Christian Schwantes
Christian Schwantes
You ran into the same seg fault? On Tue, Jun 17, 2014 at 8:39 PM, Lee-Ping [email protected] wrote: > I tried to fix this before, but I only spent ~2...
Ok that's an easy enough way to implement it. @leeping @mlawrenz @cxhernandez and anyone else, what features in LPRMSD do you need. There are multiple "align to density," or "align...
I'm working on translating it now. It slipped through the cracks during the transfer to mdtraj. It will have this functionality: 1) Align to one set of atoms and compute...
So, as robert pointed out, that is in the mdtraj.lprmsd function. If you pass `superpose=True` then it will modify the contents of the trajectory to be aligned to the reference.
@leeping do you have any data from the old version that I could use to test the implementation? I need a simple test for making sure the permute groups are...
nevermind, I came up with some simple examples. There seems to be a bug right now. I _think_ it's in mdtraj though.
There's no bug, I assumed the default for permute_groups was different than it is
This test fails: https://gist.github.com/schwancr/648d2955b2315835234f The distance is correct at zero, but the superpose isn't working because the rotation matrix cannot be converged. The warning is printed here: https://github.com/rmcgibbo/mdtraj/blob/master/MDTraj/rmsd/src/theobald_rmsd.c#L267-L319 This region...
Ok, so I found the reference code and put it in a new branch in mdtraj (rmcgibbo/mdtraj#503), but it still doesn't fix this test.
Yea, I think you're right, it seems to be working otherwise though.