emdb 0.1.8

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 3.8+ See requirements.txt for full dependencies.

🤝 Contributing

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

📄 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.