⛔️ [DEPRECATED] Active at rcsb-api

Please migrate to our new and improved package, rcsb-api, which contains all the same functionalities as rcsbsearchapi and more! New features will only be added to the new rcsb-api package. For more details, see https://github.com/rcsb/py-rcsbsearchapi/issues/51.

rcsbsearchapi - Query protein structures from Python

The rcsbsearchapi package provides a Python interface to the RCSB PDB Search API. Use it to fetch lists of PDB IDs corresponding to advanced query searches.

Contents

• Quickstart
  • Installation
  • Getting Started
  • Jupyter Notebooks
• Query Construction
  • Query Syntax and Execution
  • Search Service Types
  • Request Options
• Exploring Schema Attributes
  • search()
  • get_attribute_details()
  • get_attribute_type()
• Additional Examples
  • Sequence Search Examples
  • Sequence Motif Search Examples
  • Structure Similarity Search Examples
  • Structure Motif Search Examples
  • Chemical Similarity Search Examples
  • Faceted Query Examples
  • GroupBy Example
  • Sort Example
• API Documentation

Availability

Get it from PyPI:

pip install rcsbsearchapi

Or, download from GitHub

License

Code is licensed under the BSD 3-clause license. See the LICENSE for details.

Citing

Please cite the rcsbsearchapi package by URL:

https://rcsbsearchapi.readthedocs.io

You should also cite the RCSB PDB service this package utilizes:

Yana Rose, Jose M. Duarte, Robert Lowe, Joan Segura, Chunxiao Bi, Charmi Bhikadiya, Li Chen, Alexander S. Rose, Sebastian Bittrich, Stephen K. Burley, John D. Westbrook. RCSB Protein Data Bank: Architectural Advances Towards Integrated Searching and Efficient Access to Macromolecular Structure Data from the PDB Archive, Journal of Molecular Biology, 2020. DOI: 10.1016/j.jmb.2020.11.003