Python client for accessing RCSB.org APIs

[Dennis Piehl]

Dear RCSB PDB power users,

We’re excited to share some new developments that facilitate programmatic access to RCSB.org APIs using Python.

Over a year ago, we introduced a new Python package, rcsb-api, which initially served to provide a simple Pythonic interface to our Search API service for building complex queries and retrieving matching PDB IDs. Since then, we have extended support to additional RCSB.org APIs, including our Data API, Sequence Coordinate API, and Model API. These additions significantly expand your ability to query, access, and analyze the wealth of structural biology data available in the PDB.

Specifically, each API service is provided as a separate "module" (or sub-package) within the Python client, and offers the following set of key functionalities:

Search API module (`rcsbapi.search`):

• Perform all search types available through the RCSB.org Advanced Search builder (e.g., full-text, attribute-based, sequence and structure similarity, sequence and structure motif)

• Use simple Boolean logic to intuitively construct complex or nested queries

• Upload custom structure files for structure similarity searches

• Include computed structure models (CSMs) in search results

Data API module (`rcsbapi.data`): 

• Retrieve any subset of metadata, features, and/or annotations for a given list of PDB IDs (e.g., experimental method details, structural annotations, binding sites, etc.) 

• Easily fetch data for all structures across the archive

• Simplified GraphQL query construction using a Python syntax 

Sequence Coordinate API module (`rcsbapi.sequence`): 
    • Query alignments between structural and sequence databases as well as protein positional annotations/features integrated from multiple resources

    • Alignment data is available for NCBI RefSeq (including protein and genomic sequences), UniProt and PDB sequences
    • Protein positional features are integrated from UniProt, CATH, SCOPe and RCSB PDB and collected from the RCSB PDB Data Warehouse 

Model API module (`rcsbapi.model`): 
    • Provides access to molecular structure data (e.g., atomic coordinates) and related information (in mmCIF or BCIF formats)
    • Query for various structural data types, such as full structure, ligands, atoms, residue interactions, and more
    • Valuable for extracting out specific slices of a structure data file (not for bulk downloads, in which case see our download services)

Package documentation is provided at: https://rcsbapi.readthedocs.io/. The project source code is available on GitHub, which also contains several example notebooks. Additionally, we recently hosted a webinar to showcase the package, which provides video recordings with hands-on tutorials.

We hope you find this toolkit valuable for any of your research interests and applications.

Dennis Piehl

RCSB Protein Data Bank