Command line browser for RCSB database
Homepage Repository PyPI Python
pip install rcsb_browser==0.1.0
A command line browser for RCSB data bank: you can either query the their database for keywords or download PDB file when ID is known. This version only downloads the pdb file in tar.gz file. USAGE EXAMPLE ============= To query :: $ rcsb_browser --query adenine in human by Hurley and Parajuli Total 1 results are fetched INFO: Storing custom report: /home/dilawar/Work/GITHUB/rcsb_browser ++++++++++ structureId : 4L2O structureTitle : Crystal structure of human ALDH3A1 with its selective inhibitor 1-(4-fluorophenyl)sulfonyl-2-methylbenzimidazole experimentalTechnique : X-RAY DIFFRACTION depositionDate : 2013-06-04 releaseDate : 2014-01-29 ndbId : null resolution : 1.94 structureAuthor : Hurley, T.D., Parajuli, B. classification : OXIDOREDUCTASE/Inhibitor structureMolecularWeight : 213310.03 macromoleculeType : Protein In this example, only one result is fetched but if query is short then you might end up getting thousands for results (though it will never print more than 100 results onto the console). A file in XML format is also saved which you can open in some office-suite to see. Once ID is known (e.g. 4l20 in this case), you can download the pdb file, by using the --fetch (or -f) command. :: $ rcsb_browser --fetch 4l20 It will download and store the file in current working directory.