cation bridging interactions

[sarahvs99]

Hello, I am new to this package and was wondering if anyone has a modification/suggestion on how to do cation bridging interactions. This would be similar to the water bridging, but would allow for:
protein - water - cation - water - ligand interaction
protein - water - cation - ligand interaction
protein - cation - water - ligand interaction
protein - cation - ligand interaction

[cbouy]

Hi @sarahvs99,

The bridged interactions are still a feature in development so we haven't really generalised the concept to other interactions in a user-friendly way. With that being said, you could try something like the following:

1. create the missing cation-water interaction
2. replace the underlying fingerprint object that is used for the water bridge analysis with one that includes this new interaction and the purely ionic ones (on top of the usual HBond ones used for water-water bridges)
3. run the code as usual with fp.run or fp.run_from_iterable

from prolif.interactions.interactions import HBAcceptor
from prolif.interactions.water_bridge import WaterBridge as BaseWaterBridge

# create a new interaction for cation-water
# derives from HBondAcceptor as the WaterBridge has some hardcoded logic based on it
class CationWater(HBAcceptor):
    def __init__(self):
        super().__init__(
            acceptor="[+{1-},$([NX3&!$([NX3]-O)]-[C]=[NX3+])]",
            donor="[OH2]-[H]",
            distance=3.5,
            # disable angle checks
            DHA_angle=(0, 180),
        )

WaterCation = CationWater.invert_role("WaterCation", "")

# overwrite WaterBridge interaction
class WaterBridge(BaseWaterBridge):
    def __init__(self, *args, **kwargs):
        super().__init__(*args, **kwargs)
        self.water_fp = plf.Fingerprint(
            interactions=["HBDonor", "HBAcceptor", "Anionic", "Cationic", "CationWater", "WaterCation"],
            count=self.water_fp.count,
        )

fp = plf.Fingerprint(
    ["WaterBridge"], parameters={"WaterBridge": {"water": water_selection, "order": 3}}
)

The resulting interactions will be named "WaterBridge" and will also include bridged interactions that don't involve ions at all, you'd have to do some processing on the fp.ifp results to remove those.
I haven't tested this so make sure to compare the results on some frame with visual inspection.

Feel free to reopen the issue if you have more related questions