pdbsearch 0.2.0

A library for searching for PDB structures using the official APIs.

pdbsearch is a Python library for searching for PDB structures using the RCSB web services.

Example

>>> import pdbsearch
>>> codes = pdbsearch.search(limit=5)
>>> codes
['4CD7', '4CCW', '4CD8', '4CCX', '4CCY']

Installing

pip

pdbsearch can be installed using pip (you may need to use pip3):

$ pip install pdbsearch

If you get permission errors, try using sudo:

$ sudo pip install pdbsearch

Development

The repository for pdbsearch, containing the most recent iteration, can be found here. To clone the pdbsearch repository directly from there, use:

$ git clone git://github.com/samirelanduk/pdbsearch.git

Requirements

pdbsearch requires requests.

Testing

To test a local version of pdbsearch, cd to the pdbsearch directory and run:

$ python -m unittest discover tests

You can opt to only run unit tests or integration tests:

$ python -m unittest discover tests.unit $ python -m unittest discover tests.integration

Overview

pdbsearch is a Python library for searching for PDB structures using the RCSB web services.

Returning all PDB Codes

You can get all PDB codes without any particular search expression like so:

>>> import pdbsearch
>>> codes = pdbsearch.search(limit=None)
>>> len(codes)
174994

This will take a few seconds, and requires downloading a rather large JSON object over the network. Generally it is better to paginate the results:

>>> first_ten_codes = pdbsearch.search(limit=10)
>>> second_ten_codes = pdbsearch.search(start=10, limit=10)
>>> third_ten_codes = pdbsearch.search(start=20, limit=10)

You can sort the results by any of the terms at https://search.rcsb.org/search-attributes.html:

>>> most_recent_codes = pdbsearch.search(sort="rcsb_accession_info.deposit_date")
>>> earliest_codes = pdbsearch.search(sort="-rcsb_accession_info.deposit_date")

As these are somewhat cumbersome, some of them have a shorthand:

>>> pdbsearch.search(limit=5, sort="code")
['9XIM', '9XIA', '9WGA', '9RUB', '9RSA']
>>> pdbsearch.search(limit=5, sort="-resolution")
['3NIR', '5D8V', '1EJG', '3P4J', '5NW3']

You can sort by multiple criteria:

>>> pdbsearch.search(limit=5, sort=["-atoms", "released"])
['1ANP', '6UOU', '6UOW', '1Q7O', '6QTF']

Changelog

Release 0.2.0

25 April 2021

• Added ability to sort results.

• Created shorthand system for common sort criteria.

Release 0.1.0

2 March 2021

• Started library.

• Added ability to fetch all PDB codes.

• Basic pagination.