Performance issues

[cabergh]

Thanks for a great package for protein-lipid analysis! I would really like to test the binding site identification and binding pose extraction functionality. Unfortunately, I found that the performance is way too slow for me to test this functionality. I have an atomistic system with 1555 residues and a couple 100 lipids, but running the first steps in this tutorial (https://pylipid.readthedocs.io/en/master/tutorials/0-application-walk-through.html, up to "interaction with residues") took 4 mins on my test data (11 frames of protein and lipids), which means this analysis would take 43 days on my whole dataset. For comparison, I previously ran a similar analysis with prolintpy (https://prolint.github.io/prolintpy/#/) which took me ~20 h for the big dataset. Would it be possible to investigate the performance, remove some bottlenecks and perhaps enable multithreading to reduce the runtime?