The engines themselves are readily available from their original creators, and our custom patches and compilation instructions for usage within our game are available here: EternaJS/lib at master · eternagame/EternaJS · GitHub
We compile with emscripten to webassembly so that it’s usable within a browser, however that of course isn’t a necessity (they’re originally built to compile as CLI apps). One thing to note though is that if you use the models directly, you won’t get information on whether a design passes constraints - you just get what the model spits out (MFE, structure energies, etc).
If you want to work within the bounds of Eterna itself, you can write an in-game booster to run through the possibilities and check if it is satisfied or not.
Feel free to send questions my way on any of this - I’m happy to do what I can to clarify. 