Charlie Laughton
Charlie Laughton
I have 1.9.7, which seems to be the most recent in Pypi. I hadn't spotted the previous issue, I guess the fix just hasn't made it through yet.
With a fix that seems to solve issue #1769 (PR submitted), I get this behaviour with Python 3.11.3: >>> t = mdt.load ('alanine-dipeptide-explicit.dcd', top='alanine-dipeptide-explicit.prmtop') >>> print(t.xyz[0,0]) [1.352181 1.2696236 1.6946713] >>>...
I've done some digging into mdtraj/geometry/src/image_molecules.pxi and think I've identified a couple of bugs that could be responsible for at least some of the behaviours people are seeing. Firstly in...
Hi - just reminding folk there is a PR submitted for this - all feedback much appreciated.
I have a proposed fix according to your second paragraph above (warning raised if atom_indices are not monotonically increasing). PR on the way.
Hi, I have checked 1.9.8 and the issue is still there. The problem comes from the way `result` is instantiated when `inplace=False`: currently a new `Trajectory` is created, but many...
> Thanks for the PR submission! Left a couple of comments. > > Also - it looks like all the tests passed but could you also run this test for...
> > ... Do we think this is something of note? ... > > If it's a new warning, yeah we should avoid that I think I have just uncovered...
It seems the warning was appearing because in angles.py `ensure_type()` is used to cast box vectors to np.float32 without the `warn_on_cast` option being set to False (it defaults to True)....
OK - I have re-synced my fork - please try again!