pyPDBeREST
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Published
20 hours ago •
biomadeira
biomadeira
A python wrapper for the PDBe REST API
pyPDBeREST
|Build Status| |Coverage Status| |Health| |Python: versions| |License|
A python wrapper for the PDBe REST API, inspired by pyEnsemblRest.
Setup
Easy install from github using pip.
.. code:: bash
$ pip install --upgrade http://github.com/biomadeira/pyPDBeREST/zipball/master
If you want to mess up with the source code.
.. code:: bash
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)
.. code:: 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,
"other": 0
},
"processing_site": "RCSB",
"deposition_date": "19980526",
"assemblies": [
{
"assembly_id": "1",
"form": "homo",
"preferred": true,
"name": "tetramer"
}
]
}
]
}
POST
''''
Not all endpoints enable post requests. Those will raise a
``NotImplementedError()`` exception.
.. code:: python
# an example POST query...
# up to 1000 pdb ids can be queried with post methods
data = p.PDB.getSummary(pdbid='1cbs, 2pah', method='POST')
print(data)
.. code:: javascript
{
"1cbs": [
{
"related_structures": [],
"split_entry": [],
"title": "CRYSTAL STRUCTURE OF CELLULAR RETINOIC-ACID-BINDING PROTEINS I AND II IN COMPLEX WITH ALL-TRANS-RETINOIC ACID AND A SYNTHETIC RETINOID",
"release_date": "19950126",
"experimental_method": [
"X-ray diffraction"
],
"experimental_method_class": [
"x-ray"
],
"revision_date": "20090224",
"entry_authors": [
"Kleywegt, G.J.",
"Bergfors, T.",
"Jones, T.A."
],
"deposition_site": null,
"number_of_entities": {
"polypeptide": 1,
"dna": 0,
"ligand": 1,
"dna/rna": 0,
"rna": 0,
"sugar": 0,
"water": 1,
"other": 0
},
"processing_site": null,
"deposition_date": "19940928",
"assemblies": [
{
"assembly_id": "1",
"form": "homo",
"preferred": true,
"name": "monomer"
}
]
}
],
"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,
"other": 0
},
"processing_site": "RCSB",
"deposition_date": "19980526",
"assemblies": [
{
"assembly_id": "1",
"form": "homo",
"preferred": true,
"name": "tetramer"
}
]
}
]
}
Looking for more?
'''''''''''''''''
For a full set of examples and more details on all functionality see
these `notes`_.
Dependencies
See the necessary requirements_ for this module.
Contributing and Bug tracking
Feel free to fork, clone, share and distribute. If you find any bugs or
issues please log them in the `issue tracker`_.
License
~~~~~~~
GNU General Public License v3 (GPLv3). See `license`_ for details.
.. _notes: https://github.com/biomadeira/pyPDBeREST/blob/master/Examples.ipynb
.. _PDBe REST API: http://www.ebi.ac.uk/pdbe/api/doc/
.. _pyEnsemblRest: https://github.com/pyOpenSci/pyEnsemblRest
.. _requirements: https://github.com/biomadeira/pyPDBeREST/blob/master/requirements.txt
.. _issue tracker: https://github.com/biomadeira/pyPDBeREST/issues
.. _license: https://github.com/biomadeira/pyPDBeREST/blob/master/LICENSE.md
.. |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
.. |Python: versions| image:: https://img.shields.io/badge/python-2.7,_3.3,_3.4,_3.5,_pypy,_pypy3-blue.svg?style=flat
:target: http://travis-ci.org/biomadeira/pyPDBeREST
.. |Health| image:: https://landscape.io/github/biomadeira/pyPDBeREST/master/landscape.svg?style=flat
:target: https://landscape.io/github/biomadeira/pyPDBeREST/master
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