Source code for cobra.core.formula
# -*- coding: utf-8 -*-
from __future__ import absolute_import
import re
from warnings import warn
from cobra.core.object import Object
# Numbers are not required because of the |(?=[A-Z])? block. See the
# discussion in https://github.com/opencobra/cobrapy/issues/128 for
# more details.
[docs]class Formula(Object):
"""Describes a Chemical Formula
Parameters
---------
formula : string
A legal formula string contains only letters and numbers.
"""
def __init__(self, formula=None):
Object.__init__(self, formula)
self.formula = formula
self.elements = {}
if self.formula is not None:
self.parse_composition()
[docs] def __add__(self, other_formula):
"""Combine two molecular formulas.
Parameters
----------
other_formula : Formula, str
string for a chemical formula
Returns
-------
Formula
The combined formula
"""
return Formula(self.formula + other_formula.formula)
[docs] def parse_composition(self):
"""Breaks the chemical formula down by element."""
tmp_formula = self.formula
# commonly occuring characters in incorrectly constructed formulas
if "*" in tmp_formula:
warn("invalid character '*' found in formula '%s'" % self.formula)
tmp_formula = self.formula.replace("*", "")
if "(" in tmp_formula or ")" in tmp_formula:
warn("parenthesis found in formula '%s'" % self.formula)
return
composition = {}
parsed = element_re.findall(tmp_formula)
for (element, count) in parsed:
if count == '':
count = 1
else:
try:
count = float(count)
int_count = int(count)
if count == int_count:
count = int_count
else:
warn("%s is not an integer (in formula %s)" %
(count, self.formula))
except ValueError:
warn("failed to parse %s (in formula %s)" %
(count, self.formula))
self.elements = {}
return
if element in composition:
composition[element] += count
else:
composition[element] = count
self.elements = composition
@property
[docs] def weight(self):
"""Calculate the mol mass of the compound
Returns
-------
float
the mol mass
"""
try:
return sum([count * elements_and_molecular_weights[element]
for element, count in self.elements.items()])
except KeyError as e:
warn("The element %s does not appear in the periodic table" % e)
[docs]elements_and_molecular_weights = {
'H': 1.007940,
'He': 4.002602,
'Li': 6.941000,
'Be': 9.012182,
'B': 10.811000,
'C': 12.010700,
'N': 14.006700,
'O': 15.999400,
'F': 18.998403,
'Ne': 20.179700,
'Na': 22.989770,
'Mg': 24.305000,
'Al': 26.981538,
'Si': 28.085500,
'P': 30.973761,
'S': 32.065000,
'Cl': 35.453000,
'Ar': 39.948000,
'K': 39.098300,
'Ca': 40.078000,
'Sc': 44.955910,
'Ti': 47.867000,
'V': 50.941500,
'Cr': 51.996100,
'Mn': 54.938049,
'Fe': 55.845000,
'Co': 58.933200,
'Ni': 58.693400,
'Cu': 63.546000,
'Zn': 65.409000,
'Ga': 69.723000,
'Ge': 72.640000,
'As': 74.921600,
'Se': 78.960000,
'Br': 79.904000,
'Kr': 83.798000,
'Rb': 85.467800,
'Sr': 87.620000,
'Y': 88.905850,
'Zr': 91.224000,
'Nb': 92.906380,
'Mo': 95.940000,
'Tc': 98.000000,
'Ru': 101.070000,
'Rh': 102.905500,
'Pd': 106.420000,
'Ag': 107.868200,
'Cd': 112.411000,
'In': 114.818000,
'Sn': 118.710000,
'Sb': 121.760000,
'Te': 127.600000,
'I': 126.904470,
'Xe': 131.293000,
'Cs': 132.905450,
'Ba': 137.327000,
'La': 138.905500,
'Ce': 140.116000,
'Pr': 140.907650,
'Nd': 144.240000,
'Pm': 145.000000,
'Sm': 150.360000,
'Eu': 151.964000,
'Gd': 157.250000,
'Tb': 158.925340,
'Dy': 162.500000,
'Ho': 164.930320,
'Er': 167.259000,
'Tm': 168.934210,
'Yb': 173.040000,
'Lu': 174.967000,
'Hf': 178.490000,
'Ta': 180.947900,
'W': 183.840000,
'Re': 186.207000,
'Os': 190.230000,
'Ir': 192.217000,
'Pt': 195.078000,
'Au': 196.966550,
'Hg': 200.590000,
'Tl': 204.383300,
'Pb': 207.200000,
'Bi': 208.980380,
'Po': 209.000000,
'At': 210.000000,
'Rn': 222.000000,
'Fr': 223.000000,
'Ra': 226.000000,
'Ac': 227.000000,
'Th': 232.038100,
'Pa': 231.035880,
'U': 238.028910,
'Np': 237.000000,
'Pu': 244.000000,
'Am': 243.000000,
'Cm': 247.000000,
'Bk': 247.000000,
'Cf': 251.000000,
'Es': 252.000000,
'Fm': 257.000000,
'Md': 258.000000,
'No': 259.000000,
'Lr': 262.000000,
'Rf': 261.000000,
'Db': 262.000000,
'Sg': 266.000000,
'Bh': 264.000000,
'Hs': 277.000000,
'Mt': 268.000000,
'Ds': 281.000000,
'Rg': 272.000000,
'Cn': 285.000000,
'Uuq': 289.000000,
'Uuh': 292.000000
}