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Tool System

The tool system is the core of codemol. Every action — loading structures, measuring distances, changing representations — is implemented as a tool module.

Key Concepts

  • Tool — A Python module with a run() function
  • Tool group — A directory containing related tools (e.g., tools/measurements/)
  • Auto-discovery — Tools are found at startup by scanning the tools/ directory
  • Dispatch — The runtime that routes commands to tools, handles argument fitting and scoping

27+ Groups, 200+ Tools

Group Tools Purpose
io load, clear, density, project File I/O and PDB fetching
representations cartoon, sticks, surface, ... (15) Visual representations
color bychain, byelement, spectrum, ... (10) Coloring schemes
measurements distance, angle, dihedral, contacts, ... (11) Structural measurements
analysis align, rmsd, clashes, pockets, ... (17) Structural analysis
interactions hbonds, saltbridges, pistacking, ... (6) Interaction detection
visibility show, hide Object visibility
selection select, nearby Selection management
labels label, smart, font, color, ... (9) Atom/residue labels
camera orient, zoom, turn, clip Camera controls
presets publication, presentation, ... (14) One-click visual presets
surface area, transparency, type Surface analysis
edit hadd, remove, alter, extract, ... (13) Structure editing
rendering lighting, background, shadows, ... (11) Render settings
docking load, info, cluster, split, ... (9) Docking analysis
trajectory load, play, rmsd, align, ... (8) MD trajectories
session save, load, list, update, delete Session management
timeline add, recall, list, export, ... (8) Scene timeline
crystal symexp, contacts, info Crystal symmetry
share create, join, status, stop, ... (6) Shared sessions
agents list, use, stop, status, config AI agent control
export png, ray Image export
search search, load PDB search
config list, set, interactive, dirs Configuration
info atoms, mass, ligand, list Structure info
movie setup, play, rock, export, stop Movie creation
media list, open, rename, delete Media management
alias alias Command aliases

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