Ligands are removed from the models when using the alascan module, therefore producing wrong results

Module/Workflow/Library affected

alascan

Expected behavior

The module should score the provided complex, and not only protein chains

Actual behavior

As no parameters allow to accept ligand_top_fname and ligand_param_fname, the ligands in a complex are removed when the topology is re-generated when performing the point-mutation.

Steps to reproduce the behavior

run_dir = "alascan_bug"
molecules = ["protein-ligand-complex.pdb"]
[topoaa]
ligand_param_fname = "ligand.par"
ligand_top_fname = "ligand.top"
[alascan]
output_mutants=true

Suggestions on how to fix it

Add those two parameters in the alascan module and make sure they are used when re-generating the topology and parameters after the point mutation

Version

haddock3 - 2025.9.0

Additional context

https://ask.bioexcel.eu/t/protein-small-molecule-best-approach/5909/8?u=vgpreys