Package: pyPDBeREST
A python wrapper for thePDBe REST API, inspired bypyEnsemblRest.Setupgit clone https://github.com/biomadeira/pyPDBeREST.git
cd pyPDBeREST
sudo python setup.py installExample usageFor a full set of examples and more details on all functionality see
thesenotes. For the impatient see below.Quickstart# loading the module...frompdbeimportpyPDBeRESTp=pyPDBeREST()Alternatively overriding the base url for the endpoints…# using the dev branch of the apip=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
    PISAPrinting 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
    getMoleculesGET# 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"}]}]}POSTNot all endpoints enable post requests. Those will raise aNotImplementedError()exception.# an example POST query...# up to 1000 pdb ids can be queried with post methodsdata=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
thesenotes.DependenciesSee the necessaryrequirementsfor this module.Contributing and Bug trackingFeel free to fork, clone, share and distribute. If you find any bugs or
issues please log them in theissue tracker.LicenseGNU General Public License v3 (GPLv3). Seelicensefor details.