Exploit MDanalysis capability of reading bond information from tpr files.

[DrDomenicoMarson]

Happy new year and thank you for quickly addressing the previous issue with the importing of VDW radii!

While importing XTC files with a TPR file as a topology file, MDanalysis also has useful "bonds" information. I noticed the load_trajectory function has include_bonds = False, but it's never used inside the function.

To have the correct bonds information, it's sufficient to change around line 44 to:

    # create the initial model
    if hasattr(univ, 'bonds'):
        bonds = univ.bonds.indices
    else:
        bonds = []
    mol_object = create_object(
        name = name,
        collection = coll_mn(),
        locations = univ.atoms.positions * world_scale, 
        bonds = bonds
    )

By doing so I was able to load a TPR+XTC trajectory of a protein with proper bond data, which is quicker and "more precise" than having to calculate bonds for each frame based on distance.

[BradyAJohnston]

Ah excellent! I have been meaning to look into the bonds for the MDAnalysis import, but hadnt spent the time and I didnt realise it would be so simple.

If you want to open a pull request i could accept it through that, or i could make the changes as well. thanks for looking into it!

[BradyAJohnston]

Added here: a523d50