Waterdynamics depends on deprecated hbonds module

[RMeli]

analysis.waterdynamics uses analysis.hbonds which is deprecated in 1.0 and scheduled for removal in 2.0 (see #2739).

[RMeli]

Attribute timeseries is missing from the new HydrogenBondAnalysis but it is used in HydrogenBondLifetimes.run()

[RMeli]

@alejob @p-j-smith @MDAnalysis/coredevs I stumbled into this while trying to help @IAlibay with #2739 (see #2746 ) but I'm not very familiar with the waterdynamics.py and hbonds analysis modules. Do you have any suggestion on how to best fix this problem?

[alejob]

Hey there, is any replace for analysis.hbonds???

[orbeckst]

Yes, analysis.hydrogenbonds, see MDAnalysis.analysis.hydrogenbonds.hbond_analysis – it still has a HydrogenBondAnalysis class but it's called a little bit differently (and it's faster).

[xiki-tempula]

My suggestion would be using the water bridge analysis module. If order=0 and update_selection=True, the water bridge analysis should give the same result as the old hbonds module.
For MDAnalysis.analysis.waterdynamics.HydrogenBondLifetimes
An example could be:

    def run(self, **kwargs):
        """Analyze trajectory and produce timeseries"""
        h_list = MDAnalysis.analysis.hbonds.WaterBridgeAnalysis(self.universe,
                                                                 self.selection1,
                                                                 self.selection2,
                                                                 distance=3.5,
                                                                 angle=120.0,
                                                                 order=0,# For hydorgne bond detection
                                                                 update_selection=True, # This is default to false in water bridge analysis
)
        h_list.run(**kwargs)
        self.timeseries = self._getGraphics(h_list.timeseries, self.t0,
                                            self.tf, self.dtmax)

I'm currently moving the WaterBridgeAnalysis from hbonds to hydrogenbonds.

[alejob]

I understand that HydrogenBondLifetimes will be removed from waterdynamics, so this update is not necessary anymore.

[IAlibay]

@alejob do we have a path already defined for this? We probably need to consider what the deprecation order is going to be for this. We probably can't do a straight removal for 2.0, maybe we'd have to consider deprecating in 1.x or just a stub to the replacement if it behaves the same way?

[alejob]

The class was already removed for v2.0, see #2842.

[IAlibay]

I see the deprecation warning got added in #2798, that makes sense.

I think the only thing leftover in waterdynamics from the old hbonds is an unused import then?

mdanalysis/package/MDAnalysis/analysis/waterdynamics.py

Line 392 in 23074c6

import MDAnalysis.analysis.hbonds

That'll get itself taken care of when we remove the old hbonds code, so I'm going to go ahead and close this issue unless there's any objections.