Chemistry Rdkit logo

Chemistry Rdkit

OrganizationPopular
aiming-lab
chemistry-rdkit

Computational chemistry with RDKit for molecular analysis, descriptors, fingerprints, and substructure search. Use when working with SMILES, drug discovery, or cheminformatics tasks.

Overview

Publisheraiming-lab
RepositoryAutoResearchClaw
Skill namechemistry-rdkit
Stars
14.4K
Forks
1.7K
Bundled files
Instructions only
LicenseMIT
Links
Skill sourceRepository
  • Markdown instructions

    A SKILL.md file the model loads on demand, so it only costs tokens when a request actually matches.

  • Works with any LLM

    AI skills are plain Markdown, not provider-specific code, so this works with GPT, Claude, Gemini, Grok, or a local model.

  • Self-contained

    Everything the model needs lives in the instructions — no extra files to sync.

  • Open source

    Published by aiming-lab on GitHub. Read the source before you install it.

Installation

Install the Chemistry Rdkit AI skill in TypingMind to use it with any LLM, or drop it into another agent that reads SKILL.md.

1

Install in TypingMind

TypingMind installs a skill straight from its GitHub folder — it reads SKILL.md, bundles the resource files, and stores the result locally.

  1. Open the app and go to Plugins → Skills.
  2. Choose "Install from GitHub".
  3. Paste the skill folder URL below and confirm.
  4. Enable the skill in any chat where you want it available.
Plugins → Skills → Add skill → From GitHub URL, then paste the folder URL and press Continue.
2

Install in another agent

Any agent that reads the Agent Skills format can use this skill — copy the folder into that agent's skills directory.

Claude Code — .claude/skills
git clone --depth 1 https://github.com/aiming-lab/AutoResearchClaw.git /tmp/AutoResearchClaw
mkdir -p .claude/skills
cp -r /tmp/AutoResearchClaw/researchclaw/skills/builtin/domain/chemistry-rdkit .claude/skills/chemistry-rdkit
Restart Claude Code after copying so it picks up the new skill.

Use it in TypingMind

Enable Chemistry Rdkit in any TypingMind chat and the model takes it from there. Its name and description sit in the system prompt, and the moment a request matches, the model loads the full instructions itself — you never invoke it by hand, and it costs no tokens until it is actually used.

The model loads Chemistry Rdkit on its own as soon as a request matches it.

Works with any AI model

AI skills are plain Markdown instructions rather than provider-specific code, so Chemistry Rdkit is not tied to the model it was written for. Install it once in TypingMind and use it with GPT-5, Claude, Gemini, Grok, DeepSeek, Mistral, Llama, or a local model you run yourself — all on your own API keys.

  • Loaded only when it is needed

    The system prompt carries just the name and description. The instructions are fetched on the first matching request, so an idle skill costs nothing.

  • Switch models mid-chat

    Because the skill is instructions rather than code, changing model does not break it — the next model reads the same SKILL.md.

Skill instructions

This is the SKILL.md content the model loads. Read it before installing — a skill is instructions your model will follow.

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

Frequently asked questions

What does the Chemistry Rdkit AI skill do?

Computational chemistry with RDKit for molecular analysis, descriptors, fingerprints, and substructure search. Use when working with SMILES, drug discovery, or cheminformatics tasks.

Why use Chemistry Rdkit on TypingMind?

Because you install it once and use it with any model. Chemistry Rdkit is plain Markdown rather than provider-specific code, so the same skill runs on GPT-5, Claude, Gemini, Grok, or a local model — and you can switch model mid-chat without it breaking. TypingMind runs on your own API keys, so you pay providers directly instead of a per-seat subscription, and your skills and chats stay in your own storage.

How do I install Chemistry Rdkit in TypingMind?

Open Plugins → Skills → Install from GitHub in TypingMind and paste https://github.com/aiming-lab/AutoResearchClaw/tree/main/researchclaw/skills/builtin/domain/chemistry-rdkit. TypingMind reads its SKILL.md and installs it as a skill you can enable per chat.

Which AI models can use Chemistry Rdkit?

Any model you connect in TypingMind. AI skills are plain Markdown instructions rather than provider-specific code, so GPT, Claude, Gemini, Grok, and local models can all load this skill when a request matches it.

How many AI models can I use with Chemistry Rdkit?

As many as you like. As long as a model supports skills, you can use Chemistry Rdkit with it — GPT, Claude, Gemini, Grok, DeepSeek, Mistral, Llama and more — all on TypingMind with your own API keys.

Is the Chemistry Rdkit AI skill free?

Yes. It is published on GitHub by aiming-lab under the MIT license. You only pay your own AI provider for the tokens you use.

What are AI skills?

An AI skill is a reusable instruction bundle that teaches an AI model how to do one specific task. It follows the open Agent Skills format: a SKILL.md file with a name and description, plus any scripts, templates or reference files the model may need. The model reads the instructions only when your request matches the skill, so an installed skill costs nothing until it is used.

How are AI skills different from plugins or MCP servers?

A plugin or MCP server gives a model new tools to call — code that runs somewhere and returns a result. An AI skill gives the model knowledge and process instead: how to approach a task, which steps to follow, what good output looks like. Skills are plain Markdown, so they need no server, no API key and no runtime, and they work with any model.

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