I'm opening this issue to suggest adding support for molecular visualization as part of the future 3D roadmap. Supporting molecular visualization would broaden the impact of this repository and attract interest from communities working in drug discovery, materials design, and biomolecular simulations. Current solutions for molecular visualization are often specialized--for example, PyMOL or VMD. There are a few efforts that allow interactive visualization within Jupyter notebooks or websites, but these typically don’t integrate well with additional scientific visualization workflows and have limited ongoing development (see, for example, py3dmol and related follow-ups: https://github.com/avirshup/py3dmol, or nglview https://github.com/nglviewer/nglview). Mathematica is another alternative that continues to improve over time, but seamless integration with Python remains missing.

It would be great to add the ability to seamlessly integrate the display and animation of small molecules, materials, and biomolecules with other common scientific visualizations, while being able to address the library from python and interacting with it from a Jupyter notebook or a REPL. The simplest starting point would be the support of displaying organic small molecules, because they are super useful in many areas of science and only require a limited number of useful primitives in their representations (bonds and atoms go a really long way; eventually perhaps one could add displays of electrostatic potentials, electron densities, and wavefunctions).