pyPDBeREST

A python wrapper for the PDBe REST API, inspired by pyEnsemblRest.

Setup

Easy install from github using pip.

$ pip install --upgrade http://github.com/biomadeira/pyPDBeREST/zipball/master

If you want to mess up with the source code.

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

# loading the module...
from pdbe import pyPDBeREST
p = pyPDBeREST()

Alternatively overriding the base url for the endpoints…

# using the dev branch of the api
p = pyPDBeREST(base_url='http://wwwdev.ebi.ac.uk/pdbe/')

Printing out all the available method endpoints…

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…

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

# example of a GET query...
data = p.PDB.getSummary(pdbid='1cbs')
print(data)

{
    "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.

# 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)

{
    "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.

biomadeira / pyPDBeREST