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Description:

pdbsearch 0.4.0

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

Example

>>> import pdbsearch
>>> codes = pdbsearch.search(limit=5, ligand_name="CU")
>>> codes
['3HW7', '2WKO', '2WOF', '2WOH', '2WO0']

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/structure-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']

Search Criteria
You can search by passing keywords to the search function:

>>> pdbsearch.search(limit=5, ligand_name="ZN")
['3HW7', '3I7I', '3I7G', '2WFX', '2WGT']

You can modify the operator used with double underscores:

>>> pdbsearch.search(limit=5, ligand_name__in=["ZN", "CU"])
['3HW7', '3I7I', '3I7G', '2WFX', '2WGT']
>>> pdbsearch.search(limit=5, resolution__lt=2)
['3HW3', '3I83', '3HVS', '3HW4', '3HW5']
>>> pdbsearch.search(limit=5, atoms__within=[200, 300])
['2WH9', '2WPY', '395D', '396D', '2X8Q']

These are some shorthands, but you can search by any of the terms in the above
linked list by replacing the dot with a double underscore:

>>> pdbsearch.search(limit=5, citation__rcsb_authors="Sula, A.")
['4CAH', '4CAI', '4X8A', '4X88', '4X89']

If you use more than one term, they will be combined with AND operators:

>>> pdbsearch.search(limit=5, ligand_name="ZN", atoms__within=[200, 300])
['3WUP', '3ZNF', '2YTA', '2YTB', '2YSV']

Changelog

Release 0.4.0
24 Jul 2022

Updated library for v2 of the RCSB search API.

Release 0.3.0
29 May 2021

Added search criteria.
Added AND chaining for search criteria.

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.