{
    "info": {
        "author": "F\u00e1bio Madeira",
        "author_email": "fabiomadeira@me.com",
        "bugtrack_url": null,
        "classifiers": [
            "Development Status :: 4 - Beta",
            "Intended Audience :: Developers",
            "Intended Audience :: Science/Research",
            "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
            "Natural Language :: English",
            "Programming Language :: Python :: 2.7",
            "Programming Language :: Python :: 3.3",
            "Programming Language :: Python :: 3.4",
            "Programming Language :: Python :: 3.5",
            "Programming Language :: Python :: Implementation :: PyPy",
            "Topic :: Internet",
            "Topic :: Scientific/Engineering :: Bio-Informatics",
            "Topic :: Software Development :: Libraries :: Python Modules"
        ],
        "description": "pyPDBeREST\r\n==========\r\n\r\n|Build Status| |Coverage Status| |License|\r\n\r\nA python wrapper for the `PDBe REST API`_, inspired by `pyEnsemblRest`_.\r\n\r\nSetup\r\n~~~~~\r\n\r\n::\r\n\r\n    git clone https://github.com/biomadeira/pyPDBeREST.git \r\n    cd pyPDBeREST\r\n    sudo python setup.py install\r\n\r\nExample usage\r\n~~~~~~~~~~~~~\r\n\r\nFor a full set of examples and more details on all functionality see\r\nthese `notes`_. For the impatient see below.\r\n\r\nQuickstart\r\n~~~~~~~~~~\r\n\r\n.. code:: python\r\n\r\n    # loading the module...\r\n    from pdbe import pyPDBeREST\r\n    p = pyPDBeREST()\r\n\r\nAlternatively overriding the base url for the endpoints\u2026\r\n\r\n.. code:: python\r\n\r\n    # using the dev branch of the api\r\n    p = pyPDBeREST(base_url='http://wwwdev.ebi.ac.uk/pdbe/')\r\n\r\nPrinting out all the available method endpoints\u2026\r\n\r\n.. code:: python\r\n\r\n    print(p.endpoints())\r\n\r\n::\r\n\r\n    The following endpoints are available:\r\n        EMDB\r\n        SSM\r\n        SEARCH\r\n        SIFTS\r\n        COMPOUNDS\r\n        TOPOLOGY\r\n        VALIDATION\r\n        PDB\r\n        PISA\r\n\r\nPrinting out all the available endpoints for one of the top level\r\nmethods\u2026\r\n\r\n.. code:: python\r\n\r\n    print(p.PDB.endpoints())\r\n\r\n::\r\n\r\n    The following endpoints are available:\r\n        getReleaseStatus\r\n        getBindingSites\r\n        getObservedRanges\r\n        getRelatedPublications\r\n        getResidueListingChain\r\n        getNmrResources\r\n        getExperiments\r\n        getSecondaryStructure\r\n        getVariousUrls\r\n        getModifiedResidues\r\n        getSummary\r\n        getResidueListing\r\n        getPublications\r\n        getLigands\r\n        getMutatedResidues\r\n        getMolecules\r\n\r\nGET\r\n'''\r\n\r\n.. code:: python\r\n\r\n    # example of a GET query...\r\n    data = p.PDB.getSummary(pdbid='1cbs')\r\n    print(data)\r\n\r\n.. code:: javascript \r\n\r\n    {\r\n        \"2pah\": [\r\n            {\r\n                \"related_structures\": [], \r\n                \"split_entry\": [], \r\n                \"title\": \"TETRAMERIC HUMAN PHENYLALANINE HYDROXYLASE\", \r\n                \"release_date\": \"19991006\", \r\n                \"experimental_method\": [\r\n                    \"X-ray diffraction\"\r\n                ], \r\n                \"experimental_method_class\": [\r\n                    \"x-ray\"\r\n                ], \r\n                \"revision_date\": \"20110713\", \r\n                \"entry_authors\": [\r\n                    \"Stevens, R.C.\", \r\n                    \"Fusetti, F.\", \r\n                    \"Erlandsen, H.\"\r\n                ], \r\n                \"deposition_site\": \"BNL\", \r\n                \"number_of_entities\": {\r\n                    \"polypeptide\": 1, \r\n                    \"dna\": 0, \r\n                    \"ligand\": 1, \r\n                    \"dna/rna\": 0, \r\n                    \"rna\": 0, \r\n                    \"sugar\": 0, \r\n                    \"water\": 0, \r\n                    \"other\": 0\r\n                }, \r\n                \"processing_site\": \"RCSB\", \r\n                \"deposition_date\": \"19980526\", \r\n                \"assemblies\": [\r\n                    {\r\n                        \"assembly_id\": \"1\", \r\n                        \"form\": \"homo\", \r\n                        \"preferred\": true, \r\n                        \"name\": \"tetramer\"\r\n                    }\r\n                ]\r\n            }\r\n        ]\r\n    }\r\n\r\n\r\nPOST\r\n''''\r\n\r\nNot all endpoints enable post requests. Those will raise a\r\n``NotImplementedError()`` exception.\r\n\r\n.. code:: python\r\n\r\n    # an example POST query...\r\n    # up to 1000 pdb ids can be queried with post methods\r\n    data = p.PDB.getSummary(pdbid='1cbs, 2pah', method='POST')\r\n    print(data)\r\n\r\n.. code:: javascript\r\n\r\n    {\r\n        \"1cbs\": [\r\n            {\r\n                \"related_structures\": [], \r\n                \"split_entry\": [], \r\n                \"title\": \"CRYSTAL STRUCTURE OF CELLULAR RETINOIC-ACID-BINDING PROTEINS I AND II IN COMPLEX WITH ALL-TRANS-RETINOIC ACID AND A SYNTHETIC RETINOID\", \r\n                \"release_date\": \"19950126\", \r\n                \"experimental_method\": [\r\n                    \"X-ray diffraction\"\r\n                ], \r\n                \"experimental_method_class\": [\r\n                    \"x-ray\"\r\n                ], \r\n                \"revision_date\": \"20090224\", \r\n                \"entry_authors\": [\r\n                    \"Kleywegt, G.J.\", \r\n                    \"Bergfors, T.\", \r\n                    \"Jones, T.A.\"\r\n                ], \r\n                \"deposition_site\": null, \r\n                \"number_of_entities\": {\r\n                    \"polypeptide\": 1, \r\n                    \"dna\": 0, \r\n                    \"ligand\": 1, \r\n                    \"dna/rna\": 0, \r\n                    \"rna\": 0, \r\n                    \"sugar\": 0, \r\n                    \"water\": 1, \r\n                    \"other\": 0\r\n                }, \r\n                \"processing_site\": null, \r\n                \"deposition_date\": \"19940928\", \r\n                \"assemblies\": [\r\n                    {\r\n                        \"assembly_id\": \"1\", \r\n                        \"form\": \"homo\", \r\n                        \"preferred\": true, \r\n                        \"name\": \"monomer\"\r\n                    }\r\n                ]\r\n            }\r\n        ], \r\n        \"2pah\": [\r\n            {\r\n                \"related_structures\": [], \r\n                \"split_entry\": [], \r\n                \"title\": \"TETRAMERIC HUMAN PHENYLALANINE HYDROXYLASE\", \r\n                \"release_date\": \"19991006\", \r\n                \"experimental_method\": [\r\n                    \"X-ray diffraction\"\r\n                ], \r\n                \"experimental_method_class\": [\r\n                    \"x-ray\"\r\n                ], \r\n                \"revision_date\": \"20110713\", \r\n                \"entry_authors\": [\r\n                    \"Stevens, R.C.\", \r\n                    \"Fusetti, F.\", \r\n                    \"Erlandsen, H.\"\r\n                ], \r\n                \"deposition_site\": \"BNL\", \r\n                \"number_of_entities\": {\r\n                    \"polypeptide\": 1, \r\n                    \"dna\": 0, \r\n                    \"ligand\": 1, \r\n                    \"dna/rna\": 0, \r\n                    \"rna\": 0, \r\n                    \"sugar\": 0, \r\n                    \"water\": 0, \r\n                    \"other\": 0\r\n                }, \r\n                \"processing_site\": \"RCSB\", \r\n                \"deposition_date\": \"19980526\", \r\n                \"assemblies\": [\r\n                    {\r\n                        \"assembly_id\": \"1\", \r\n                        \"form\": \"homo\", \r\n                        \"preferred\": true, \r\n                        \"name\": \"tetramer\"\r\n                    }\r\n                ]\r\n            }\r\n        ]\r\n    }\r\n\r\n\r\nLooking for more?\r\n'''''''''''''''''\r\n\r\nFor a full set of examples and more details on all functionality see\r\nthese `notes`_.\r\n\r\nDependencies\r\n~~~~~~~~~~~~\r\n\r\n|Python: versions|\r\n\r\nSee the necessary `requirements`_ for this module.\r\n\r\nContributing and Bug tracking\r\n~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\r\n\r\nFeel free to fork, clone, share and distribute. If you find any bugs or\r\nissues please log them in the `issue tracker`_.\r\n\r\nLicense\r\n~~~~~~~\r\n\r\nGNU General Public License v3 (GPLv3). See `license`_ for details.\r\n\r\n.. _notes: https://github.com/biomadeira/pyPDBeREST/blob/master/Examples.ipynb\r\n.. _PDBe REST API: http://www.ebi.ac.uk/pdbe/api/doc/\r\n.. _pyEnsemblRest: https://github.com/pyOpenSci/pyEnsemblRest\r\n.. _requirements: https://github.com/biomadeira/pyPDBeREST/blob/master/requirements.txt\r\n.. _issue tracker: https://github.com/biomadeira/pyPDBeREST/issues\r\n.. _license: https://github.com/biomadeira/pyPDBeREST/blob/master/LICENSE.md\r\n\r\n.. |Build Status| image:: https://secure.travis-ci.org/biomadeira/pyPDBeREST.png?branch=master\r\n   :target: http://travis-ci.org/biomadeira/pyPDBeREST\r\n.. |Coverage Status| image:: https://coveralls.io/repos/biomadeira/pyPDBeREST/badge.svg?branch=master&service=github\r\n   :target: https://coveralls.io/github/biomadeira/pyPDBeREST?branch=master\r\n.. |License| image:: http://img.shields.io/badge/license-GPLv3-brightgreen.svg?style=flat\r\n   :target: https://github.com/biomadeira/pyPDBeREST/blob/master/LICENSE.md\r\n.. |Twitter: @biomadeira| image:: https://img.shields.io/badge/contact-@biomadeira-blue.svg?style=flat\r\n   :target: https://twitter.com/biomadeira\r\n.. |Python: versions| image:: https://img.shields.io/badge/python-2.7,_3.3,_3.4,_3.5,_pypy,_pypy3-blue.svg?style=flat\r\n   :target: http://travis-ci.org/biomadeira/pyPDBeREST",
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