Hi BioBB team!
I think I found a possible bug, let me know if I'm mistaken or I understood something wrong :)
I was trying to use cat_pdb recursively to concatenate different ligands to a main structure:
First iteration:
input_structure1: ligand_1.pdb
input_structure2: structure.pdb
output_structure_path: complex.pdb
Second iteration:
input_structure1: ligand_2.pdb
input_structure2: complex.pdb
output_structure_path: complex.pdb
Doing this I noticed that if input_structure2 (or input_structure1 I guess) has the same file name as output_structure_path, what I get after executing the second iteration is not the concatenated ligand_1.pdb, ligand_2.pdb and structure.pdb but just the concatenation of ligand_1.pdb and structure.pdb. What I already had after iteration 1. I think there is a file name conflict in the sandbox of cat_pdb whenever output and input files are named the same. I could solve it by changing the output_structure_path for each iteration.
To me it's weird that this is the case, as if would happen for other BioBBs as well - so maybe I understood something wrong.
To Reproduce
You can try to reproduce this trying to use cat_pdb recursively as mentioned before.
Expected behaviour
I would expect that even if one of the input structures and the output structure have the same name, the output structure contains both input structure 1 and 2
- Python version: 3.10
- BioBB version 5.0.0
Thank you! :)
Hi BioBB team!
I think I found a possible bug, let me know if I'm mistaken or I understood something wrong :)
I was trying to use cat_pdb recursively to concatenate different ligands to a main structure:
First iteration:
Second iteration:
Doing this I noticed that if input_structure2 (or input_structure1 I guess) has the same file name as output_structure_path, what I get after executing the second iteration is not the concatenated ligand_1.pdb, ligand_2.pdb and structure.pdb but just the concatenation of ligand_1.pdb and structure.pdb. What I already had after iteration 1. I think there is a file name conflict in the sandbox of cat_pdb whenever output and input files are named the same. I could solve it by changing the output_structure_path for each iteration.
To me it's weird that this is the case, as if would happen for other BioBBs as well - so maybe I understood something wrong.
To Reproduce
You can try to reproduce this trying to use cat_pdb recursively as mentioned before.
Expected behaviour
I would expect that even if one of the input structures and the output structure have the same name, the output structure contains both input structure 1 and 2
Thank you! :)