rcsbsearch 0.1.0

Access the RCSB Search API

rcsbsearch

Python interface for the RCSB search API.

Currently the 'text search' part of the API has been implemented.

This package requires python 3.7 or later.

Usage

Searches are built up from a series of Terminal nodes. For example:

from rcsbsearch import Terminal
q1 = Terminal("rcsb_struct_symmetry.symbol", "exact_match", "C2")
q2 = Terminal("rcsb_struct_symmetry.kind", "exact_match", "Global Symmetry")
q3 = Terminal(value='"heat-shock transcription factor"')
q4 = Terminal("rcsb_entry_info.polymer_entity_count_DNA", "greater_or_equal", 1)

These are combined using python's bitwise operators as if they were sets of results:

q = q1 & q2 & q3 & q4  # AND of all queries

AND (&), OR (|), and terminal negation (~) are implemented directly by the API, but the python package also implements set difference (-), symmetric difference (^), and general negation by transforming the query.

Queries are executed by calling them as functions. They return an iterator of result identifiers. Paging is handled transparently by the query.

results = set(q())

By default PDB IDs are returned, but other result types are also supported:

results = set(q("assembly"))

More control is available by executing the query using a Session object. For instance, the Session.iquery() returns a list of all results. It uses the optional tqdm package to track the progress of the query interactively.

from rcsbsearch import Session
session = Session(q)
results = session.iquery()

Tests are run using tox and/or pytest.

tox -e py37

or directly:

pytest

Code Style

Code conforms to the black and PEP8 style guides. Before checking in code, please run the linters:

black .
flake8
mypy rcsbsearch

These are tested by the 'lint' tox environment:

tox -e lint