OverflowError: Python integer -1000 out of bounds for uint32 int32_to_negative(int32) in supplemental.py

[gmrandazzo]

Describe the bug

program crash while running the example with an OverflowError: Python integer -1000 out of bounds for uint32

To Reproduce
Steps to reproduce the behavior:

1. Install python3.12, openbabel and all the dependencies.
2. Install plip in python3.12
3. Run the example plipcmd.py -i 1vsn -yv

Expected behavior

plipcmd.py -i 1vsn -yv
2024-08-16 15:56:28,763 [INFO] [plipcmd.py:124] plip: Protein-Ligand Interaction Profiler (PLIP) 2.3.0
2024-08-16 15:56:28,763 [INFO] [plipcmd.py:125] plip: brought to you by: PharmAI GmbH (2020-2021) - www.pharm.ai - [email protected]
2024-08-16 15:56:28,763 [INFO] [plipcmd.py:126] plip: please cite: Adasme,M. et al. PLIP 2021: expanding the scope of the protein-ligand interaction profiler to DNA and RNA. Nucl. Acids Res. (05 May 2021), gkab294. doi: 10.1093/nar/gkab294
2024-08-16 15:56:28,763 [INFO] [webservices.py:41] plip.exchange.webservices: downloading file from PDB
2024-08-16 15:56:29,389 [INFO] [plipcmd.py:99] plip: file downloaded as ./1vsn.pdb
2024-08-16 15:56:29,389 [INFO] [plipcmd.py:49] plip: starting analysis of 1vsn.pdb
2024-08-16 15:56:29,403 [DEBUG] [supplemental.py:413] plip.basic.supplemental: detected pdb as format, trying to read file with OpenBabel
2024-08-16 15:56:29,661 [DEBUG] [supplemental.py:430] plip.basic.supplemental: molecule successfully read
2024-08-16 15:56:29,663 [INFO] [preparation.py:1389] plip.structure.preparation: PDB structure successfully read
2024-08-16 15:56:29,663 [DEBUG] [preparation.py:1400] plip.structure.preparation: PyMOL name set as: 1vsn
2024-08-16 15:56:29,665 [DEBUG] [preparation.py:415] plip.structure.preparation: 1 ligand(s) after first filtering step
2024-08-16 15:56:29,666 [DEBUG] [preparation.py:276] plip.structure.preparation: 1 ligand kmer(s) detected for closer inspection
Traceback (most recent call last):
  File "/Users/marco/Library/Python/3.12/bin/plipcmd.py", line 313, in <module>
    main()
  File "/Users/marco/Library/Python/3.12/bin/plipcmd.py", line 309, in main
    run_analysis(expanded_path, arguments.pdbid)  # Start main script
    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/marco/Library/Python/3.12/bin/plipcmd.py", line 159, in run_analysis
    process_pdb(pdbpath, config.OUTPATH, outputprefix=output_prefix)
  File "/Users/marco/Library/Python/3.12/bin/plipcmd.py", line 52, in process_pdb
    mol.load_pdb(pdbfile, as_string=as_string)
  File "/Users/marco/Library/Python/3.12/lib/python/site-packages/plip/structure/preparation.py", line 1403, in load_pdb
    ligandfinder = LigandFinder(self.protcomplex, self.altconf, self.modres, self.covalent, self.Mapper)
                   ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/marco/Library/Python/3.12/lib/python/site-packages/plip/structure/preparation.py", line 237, in __init__
    self.ligands = self.getligs()
                   ^^^^^^^^^^^^^^
  File "/Users/marco/Library/Python/3.12/lib/python/site-packages/plip/structure/preparation.py", line 282, in getligs
    ligands.append(self.extract_ligand(kmer))
                   ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/marco/Library/Python/3.12/lib/python/site-packages/plip/structure/preparation.py", line 300, in extract_ligand
    members = [(res.GetName(), res.GetChain(), int32_to_negative(res.GetNum())) for res in kmer]
                                               ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/marco/Library/Python/3.12/lib/python/site-packages/plip/basic/supplemental.py", line 378, in int32_to_negative
    dct[np.uint32(i)] = i
        ^^^^^^^^^^^^
OverflowError: Python integer -1000 out of bounds for uint32

Screenshots

Desktop (please complete the following information):

• OS: MacOS
• CPU: M2
• Version Sonoma 14.6.1