Menu

Individual skill

molecule-visualization

Publication-quality molecular visualization. 2D structure drawings (PNG/SVG), molecule grids with property annotations, scaffold highlighting, protein-ligand interaction diagrams, and interactive 3D views.

backend/cli/skills/chemistry/molecule-visualization/SKILL.md

Read pinned source

Source commit a08e0ad0ad3d6448123039ee4659163eb2e35d99

What was checked

Matches the observed repository HEAD
Yes
Scanner rules are current
Yes
Repository scan complete
No
Skill scan complete
No
Observed behavior
Network or broad shell
Last checked
Nov 2, 2026

These are observations at the recorded commit, not a guarantee of safety. Review the source before running it.

Install this skill

Choose an agent in your Stack or copy a command below. Commands fetch the pinned commit and copy only this skill directory. Existing destinations are refused. Copying a command does not install anything.

An install command is unavailable: current rules, complete repository and skill scans, an eligible behavior level and a permitted license are required.

Repository context

Repository stars (not skill ratings)
4,351
Repository last updated
Nov 6, 2026
License
Apache-2.0

Observed agent integration: No specific integration evidence. Standard SKILL.md installation does not imply verified compatibility.

Files and excerpt

File metadata and permitted, redacted excerpts come from the recorded scan. Source links are pinned to that commit.

Browse files
Read excerpt

# Molecule Visualization

Generate publication-quality molecular images for drug discovery, medicinal chemistry, and computational chemistry workflows. This skill provides a comprehensive suite of tools for rendering 2D structural drawings, annotated molecule grids, scaffold decomposition views, protein-ligand interaction diagrams, and interactive 3D molecular viewers.

## When to Use

- **2D structure drawings**: Generate clean, high-resolution depictions of small molecules for papers, patents, reports, and presentations.
- **Molecule grids**: Compare compound series side-by-side with property annotations (QED, LogP, MW, etc.).
- **Scaffold highlighting**: Visualize SAR by decomposing molecules into core scaffolds and R-groups.
- **Interaction diagrams**: Summarize protein-ligand binding modes from docking or crystal structures.
- **3D interactive views**: Create browser-based 3D viewers for proteins, ligands, and complexes.

## Installation