SMARTSViewer

Streamlit application for visualizing SMARTS patterns of individual compounds and chemical reactions.

Features

• Interactive molecule drawing with Ketcher editor
• SMARTS pattern matching and highlighting in molecular structures
• Chemical reaction analysis using reaction SMARTS
• Product generation and visualization
• Pre-configured examples for common patterns and reactions

Quickstart

Prerequisites

• Python 3.13 or higher
• uv package manager (recommended) or pip

Installation

1. Clone the repository:

git clone <repository-url>
cd SMARTSViewer

2. Install dependencies:

# Using uv (recommended)
uv sync

# Or using pip
pip install -e .

3. Run the application:

# Using uv
uv run streamlit run app.py

# Or using pip
streamlit run app.py

The application will open in your browser at http://localhost:8501.

How to Use

Compound Page

1. Draw or edit molecules: Use the interactive Ketcher molecular editor to draw your compound
2. Enter SMARTS pattern: Input a SMARTS pattern in the text field to search for specific substructures
3. View results: The molecule will be highlighted showing all matching fragments

Example SMARTS patterns:

• Aromatic ring: c1ccccc1
• Hydroxyl group: [OH]
• Carbonyl: [#6]=[#8]
• Amine: [NH2]
• Carboxylic acid: [CX3](=O)[OX2H1]

Reaction Page

1. Define reactants: Draw all reactant molecules in the editor (separate multiple reactants with dots)
2. Apply changes: Click "Apply Changes" to parse the reactants
3. Enter reaction SMARTS: Input a reaction SMARTS pattern defining the transformation
4. View products: All generated products will be displayed

Example reaction SMARTS:

• Alcohol oxidation: [C:1][OH:2]>>[C:1][O:2]
• Ester hydrolysis: [C:1](=[O:2])[O:3][C:4]>>[C:1](=[O:2])[OH:3].[C:4][O:5]
• Esterification: [C:1][OH:2].[C:3](=[O:4])[OH:5]>>[C:1][O:2][C:3](=[O:4]).[O:5]

Tips for reactions:

• Separate multiple reactants with dots: CCO.CC(=O)O
• Use atom mapping in reactions: [C:1][OH:2]>>[C:1][O:2]
• Ensure proper SMARTS syntax for reliable product generation

Dependencies

• RDKit: Chemical informatics toolkit
• Streamlit: Web application framework
• Streamlit-Ketcher: Interactive molecule editor
• NumPy: Numerical computing
• Plotly: Interactive plotting
• PyYAML: Configuration file parsing

Configuration

The application behavior can be customized through config.yaml:

• Default molecules and reaction patterns
• UI settings and styling
• Example patterns for quick testing
• Error messages and validation settings

License

See LICENSE file for details.