#
# The high-throughput toolkit (httk)
# Copyright (C) 2012-2015 Rickard Armiento
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.
#
# This program 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 Affero General Public License for more details.
#
# You should have received a copy of the GNU Affero General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
symbols = ['0', 'H', 'He', 'Li', 'Be', 'B', 'C', 'N', 'O', 'F', 'Ne', 'Na', 'Mg', 'Al', 'Si', 'P', 'S', 'Cl', 'Ar', 'K', 'Ca', 'Sc', 'Ti', 'V', 'Cr', 'Mn', 'Fe', 'Co',
'Ni', 'Cu', 'Zn', 'Ga', 'Ge', 'As', 'Se', 'Br', 'Kr', 'Rb', 'Sr', 'Y', 'Zr', 'Nb', 'Mo', 'Tc', 'Ru', 'Rh', 'Pd', 'Ag', 'Cd', 'In', 'Sn', 'Sb', 'Te',
'I', 'Xe', 'Cs', 'Ba', 'La', 'Ce', 'Pr', 'Nd', 'Pm', 'Sm', 'Eu', 'Gd', 'Tb', 'Dy', 'Ho', 'Er', 'Tm', 'Yb', 'Lu', 'Hf', 'Ta', 'W', 'Re', 'Os', 'Ir',
'Pt', 'Au', 'Hg', 'Tl', 'Pb', 'Bi', 'Po', 'At', 'Rn', 'Fr', 'Ra', 'Ac', 'Th', 'Pa', 'U', 'Np', 'Pu', 'Am', 'Cm', 'Bk', 'Cf', 'Es', 'Fm', 'Md', 'No',
'Lr', 'Rf', 'Db', 'Sg', 'Bh', 'Hs', 'Mt', 'Ds', 'Rg', 'Cn', 'Uut', 'Uuq', 'Uup', 'Uuh', 'Uus', 'Uuo']
names = ['0', 'Hydrogen', 'Helium', 'Lithium', 'Beryllium', 'Boron', 'Carbon', 'Nitrogen', 'Oxygen', 'Fluorine', 'Neon', 'Sodium', 'Magnesium', 'Aluminum,',
'Silicon', 'Phosphorus', 'Sulfur', 'Chlorine', 'Argon', 'Potassium', 'Calcium', 'Scandium', 'Titanium', 'Vanadium', 'Chromium', 'Manganese',
'Iron', 'Cobalt', 'Nickel', 'Copper', 'Zinc', 'Gallium', 'Germanium', 'Arsenic', 'Selenium', 'Bromine', 'Krypton', 'Rubidium', 'Strontium',
'Yttrium', 'Zirconium', 'Niobium', 'Molybdenum', 'Technetium', 'Ruthenium', 'Rhodium', 'Palladium', 'Silver', 'Cadmium', 'Indium', 'Tin',
'Antimony', 'Tellurium', 'Iodine', 'Xenon', 'Cesium', 'Barium', 'Lanthanum', 'Cerium', 'Praseodymium', 'Neodymium', 'Promethium', 'Samarium',
'Europium', 'Gadolinium', 'Terbium', 'Dysprosium', 'Holmium', 'Erbium', 'Thulium', 'Ytterbium', 'Lutetium', 'Hafnium', 'Tantalum', 'Tungsten',
'Rhenium', 'Osmium', 'Iridium', 'Platinum', 'Gold', 'Mercury', 'Thallium', 'Lead', 'Bismuth', 'Polonium', 'Astatine', 'Radon', 'Francium', 'Radium',
'Actinium', 'Thorium', 'Protactinium', 'Uranium', 'Neptunium', 'Plutonium', 'Americium', 'Curium', 'Berkelium', 'Californium', 'Einsteinium',
'Fermium', 'Mendelevium', 'Nobelium', 'Lawrencium', 'Rutherfordium', 'Dubnium', 'Seaborgium', 'Bohrium', 'Hassium', 'Meitnerium', 'Darmstadtium',
'Roentgenium', 'Copernicium', 'Ununtrium', 'Ununquadium', 'Ununpentium', 'Ununhexium', 'Ununseptium', 'Ununoctium']
numbers = {'H': 1, 'He': 2, 'Li': 3, 'Be': 4, 'B': 5, 'C': 6, 'N': 7, 'O': 8, 'F': 9, 'Ne': 10, 'Na': 11, 'Mg': 12, 'Al': 13, 'Si': 14, 'P': 15, 'S': 16, 'Cl': 17, 'Ar': 18,
'K': 19, 'Ca': 20, 'Sc': 21, 'Ti': 22, 'V': 23, 'Cr': 24, 'Mn': 25, 'Fe': 26, 'Co': 27, 'Ni': 28, 'Cu': 29, 'Zn': 30, 'Ga': 31, 'Ge': 32, 'As': 33, 'Se': 34,
'Br': 35, 'Kr': 36, 'Rb': 37, 'Sr': 38, 'Y': 39, 'Zr': 40, 'Nb': 41, 'Mo': 42, 'Tc': 43, 'Ru': 44, 'Rh': 45, 'Pd': 46, 'Ag': 47, 'Cd': 48, 'In': 49, 'Sn': 50,
'Sb': 51, 'Te': 52, 'I': 53, 'Xe': 54, 'Cs': 55, 'Ba': 56, 'La': 57, 'Ce': 58, 'Pr': 59, 'Nd': 60, 'Pm': 61, 'Sm': 62, 'Eu': 63, 'Gd': 64, 'Tb': 65, 'Dy': 66,
'Ho': 67, 'Er': 68, 'Tm': 69, 'Yb': 70, 'Lu': 71, 'Hf': 72, 'Ta': 73, 'W': 74, 'Re': 75, 'Os': 76, 'Ir': 77, 'Pt': 78, 'Au': 79, 'Hg': 80, 'Tl': 81, 'Pb': 82,
'Bi': 83, 'Po': 84, 'At': 85, 'Rn': 86, 'Fr': 87, 'Ra': 88, 'Ac': 89, 'Th': 90, 'Pa': 91, 'U': 92, 'Np': 93, 'Pu': 94, 'Am': 95, 'Cm': 96, 'Bk': 97, 'Cf': 98,
'Es': 99, 'Fm': 100, 'Md': 101, 'No': 102, 'Lr': 103, 'Rf': 104, 'Db': 105, 'Sg': 106, 'Bh': 107, 'Hs': 108, 'Mt': 109, 'Ds': 110, 'Rg': 111, 'Cn': 112,
'Uut': 113, 'Uuq': 114, 'Uup': 115, 'Uuh': 116, 'Uus': 117, 'Uuo': 118}
#TODO: This table is not correct, lift data from http://en.wikipedia.org/wiki/List_of_elements_by_stability_of_isotopes
most_common_masses = {'H': 1, 'He': 2, 'Li': 3, 'Be': 4, 'B': 5, 'C': 6, 'N': 7, 'O': 8, 'F': 9, 'Ne': 10, 'Na': 11, 'Mg': 12, 'Al': 13, 'Si': 14, 'P': 15, 'S': 16, 'Cl': 17, 'Ar': 18,
'K': 19, 'Ca': 20, 'Sc': 21, 'Ti': 22, 'V': 23, 'Cr': 24, 'Mn': 25, 'Fe': 26, 'Co': 27, 'Ni': 28, 'Cu': 29, 'Zn': 30, 'Ga': 31, 'Ge': 32, 'As': 33, 'Se': 34,
'Br': 35, 'Kr': 36, 'Rb': 37, 'Sr': 38, 'Y': 39, 'Zr': 40, 'Nb': 41, 'Mo': 42, 'Tc': 43, 'Ru': 44, 'Rh': 45, 'Pd': 46, 'Ag': 47, 'Cd': 48, 'In': 49, 'Sn': 50,
'Sb': 51, 'Te': 52, 'I': 53, 'Xe': 54, 'Cs': 55, 'Ba': 56, 'La': 57, 'Ce': 58, 'Pr': 59, 'Nd': 60, 'Pm': 61, 'Sm': 62, 'Eu': 63, 'Gd': 64, 'Tb': 65, 'Dy': 66,
'Ho': 67, 'Er': 68, 'Tm': 69, 'Yb': 70, 'Lu': 71, 'Hf': 72, 'Ta': 73, 'W': 74, 'Re': 75, 'Os': 76, 'Ir': 77, 'Pt': 78, 'Au': 79, 'Hg': 80, 'Tl': 81, 'Pb': 82,
'Bi': 83, 'Po': 84, 'At': 85, 'Rn': 86, 'Fr': 87, 'Ra': 88, 'Ac': 89, 'Th': 90, 'Pa': 91, 'U': 92, 'Np': 93, 'Pu': 94, 'Am': 95, 'Cm': 96, 'Bk': 97, 'Cf': 98,
'Es': 99, 'Fm': 100, 'Md': 101, 'No': 102, 'Lr': 103, 'Rf': 104, 'Db': 105, 'Sg': 106, 'Bh': 107, 'Hs': 108, 'Mt': 109, 'Ds': 110, 'Rg': 111, 'Cn': 112,
'Uut': 113, 'Uuq': 114, 'Uup': 115, 'Uuh': 116, 'Uus': 117, 'Uuo': 118}
#masses=[0.0]*118
[docs]def atomic_symbol(parse):
"""
Helper function to produce an atomic symbol if you have some kind of identifier, but does not know what it is.
"""
try:
return parse.to_atomic_symbol()
except AttributeError:
pass
if isinstance(parse, int):
return symbols[parse]
if isinstance(parse, (list, tuple)):
return atomic_symbol(parse[0])
s = str(parse)
if s in symbols:
return s
if s in names:
return symbols[names.index(s)]
if s == 'D':
return 'D'
raise Exception("Do not know how to parse input: "+str(parse))
[docs]def atomic_number(parse):
"""
Helper function to produce an atomic symbol if you have some kind of identifier, but does not know what it is.
"""
try:
return parse.to_atomic_number()
except Exception:
pass
if isinstance(parse, int):
return parse
if isinstance(parse, (list, tuple)):
return atomic_number(parse[0])
s = str(parse)
if s in symbols:
return symbols.index(s)
if s in names:
return names.index(s)
raise Exception("Do not know how to parse input: "+str(parse))
[docs]def atomic_number_isotope(parse):
"""
Helper function to produce an atomic symbol if you have some kind of identifier, but does not know what it is.
"""
try:
return parse.to_atomic_number()
except AttributeError:
pass
if isinstance(parse, int):
return parse
if isinstance(parse, (list, tuple)):
return atomic_number(parse[0])
s = str(parse)
if s in symbols:
return symbols.index(s)
if s in names:
return names.index(s)
if s == 'D':
return 1
raise Exception("Do not know how to parse input: ", str(parse))
[docs]def most_common_mass(parse):
parsed = atomic_number(parse)
raise Exception("periodictable.most_common_mass: not implemented yet")
return most_common_masses[parsed]