water dynamics without needing to order atom IDs

[yjw0510]

Is your feature request related to a problem?

The current (2.4.0-dev) version of MDAnalysis requires a user to order the atom IDs in advance.
The module (water dynamics) expects OHHOHH... ordered data as input.

Describe the solution you'd like

Probably the direct way to solve this is to reuse parts of hydrogen bonding code (mdanalysis/package/MDAnalysis/analysis/hydrogenbonds/hbond_analysis.py: line 362~367)
I think both functions (hydrogen bonding and water dynamics) are deeply related and, for that, it is also good for consistency.

    def guess_hydrogens(self,
                        select='all',
                        max_mass=1.1,
                        min_charge=0.3,
                        min_mass=0.9
                        ):

I am not sure but it might potentially degrade the computation performance significantly as there is an additional overhead of detecting oxygens and hydrogens. Thus, it might be more adequate to add this function as an optional parameter (i.e. guess_atom_type=bool).

Describe alternatives you've considered

I have no other idea

Additional context

[bhaumikpatel7]

we can reuse parts of the hydrogen bonding code in MDAnalysis to create a function that can guess which atoms are oxygens and hydrogens, which is useful for water dynamics analysis. This could potentially be added as an optional parameter in the water dynamics function.

This solution would likely improve consistency between the two functions and make it easier for users to apply the water dynamics analysis to their systems. However, as you mentioned, there may be a performance cost associated with the additional overhead of detecting atoms, so it would be important to carefully consider the trade-offs and test the performance impact before implementing this solution.

[kumarvaastavi]

I would like to work on this problem, can you guide how to start?