atomworks documentation

Welcome to atomworks — a toolkit for converting, parsing, and manipulating biological structure and sequence data, inspired by the Biotite library. Quickly convert between formats, extract features, and prepare data for machine learning or structural analysis.

Navigation

• Tutorial
  • Getting Started
• Installation
  • 1. Installing via pip (recommended)
  • 2. Using the Standalone Apptainer
  • 2. Local Conda Environment
  • 3. As a Dependency in Your Apptainer
• Glossary
  • Entities vs. Instances
  • Suffixes
  • Chains, PN_Units, and Molecules
  • Combinatorial Nomenclature - Worked Example
• API
  • IO
  • ML
• Examples
• Contributing
  • As you code
  • As you commit
  • As you finalize a PR
  • As you review
  • Visual Aids
  • More detail