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Chemistry Agent

The Chemistry Agent provides a natural language interface for working with chemical structures, reactions, and molecular properties. It can process SMILES strings, render chemical structures, calculate molecular properties, and assist with chemical analysis tasks.

Features

  • Process SMILES strings and render molecular structures
  • Calculate common molecular properties and descriptors
  • Convert between different chemical formats
  • Search for chemical compounds by name or structure
  • Analyze chemical reactions and transformations
  • Generate high-quality visualizations of molecules

Usage

Python API

from aurelian.agents.chemistry import chemistry_agent, get_config

# Initialize dependencies
deps = get_config()

# Process a chemical query
result = await chemistry_agent.run(
    "Draw the structure of caffeine and calculate its molecular weight",
    deps=deps
)

# Get the analysis results
print(result.data)

Command Line Interface

aurelian chemistry "Draw the structure of caffeine and calculate its molecular weight"

Gradio Interface

from aurelian.agents.chemistry import chat

# Launch Gradio interface
interface = chat()
interface.launch()

Tools

The Chemistry Agent provides the following tools:

process_smiles

Processes a SMILES string to generate a molecular structure and calculate basic properties.

draw_molecule

Creates a visual representation of a molecule from its SMILES string.

calculate_descriptors

Calculates detailed molecular descriptors and properties for a given molecule.

search_pubchem

Searches PubChem for compounds matching a name or partial structure.

Examples

Example 1: Analyzing a molecule

Draw the structure of aspirin and calculate its molecular weight

Example 2: Converting chemical representations

Convert "caffeine" to a SMILES string

Example 3: Comparing molecules

Compare the structures and properties of ibuprofen and paracetamol