Implement Trj method for selecting a subset of atoms

[matteobecchi]

Something along the lines of

import MDAnalysis as mda
import numpy as np
from MDAnalysis.coordinates.memory import MemoryReader

def expensive_atom_selection(trj: Trj, selection: str) -> Trj:
    """Create a trj with a selection of atoms."""
    oxygen_atoms = trj.universe.select_atoms(selection)
    coords = []
    for ts in trj.universe.trajectory:
        coords.append(oxygen_atoms.positions.copy())
    u_oxygen = mda.Merge(oxygen_atoms)
    u_oxygen.load_new(np.array(coords), format=MemoryReader)
    return Trj(u_oxygen)

?

[andrewtarzia]

Is this necessary for something in dynsight? Because it just seems like mdanalysis code - and the user knows that a Trj is just a universe container, so they can do any mdanalysis thing they want with it.

Maybe just linking to useful mdanalysis methods might be better?

[matteobecchi]

Yes, in theory I agree. But then every time I need to do this stuff I need to look ad MDA docs to write some kind of convoluted code.... if the "easier" solution still requires something like ten lines of code, doesn't it make sense to wrap it in a one-line Trj method?

Anyway, I will look for the easier method to do this, so we can decide!

[andrewtarzia]

I agree with you. Just have to ask the question "how often will this be used?" Before adding more stuff that is technically elsewhere.

If the answer is significant, then I always say yes.