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A package for managing simple chemical species and states

Project description

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Introduction to PyValem

PyValem is a Python package for parsing, validating, manipulating and interpreting the chemical formulas, quantum states and labels of atoms, ions and small molecules.

Species and states are specified as strings using a simple and flexible syntax, and may be compared, output in different formats and manipulated using a variety of predefined Python methods.

Installation:

The PyValem package can be installed either from PyPI using pip

python3 -m pip install pyvalem

or from the source by running (one of the two) from the project source directory.

# either
python setup.py install

# or
python3 -m pip install .

Examples:

Formula

The basic (state-less) chemical formulas are represented by the Formula class. A Formula object is instantiated from a valid formula string and supports ions, isotopologues, as well as a few special species. The object contains attributes with its HTML and LaTeX representations, and its molar mass.

>>> from pyvalem.formula import Formula

>>> # neutral formulas:
>>> Formula('C2H5OH')
C2H5OH

>>> # isotopes:
>>> Formula('(14C)')
(14C)

>>> # ions
>>> [Formula('H3O+'), Formula('(1H)(2H)+'), Formula('Co(H2O)6+2')]
[H3O+, (1H)(2H)+, Co(H2O)6+2]

>>> # special species
>>> [Formula('e-'), Formula('hv')]
[e-, hν]

>>> # formula attributes:
>>> Formula('Ar+2').charge
2

>>> Formula('H2(18O)').html
'H<sub>2</sub><sup>18</sup>O'

>>> print(Formula('H2(18O)').latex)
\mathrm{H}_{2}{}^{18}\mathrm{O}

>>> Formula('(235U)').mass
235.04392819

“Stateful” Species

The “stateful” species represent species with (or without) any number of states attached. The StatefulSpecies object can be instantiated from a valid string, which consist of a valid Formula string, followed by a whitespace, followed by a semicolon-delimited sequence of valid State strings. PyValem supports several different types of state notation. For further information on valid PyValem State strings, consult the documentation.

Examples:

>>> from pyvalem.stateful_species import StatefulSpecies

>>> stateful_species = StatefulSpecies('Ne+ 1s2.2s2.2p5; 2P_1/2')
>>> stateful_species.formula
Ne+

>>> type(stateful_species.formula)
<class 'pyvalem.formula.Formula'>

>>> stateful_species.states
[1s2.2s2.2p5, 2P_1/2]

>>> state1, state2 = stateful_species.states
>>> type(state1)
<class 'pyvalem.states.atomic_configuration.AtomicConfiguration'>

>>> state1.orbitals
[1s2, 2s2, 2p5]

>>> type(state2)
<class 'pyvalem.states.atomic_term_symbol.AtomicTermSymbol'>

>>> state2.L, state2.J
(1, 0.5)

As Formula, also StatefulSpecies have html and latex attributes.

>>> print(stateful_species.latex)
\mathrm{Ne}^{+} \; 1s^{2}2s^{2}2p^{5} \; {}^{2}\mathrm{P}_{1/2}

>>> StatefulSpecies('(52Cr)(1H) 1sigma2.2sigma1.1delta2.1pi2; 6SIGMA+; v=0; J=2').html
'<sup>52</sup>Cr<sup>1</sup>H 1σ<sup>2</sup>.2σ<sup>1</sup>.1δ<sup>2</sup>.1π<sup>2</sup> <sup>6</sup>Σ<sup>+</sup> v=0 J=2'

Reaction

Finally, the Reaction class represents a reaction or a collisional process between species. A Reaction object is instantiated with a string consisting of valid Formula or StatefulSpecies strings delimited by ' + ', and reaction sides separated by ' -> ', such as

>>> from pyvalem.reaction import Reaction
>>> reaction = Reaction('He+2 + H -> He+ 3p1 + H+ + hv')
>>> reaction
He+2 + H → He+ 3p + H+ + hν

>>> reaction.html
'He<sup>2+</sup> + H → He<sup>+</sup> 3p + H<sup>+</sup> + hν'

>>> print(reaction.latex)
\mathrm{He}^{2+} + \mathrm{H} \rightarrow \mathrm{He}^{+} \; 3p + \mathrm{H}^{+} + h\nu

The Reaction class also watches out for charge balance and stoichiometry conservation during instantiation.

>>> Reaction('(2H) + (3H) -> (4He)')
Traceback (most recent call last):
...
pyvalem.reaction.ReactionStoichiometryError: Stoichiometry not preserved for reaction: (2H) + (3H) -> (4He)

>>> Reaction('e- + Ar -> Ar+ + e-')
Traceback (most recent call last):
...
pyvalem.reaction.ReactionChargeError: Charge not preserved for reaction: e- + Ar -> Ar+ + e-

For Developers:

It goes without saying that any development should be done in a clean virtual environment. After cloning or forking the project from its GitHub page, pyvalem might be installed into the virtual environment in editable mode with

pip install -e .[dev]

The [dev] extra installs (apart from the package dependencies) also several development-related packages, such as pytest, black, tox or ipython. The tests can then be executed by running (from the project root directory)

# either
pytest

# or
tox

The project does not have requirements.txt by design, all the package dependencies are rather handled by setup.py. The package needs to be installed to run the tests, which grants the testing process another layer of usefulness.

Docstrings in the project adhere to the numpydoc styling. The project code is formatted by black. Always make sure to format your code before submitting a pull request, by running black on all your python files.

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