add tests for rigid body custom atom_indices
angle axis c++ now supports atom_indices.

It's not yet tested
add python test for c++ atom_indices.

Remove the warning that custom atom_indices should not be used with c++
add fire cpp test
formatting
formatting
Merge pull request #114 from js850/rb_atom_indices

generalize the c++ rigid body framework so it works with custom atom indices.
Merge pull request #115 from kjs73/fire_test

 add fire cpp test
remove Qt requirement from the travis build

We don't currently don't test the gui
Revert "remove Qt requirement from the travis build"

This reverts commit e6f475666ae963636714e40f1893faf345d23892.

Travis registers failure just because nose can't import pele/gui.
Besides, it doesn't really speed up the installation because conda
installs QT anyway
add the framework for the amber12 cython interface
Merge branch 'master' into periodic_boundaries