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name: pharmaclaw-chemistry-query description: 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. type: code dependencies: python: ">=3.10" python-packages: - rdkit - gradio - pandas - Pillow system: - java (JRE 8+ for OPSIN, optional — only needed for IUPAC name→SMILES conversion) external-apis: - PubChem REST API (public, no key required) - ChEMBL API (public, no key required) - PubMed/NCBI E-utilities (public, no key required) notes: > OPSIN JAR (13.8MB) is auto-downloaded on first use of IUPAC name conversion with pinned SHA-256 checksum verification (d25bc08f...). All other functionality works without Java/OPSIN.

Chemistry 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>

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

1. Name → Full Profile: chain_entry.py with {"name": "ibuprofen"} → props + draw + retro
2. Chemistry → Pharmacology: Output feeds directly into pharma-pharmacology-agent
3. Retro + Viz: Get precursors, then draw each one
4. 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+:

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

v1.4.1 (2026-02-25)

• Security hardening: input sanitization for all subprocess calls (SMILES, compound names, output paths)
• Added _sanitize_input() — length limits, null-byte rejection for all user inputs
• Added _sanitize_output_path() — prevents path traversal, restricts extensions, blocks arbitrary file writes
• Added shell metacharacter rejection in resolve_target()
• Added SMILES validation via RDKit in chem_ui.py before subprocess calls
• Added compound input validation in query_pubchem.py (length/null-byte checks)
• Added timeout to resolve_target() PubChem subprocess call
• Addresses VirusTotal "suspicious" classification for argument injection vectors

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