emdb 0.1.12

A Python client for accessing the Electron Microscopy Data Bank (EMDB)

EMDB Python Client

A Python client for accessing and interacting with the Electron Microscopy Data Bank (EMDB).
This package provides an easy-to-use interface to query EMDB entries, access metadata, and download associated files.

🚀 Features

• Retrieve EMDB entries by ID
• Query metadata such as resolution, sample description, and related PDBs
• Download associated files (maps, images, metadata)
• Utility models for plotting and file handling
• Access to validation analysis and annotation data

📚 Documentation

Full API documentation is available at:
👉 https://emdb.readthedocs.io/en/latest/

🔧 Installation

You can install the EMDB client via pip:

pip install emdb

✨ Quick Start

from emdb.client import EMDB
from emdb.exceptions import EMDBNotFoundError

client = EMDB()

try:
    # Retrieve an entry by ID
    entry = client.get_entry("EMD-8117")
    print(entry.resolution)
    
    # Access cross-reference annotations
    annotations = entry.get_annotations()
    for annotation in annotations:
        print(annotation)
    
    # Access validation data and plot FSC
    validation = entry.get_validation()
    validation.plots.fsc.plot()
    
    # Download all files
    entry.download_all_files(output_dir="/tmp/emd1234/")
    
    # Perform a query to return EMDB entries
    results = client.search("HIV")
    for entry in results:
        print(entry.id, entry.method, entry.resolution)
    
    # Perform a query to return a DataFrame
    table = client.csv_search("HIV")
    print(table)
except EMDBNotFoundError:
    print("Entry not found.")

🛠 Requirements

• Python 3.10+ See requirements.txt for full dependencies.

🤝 Contributing

Contributions are welcome! Feel free to open issues or submit pull requests.

For detailed contributing guidelines, see CONTRIBUTING.md.

Running Tests

This project uses pytest for testing. To run the tests:

# Install test dependencies
pip install -e ".[test]"

# Run all tests
pytest

# Run with coverage report
pytest --cov=emdb --cov-report=html

# Run specific test file
pytest tests/test_client.py

📄 License

This project is licensed under the Apache License 2.0.

📧 Contact

For questions or feedback, please open an issue on GitHub or contact the maintainers.