Pharmaclaw Chemistry Query

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

scripts/advanced_chem.py

Advanced cheminformatics engine with 6 Tier 1 capabilities.

--action <standardize|descriptors|scaffold|mcs|mmpa|chemspace> --smiles <SMILES> [options]

Examples:

# Standardize a salt form
python scripts/advanced_chem.py --action standardize --smiles "[Na+].CC(=O)[O-]"

# Full descriptors (217+)
python scripts/advanced_chem.py --action descriptors --smiles "CC(=O)Oc1ccccc1C(=O)O" --descriptor_set all

# Scaffold diversity of a set
python scripts/advanced_chem.py --action scaffold --target_smiles "CC(=O)Oc1ccccc1C(=O)O,CN1C=NC2=C1C(=O)N(C(=O)N2C)C,CC(C)Cc1ccc(cc1)C(C)C(=O)O"

# MCS of aspirin and salicylic acid
python scripts/advanced_chem.py --action mcs --target_smiles "CC(=O)Oc1ccccc1C(=O)O,c1ccccc1C(=O)O"

# Matched molecular pairs
python scripts/advanced_chem.py --action mmpa --target_smiles "c1ccc(CC(=O)O)cc1,c1ccc(CCC(=O)O)cc1"

# Chemical space PCA plot
python scripts/advanced_chem.py --action chemspace --target_smiles "CC(=O)Oc1ccccc1C(=O)O,CN1C=NC2=C1C(=O)N(C(=O)N2C)C,c1ccccc1" --method pca --output space.png

Changelog

v2.0.0 (2026-02-28)

• NEW: advanced_chem.py with 6 Tier 1 cheminformatics capabilities
  • Molecular Standardization & Tautomer Enumeration (salt stripping, charge normalization, canonical tautomers)
  • Extended Descriptors (217+ RDKit descriptors, QED, SA Score, Lipinski, Veber)
  • Scaffold Analysis (Murcko, generic scaffolds, diversity ratio, R-group decomposition)
  • Maximum Common Substructure (rdFMCS with coverage per molecule)
  • Matched Molecular Pair Analysis (rdMMPA fragmentation, transformation detection)
  • Chemical Space Visualization (PCA/t-SNE/UMAP with matplotlib scatter plots)
• Dependencies: scikit-learn, matplotlib (added)

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