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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

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