synthetic-sciences/openscience is an AI workbench that carries out scientific research by reading papers, forming hypotheses, writing and running code, conducting experiments, analyzing results, and preparing reports. Researchers use it for work in machine learning, biology, physics, and chemistry with remote or local models. Catalogue add-ons extend its scientific workflows through skills and instructions.
Getting it into your agent
One page per mod, every tool's command on it. A separate URL per tool would split the same page into five that compete with each other.
npx agentmods add skills/synthetic-sciences/openscience/molecule-visualizationnpx skills add synthetic-sciences/openscience --skill molecule-visualizationgit clone --depth 1 https://github.com/synthetic-sciences/openscienceWrote this? Show the measurements
A badge with what this costs and how it scanned, read live from this page, so it follows the numbers instead of freezing them. Markdown for a README, HTML for a documentation site or a project page.
[](https://agentmods.dev/skills/synthetic-sciences/openscience/molecule-visualization)<a href="https://agentmods.dev/skills/synthetic-sciences/openscience/molecule-visualization"><img src="https://agentmods.dev/badge/skills/synthetic-sciences/openscience/molecule-visualization.svg" alt="Measured on agentmods" height="20"></a>What it costs to keep this loaded
Counted locally with the o200k_base tokenizer, which is exact for GPT models; Claude uses its own tokenizer and its counts differ. Treat this as one consistent yardstick across the catalogue rather than a bill. Prices are per million input tokens.
| Model | Per session | Once invoked |
|---|---|---|
| Fable 5 | $0.00044 | $0.01746 |
| Opus 5 | $0.00022 | $0.00873 |
| Sonnet 5 | $0.00009 | $0.00349 |
| Haiku 4.5 | $0.00004 | $0.00175 |
Grade A, and why
molecule-visualization scanned grade A with 0 findings against 26 rules in 11 categories — prompt injection, anti-refusal, data exfiltration, privilege escalation, supply chain, agent snooping, system-prompt leakage, SSRF and excessive agency — measured 2d ago.
A static scan of the body, not an audit. Every finding is printed with the line that produced it so you can judge whether it matters here. A mod is markdown that instructs an agent; that is exactly why what it instructs is worth reading.
Nothing flagged
None of the 26 patterns this scan looks for appear in this file: no shell pipes, no recursive deletes, no credential paths, no hidden text, no instruction-override or anti-refusal phrasing, no agent-config snooping. That is not a guarantee, it is the absence of the things that are checkable.
How it starts
The opening of the file, as written. The whole thing — 198 lines — stays where its author put it; the contents beside it link to each section on GitHub.
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
All scripts require Python 3.8+ and the following packages:
# Core (required for all scripts)
pip install rdkit-pypi pillow matplotlib
# For protein-ligand interaction diagrams
pip install biopython
# For 3D interactive views
pip install py3Dmol
# Full installation
pip install rdkit-pypi pillow matplotlib biopython py3Dmol
Core Workflows
1. Single Molecule Drawing (scripts/draw_2d.py)
Render a single molecule as a high-quality PNG or SVG image.
# Basic usage
python scripts/draw_2d.py --smiles "c1ccccc1" --output benzene.png
# With atom highlighting and title
python scripts/draw_2d.py \
--smiles "CC(=O)Oc1ccccc1C(=O)O" \
--output aspirin.svg \
--title "Aspirin" \
--highlight-atoms 0,1,2,3 \
--highlight-color "#4A90D9"
# Show atom indices for reference
python scripts/draw_2d.py \
--smiles "c1ccc(NC(=O)c2ccccc2)cc1" \
--output benzanilide.png \
--show-atom-indices \
--size 600x400
2. Molecule Grid (scripts/draw_grid.py)
Compare multiple molecules in a grid layout with optional property annotations.
What ships with it
6 files beside SKILL.md in the same directory: the scripts, references and assets a skill reads on demand. Not counted in the per-session cost; read them before you install if any of them is executable.
What this file has done since we first saw it
Hashed on every crawl. A supply-chain change to an agent config is a question of when, not whether, so the history is kept rather than the latest state alone.
- 2d ago First seen · 198 lines · 44 tokens per session scan A b1ecad8b4e5c
molecule-visualization is a skill published in the GitHub repository synthetic-sciences/openscience (3,473 stars, last pushed today), licensed Apache-2.0. It adds 44 tokens to every session and 1,746 once invoked, about $0.0002 per session on Opus 5. A static security scan graded it A with 0 findings. No closer match exists in the catalogue, so it is treated as the original; first seen 2026-09-03.
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