Documentation

• Project README (overview, installation, quickstart)
• File Formats
• What 1.x keeps stable
• Networks in the Domainator Viewer
• Examples
• Agent-driven workflows
• Key algorithms
• Developing Domainator
• 1.0 release plan
• Structure search and annotation
• ESM-2 3B 3Di and foldseek integration
• Limitations and FAQ
• Command-line reference: every command's options, generated from its parser
• Tool manifest: domainator describe, for GUIs and other programs that drive Domainator