Cactus cheminformatics guide

Skill brycewang-stanford/Auto-Empirical-Research-Skills/skills/43-wentorai-research-plugins/skills/domains/chemistry/cactus-cheminformatics-guide

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PNNL cheminformatics LLM agent for molecular analysis

SKILL.md

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CACTUS Cheminformatics Agent Guide

Overview

CACTUS is a cheminformatics LLM agent developed at Pacific Northwest National Laboratory (PNNL) that provides AI-assisted molecular analysis, property prediction, and chemical reasoning. It wraps RDKit, molecular databases, and ML models behind a conversational interface, enabling researchers to query molecular properties, perform similarity searches, and run cheminformatics workflows using natural language.

Usage

from cactus import ChemAgent

agent = ChemAgent(llm_provider="anthropic")

# Natural language chemistry queries
result = agent.ask(
    "What is the molecular weight and LogP of aspirin? "
    "Is it drug-like by Lipinski's rules?"
)
print(result.answer)
# Aspirin (CC(=O)Oc1ccccc1C(=O)O):
# MW: 180.16, LogP: 1.24
# Lipinski: PASS (MW<500, LogP<5, HBD=1≤5, HBA=4≤10)

# Molecular property calculation
props = agent.calculate_properties(
    smiles="CC(=O)Oc1ccccc1C(=O)O",
    properties=["mw", "logp", "tpsa", "hbd", "hba", "rotatable"],
)
print(props)

Similarity Search

# Find similar molecules
similar = agent.similarity_search(
    query_smiles="CC(=O)Oc1ccccc1C(=O)O",  # Aspirin
    database="chembl",
    threshold=0.7,  # Tanimoto similarity
    max_results=10,
)

for mol in similar:
    print(f"{mol.name}: {mol.smiles} "
          f"(similarity: {mol.tanimoto:.3f})")

Substructure Analysis

# Substructure search
matches = agent.substructure_search(
    pattern="c1ccccc1C(=O)O",  # Benzoic acid motif
    database="drugbank",
    max_results=20,
)

# Functional group identification
groups = agent.identify_functional_groups(
    smiles="CC(=O)Oc1ccccc1C(=O)O"
)
# ["ester", "carboxylic_acid", "aromatic_ring"]

Use Cases

Molecular analysis: Property calculation via natural language
Drug screening: Lipinski/Veber rule checking
Similarity search: Find analogs in chemical databases
Structure analysis: Substructure and functional group ID
Chemical education: Interactive chemistry exploration