[BUG] fixes pdb file cause `FileNotFoundError` when using `--nofixfile` and `--pymol`

[chAwater]

To Reproduce

1. Edit the 1vsn.pdb file, add an empty line in the end. (mimic the fix will be applied to the pdb)
2. Run the code

docker run --rm \
    -v ${PWD}:/results \
    -w /results \
    -u $(id -u ${USER}):$(id -g ${USER}) \
    pharmai/plip:latest -f 1vsn.pdb -yv --nofixfile

3. See the error

Traceback (most recent call last):
  File "/usr/lib/python3/dist-packages/pymol/internal.py", line 293, in file_read
    handle = open(finfo, 'rb')
             ^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: './plipfixed.1vsn_1vfawm8i.pdb'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/src/plip/plipcmd.py", line 355, in <module>
    main()
  File "/src/plip/plipcmd.py", line 351, in main
    run_analysis(expanded_path, arguments.pdbid)  # Start main script
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/src/plip/plipcmd.py", line 160, in run_analysis
    process_pdb(inputstruct, config.OUTPATH, as_string=read_from_stdin, outputprefix=output_prefix)
  File "/src/plip/plipcmd.py", line 87, in process_pdb
    [visualize_in_pymol(plcomplex) for plcomplex in complexes]
  File "/src/plip/plipcmd.py", line 87, in <listcomp>
    [visualize_in_pymol(plcomplex) for plcomplex in complexes]
     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/src/plip/visualization/visualize.py", line 40, in visualize_in_pymol
    cmd.load(plcomplex.sourcefile)
  File "/usr/lib/python3/dist-packages/pymol/importing.py", line 819, in load
    kw['contents'] = _self.file_read(filename)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/usr/lib/python3/dist-packages/pymol/internal.py", line 297, in file_read
    raise pymol.CmdException('failed to open file "%s"' % finfo)
pymol.CmdException:  Error: failed to open file "./plipfixed.1vsn_1vfawm8i.pdb"

Debug
After applied fixes pdb

• self.sourcefiles['pdbcomplex'] = pdbpath_fixed
• but the file was not saved when --nofixfile

plip/plip/structure/preparation.py

Lines 1430 to 1445 in e4181b2

	if not config.PLUGIN_MODE:
	if pdbparser.num_fixed_lines > 0:
	logger.info(f'{pdbparser.num_fixed_lines} lines automatically fixed in PDB input file')
	# Save modified PDB file
	if not as_string:
	basename = os.path.basename(pdbpath).split('.')[0]
	else:
	basename = "from_stdin"
	pdbpath_fixed = tmpfile(prefix='plipfixed.' + basename + '_', direc=self.output_path)
	create_folder_if_not_exists(self.output_path)
	self.sourcefiles['pdbcomplex'] = pdbpath_fixed
	self.corrected_pdb = re.sub(r'[^\x00-\x7F]+', ' ', self.corrected_pdb) # Strip non-unicode chars
	if not config.NOFIXFILE: # Only write to file if this option is not activated
	with open(pdbpath_fixed, 'w') as f:
	f.write(self.corrected_pdb)
	self.information['pdbfixes'] = True

Expected behavior

• Maybe remove the fixed file in the end of the program?

Related issues (maybe)

• pymol.CmdException: Error: Object not found #135