Fitness function
General
- Given two molecules, decides which is better
- Return a number for each molecule
- Must operate on any molecule, including very bad ones
- Must provide routes for evolution to reach good molecules
- Must make fine distinctions
Evolve towards molecular target
- All-pairs-shortest-path (APSP) distance
- Assign extended types to each atom (element plus bond pattern)
- Find shortest path between each pair of atoms
- Create bag with one element per shortest path. Each element is the (sorted) extended types of the end point and the number of bonds in the (shortest) path
- A bag is a set with duplicate elements
- Tanimoto distance between bags