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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.
The PyValem package can be installed either from PyPI_ using pip
.. code-block:: bash
python3 -m pip install pyvalem
or from the source by running (one of the two) from the project source directory.
.. code-block:: bash
# either
python setup.py install
# or
python3 -m pip install .
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.
.. code-block:: pycon
>>> 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
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:
.. code-block:: pycon
>>> 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.
.. code-block:: pycon
>>> 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'
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
.. code-block:: pycon
>>> 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.
.. code-block:: pycon
>>> 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-
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
.. code-block:: bash
pip install -e .[dev]
or on zsh:
.. code-block:: zsh
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)
.. code-block:: bash
# 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.
.. _GitHub: https://github.com/xnx/pyvalem .. _PyPI: https://pypi.org/project/pyvalem/ .. _numpydoc: https://numpydoc.readthedocs.io/en/latest/format.html
FAQs
A package for managing simple chemical species and states
We found that pyvalem demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 2 open source maintainers collaborating on the project.
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