-
Notifications
You must be signed in to change notification settings - Fork 1
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
63d4d96
commit 5c92476
Showing
1 changed file
with
114 additions
and
0 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,114 @@ | ||
pyPDBeREST | ||
========== | ||
|
||
|Twitter: @biomadeira| |Build Status| |Coverage Status| |License| | ||
|
||
A python wrapper for the `PDBe REST API`_, inspired by `pyEnsemblRest`_. | ||
|
||
Setup | ||
~~~~~ | ||
|
||
:: | ||
|
||
git clone https://github.com/biomadeira/pyPDBeREST.git | ||
cd pyPDBeREST | ||
sudo python setup.py install | ||
|
||
Example usage | ||
~~~~~~~~~~~~~ | ||
|
||
For a full set of examples and more details on all functionality see | ||
these `notes`_. For the impatient see below. | ||
|
||
Quickstart | ||
~~~~~~~~~~ | ||
|
||
.. code:: python | ||
# loading the module... | ||
from pdbe import pyPDBeREST | ||
p = pyPDBeREST() | ||
Alternatively overriding the base url for the endpoints… | ||
|
||
.. code:: python | ||
# using the dev branch of the api | ||
p = pyPDBeREST(base_url='http://wwwdev.ebi.ac.uk/pdbe/') | ||
Printing out all the available method endpoints… | ||
|
||
.. code:: python | ||
print(p.endpoints()) | ||
:: | ||
|
||
The following endpoints are available: | ||
EMDB | ||
SSM | ||
SEARCH | ||
SIFTS | ||
COMPOUNDS | ||
TOPOLOGY | ||
VALIDATION | ||
PDB | ||
PISA | ||
|
||
Printing out all the available endpoints for one of the top level | ||
methods… | ||
|
||
.. code:: python | ||
print(p.PDB.endpoints()) | ||
:: | ||
|
||
The following endpoints are available: | ||
getReleaseStatus | ||
getBindingSites | ||
getObservedRanges | ||
getRelatedPublications | ||
getResidueListingChain | ||
getNmrResources | ||
getExperiments | ||
getSecondaryStructure | ||
getVariousUrls | ||
getModifiedResidues | ||
getSummary | ||
getResidueListing | ||
getPublications | ||
getLigands | ||
getMutatedResidues | ||
getMolecules | ||
|
||
GET | ||
''' | ||
|
||
.. code:: python | ||
# example of a GET query... | ||
data = p.PDB.getSummary(pdbid='1cbs') | ||
print(data) | ||
\`\`\`javascript { “2pah”: [ { “related\_structures”: [], | ||
“split\_entry”: [], “title”: “TETRAMERIC HUMAN PHENYLALANINE | ||
HYDROXYLASE”, “release\_date”: “19991006”, “experimental\_method”: [ | ||
“X-ray diffraction” ], “experimental\_method\_class”: [ “x-ray” ], | ||
“revision\_date”: “20110713”, “entry\_authors”: [ “Stevens, R.C.”, | ||
“Fusetti, F.”, “Erlandsen, H.” ], “deposition\_site”: “BNL”, | ||
“number\_of\_entities”: { “polypeptide”: 1, “dna”: 0, “ligand”: 1, | ||
“dna/rna”: 0, “rna”: 0, “sugar”: 0, “water”: 0, | ||
|
||
.. _PDBe REST API: http://www.ebi.ac.uk/pdbe/api/doc/ | ||
.. _pyEnsemblRest: https://github.com/pyOpenSci/pyEnsemblRest | ||
.. _notes: Examples.ipynb | ||
|
||
.. |Twitter: @biomadeira| image:: https://img.shields.io/badge/contact-@biomadeira-blue.svg?style=flat | ||
:target: https://twitter.com/biomadeira | ||
.. |Build Status| image:: https://secure.travis-ci.org/biomadeira/pyPDBeREST.png?branch=master | ||
:target: http://travis-ci.org/biomadeira/pyPDBeREST | ||
.. |Coverage Status| image:: https://coveralls.io/repos/biomadeira/pyPDBeREST/badge.svg?branch=master&service=github | ||
:target: https://coveralls.io/github/biomadeira/pyPDBeREST?branch=master | ||
.. |License| image:: http://img.shields.io/badge/license-GPLv3-brightgreen.svg?style=flat | ||
:target: https://github.com/biomadeira/pyPDBeREST/blob/master/LICENSE.md |