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.

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>

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

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+:

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

scripts/advanced_chem.py

Advanced cheminformatics engine with 6 Tier 1 capabilities.

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

Action	Description	Key Args
standardize	Salt stripping, charge normalization, tautomer enumeration	--smiles
descriptors	217+ molecular descriptors (RDKit full set), QED, SA Score, Lipinski/Veber rules	--smiles --descriptor_set all|druglike|physical|topological
scaffold	Murcko scaffold extraction, generic scaffolds, diversity analysis, R-group decomposition	--smiles or --target_smiles "smi1,smi2,..." --rgroup_core <SMARTS>
mcs	Maximum Common Substructure across 2+ molecules	--target_smiles "smi1,smi2,..."
mmpa	Matched Molecular Pair Analysis — find single-point transformations	--target_smiles "smi1,smi2,..."
chemspace	Chemical space visualization (PCA/t-SNE/UMAP scatter plot PNG)	--target_smiles "smi1,smi2,..." --method pca|tsne|umap --output plot.png

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