Tutorials

These tutorials are the main MolScope paths. They start from ordinary PDB files and end with the three outputs the project is designed to make polished: descriptor tables, graph ML inputs, and coarse-grained bead models.

Choose a workflow

Tutorial	Output	Use when
PDB to descriptors	A fixed-width CSV feature table	You want classical ML features, quick structure summaries, or batch descriptors.
PDB to graph/GNN	Atom/residue graphs and a PyTorch Geometric toy dataset	You want message-passing inputs or a minimal graph neural network workflow.
PDB to coarse-grained beads	Residue and backbone/sidechain bead models	You want an interpretable reduced representation for inspection or graph prototyping.

Run commands from the repository root so paths like examples/data/1fqy.pdb resolve correctly.