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Tutorials

These notebooks are the main “how to use this in practice” part of the docs.

Note: the MkDocs build is configured not to execute notebooks (execute: false). To see SVG depictions and computed outputs, run notebooks locally.

  1. Tutorial 00 — Overview (00_overview.ipynb)
    What cTopo is for, and the high-level workflow.

  2. Tutorial 01 — Ligand basics (01_ligand_basics.ipynb)
    Donor marking, skeleton definition, and atom roles (DONOR / SKELETON / SUBSTITUENT).

  3. Tutorial 02 — Skeleton and topology (02_skeleton_topology.ipynb)
    How topology reduction works and how to use topology/skeleton keys for grouping.

  4. Tutorial 03 — Dataset hierarchy and HTML reports (03_dataset_tree_reports.ipynb)
    Build denticity → topology → skeleton → ligand trees and export a shareable HTML report.

  5. Tutorial 04 — Role-aware fingerprints (04_role_aware_fingerprints.ipynb)
    Compare full-ligand vs skeleton-only vs substituent-only fingerprints and similarity.

  6. Tutorial 05 — Complexes and ligand extraction (05_complexes_and_extraction.ipynb)
    Dative-bond encoding convention and extracting ligands from complex datasets.

Figures

Where a tutorial benefits from a diagram, the notebooks link to placeholder SVGs in docs/assets/figs/. Replace them later with your final figures without changing notebook content.