A library for searching for PDB structures using the official APIs.
Project description
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(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)
Changelog
Release 0.1.0
2 March 2021
Started library.
Added ability to fetch all PDB codes.
Basic pagination.
Project details
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distributions
Built Distribution
Hashes for pdbsearch-0.1.0-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | c027413bc5e7e91386999dab1cb6f9ae6748d0a8b2f5828483efcccc6972693e |
|
MD5 | dbd330b1af0d459d0564949d00471674 |
|
BLAKE2b-256 | d04793807d415f24ab07efbb4f955f0c76b5f3685359e2226515f2c263f4baab |