Chemistry demos

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Some possible useful examples here: https://github.com/chrisjsewell/chrisjsewell.github.io/blob/master/3d_atomic/3D%20Atomic%20Visualisation.ipynb

See also: https://ipymd.readthedocs.io/en/latest/ ("Molecular Dynamics Analysis for IPython (ipyMD)")

More recent work appears to be:

https://github.com/chrisjsewell/ipyatom https://github.com/chrisjsewell/ase-notebook ("create atomic configuration visualisations, principally within a Jupyter Notebook")

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Crstallographic electron microscopy https://github.com/pyxem/pyxem-demos

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Molecular viewers compilation: https://www.macinchem.org/scientificsoftware/jsmolviewers.php

Reviews of viewers: https://medevel.com/15-3d-molecular-protein-modelling/

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This looks interesting — icn3d: https://www.ncbi.nlm.nih.gov/Structure/icn3d/icn3d.html#gallery — but not Jupyter embeddings as yet?

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Materials / structure visualisations:

https://pymatgen.org/

https://www.ovito.org/

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Handy mhchem guide: https://mhchem.github.io/MathJax-mhchem/

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Molecule editor, based on RDKit https://www.wildcardconsulting.dk/rdeditor-an-open-source-molecular-editor-based-using-python-pyside2-and-rdkit/

Repo: https://github.com/EBjerrum/rdeditor

Another molecule editor, https://peter-ertl.com/jsme/ , embeddable in notebook via https://github.com/apahl/rdkit_ipynb_tools

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Lewis structures https://tex.stackexchange.com/questions/137227/draw-lewis-structures-like-a-book

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Visualise atoms:

https://github.com/VHchavez/blobs Cube files plotting machine: Plot cube files produced with Psi4 directly in a Jupyter Notebook - Psi4 - https://github.com/fevangelista/vmd_cube

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Molecular Visualization powered by Plotly

https://github.com/VHchavez/moly

Molecules via https://github.com/MolSSI/QCPortal