Add high throughput simulation option to file configuration

[NDoering99]

Fixes #

Changes made:

• Added High Throughput Simulation option to the PDB configuration form, allowing users to generate individual simulation setups for each ligand in a multi-ligand SDF file
• Extended configureFiles() to store the highThroughputSimulation session value
• Refactored downloadPackage(): when high throughput mode is active, the zip archive contains a separate subdirectory per ligand (named after the molecule's _Name property), each holding its own SDF and OpenMMDL_Simulation.py script
• Extended createScript() with ligand_sdf_override and protein_path_override parameters so per-ligand scripts reference the correct filenames