It's a good little puzzle bit but there are a few things that make it unnecessarily obfuscated. So here are my suggestions to tweak this part.
1. First of all, why atoms? Atoms in this context makes zero sense, never mind the "negative atoms".. To make it clear, these should be called mutation effects or traits, so all mutagens facilitate some effects and inhibit some. And we would be composing a complex mutagen from other mutagens. I am sure relevant logs would also sound better this way.
2. There really is no need for these effects (or atoms as they are called in the game) to be represented by two letters/numbers. 10-20 single letter codes should suffice. (also a list of these acronyms with rudimentary details about the relevant mutation can be included in the lore)
3. Once a mutagen is scanned, its sequence information can be added to its item information, replacing the generic mutagen info text. This removes the need to actually use a pen and paper while playing. After all, my Player Character should have the ability to note and remember stuff.
EDIT: ( another suggestion that came as an afterthought )
4. It would be nice to have the possibility to lower the difficulty of this puzzle with some INT (or some other) skill check. I liked that it required me to do some algebra on paper but IF someone is role playing a smart person you should let them be. This could work by partially revealing the generator sequence. It would still not be trivial.
