Chemistry Query Agent v1.4.0

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.

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(O)O>>[c:1][c:3]"

Tested With

All features verified end-to-end with RDKit 2024.03+:

Molecule	SMILES	Tests Passed
Caffeine	`CN1C=NC2=C1C(=O)N(C(=O)N2C)C`	info, structure, props, draw, retro, plan, chain
Aspirin	`CC(=O)Oc1ccccc1C(=O)O`	info, structure, props, draw, retro, plan, chain
Sotorasib	PubChem name lookup	info, structure, props, draw, retro, chain
Ibuprofen	PubChem name lookup	info, structure, props, chain
Invalid SMILES	`XXXINVALID`	Graceful JSON error
Empty 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

chemistry-query

Installation