Your idea is briliant but for me it miss a bit of something.
I started making something given the idea of Factorio x Spacechem
What I have done differently :
- the atoms icons are freshly made to looks like signal but in circle
- bonds are embeded in the atom equipment
- molecules all have 4x4 grid, the molecule icon represent the grid state but only display where there is an atom, no coloring and no bound
- molecules could be freely manualy handled by the engineer, which make experimentation a way to play (making).
- this correspond to 11507 registered molecules and 9047 registered atoms (all 118 atoms with their corresponding bounding variants) which is less than 50000 prototypes
- since it always use a 4x4 grid, it could theorically works like spacechem
- I plan to make programmable reactors that execute one instruction per tick, for now it will be classic programming, but in the long term I think that waldo programming would replace it (waldo will only be classic programming but with a visual layer)
https://i.imgur.com/zkwG9qy.jpg