Gephi is an award-winning open-source platform for visualizing and manipulating large graphs. It runs on Windows, Mac OS X and Linux. Localization is available in English, French, Spanish, Japanese, ...

"I see in 3D" (iCn3D) Structure Viewer is not only a web-based 3D viewer, but also a structure analysis tool interactively or in the batch mode using NodeJS scripts based on the npm package icn3d.