[Biopython-dev] General Clean-up of Bio.PDB

[João Rodrigues]

Hi all,

I got a notification from Landscape.io today about a repo of mine and
decided to check Biopython's. I focused only on the Bio.PDB module and
friends. Besides cleaning indentation problems and others, a few questions
arose:


   - Is Bio.PDB.mmCIF (the folder with the lex.yy files) still used at all?
   Otherwise we could remove it.


   - DSSP is silently ignoring errors. Running the function
   dssp_dict_from_pdb_file on a bad PDB file does not give any hint the
   process failed. I added a warning in case STDERR is not empty and an
   exception in case this happens and STDOUT is empty.


   - Same with NACCESS. Added a warning and an exception in case of
   failure. Checks if the rsa and asa files are not created.


Issued a pull request with all these changes. Feel free to apply or
cherry-pick the white-space and cleaning only. All tests passed here on my
machine.

Cheers,

João
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