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Fast and efficient theoretical isotopic profile generation

Project description

:mod:brainpy is a small Python library implementing the B afflingly R ecursive A lgorithm for I sotopic Patter N generation [Dittwald2014]_. It includes three implementations, a pure-Python object oriented implementation, a :title-reference:Cython accelerated version of the object oriented implementation, and a pure :title-reference:C implementation, listed in order of ascending speed. The C implementation is used by default when available.

BRAIN, implemented in :func:brainpy.isotopic_variants, takes an elemental composition represented by any :class:~.collections.abc.Mapping-like Python object and uses it to compute its aggregated isotopic distribution. All isotopic variants of the same number of neutrons are collapsed into a single centroid peak, meaning it does not consider isotopic fine structure.

Installing

:mod:brainpy has three implementations, a pure Python implementation, a Cython translation of that implementation, and a pure C implementation that releases the :title-reference:GIL.

To install from a package index, you will need to have a C compiler appropriate to your Python version to build these extension modules. Additionally, there are prebuilt wheels for Windows available on PyPI <https://pypi.org/project/brain-isotopic-distribution/>_:

.. code-block:: sh

$ pip install brain-isotopic-distribution

To build from source, in addition to a C compiler you will also need to install a recent version of Cython <https://pypi.org/project/Cython/>_ to transpile C code.

References

This package is an implementation of the algorithm originally described in P. Dittwald, J. Claesen, T. Burzykowski, D. Valkenborg, and A. Gambin, "BRAIN: a universal tool for high-throughput calculations of the isotopic distribution for mass spectrometry.", Anal. Chem., vol. 85, no. 4, pp. 1991–4, Feb. 2013.

H. Hu, P. Dittwald, J. Zaia, and D. Valkenborg,
"Comment on 'Computation of isotopic peak center-mass distribution by fourier transform'.",
Anal. Chem., vol. 85, no. 24, pp. 12189–92, Dec. 2013.

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