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Chemistry Query

Chemistry agent skill for PubChem API queries (compound info/properties, structures/SMILES/images, synthesis routes/references) + RDKit cheminformatics (SMIL...

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Chemistry agent skill for PubChem API queries (compound info/properties, structures/SMILES/images, synthesis routes/references) + RDKit cheminformatics (SMIL...

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Requirements

Target platform: OpenClaw
Install method: Manual import
Extraction: Extract archive
Prerequisites: OpenClaw
Primary doc: SKILL.md

Package facts

Download mode: Yavira redirect
Package format: ZIP package
Source platform: Tencent SkillHub
What's included: scripts/chembl_query.py, scripts/pubmed_search.py, scripts/templates.json, scripts/admet_predict.py, scripts/rdkit_mol.py, scripts/chain_entry.py

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Release facts

Source: Tencent SkillHub
Verification: Indexed source record
Version: 1.0.0

Provenance

Publisher: Cheminem
Source page: View original listing
Canonical URL: Open canonical page

Documentation

ClawHub primary doc Primary doc: SKILL.md 10 sections Open source page

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/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> ActionDescriptionKey ArgspropsMW, logP, TPSA, HBD, HBA, rotB, aromRings--smilesdraw2D PNG/SVG (300×300)--smiles --output file.png --format png|svgretroBRICS recursive retrosynthesis--target <SMILES|name> --depth NplanMulti-step retro route--target <SMILES|name> --steps NreactForward reaction via SMARTS--reactants "smi1 smi2" --smarts "<SMARTS>"fingerprintMorgan fingerprint bitvector--smiles --radius 2similarityTanimoto similarity scoring--query_smiles --target_smiles "smi1,smi2"substructSubstructure matching--query_smiles --target_smiles "smi1,smi2"xyz3D 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. python scripts/chain_entry.py --input-json '{"name": "sotorasib", "context": "user"}' Output schema: { "agent": "chemistry-query", "version": "1.4.0", "smiles": "<canonical>", "status": "success|error", "report": {"props": {...}, "draw": {...}, "retro": {...}}, "risks": [], "viz": ["path/to/image.png"], "recommend_next": ["pharmacology", "toxicology"], "confidence": 0.95, "warnings": [], "timestamp": "ISO8601" }

scripts/templates.json

21 named reaction templates with SMARTS, expected yields, conditions, and references. Includes: Suzuki, Heck, Buchwald-Hartwig, Grignard, Wittig, Diels-Alder, Click, Sonogashira, Negishi, and more.

Chaining

Name → Full Profile: chain_entry.py with {"name": "ibuprofen"} → props + draw + retro Chemistry → Pharmacology: Output feeds directly into pharma-pharmacology-agent Retro + Viz: Get precursors, then draw each one Suzuki Test: --action react --reactants "c1ccccc1Br c1ccccc1B(O)O" --smarts "[c:1][Br:2].[c:3][B]([c:4])(O)O>>[c:1][c:3]"

Tested With

All features verified end-to-end with RDKit 2024.03+: MoleculeSMILESTests PassedCaffeineCN1C=NC2=C1C(=O)N(C(=O)N2C)Cinfo, structure, props, draw, retro, plan, chainAspirinCC(=O)Oc1ccccc1C(=O)Oinfo, structure, props, draw, retro, plan, chainSotorasibPubChem name lookupinfo, structure, props, draw, retro, chainIbuprofenPubChem name lookupinfo, structure, props, chainInvalid SMILESXXXINVALIDGraceful JSON errorEmpty input{}Graceful JSON error

Resources

references/api_endpoints.md — PubChem API endpoint reference and rate limits scripts/rdkit_reaction.py — Legacy reaction module scripts/chembl_query.py, scripts/pubmed_search.py, scripts/admet_predict.py — Additional query modules

Changelog

v1.4.0 (2026-02-14) Fixed PubChem SMILES/InChI endpoint (property/CanonicalSMILES/TXT) Fixed chain_entry.py HTML entity corruption Fixed brics_retro to handle BRICSDecompose string output correctly Added request timeouts (15s) to all PubChem calls Graceful error handling for invalid SMILES and empty input Updated chain output version and schema Comprehensive end-to-end testing v1.3.0 RDKit props NoneType fixes, invalid SMILES graceful errors React fix: ReactionFromSmarts import Name resolution via PubChem for all RDKit actions v1.2.0 BRICS retrosynthesis + 21 reaction templates library Multi-step synthesis planning

Category context

Code helpers, APIs, CLIs, browser automation, testing, and developer operations.

Source: Tencent SkillHub

Largest current source with strong distribution and engagement signals.

Package contents

Included in package

5 Scripts1 Config

scripts/admet_predict.py Scripts
scripts/chain_entry.py Scripts
scripts/chembl_query.py Scripts
scripts/pubmed_search.py Scripts
scripts/rdkit_mol.py Scripts
scripts/templates.json Config