Big Issue: plip can't batch generate pse-files for multiple complex.pdb files.

[FeizhenWu]

Describe the bug

I can successfully run plip command in terminal one by one,
[uxxx@cpu10 test_pdbs]$ plip -f rep_2_160_with_D001-01_4278.pdb -o output --pymol --txt
2025-03-19 14:16:13,031 [INFO] [plipcmd.py:124] plip.plipcmd: Protein-Ligand Interaction Profiler (PLIP) 2.3.0
2025-03-19 14:16:13,031 [INFO] [plipcmd.py:125] plip.plipcmd: brought to you by: PharmAI GmbH (2020-2021) - www.pharm.ai - [email protected]
2025-03-19 14:16:13,031 [INFO] [plipcmd.py:126] plip.plipcmd: 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
2025-03-19 14:16:13,065 [INFO] [plipcmd.py:49] plip.plipcmd: starting analysis of rep_2_160_with_D001-01_4278.pdb
2025-03-19 14:16:16,634 [INFO] [plipcmd.py:165] plip.plipcmd: finished analysis, find the result files in output/
[uxxx@cpu10 test_pdbs]$

*but I can't run the following command:
ls rep_pdb |while read a; do plip -f $a -o output --pymol --txt; done

2025-03-19 14:07:58,452 [INFO] [plipcmd.py:124] plip.plipcmd: Protein-Ligand Interaction Profiler (PLIP) 2.3.0
2025-03-19 14:07:58,452 [INFO] [plipcmd.py:125] plip.plipcmd: brought to you by: PharmAI GmbH (2020-2021) - www.pharm.ai - [email protected]
2025-03-19 14:07:58,452 [INFO] [plipcmd.py:126] plip.plipcmd: 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
2025-03-19 14:07:58,452 [INFO] [plipcmd.py:49] plip.plipcmd: starting analysis of rep_2_160_with_D001-01_4278.pdb
PyMOL>rep_2_160_with_TopSci_Sel_17901.pdb
NameError: name 'rep_2_160_with_TopSci_Sel_17901' is not defined
PyMOL>rep_5_127_with_Bioactivate_4132.pdb
NameError: name 'rep_5_127_with_Bioactivate_4132' is not defined
PyMOL>rep_6_75_with_Nat_Comp_80868.pdb
NameError: name 'rep_6_75_with_Nat_Comp_80868' is not defined
PyMOL>rep_6_75_with_S_Nat_Comp_3017.pdb
NameError: name 'rep_6_75_with_S_Nat_Comp_3017' is not defined
PyMOL>rep_6_75_with_TopSci_Ext_89078.pdb
NameError: name 'rep_6_75_with_TopSci_Ext_89078' is not defined
PyMOL>rep_7_68_with_D001-01_3802.pdb
File "toplevel", line 1
rep_7_68_with_D001-01_3802.pdb
^
SyntaxError: invalid syntax
PyMOL>rep_7_68_with_TopSci_Ext_2207.pdb
NameError: name 'rep_7_68_with_TopSci_Ext_2207' is not defined
2025-03-19 14:08:01,996 [INFO] [plipcmd.py:165] plip.plipcmd: finished analysis, find the result files in output/

How to revise this bug?
The issue may be linked to plip.visualization.visualize, where the PyMOL visualization object is not being closed after the .pse file generation is completed.

please revise it.