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Local environment after installation of all external dependencies
Bug Description
When running the surfmap script with input files that have filenames exceeding 50 characters, the script encounters a UnicodeDecodeError. This issue arises due to the improper handling of long filenames by MSMS, resulting in invalid characters being introduced in the processing pipeline.
Steps to Reproduce
Prepare an input .pdb file with a filename longer than 50 characters, e.g., a_very_long_filename_with_more_than_50_characters.pdb.
Run the surfmap script with this input file: surfmap -pdb a_very_long_filename_with_more_than_50_characters.pdb -tomap stickiness
Observe the UnicodeDecodeError in the console output.
Relevant Log Output
...
SURFACE MAPPING OF THE STICKINESS PROPERTY
Step 1: computing a shell around the protein surface
Traceback (most recent call last):
File "/home/nchenche/.venvs/surfmap/bin/surfmap", line 33, in<module>
sys.exit(load_entry_point('surfmap', 'console_scripts', 'surfmap')())
File "/home/nchenche/projects/SURFMAP/surfmap/bin/surfmap.py", line 63, in main
surfmap_local(params=params)
File "/home/nchenche/projects/SURFMAP/surfmap/bin/surfmap.py", line 18, in surfmap_local
surfmap_from_pdb(params=params)
File "/home/nchenche/projects/SURFMAP/surfmap/lib/core.py", line 171, in surfmap_from_pdb
csv_coords, shell = run_compute_shell(pdb_filename=params.pdbarg, out_dir=outdir_shell, extra_radius=extra_radius)
File "/home/nchenche/projects/SURFMAP/surfmap/tools/compute_shell.py", line 117, in run
vert2csv(vertfile=outfile_vert, outfile=outfile_csv, skiplines=list(range(3)))
File "/home/nchenche/projects/SURFMAP/surfmap/tools/compute_shell.py", line 72, in vert2csv
fori, linein enumerate(_readfile):
File "/usr/lib/python3.10/codecs.py", line 322, in decode
(result, consumed) = self._buffer_decode(data, self.errors, final)
UnicodeDecodeError: 'utf-8' codec can't decode byte 0xcd in position 177: invalid continuation byte
Additional context (optional)
This bug affects the vert2csv function where the ".vert" file from MSMS contains invalid bytes characters (a_very_long_filename_with_more_than_50_characters�̌@r) introduced in its header part:
Operating System
Unix (e.g., Ubuntu 20.04)
Version
2.2.0
Python Version (optional)
3.10.12
Python Virtual Environment
venv/virtualenv/other
Execution Environment
Local environment after installation of all external dependencies
Bug Description
When running the surfmap script with input files that have filenames exceeding 50 characters, the script encounters a UnicodeDecodeError. This issue arises due to the improper handling of long filenames by MSMS, resulting in invalid characters being introduced in the processing pipeline.
Steps to Reproduce
a_very_long_filename_with_more_than_50_characters.pdb
.surfmap -pdb a_very_long_filename_with_more_than_50_characters.pdb -tomap stickiness
Relevant Log Output
Additional context (optional)
This bug affects the vert2csv function where the ".vert" file from MSMS contains invalid bytes characters (a_very_long_filename_with_more_than_50_characters�̌@r) introduced in its header part:
Confirmation
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