penguins 0.2.0

Penguins: an Easy, NPE-free Gateway to Unpacking and Illustrating NMR Spectra

Penguins: an Easy, NPE-free Gateway to Unpacking and Illustrating NMR Spectra

pip install penguins

penguins is a Python 3 package intended mainly for generating publication-quality plots of NMR spectra in a programmatic, reproducible fashion.

Documentation can be found at https://yongrenjie.github.io/penguins. Everything is documented in one form or another, although I'm still working on tutorial-type pages which are easier to read than the docstrings.

Note that penguins is still in development, so the interface should not be assumed to be (too) stable. For now, I am working directly on the master branch, and rebasing/force pushing may occur without warning.

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As an example of the output, here's Figure 2 from Angew. Chem. Int. Ed. 2017, 56 (39), 11779–11783:

And here's a similar plot that can be done in under 20 lines of PEP8-compliant code using penguins (it's the same compound, but not the same data):

import penguins as pg
hmqc, hsqc, cosy, noesy = (pg.read("tests/data/noah", i, 1)
                           for i in range(1, 5))

fig, axs = pg.subplots2d(2, 2)
hmqc.stage(axs[0, 0], levels=7e3, f1_bounds="110..130", f2_bounds="7..9.5")
hsqc.stage(axs[0, 1], levels=4e4, f1_bounds="12..65", f2_bounds="0.5..5")
cosy.stage(axs[1, 0], levels=8e5)
noesy.stage(axs[1, 1], levels=9e4)

titles = [r"$^{15}$N HMQC", r"$^{13}$C HSQC", "COSY", "NOESY"]
for ax, title, char in zip(axs.flat, titles, "abcd"):
    pg.mkplot(ax, title=title, autolabel="nucl")
    ax.text(x=0.02, y=0.98, s=f"({char})", transform=ax.transAxes,
            fontweight="semibold", verticalalignment="top")
    pg.move_ylabel(ax, pos="topright")

pg.cleanup_axes()
pg.show()

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[Regarding the 'NPE' in the name: I made this package after getting fed up of getting java.lang.NullPointerException in TopSpin's Plot tab. It's especially bad on OS X Catalina, but even on Windows it's rather buggy. Also, penguins are cute. 🐧]