Code does not work unless given specific file name

[ejmeitz]

I was debugging an issue where FLIPPER was not outputting the correct LIP scores on the 1jsu complex which has results in the README. It turns out unless I name my pdb as <3-letters><4-letter-pdb-id>.<anything>.gz the code does not work. I had my file just name 1jsu.pdb.gz. Specifically, the keys in the flipper.dssp_dict do not match the expected keys which causes the secondary structure to count in LipsFinder.extract_features to incorrectly count the helixes, sheets etc. I'm sure there's other places this breaks since the final LIP score was also broken. I just fixed it by changing the name.

It would be nice to either document this requirement or update code like:
pdb_id = os.path.basename(pdb_file_gz)[3:7] to be more generic.

Thanks