Cédric Bouysset

Hi @CAODH, The best for this is to do it with a dataframe. Supposing you've already run the interaction calculation, you can then do `df = fp.to_dataframe(return_atoms=True)`. The resulting dataframe...

Indeed, those index correspond to the atom numbering in the residue, not in the input. To retrieve the index in the actual file, you could try this (assuming you already...

Hi @martutebon and thank you! > Am I doing something wrong? Nope! It's just that by default the RDKitConverter in MDAnalysis was set to automatically fail if a user is...

Hi, This sounds more like an issue with the `RDKitConverter` from MDAnalysis, so I suggest that you open an issue with them for this. Best, Cédric

Hi Amir, I'll need a bit more info to solve this. The error means that there is no `PiStacking` interaction detected, but it could come from multiple things: - it...

Since both files have all hydrogen atoms explicit and there shouldn't be anything wrong with the code snippet, I think it might be the default parameters for that interaction which...

Hi @eschoo, Have you looked at [this part of the documentation](https://prolif.readthedocs.io/en/latest/notebooks/how-to.html#Using-PDBQT-files)? The only catch is that you'll require either a MOL2 file or SMILES to map the bond orders and...

Sorry for the very late response, I'm quite busy these days! ProLIF doesn't have a way to directly read files from a tar collection, but the Python standard library has...

There isn't currently a way to directly obtain that from the fingeprint calculation but I'll definitely consider adding some interactions metadata in the updates to come! @noahharrison64 's script shows...

Hi @alfredoq and sorry for the late response. If you set `match3D=False`, it will generate new 2D coordinates for your ligand, a bit as if you generated the structure from...