initial commit
sketch the public API

added munkres files

Add the assignment problem solver

add test for munkres

test

fix test

junk

some more work on lprmsd

Working minimally.

Add quaternion code adapted from yank

Work on progress

I think it's working now. A couple tests passing

some assert on rotation matrix

relax condtion slightly

fix bug

Change docs a little, add todo

tests

taking views could be unsafe, because some subset of the structure might get rotated but then another doesn't -- that would corrupt the coordinates

docstring

(1) factor out some of the input validation into separate functions, (2) avoid large copies as much as possible

port fancy indexing to c so that we can do it without the gil and thus run the parallel loop

fix docstring to be more explicit

merge with master

I think this is finally fixed

minor cleanup. better name for file
Add superpose kwarg to lprmsd
merge
Merge pull request #388 from rmcgibbo/lprmsd

Add LPRMSD to mdtraj