Route Node IDs¶

RetroCast uses deterministic route-local ids when evaluation annotations need to point back into a Route. These ids are not chemical identities; they are addresses inside one serialized route tree.

Example Route¶

graph TD
    m_root["rc:m:_ target"] --> r_root["rc:r:_"]
    r_root --> m_0["rc:m:0 intermediate a"]
    r_root --> m_1["rc:m:1 intermediate b"]
    r_root --> m_2["rc:m:2 stock leaf"]

    m_0 --> r_0["rc:r:0"]
    r_0 --> m_00["rc:m:0.0 stock leaf"]
    r_0 --> m_01["rc:m:0.1 stock leaf"]

    m_1 --> r_1["rc:r:1"]
    r_1 --> m_10["rc:m:1.0 intermediate c"]
    r_1 --> m_11["rc:m:1.1 stock leaf"]

    m_10 --> r_10["rc:r:1.0"]
    r_10 --> m_100["rc:m:1.0.0 stock leaf"]

The same route as a trimmed Route tree, with ids shown as annotations:

{
  "target": {
    "id": "rc:m:_",
    "synthesis_step": {
      "id": "rc:r:_",
      "reactants": [
        {
          "id": "rc:m:0",
          "synthesis_step": {
            "id": "rc:r:0",
            "reactants": [{ "id": "rc:m:0.0" }, { "id": "rc:m:0.1" }]
          }
        },
        {
          "id": "rc:m:1",
          "synthesis_step": {
            "id": "rc:r:1",
            "reactants": [
              {
                "id": "rc:m:1.0",
                "synthesis_step": {
                  "id": "rc:r:1.0",
                  "reactants": [{ "id": "rc:m:1.0.0" }]
                }
              },
              { "id": "rc:m:1.1" }
            ]
          }
        },
        { "id": "rc:m:2" }
      ]
    }
  }
}

Grammar¶

route_id  := "rc:" node_kind ":" path
node_kind := "m" | "r"
path      := "_" | index ("." index)*
index     := nonnegative integer

Semantics:

• rc:m:_ is the target molecule.
• rc:r:_ is the reaction producing the target molecule.
• rc:m:0 is the first reactant molecule of rc:r:_.
• rc:r:0 is the reaction producing rc:m:0, when that molecule is not a leaf.
• rc:m:0.1 is the second reactant molecule under rc:r:0.

The reaction id is always the product molecule path with rc:r: instead of rc:m:. Child indices follow the route's canonical reactant list order.

Library Access¶

for route_reaction in route.iter_reactions():
    print(route_reaction.reaction_id, route_reaction.product_id)

route_reaction = route.get_reaction_by_id("rc:r:1.0")

Evaluation annotations use these ids:

{
  "reaction_id": "rc:r:1.0",
  "validity": {
    "tier 0": { "status": "pass" }
  }
}