Concepts

cTopo is built around a small set of abstractions that are easy to reason about in coordination chemistry.

Recommended reading order:

1. Skeleton — what part of a ligand “defines the cage”.
2. Topology — how skeletons are reduced into a small set of patterns.
3. Denticity → topology → skeleton → ligand — how cTopo organizes datasets.
4. Atom roles — donor/skeleton/substituent typing used for fingerprints and analysis.
5. Complex encoding — conventions for RDKit dative bonds (optional feature).

The tutorials then show how to apply these ideas to real datasets.