Choose the UML style for Zendock

All options include both a class diagram and a workflow/activity diagram. I recommend Option A.

A. Balanced Documentation
DockingRunner
Receptor
Ligand
Results

Core classes + important helpers + clean workflow

Balanced update

Keep `PROJECT_UML.md`, correct details from the code, and make the diagrams readable for README/docs use.

Pros

  • Best fit for project docs
  • Not too noisy
  • Maintains current file

Cons

  • Omits some private helpers
B. Public API Overview
Receptor
→
DockingRunner
←
Ligand

Small, teaching-oriented diagram

Compact overview

Focus only on the notebook-facing API and the main docking sequence.

Pros

  • Easy for users to understand
  • Great for README

Cons

  • Less useful for contributors
  • Hides internal architecture
C. Detailed Architecture Pack
Facades
Models
Tools
Fetchers
Visualizers
Exceptions

More diagrams, more relationships

Detailed contributor docs

Add class, workflow, module/dependency, and artifact-output diagrams.

Pros

  • Most complete
  • Good onboarding reference

Cons

  • Longer file
  • More maintenance burden