https://github.com/dilawar/rcsb_browser

A command line browser for RCSB data bank.
https://github.com/dilawar/rcsb_browser

Last synced: about 2 months ago
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A command line browser for RCSB data bank.

• Host: GitHub
• URL: https://github.com/dilawar/rcsb_browser
• Owner: dilawar
• Created: 2014-08-29T09:51:15.000Z (over 10 years ago)
• Default Branch: master
• Last Pushed: 2014-09-11T08:27:06.000Z (over 10 years ago)
• Last Synced: 2023-03-22T15:28:30.804Z (almost 2 years ago)
• Language: Python
• Size: 215 KB
• Stars: 0
• Watchers: 0
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README

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README

        
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.