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Having to change tabs to take a screenshot means visualisation can behave in unpredictable ways. Better to have a button on the main body to do that, to avoid these side effects.

The visualization of bonding and J-coupling networks fails when using the _repr_png_() method of the MagresAtomsView class. The failure occurs when calling:

...
atoms_set = set(self.atoms)
...

with the error:

TypeError: unhashable type: 'MagresAtom`

Environment Details

OS: Windows Subsystem for Linux 2 (Ubuntu 20.04)
Kernel: 4.19.104-microsoft-standard

Using Miniconda3

$ conda --version
conda 4.9.2

Example

In the example notebook Bonding and J-coupling network output example.ipynb

from __future__ import print_function

from magres.atoms import MagresAtoms, MagresAtomsView

ethanol_atoms = MagresAtoms.load_magres('../samples/ethanol-all.magres')

castep_file = open('../samples/ethanol.castep').read()

ethanol_atoms.calculate_bonds()

At this point, no output is generated in the notebook (note: this is true even after removing the return None from the _repr_png_() method in MagresAtomsView.)

Explicitly calling ethanol_atoms._repr_png_() will then throw the TypeError.

Suggested Fix

Define a __dict__ and __key attribute for the MagresAtom class to make it "hashable".

See this Stackoverflow question