chemistry_tools.formulae.parser

Attention

This module has the following additional requirements:

cawdrey>=0.5.0
mathematical>=0.5.1
pyparsing>=2.4.6
tabulate>=0.8.9

These can be installed as follows:

python -m pip install chemistry-tools[formulae]

Functions and parsing formulae.

Functions:

mass_from_composition(composition[, charge])

Calculates molecular mass, in atomic mass units, from atomic weights.

string_to_composition(formula[, prefixes, …])

Parse composition of formula representing a chemical formula.
mass_from_composition(composition, charge=0)[source]

Calculates molecular mass, in atomic mass units, from atomic weights.

Note

Atomic number 0 denotes charge or “net electron defficiency”

Example:

>>> f'{mass_from_composition({0: -1, "H": 1, 8: 1}):.2f}'
'17.01'
Parameters

  • composition (Mapping[Union[str, int], int]) – Mapping of str or int (element symbol or atomic number) to int (coefficient)

  • charge (int) – The charge of the composition. Default 0.

Return type

float

string_to_composition(formula, prefixes=None, suffixes=('(s)', '(l)', '(g)', '(aq)'))[source]

Parse composition of formula representing a chemical formula.

Examples:

>>> string_to_composition('NH4+') == {0: 1, "H": 4, "N": 1}
True
>>> string_to_composition('.NHO-(aq)') == {0: -1, "H": 1, "N": 1, "O": 1}
True
>>> string_to_composition('Na2CO3.7H2O') == {"Na": 2, "C": 1, "O": 10, "H": 14}
True
Parameters

  • formula (str) – Chemical formula, e.g. 'H2O', 'Fe+3', 'Cl-'

  • prefixes (Optional[Iterable[str]]) – Prefixes to ignore, e.g. ('.', 'alpha-'). Default None.

  • suffixes (Sequence[str]) – Suffixes to ignore. Default ('(s)', '(l)', '(g)', '(aq)').

Return type

Dict[int, int]

Returns

The composition, as a dictionary mapping atomic number -> multiplicity. “Atomic number” 0 represents net charge.