salp-rs 0.2.0

A Rust library with a python wrapper that allows fetching and (processing) big PDB data via queries by communicating with the RCSB API

salp

Original image credit: By Peter Southwood - Own work, CC BY-SA 3.0

A Python library for querying and fetching protein structures from the RCSB PDB, written in Rust.

Installation

pip install salp-rs

With uv:

uv add salp-rs

Example usage

from salp import Query, search, fetch_and_save
# btw these are the only 2 functions you got

query = Query.and_([
    Query.organism("Homo sapiens"),
    Query.max_resolution(2.5),
    Query.keyword("kinase"),
])

# This returns the total count and list of PDB IDs
# RCSB returns up to 10 results by default. Control this with `start` and `rows`:
total, ids = search(query, start=0, rows=50)
print(f"Found {total} structures, fetching first {len(ids)}")

# Fetch and save, filter_proteins removes non-protein atoms
fetch_and_save(ids, filter_proteins=True, output_dir="./structures")

Contributing

Issues and PRs welcome on GitHub.