Skip to main content

Access the RCSB Search API

Project description

PyPi Release Build Status Documentation Status Code style: black Binder

rcsbsearch

Python interface for the RCSB search API.

Currently the 'text search' part of the API has been implemented. See 'Supported features' below.

This package requires python 3.7 or later.

Example

Here is a quick example of how the package is used. Two syntaxes are available for constructing queries: an "operator" API using python's comparators, and a "fluent" syntax where terms are chained together. Which to use is a matter of preference.

A runnable jupyter notebook with this example is available in notebooks/quickstart.ipynb, or can be run online using binder: Binder

An additional example including a Covid-19 related example is in notebooks/covid.ipynb: Binder

Operator example

Here is an example from the RCSB Search API page, using the operator syntax. This query finds symmetric dimers having a twofold rotation with the DNA-binding domain of a heat-shock transcription factor.

from rcsbsearch import TextQuery
from rcsbsearch import rcsb_attributes as attrs

# Create terminals for each query
q1 = TextQuery('"heat-shock transcription factor"')
q2 = attrs.rcsb_struct_symmetry.symbol == "C2"
q3 = attrs.rcsb_struct_symmetry.kind == "Global Symmetry"
q4 = attrs.rcsb_entry_info.polymer_entity_count_DNA >= 1

# combined using bitwise operators (&, |, ~, etc)
query = q1 & q2 & q3 & q4  # AND of all queries

# Call the query to execute it
for assemblyid in query("assembly"):
    print(assemblyid)

For a full list of attributes, please refer to the RCSB schema.

Fluent Example

Here is the same example using the fluent syntax.

from rcsbsearch import TextQuery

# Start with a Attr or TextQuery, then add terms
results = TextQuery('"heat-shock transcription factor"') \
    .and_("rcsb_struct_symmetry.symbol").exact_match("C2") \
    .and_("rcsb_struct_symmetry.kind").exact_match("Global Symmetry") \
    .and_("rcsb_entry_info.polymer_entity_count_DNA").greater_or_equal(1) \
    .exec("assembly")

# Exec produces an iterator of IDs
for assemblyid in results:
    print(assemblyid)

Supported Features

The following table lists the status of current and planned features.

  • Attribute Comparison operations
  • Query set operations
  • Attribute contains, in_ (fluent only)
  • Sequence search
  • Sequence motif search
  • Structural search
  • Structural motif search
  • Chemical search

Contributions are welcome for unchecked items!

Installation

Get it from pypi:

pip install rcsbsearch

Or, download from github

Documentation

Detailed documentation is at rcsbsearch.readthedocs.io

License

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

Citing rcsbsearch

Please cite the rcsbsearch package by URL:

https://rcsbsearch.readthedocs.io

You should also cite the RCSB 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

Developers

For information about building and developing rcsbsearch, see CONTRIBUTING.md

Project details


Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

rcsbsearch-0.2.3.tar.gz (131.0 kB view details)

Uploaded Source

Built Distribution

rcsbsearch-0.2.3-py3-none-any.whl (131.2 kB view details)

Uploaded Python 3

File details

Details for the file rcsbsearch-0.2.3.tar.gz.

File metadata

  • Download URL: rcsbsearch-0.2.3.tar.gz
  • Upload date:
  • Size: 131.0 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.3.0 pkginfo/1.7.0 requests/2.25.1 setuptools/49.6.0.post20210108 requests-toolbelt/0.9.1 tqdm/4.56.0 CPython/3.9.1

File hashes

Hashes for rcsbsearch-0.2.3.tar.gz
Algorithm Hash digest
SHA256 63b29e6df4809a6e47a83874cd166bd3753a0df0db96e644bebff1743c08faa8
MD5 780a4ec8fd3389751a51bc0539b5977e
BLAKE2b-256 e710253b47e8b2f1451403461d3086273f7d517f422e65f85a751357113e7e40

See more details on using hashes here.

File details

Details for the file rcsbsearch-0.2.3-py3-none-any.whl.

File metadata

  • Download URL: rcsbsearch-0.2.3-py3-none-any.whl
  • Upload date:
  • Size: 131.2 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/3.3.0 pkginfo/1.7.0 requests/2.25.1 setuptools/49.6.0.post20210108 requests-toolbelt/0.9.1 tqdm/4.56.0 CPython/3.9.1

File hashes

Hashes for rcsbsearch-0.2.3-py3-none-any.whl
Algorithm Hash digest
SHA256 a04e4167d43ce3ebe83fe3dd20ffd6c0fae3a0a7fab75991fbcca53ad430481c
MD5 692e6c13b610c01e8950140df573539b
BLAKE2b-256 8a091175e109ac509a271dfc811fee0fe3e9cf44b192fdba72580693804a6fa5

See more details on using hashes here.

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page