nickel =         Element( 28,"nickel","Ni", 58.69342, 0.163)
copper =         Element( 29,"copper","Cu", 63.5463, 0.14)
zinc =           Element( 30,"zinc","Zn", 65.4094, 0.139)
gallium =        Element( 31,"gallium","Ga", 69.7231, 0.107)
germanium =      Element( 32,"germanium","Ge", 72.641, 0.2)
arsenic =        Element( 33,"arsenic","As", 74.921602, 0.185)
selenium =       Element( 34,"selenium","Se", 78.963, 0.19)
bromine =        Element( 35,"bromine","Br", 79.9041, 0.185)
krypton =        Element( 36,"krypton","Kr", 83.7982, 0.202)
rubidium =       Element( 37,"rubidium","Rb", 85.46783, 0.2)
strontium =      Element( 38,"strontium","Sr", 87.621, 0.2)
yttrium =        Element( 39,"yttrium","Y", 88.905852, 0.2)
zirconium =      Element( 40,"zirconium","Zr", 91.2242, 0.2)
niobium =        Element( 41,"niobium","Nb", 92.906382, 0.2)
molybdenum =     Element( 42,"molybdenum","Mo", 95.942, 0.2)
technetium =     Element( 43,"technetium","Tc", 98, 0.2)
ruthenium =      Element( 44,"ruthenium","Ru", 101.072, 0.2)
rhodium =        Element( 45,"rhodium","Rh", 102.905502, 0.2)
palladium =      Element( 46,"palladium","Pd", 106.421, 0.163)

mdtraj / mdtraj / mdtraj / core / element.py View on Github

boron =          Element(  5,"boron","B", 10.8117, 0.2)
carbon =         Element(  6,"carbon","C", 12.01078, 0.17)
nitrogen =       Element(  7,"nitrogen","N", 14.00672, 0.155)
oxygen =         Element(  8,"oxygen","O", 15.99943, 0.152)
fluorine =       Element(  9,"fluorine","F", 18.99840325, 0.147)
neon =           Element( 10,"neon","Ne", 20.17976, 0.154)
sodium =         Element( 11,"sodium","Na", 22.989769282, 0.136)
magnesium =      Element( 12,"magnesium","Mg", 24.30506, 0.118)
aluminum =       Element( 13,"aluminum","Al", 26.98153868, 0.2)
silicon =        Element( 14,"silicon","Si", 28.08553, 0.21)
phosphorus =     Element( 15,"phosphorus","P", 30.9737622, 0.18)
sulfur =         Element( 16,"sulfur","S", 32.0655, 0.18)
chlorine =       Element( 17,"chlorine","Cl", 35.4532, 0.227)
argon =          Element( 18,"argon","Ar", 39.9481, 0.188)
potassium =      Element( 19,"potassium","K", 39.09831, 0.176)
calcium =        Element( 20,"calcium","Ca", 40.0784, 0.137)
scandium =       Element( 21,"scandium","Sc", 44.9559126, 0.2)
titanium =       Element( 22,"titanium","Ti", 47.8671, 0.2)
vanadium =       Element( 23,"vanadium","V", 50.94151, 0.2)
chromium =       Element( 24,"chromium","Cr", 51.99616, 0.2)
manganese =      Element( 25,"manganese","Mn", 54.9380455, 0.2)
iron =           Element( 26,"iron","Fe", 55.8452, 0.2)
cobalt =         Element( 27,"cobalt","Co", 58.9331955, 0.2)
nickel =         Element( 28,"nickel","Ni", 58.69342, 0.163)
copper =         Element( 29,"copper","Cu", 63.5463, 0.14)
zinc =           Element( 30,"zinc","Zn", 65.4094, 0.139)
gallium =        Element( 31,"gallium","Ga", 69.7231, 0.107)
germanium =      Element( 32,"germanium","Ge", 72.641, 0.2)
arsenic =        Element( 33,"arsenic","As", 74.921602, 0.185)
selenium =       Element( 34,"selenium","Se", 78.963, 0.19)
bromine =        Element( 35,"bromine","Br", 79.9041, 0.185)
krypton =        Element( 36,"krypton","Kr", 83.7982, 0.202)

How to use the mdtraj.core.element.Element function in mdtraj

To help you get started, we’ve selected a few mdtraj examples, based on popular ways it is used in public projects.

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