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chemosim-lab / ProLIF

Interaction Fingerprints for protein-ligand complexes and more
https://prolif.readthedocs.io
Apache License 2.0
337 stars 66 forks source link

Random result of ifp? #194

Closed tom832 closed 1 week ago

tom832 commented 3 months ago

When I use prolif to analyze the ifp of following receptor and ligand, it gave me different ifp results. So is there any random module or algorithm in proliferation? BTW, I use plf.Fingerprint(count=True) in my code.

receptor file: 7en8_clean_H.pdbfixer.pdb.txt

ligand file:7en8_lig_H.sdf.txt

cbouy commented 3 months ago

Well at least not intentionally. I gave your files a go and the results for 10 repeats are the exact same, are you sure you tried on the same python installation? Which version are you using?

tom832 commented 2 months ago

I found it might be the random positions of added H with pdbfixer I used. Have you ever found this issue? or how can I get solid added Hs‘ positions?

cbouy commented 2 months ago

Ah right, then yes different H positions are going to affect the HBond detection. Can't offer support for pdbfixer though, but hopefully there's a random seed that you can set there to help with that