aai-research-lab/FastMDXplora ? reverse-engineered prompt

Build me a Python tool that can take a simple PDB ID or a small config file and run a whole molecular dynamics study for me from start to finish.

I want it to handle setup, simulation, analysis, and then generate a clean report at the end, ideally as a PDF plus a saved results folder with everything needed to reproduce the run. It should also have a simple command line interface and a small GUI so I can either type a command or fill out a form. If possible, add a way to start a study from a plain English request too, but it should still validate everything and refuse to guess when something is unclear.

It should work for a protein alone, a protein with a ligand, and basic analysis of trajectories from common MD formats. Make the config the main source of truth, and save the resolved settings and run manifest every time. If you need to, look up current docs for the best library choices.