ucd-softmatterlab/NPCoronaPredict — reverse-engineered prompt

Build me a research tool for predicting what biomolecules end up coating a nanoparticle in a biological mixture. I want it to support the NPCoronaPredict workflow, where a user can define a nanoparticle material and shape, provide proteins or other adsorbates with concentrations, estimate adsorption affinity with a coarse grained UnitedAtom style model, then use CoronaKMC to predict the final corona abundances.

Please make it usable both from the command line and through a simple desktop GUI. Include sample config files and example data so someone can run a demo without knowing all the science first. The outputs should be easy to understand, with result tables, saved run files, and basic summary statistics for the predicted corona composition.

Set up the build and install process clearly for Linux, including Python dependencies, compiled tools, and the Qt based interfaces. Add documentation that explains the full workflow, inputs, outputs, and citations for the underlying methods.