#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (C) 2014 The ProteinDF development team.
# see also AUTHORS and README if provided.
#
# This file is a part of the ProteinDF software package.
#
# The ProteinDF is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# The ProteinDF 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 General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with ProteinDF. If not, see <http://www.gnu.org/licenses/>.
import logging
logger = logging.getLogger(__name__)
[docs]
class PeriodicTable(object):
"""
>>> PeriodicTable.get_symbol(1)
'H'
>>> PeriodicTable.get_symbol(20)
'Ca'
>>> PeriodicTable.get_atomic_number('C')
6
>>> PeriodicTable.get_atomic_number('Cu')
29
"""
__table = [
'X',
'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', 'Fl', 'Lv', 'Uup', 'Uuh', 'Uus', 'Uuo'
]
__atomic_weights = [
0.0,
1.008, 4.003,
6.941, 9.012, 10.81, 12.01, 14.01, 16.00, 19.00, 20.18,
22.00, 24.31, 26.98, 28.09, 30.97, 32.07, 35.45, 39.95,
39.10, 40.08, 44.96, 47.87, 50.94, 52.00, 54.94, 55.85, 58.93, 58.69, 63.55, 65.38, 69.72, 72.63, 74.92, 78.97, 79.90, 83.80,
85.47, 87.62, 88.91, 91.22, 92.91, 95.95, 99.00, 101.1, 102.9, 106.4, 107.9, 112.4, 114.8, 118.7, 121.8, 127.6, 169.9, 131.3,
132.9, 137.3,
138.9, 140.1, 140.9, 144.2, 145.0, 150.4, 152.0, 157.3, 158.9, 162.5, 164.9, 167.3, 168.9, 173.1, 175.0,
178.5, 180.9, 183.8, 186.2, 190.2, 192.2, 195.1, 197.0, 200.6, 204.4, 207.2, 209.0, 210, 210, 222,
223, 226,
227, 232.0, 231.0, 238.0, 237, 239, 243, 247, 252, 252, 257, 258, 259, 262, 267, 268, 271, 272, 277, 276, 281, 280, 285, 289, 293
]
__vdw = [
0.0,
1.2, 1.4,
1.82, 0.0, 0.0, 1.70, 1.55, 1.52, 1.47, 1.54,
2.27, 1.73, 0.0, 2.10, 1.80, 1.80, 1.75, 1.88,
2.75, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
1.63, 1.40, 1.39, 1.87, 0.0, 1.85, 2.02,
0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0,
1.63, 1.72, 1.58, 1.93, 2.17, 0.0, 2.06, 1.98, 2.16
]
[docs]
@staticmethod
def get_num_of_atoms():
return len(PeriodicTable.__table)
[docs]
@staticmethod
def get_symbol(atomic_number):
atomic_number = int(atomic_number)
try:
answer = PeriodicTable.__table[atomic_number]
return answer
except IndexError:
logger.error("PeriodicTable.get_symbol(): atomic number %s not found.", atomic_number)
raise
[docs]
@staticmethod
def get_atomic_number(symbol):
symbol = str(symbol).lower().capitalize()
try:
answer = PeriodicTable.__table.index(symbol)
return answer
except ValueError:
logger.error("PeriodicTable.get_atomic_number(): symbol '%s' not found.", symbol)
raise
def __contains__(self, symbol):
symbol = str(symbol)
symbol = symbol.lower()
symbol = symbol.capitalize()
answer = False
for i in PeriodicTable.__table:
if symbol == i:
answer = True
break
return answer
__covalent_radius = [
0.0, # X (dummy)
0.31, # 1: H
0.28, # 2: He
1.28, # 3: Li
0.96, # 4: Be
0.84, # 5: B
0.76, # 6: C
0.71, # 7: N
0.66, # 8: O
0.57, # 9: F
0.58, # 10: Ne
1.66, # 11: Na
1.41, # 12: Mg
1.21, # 13: Al
1.11, # 14: Si
1.07, # 15: P
1.05, # 16: S
1.02, # 17: Cl
1.06, # 18: Ar
2.03, # 19: K
1.76, # 20: Ca
1.70, # 21: Sc
1.60, # 22: Ti
1.53, # 23: V
1.39, # 24: Cr
1.39, # 25: Mn
1.32, # 26: Fe
1.26, # 27: Co
1.24, # 28: Ni
1.32, # 29: Cu
1.22, # 30: Zn
1.22, # 31: Ga
1.20, # 32: Ge
1.19, # 33: As
1.20, # 34: Se
1.20, # 35: Br
1.16, # 36: Kr
2.20, # 37: Rb
1.95, # 38: Sr
1.90, # 39: Y
1.75, # 40: Zr
1.64, # 41: Nb
1.54, # 42: Mo
1.47, # 43: Tc
1.46, # 44: Ru
1.42, # 45: Rh
1.39, # 46: Pd
1.45, # 47: Ag
1.44, # 48: Cd
1.42, # 49: In
1.39, # 50: Sn
1.39, # 51: Sb
1.38, # 52: Te
1.39, # 53: I
1.40, # 54: Xe
2.44, # 55: Cs
2.15, # 56: Ba
2.07, # 57: La
2.04, # 58: Ce
2.03, # 59: Pr
2.01, # 60: Nd
1.99, # 61: Pm
1.98, # 62: Sm
1.98, # 63: Eu
1.96, # 64: Gd
1.94, # 65: Tb
1.92, # 66: Dy
1.92, # 67: Ho
1.89, # 68: Er
1.90, # 69: Tm
1.87, # 70: Yb
1.87, # 71: Lu
1.75, # 72: Hf
1.70, # 73: Ta
1.62, # 74: W
1.51, # 75: Re
1.44, # 76: Os
1.41, # 77: Ir
1.36, # 78: Pt
1.36, # 79: Au
1.32, # 80: Hg
1.45, # 81: Tl
1.46, # 82: Pb
1.48, # 83: Bi
1.40, # 84: Po
1.50, # 85: At
1.50, # 86: Rn
2.60, # 87: Fr
2.21, # 88: Ra
2.15, # 89: Ac
2.06, # 90: Th
2.00, # 91: Pa
1.96, # 92: U
1.90, # 93: Np
1.87, # 94: Pu
1.80, # 95: Am
1.69, # 96: Cm
]
[docs]
@staticmethod
def vdw(atom):
if isinstance(atom, str):
atom = PeriodicTable.get_atomic_number(atom)
try:
return PeriodicTable.__vdw[atom]
except (IndexError, KeyError):
logger.error("PeriodicTable.vdw(): no VDW radius for atom %s", atom)
raise
[docs]
@staticmethod
def covalent_radius(atom):
if isinstance(atom, str):
atom = PeriodicTable.get_atomic_number(atom)
if atom == 0:
logger.error("PeriodicTable.covalent_radius(): atomic number 0 has no covalent radius")
raise IndexError("PeriodicTable.covalent_radius(): atomic number 0 has no covalent radius")
try:
return PeriodicTable.__covalent_radius[atom]
except (IndexError, KeyError):
logger.error("PeriodicTable.covalent_radius(): no covalent radius for atom %s", atom)
raise
[docs]
@staticmethod
def atomic_weight(atom):
if isinstance(atom, str):
atom = PeriodicTable.get_atomic_number(atom)
try:
return PeriodicTable.__atomic_weights[atom]
except (IndexError, KeyError):
logger.error("PeriodicTable.atomic_weight(): no atomic weight for atom %s", atom)
raise
if __name__ == "__main__":
import doctest
doctest.testmod()