atoms.positions returns a copy of the underlying array

[kain88-de]

Expected behavior

atoms.positions returns a view to the underlying array. This means code like u.atoms[:n].positions[:] = np.ones((n,3)) does an inplace update of the coordinates.

Actual behavior

atoms.positions returns a copy. This is especially true if only a selection of atoms in the universe is used.

Code to reproduce the behavior

import MDAnalysis as mda
import numpy as np

u = mda.fetch_mmtf('1UBQ')
u.atoms[:5].positions[:] = np.ones((5, 3))
print(np.allclose(np.ones((5,3)), u.atoms[:5].positions))

Comments

I know this a limitation of numpy when indexing. I'm also aware that my code example is not how one would ideally write the code. However, this is still potentially confusing behavior and I think we get questions about this on the mailing list once in a while.

I also do not know a good solution to this problem. Or even if there is one using numpy. It would still be nice to have this in a Common Pitfalls section of the documentation. (Maybe this is already there and I just don't know?)

It is definitely possible to write our own array structure in C that supports to create views to individual atoms. I don't think the effort this would involve is worth it though.

Currently version of MDAnalysis

• Which version are you using? (run python -c "import MDAnalysis as mda; print(mda.__version__)")
  0.18.0
• Which version of Python (python -V)?
  3.6
• Which operating system?
  Arch Linux