clean_pdb script does not successfully PDB files from RSCB on mac (M1)

[rclune]

I am trying to run the following command:
python /path/to/rosetta.binary.m1.release-371/main/tools/protein_tools/scripts/clean_pdb.py 1QYS A
however I get the following error:

zcat: can't stat: /path/to/current/working/directory/1QYS.pdb.gz (/path/to/current/working/directory/1QYS.pdb.gz.Z): No such file or directory

I am using the most recently released binaries for Mn Macs - my specific machine is M4.

It appears that the zcat command (on mac) is attaching an extra .Z to the suffix of the PDB file.

Switching from zcat to gzip -d in the script results in the following error:

Traceback (most recent call last):
File "/path/to/rosetta.binary.m1.release-371/main/tools/protein_tools/scripts/clean_pdb.py", line 346, in
os.unlink(file)
FileNotFoundError: [Errno 2] No such file or directory: '/path/to/current/working/directory/1QYS.pdb.gz'

The script works fine if I pre-download the file as just a .pdb, but is not working for the .pdb.gz file format.

[roccomoretti]

I think the changes in PR #111 should fix this. (It avoids using zcat altogether.)

I don't have a Mac to test it, though.