Metadata

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.\n"}

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

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+:

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

Pharmaclaw Chemistry Query

安装技能