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Tutorials

Runnable examples and helper scripts for Nesso-1. Run all commands from the repository root.

Prediction Examples

Three YAML inputs demonstrate the supported ligand formats (SMILES, CCD, SDF). Each uses the same protein sequence with tyrosine as the ligand.

nesso predict tutorial/smiles.yaml --out_dir ./output/tutorial_smiles
nesso predict tutorial/ccd.yaml --out_dir ./output/tutorial_ccd
nesso predict tutorial/sdf.yaml --out_dir ./output/tutorial_sdf
nesso predict tutorial/multi_ligand.yaml --out_dir ./output/tutorial_multi_ligand  # two ligands; binder set in YAML

Feature Extraction

tutorial/extract_features.py reads predictions.safetensors produced when running with --save_metadata. It slices the Pairformer z tensor into protein/ligand blocks and prints tensor shapes for quick inspection.

nesso predict tutorial/smiles.yaml --out_dir ./output/tutorial_smiles --save_metadata
python tutorial/extract_features.py \
  ./output/tutorial_smiles/predictions/smiles/predictions.safetensors

Outputs:

  • z_pp, z_pl, z_ll: pairwise protein/ligand blocks from z
  • s_prot, s_lig: per-token features from row means of z