agentmods.dev

AutoResearchClaw: Skill for Claude Code

.claude/skills/chemistry-rdkit/SKILL.md

chemistry-rdkit is a skill for Claude Code from aiming-lab/AutoResearchClaw. It costs 41 tokens per session (812 once invoked), scanned A, original, MIT.

A Python toolkit for computational chemistry, the use of software to represent and study molecules. It works with molecular structures, chemical descriptors, fingerprints, and substructure searches.

In plain words
What is it for?
It is for reading SMILES or SDF files, calculating properties such as molecular weight and lipophilicity, comparing molecules, and finding chemical substructures.
Why use it?
It turns chemical structures into data that can be measured, compared, and searched programmatically.

Skill for Claude Code

Written for Claude Code: installed under .claude/.

This is aiming-lab/AutoResearchClaw's own configuration. It tells Claude Code how to work on AutoResearchClaw itself, so it is not a mod to install elsewhere. Copy it as a starting point and replace the rules that are about this project. Everything AutoResearchClaw configures →

not rated 15krepo +34 2mo ago A scan SkillSpector: pass 41 tokens original MIT
View source ↗ aiming-lab/AutoResearchClaw
About the project

AutoResearchClaw is a system that turns a research idea into a scientific paper through autonomous and collaborative AI research workflows. It is for researchers who want agents to investigate questions, run experiments, and produce papers, with optional human guidance. Catalogue skills and agents provide parts of its research workflow.

aiming-lab/AutoResearchClaw · 14,822 stars · on GitHub

Reuse

Borrowing it

Nothing to install: this file belongs to aiming-lab/AutoResearchClaw. Take a copy, put it at the same path in your own repository, and replace the rules that are about this project with yours.

Copy the file
curl -O https://raw.githubusercontent.com/aiming-lab/AutoResearchClaw/main/.claude/skills/chemistry-rdkit/SKILL.md
Clone the repo
git clone --depth 1 https://github.com/aiming-lab/AutoResearchClaw

Made for: Claude Code.

Wrote 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.

agentmods badge for chemistry-rdkit

README.md
[![agentmods](https://agentmods.dev/badge/skills/aiming-lab/autoresearchclaw/chemistry-rdkit/github.svg)](https://agentmods.dev/skills/aiming-lab/autoresearchclaw/chemistry-rdkit)
Your own site
<a href="https://agentmods.dev/skills/aiming-lab/autoresearchclaw/chemistry-rdkit"><img src="https://agentmods.dev/badge/skills/aiming-lab/autoresearchclaw/chemistry-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.

agentmods 80×15 button for chemistry-rdkit

Your own site · 80×15
<a href="https://agentmods.dev/skills/aiming-lab/autoresearchclaw/chemistry-rdkit"><img src="https://agentmods.dev/badge/skills/aiming-lab/autoresearchclaw/chemistry-rdkit.svg" alt="Reviewed on agentmods" width="80" height="20"></a>
Per session 41 Skills are progressive disclosure: only the name and description are preloaded; the body loads when the skill is used.
When invoked 812 The whole file, excluding the scripts and references it only reads on demand.
Security scan A 0 findings. A grade says what 26 rules found in the file — not that it is safe. Third-party audits
  • NVIDIA SkillSpector pass 7 Sept 2026
How audits are shown
Origin original No closer match found in the catalogue.
Token cost

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.

ModelPer sessionOnce invoked
Fable 5.1 $0.00041 $0.00812
Opus 5.5 $0.00016 $0.00325
Sonnet 5.5 $0.00008 $0.00162
Haiku 4.5 $0.00004 $0.00081

Measured 2mo ago against content hash 7cae29200713, method: parsed. Prices are Anthropic first-party input rates as of 2026-10-07, from the pricing page.

Security

Grade A, and why

chemistry-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 2mo 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.

.claude/skills/chemistry-rdkit/SKILL.md · 60 lines

How it starts

The opening of the file, as written. The whole thing — 60 lines — stays where its author put it; the contents beside it link to each section on GitHub.

RDKit Cheminformatics Best Practice

Molecular I/O

  1. Create molecules from SMILES: mol = Chem.MolFromSmiles('CCO')
  2. Always check for None: MolFromSmiles returns None on invalid input
  3. Convert to canonical SMILES: Chem.MolToSmiles(mol)
  4. Read SDF files: suppl = Chem.SDMolSupplier('file.sdf')
  5. Read SMILES files: suppl = Chem.SmilesMolSupplier('file.smi')
  6. Write molecules: writer = Chem.SDWriter('output.sdf')

Molecular Descriptors

  1. Molecular weight: Descriptors.MolWt(mol)
  2. LogP (lipophilicity): Descriptors.MolLogP(mol)
  3. TPSA (polar surface area): Descriptors.TPSA(mol)
  4. H-bond donors/acceptors: Descriptors.NumHDonors(mol), Descriptors.NumHAcceptors(mol)
  5. Rotatable bonds: Descriptors.NumRotatableBonds(mol)
  6. Lipinski Rule of 5: MW <= 500, LogP <= 5, HBD <= 5, HBA <= 10

Fingerprints and Similarity

  1. Morgan (circular) fingerprints: AllChem.GetMorganFingerprintAsBitVect(mol, radius=2, nBits=2048)
  2. RDKit fingerprints: Chem.RDKFingerprint(mol)
  3. MACCS keys: MACCSkeys.GenMACCSKeys(mol)
  4. Tanimoto similarity: DataStructs.TanimotoSimilarity(fp1, fp2)
  5. Use radius=2 (ECFP4 equivalent) as default for most applications
  6. For virtual screening, Tanimoto > 0.7 suggests structural similarity

Substructure Search

  1. SMARTS patterns: pattern = Chem.MolFromSmarts('[OH]')
  2. Check match: mol.HasSubstructMatch(pattern)
  3. Get all matches: mol.GetSubstructMatches(pattern)
  4. Common SMARTS: [#6](=O)[OH] (carboxylic acid), [NH2] (primary amine)
  5. Filter compound libraries by functional group presence

Property Calculation Patterns

  1. Batch processing: iterate over SDMolSupplier, skip None entries
  2. Use Chem.Descriptors.descList for all available descriptors
  3. For ADMET filtering, calculate Lipinski, Veber, and PAINS filters
  4. Generate 3D coordinates: AllChem.EmbedMolecule(mol, AllChem.ETKDG())
  5. Minimize energy: AllChem.MMFFOptimizeMolecule(mol)

Common Pitfalls

  1. Always sanitize molecules (default behavior) — disable only when needed
  2. Add hydrogens explicitly for 3D work: Chem.AddHs(mol)
  3. Handle stereochemistry: use Chem.AssignStereochemistry(mol)
  4. Large SDF files: use ForwardSDMolSupplier for memory efficiency
  5. Kekulization errors usually indicate invalid SMILES input

Read the full file on GitHub · 60 lines

Changes

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.

  1. 2mo ago First seen · 60 lines · 41 tokens per session scan A 7cae29200713

Subscribe to this mod's changes

chemistry-rdkit is a skill published in the GitHub repository aiming-lab/AutoResearchClaw (14,822 stars, last pushed 2mo ago), licensed MIT. It adds 41 tokens to every session and 812 once invoked, about $0.0002 per session on Opus 5.5. 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.

LanguagesPythonScientificautonomous-researchcitation-verificationllm-agentsmulti-agent-debateopenclawpaper-generation
Related

chemistry-rdkit compared with skills from other repositories

chemistry-rdkit next to 6 skills from other repositories
ModTypeStarsLast pushLicenceScanTokensWorks with
chemistry-rdkitaiming-lab/AutoResearchClawSkill15k2mo agoMITA41Claude Code
evo-stl-binary-parserOpenLAIR/OpenSkillSkill971mo agoApache-2.0A49Claude Code, Codex
pymatgen-structurejinzhezenggroup/computational-chemistry-agent-skillsSkill1564d agoLGPL-3.0A64Claude Code, Codex
xtbloom-run-python-inferencejinzhezenggroup/computational-chemistry-agent-skillsSkill1564d agoLGPL-3.0A112Codex
dpdata-driverjinzhezenggroup/computational-chemistry-agent-skillsSkill1564d agoLGPL-3.0A88Claude Code, Codex
python-packagesA-EVO-Lab/a-evolveSkill842todaynoneB27Claude Code, Codex
anndataFreedomIntelligence/OpenClaw-Medical-SkillsSkill3.1k3mo agononeA67Claude Code, Codex