Request to Use All Three VDW Presets in ProLIF

[fajardo01]

I would like to request the ability to use all three Van der Waals (VdW) presets available (Specifically, I would like to use the mdanalysis, rdkit, and csd presets) in ProLIF for evaluating differences in interactions.

In the latest version of ProLIF, it appears that specifying the preset is not currently supported. Could you please help me with a way to specify the preset for VdW interactions?

[cbouy]

Hi @fajardo01,

The addition of the van der Waals presets have not been released yet, but you can install the development version from github directly:

pip install 'git+https://github.com/chemosim-lab/ProLIF.git'

Once that's installed, you should be able to specify them individually:

fp = plf.Fingerprint(interactions=["VdWContact"], parameters={"VdWContact": {"preset": "rdkit"}})

If you want to calculate all of them in one go to have the results in the same dataframe, you can define your own interactions that subclass VdWContact (one for each preset):

from prolif.interactions import VdWContact

class MDAnalysisVdW(VdWContact):
    def __init__(self):
        super().__init__(preset="mdanalysis")

class RDKitVdW(VdWContact):
    def __init__(self):
        super().__init__(preset="rdkit")

class CSDVdW(VdWContact):
    def __init__(self):
        super().__init__(preset="csd")

fp = plf.Fingerprint(interactions=["MDAnalysisVdW", "RDKitVdW", "CSDVdW"])

Feel free to reopen the issue if you still need help on this.