Fix docstring for topology.select_atom_indices. closes #538
Merge branch 'master' of github.com:rmcgibbo/mdtraj
Fix running test_geometric kernels. closes #491
DSSP stuff
Proline bugfix in kabsch_sander. Previously, all proline residues were ignored, but they're actually only supposed to be ignored on one side of the calculation
One test is passing
c++
minor bugfix
eroneuous static
Remove dead code
Fix tabs to spaces
Fix windows compilation
Merge pull request #541 from proteneer/dssp

Fix windows compilation
Small cleanup. Free memory and deal w/ unused parameters
working
Fix the initialization of the energies
copyright
testing
merge in opther branch
some bug fixing