Workflow reference

Details for workflows introduced in the Quickstart. For definitions and visual explanations, use the Glossary; for runnable notebooks, use Tutorials.

Structures and tensors

• Concepts
• Structure I/O and visualization
• Model and structure integrations
• Model coordinate inputs
• GPU batching
• CPU threading

Scoring and modeling

• Scoring and analysis
• Packing
• Minimization and FastRelax
• Protein-interface analysis
• Ligand Preparation
• Nucleic acids

Extension and performance

• Extending TMol
• Benchmarking

Packing can change block types and atom counts: render a new scorer for its output. Coordinate-only minimization can reuse a scorer for the same layout. See Scorer reuse for details.