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BytesAgain β€Ί Skills β€Ί Pharmaclaw Chemistry Query
πŸ¦€ ClawHub

Pharmaclaw Chemistry Query

by @cheminem

Chemistry agent skill for PubChem API queries (compound info/properties, structures/SMILES/images, synthesis routes/references) + RDKit cheminformatics (SMIL...

Versionv2.0.1
Downloads1,129
Installs4
Stars⭐ 3
#clawhub
TERMINAL
clawhub install pharmaclaw-chemistry-query

πŸ“– About This Skill

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 β†’ 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  --type  [--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  --action

    | Action | Description | Key Args | |--------|-------------|----------| | props | MW, logP, TPSA, HBD, HBA, rotB, aromRings | --smiles | | draw | 2D PNG/SVG (300Γ—300) | --smiles --output file.png --format png\|svg | | retro | BRICS recursive retrosynthesis | --target --depth N | | plan | Multi-step retro route | --target --steps N | | react | Forward reaction via SMARTS | --reactants "smi1 smi2" --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": "",
  "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 β†’ Full Profile: chain_entry.py with {"name": "ibuprofen"} β†’ props + draw + retro 2. Chemistry β†’ 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(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 β€” PubChem API endpoint reference and rate limits
  • scripts/rdkit_reaction.py β€” Legacy reaction module
  • scripts/chembl_query.py, scripts/pubmed_search.py, scripts/admet_predict.py β€” Additional query modules

    • scripts/advanced_chem.py

    Advanced cheminformatics engine with 6 Tier 1 capabilities.

    --action  --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 | | mcs | Maximum Common Substructure across 2+ molecules | --target_smiles "smi1,smi2,..." | | mmpa | Matched Molecular Pair Analysis β€” 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() β€” length limits, null-byte rejection for all user inputs
  • Added _sanitize_output_path() β€” 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

    • πŸ’‘ Examples

    # 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 β†’ props + draw + retro)
    
exec python scripts/chain_entry.py --input-json '{"name": "caffeine", "context": "user"}'