pharmaclaw-chemistry-query
Chemistry agent skill for PubChem API queries (compound info/properties, structures/SMILES/images, synthesis routes/references) + RDKit cheminformatics (SMILES to molecule props/logP/TPSA, 2D PNG/SVG viz, Morgan fingerprints, retrosynthesis/BRICS disconnects, multi-step synth planning). Use for chemistry tasks involving compounds, molecules, structures, PubChem data, RDKit analysis, SMILES processing, synthesis routes, retrosynthesis, reaction simulation. Triggers on chemistry, compounds, molecules, chemical data/properties, PubChem, RDKit, SMILES, structures, synthesis, reactions, retrosynthesis, synth plan/route.
Install via CLI (Recommended)
clawhub install openclaw/skills/skills/cheminem/pharmaclaw-chemistry-queryChemistry Query Agent v1.4.1
Overview
Full-stack chemistry toolkit combining PubChem data retrieval with RDKit molecule processing, visualization, analysis, retrosynthesis, and synthesis planning. All outputs are structured JSON for easy downstream chaining. Generates PNG/SVG images on demand.
Key capabilities:
- PubChem compound lookup (info, structure, synthesis refs, similarity search)
- RDKit molecular properties (MW, logP, TPSA, HBD/HBA, rotatable bonds, aromatic rings)
- 2D molecule visualization (PNG/SVG)
- BRICS retrosynthesis with recursive depth control
- Multi-step synthesis route planning
- Forward reaction simulation with SMARTS templates
- Morgan fingerprints and similarity/substructure search
- 21 named reaction templates (Suzuki, Heck, Grignard, Wittig, Diels-Alder, etc.)
Quick Start
# PubChem compound info
exec python scripts/query_pubchem.py --compound "aspirin" --type info
# Molecular properties from SMILES
exec python scripts/rdkit_mol.py --smiles "CC(=O)Oc1ccccc1C(=O)O" --action props
# Retrosynthesis
exec python scripts/rdkit_mol.py --target "CC(=O)Oc1ccccc1C(=O)O" --action retro --depth 2
# Full chain (name → props + draw + retro)
exec python scripts/chain_entry.py --input-json '{"name": "caffeine", "context": "user"}'
Scripts
scripts/query_pubchem.py
PubChem REST API queries with automatic name→CID resolution and timeout handling.
--compound <name|CID> --type <info|structure|synthesis|similar> [--format smiles|inchi|image|json] [--threshold 80]
- info: Formula, MW, IUPAC name, InChIKey (JSON)
- structure: SMILES, InChI, image URL, or full JSON
- synthesis: Synonyms/references for a compound
- similar: Similar compounds by 2D fingerprint (top 20)
scripts/rdkit_mol.py
RDKit cheminformatics engine. Resolves names via PubChem automatically.
--smiles <SMILES> --action <props|draw|fingerprint|similarity|substruct|xyz|react|retro|plan>
| Action | Description | Key Args |
|---|---|---|
| props | MW, logP, TPSA, HBD, HBA, rotB, aromRings | --smiles |
| draw | 2D PNG/SVG (300×300) | --smiles --output file.png --format png|svg |
| retro | BRICS recursive retrosynthesis | --target <SMILES|name> --depth N |
| plan | Multi-step retro route | --target <SMILES|name> --steps N |
| react | Forward reaction via SMARTS | --reactants "smi1 smi2" --smarts "<SMARTS>" |
| fingerprint | Morgan fingerprint bitvector | --smiles --radius 2 |
| similarity | Tanimoto similarity scoring | --query_smiles --target_smiles "smi1,smi2" |
| substruct | Substructure matching | --query_smiles --target_smiles "smi1,smi2" |
| xyz | 3D coordinates (MMFF optimized) | --smiles |
scripts/chain_entry.py
Standard agent chain interface. Accepts {"smiles": "...", "context": "..."} or {"name": "...", "context": "..."}. Returns unified JSON with props, visualization, and retrosynthesis.
Metadata
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Find the right skillPaste this into your clawhub.json to enable this plugin.
{
"plugins": {
"official-cheminem-pharmaclaw-chemistry-query": {
"enabled": true,
"auto_update": true
}
}
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