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 skills add K-Dense-AI/drug-discovery-agent-skills --skill rdkitgit clone --depth 1 https://github.com/K-Dense-AI/drug-discovery-agent-skillsWrote 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/k-dense-ai/drug-discovery-agent-skills/rdkit)<a href="https://agentmods.dev/skills/k-dense-ai/drug-discovery-agent-skills/rdkit"><img src="https://agentmods.dev/badge/skills/k-dense-ai/drug-discovery-agent-skills/rdkit/github.svg" alt="Measured on agentmods" height="20"></a>Or the 80×15 button, for a site that already has a row of RSS and ATOM ones. Only the verdict fits; the numbers stay here.
<a href="https://agentmods.dev/skills/k-dense-ai/drug-discovery-agent-skills/rdkit"><img src="https://agentmods.dev/badge/skills/k-dense-ai/drug-discovery-agent-skills/rdkit.svg" alt="Reviewed on agentmods" width="80" height="20"></a>- NVIDIA SkillSpector pass
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 5.1 | $0.00189 | $0.01794 |
| Opus 5 | $0.00095 | $0.00897 |
| Sonnet 5 | $0.00038 | $0.00359 |
| Haiku 4.5 | $0.00019 | $0.00179 |
Grade A, and why
rdkit 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 12d 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 — 115 lines — stays where its author put it; the contents beside it link to each section on GitHub.
RDKit Cheminformatics Toolkit
Overview
RDKit is a comprehensive cheminformatics library providing Python APIs for molecular analysis and manipulation. This skill provides guidance for reading/writing molecular structures, calculating descriptors, fingerprinting, substructure searching, chemical reactions, 2D/3D coordinate generation, and molecular visualization. Use this skill for drug discovery, computational chemistry, and cheminformatics research tasks.
Checked against: RDKit 2026.03.5 (rdkit 2026.3.5 on PyPI, released 2026-08-03), August 2026. Official installation docs continue to recommend conda-forge for most users, while cross-platform PyPI wheels are published under the rdkit package name. rdkit-pypi is the old PyPI package name and should only appear when maintaining legacy environments.
Installation and Setup
Use uv when installing into an existing Python environment:
uv pip install rdkit
For reproducible chemistry environments, especially when mixing compiled scientific packages, conda-forge remains the upstream recommendation:
conda create -c conda-forge -n my-rdkit-env rdkit
conda activate my-rdkit-env
Avoid installing both conda rdkit and PyPI rdkit/rdkit-pypi into the same environment unless you are deliberately debugging packaging behavior. Mixed installs can make it unclear which binary extension is being imported.
Core Capabilities
Twelve capability areas, each with worked code, are documented in references/core_capabilities.md:
| # | Area | Covers |
|---|---|---|
| 1 | Molecular I/O and creation | SMILES, MOL files and blocks, InChI, SDF and SMILES suppliers, multithreaded reading, writers |
| 2 | Sanitization and validation | disabling automatic sanitization, manual and partial sanitization, detecting problems first |
| 3 | Analysis and properties | atom and bond iteration, ring information and SSSR, chirality and stereochemistry, fragments |
| 4 | Descriptors | MW, LogP, TPSA, H-bond donors/acceptors, rotatable bonds, aromatic rings, bulk calculation, drug-likeness |
| 5 | Fingerprints and similarity | topological, Morgan/ECFP via rdFingerprintGenerator, MACCS, atom pair, torsion, Avalon; Tanimoto and other metrics; Butina clustering |
| 6 | Substructure searching | SMARTS queries, match retrieval, and a library of common patterns |
| 7 | Chemical reactions | reaction SMARTS, applying reactions, reaction fingerprints |
| 8 | 2D and 3D coordinates | depiction, template alignment, ETKDG embedding, force-field optimization, RMSD, constrained embedding |
| 9 | Visualization | single and grid images, substructure highlighting, custom drawer options, Jupyter integration, fingerprint bit environments |
| 10 | Molecular modification | explicit hydrogens, Kekulization, aromaticity, substructure replacement, charge neutralization |
| 11 | Hashes and standardization | Murcko scaffold and canonical hashes, regioisomer hashes, randomized SMILES for augmentation |
| 12 | Pharmacophore and 3D features | feature factories and feature extraction |
What ships with it
8 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.
- references/api_reference.md 17 KB
- references/core_capabilities.md 15 KB
- references/descriptors_reference.md 12 KB
- references/smarts_patterns.md 8.0 KB
- references/workflows_and_best_practices.md 5.2 KB
- scripts/molecular_properties.py 8.0 KB runs code
- scripts/similarity_search.py 10 KB runs code
- scripts/substructure_filter.py 13 KB runs code
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.
- 12d ago First seen · 115 lines · 189 tokens per session scan A c3765cdab00a
rdkit is a skill published in the GitHub repository K-Dense-AI/drug-discovery-agent-skills (28 stars, last pushed 4d ago), licensed MIT. It adds 189 tokens to every session and 1,794 once invoked, about $0.0009 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 2026-08-30.
Other skills, from other repositories
patsnap-biological-modality
Biological sequence and modality intelligence via Patsnap MCP.
patsnap-chemical-molecular
Patsnap Chemical Molecular MCP for AI agents. Search 160M+ chemical structures, synthetic routes, and bioactivity data via specialized chemistry tools.
patsnap-scientific-translational-evidence
Patsnap Scientific & Translational Evidence MCP for AI agents. Retrieval platform focusing on scientific literature and translational outcomes, covering academic publication queries and translational medicine record tracking.
patsnap-solution-engine
Patsnap TRIZ Concept Solution Engine MCP for AI agents. Generates innovation or product cost-reduction concepts through asynchronous TRIZ and TRIZ/DFMA workflows. Use for engineering problem solving, concept alternatives, cost-reduction analysis, task-progress retrieval, and selected-solution details.
patsnap-clinical-trials
Patsnap Clinical Trials MCP for AI agents. Intelligent clinical trial retrieval system, covering registered trial tracking, trial details and results analysis, and supporting clinical semantic search.
patsnap-current-awareness
Patsnap Current Awareness MCP for AI agents. Tracking system for pharmaceutical industry dynamics and cutting-edge news, covering global medical news search and in-depth news detail mining.