Examples

The examples here are small scripts that can be copied into notebooks or Python files. They support the three main tutorials rather than introducing separate product pillars: PDB to descriptors, PDB to graph/GNN, and PDB to coarse-grained beads.

The repository also includes:

• examples/tour.py: an end-to-end tour over the bundled sample structures.
• examples/geometry.py: a tour of every geometry quantity (see Molecular geometry tour).
• examples/protein_analysis.py: protein metadata, contacts, simplified DSSP, NMR ensemble contacts, and binding sites.
• examples/coarse_graining.py: residue COM, centroid, and simplified BB/SC coarse-graining with a visual mapping comparison.
• examples/data/: small bundled structures used by the examples and tests.
• notebooks/molscope_tour.ipynb: a notebook version of the tour.
• notebooks/protein_analysis_from_scratch.ipynb: a tutorial notebook over 1fqy, 1aml, and 3ptb.
• docs/examples/protein-analysis-from-scratch.md: the short doc version of the same workflow.
• docs/examples/pdb-to-graph-cg.md: a focused PDB to graph and coarse-grain walkthrough.
• docs/examples/residue-contact-graphs.md: residue nodes plus spatial contact edges.
• docs/examples/pdb-to-pyg-ml.md: PDB to PyTorch Geometric classifier/regressor.
• examples/graph_to_gnn.py: graph export and a PyTorch Geometric GNN forward pass.
• examples/pdb_to_pyg_ml.py: runnable graph-level PyG toy ML example.
• examples/residue_contact_graph.py: runnable residue-contact graph drawing example.

Suggested notebook examples for future work:

• 01_read_plot_structure.ipynb
• 02_selections_geometry.ipynb
• 03_nmr_ensemble_analysis.ipynb
• 04_molecular_graphs_for_ml.ipynb
• 05_coarse_graining.ipynb