Bioinformatics with Python Cookbook

Optimizing code with Cython and Numba

Here, we will have a short introduction on how to optimize code with Cython and Numba. These are competitive approaches; Cython is a superset of Python that allows you to call C functions and specify C types. Numba is a just-in-time compiler that optimizes the Python code.

As an example, we will reuse the distance recipe from the proteomics chapter. We will compute the distance between all atoms in a PDB file.

Getting ready

Cython normally requires specifying your optimized code in a separate .pyx file (Numba is a more declarative solution without this requirement). As IPython provides a magic to hide this, we will use IPython here. However, note that if you are on plain Python, the Cython development will be ...