As we only model construction reactions, all heads are singletons in this paper.
We assume the chemistry is described by a (possibly large) set of construction reactions, i.e., affixations and cyclizations.
Synthesis planning often proceeds in two phases, the first of which is identification of a set of construction reactions, and the second is consideration of functionalization reactions.
Construction reactions are often said to fix a bond in the target, and the set of bonds fixed in the plan is denoted the bond set.
Following most of the work on formal methods for synthesis planning, we therefore focus on the first phase and model construction reactions only.
There are two main types of reactions [8]: construction reactions, which create new carbon carbon bonds in the target's skeleton, and functionalization reactions, which alter the functional groups attached to the skeleton but do not alter the skeleton itself.
As discussed earlier, synthesis planning often proceeds in two phases, the first of which is identification of a set of construction reactions, and the second is consideration of functionalization reactions.
Construction reactions come in two variants: affixations which add target bonds by uniting two separate precursor molecules, and cyclizations which add target bonds by closing a ring in a single molecule.
The DNA is then purified and subjected to library construction reactions, where the fragment ends are made double stranded, phosphorylated and A-tailed before sequencer-specific adaptors are ligated to allow amplification and sequencing of the sample.
After the construction of reaction rules, all the reactions in the database were classified according to the reaction rules.
