electrolytes 0.4.4

Electrolyte database manager

electrolytes

electrolytes provides command-line and programmatic access to a database of electrolytes and their properties. It includes 518 components by default (see credits). The package covers basic management of the database, including support for storing user-defined electrolytes.

electroMicroTransport

electrolytes is primarily developed as a utility to assist in preparing simulation cases for the electroMicroTransport toolbox for electromigrative separations. However, it is an independent package and can be installed and used separately.

Installation

Install with pip:

$ python3 -m pip install electrolytes

electrolytes currently requires Python 3.7 or later, and a relatively recent version of pip (pip may be upgraded with python3 -m pip install --upgrade pip).

Command-line usage

Invoke the electrolytes command-line application to search the database, find the details of a particular component, or to add/remove user-defined components. In your terminal, run:

$ electrolytes

or, alternatively:

$ python3 -m electrolytes

Add the --help flag to learn what options are available.

Python API

The Python API is provided for electroMicroTransport case initialization scripts.

from electrolytes import database, Properties

You can look up components in the database as you would with dict (with component names as keys), and also add user-defined components with the add method (as if database were a set). Components are instances of the Constituent class. Extra methods are also defined for database:

    def user_defined(self) -> Iterable[str]: ...

    def is_user_defined(self, name: str) -> bool: ...

The database object is also usable as a context manager (i.e. with database:), which allows multiple operations to be performed with exclusive access to the database (locking out any other processes for the duration).

Constituent names are case insensitive and will be automatically converted to all uppercase. Any instances added to (or removed from) the database will be saved for the current operating system user. Default components cannot be changed or removed (expect a ValueError if you try).

The public interface of the Constituent class is:

class Constituent:
    name: str
    u_neg: Sequence[float] = []  # mobilities for [..., -3, -2, -1], SI units*1e-9
    u_pos: Sequence[float] = []  # mobilities for [+1, +2, +3, ...], SI units*1e-9
    pkas_neg: Sequence[float] = []  # pKas for [..., -3, -2, -1]
    pkas_pos: Sequence[float] = []  # pKas for [+1, +2, +3, ...]

    # Interface for electroMicroTransport
    def mobilities(self) -> Sequence[float]: ...  # for [..., +3, +2, +1, -1, -2, -3, ...], SI units
    def pkas(self) -> Sequence[float]: ...  # for [..., +3, +2, +1, -1, -2, -3, ...]
    # NOTE: the above are padded if needed so that +3 and -3 are always present (len >= 6)
    def diffusivity(self) -> float: ...  # SI units

Data credits

Electrolyte data taken from the Simul 6 application[^simul6] (homepage, GitHub). The dataset of different electrolytes was originally compiled by Prof. Hirokawa[^Hirokawa].

[^simul6]: GAŠ, Bohuslav; BRAVENEC, Petr. Simul 6: A fast dynamic simulator of electromigration. Electrophoresis, 2021, vol. 42, no. 12-13, pp. 1291-1299. DOI: 10.1002/elps.202100048

[^Hirokawa]: HIROKAWA, Takeshi, et al. Table of isotachophoretic indices: I. Simulated qualitative and quantitative indices of 287 anionic substances in the range ph 3–10. Journal of Chromatography A, 1983, vol. 271, no. 2, pp. D1-D106. DOI: 10.1016/S0021-9673(00)80225-3