structure of edges yamls

[richardjgowers]

Currently the edges yaml is structured as

mapper: <mapper algorithm>
planner: <planner algorithm>
edges:
  <name>:
    ligand_a: <a_name>
    ligand_b: <b_name>
    atom_mapping: <mapping dict>
    score: <score>

IMO The mapper isn't a per-network property but instead a per-edge property. Also arbitrary remarks would also be useful (e.g. annotating that a certain edge was hand tweaked and why).

planner: <planner algorithm>
remarks: <freeform description of this network>
edges:
  <name>:
    ligand_a: <a_name>
    ligand_b: <b_name>
    atom_mapping: <mapping dict>
    score: <score>
    mapper: <mapper>
    remarks: <freeform remarks>

[dfhahn]

I like the suggestion. Maybe you want to be more specific about the score to accommodate for various different scores? E.g.,

score:
    lomap: <lomap_score>
    shape_sim: <shape similarity>
    …

[dotsdl]

@jchodera: I like the per-edge approach given by @richardjgowers above.