new-rmsd2

Close rmcgibbo/mdtraj#103

Squashed commit of the following:

commit e4ef64808172bee926e26663ec61c51b0df62e74
Merge: c643c28 13a996b
Author: Robert McGibbon <rmcgibbo@gmail.com>
Date:   Sat Jun 29 15:13:50 2013 -0700

    merge in master to this branch

commit c643c281156169415e80717e7a638358f86e4d95
Author: Robert McGibbon <rmcgibbo@gmail.com>
Date:   Sat Jun 29 15:01:03 2013 -0700

    added a Note about setting OMP_NUM_THREADS

commit b8b8680e4f629c67de66606a795dd2737c9e272b
Author: Robert McGibbon <rmcgibbo@gmail.com>
Date:   Sat Jun 29 14:54:10 2013 -0700

    move the rmsd code into a module in the main mdtraj package, instead of a subpackage that really only made the import harder for the end user. also, set the random seed in one of the rmsd tests so we don't get an unpredicable failure

commit 9b67d3c1a17a65e6c6ed431658cc71fd94a305ad
Author: Robert McGibbon <rmcgibbo@gmail.com>
Date:   Fri Jun 28 20:21:18 2013 -0700

    Added documentation and changed the API a little bit, making some methods on RMSDCache private to simplify things

commit 92e546f48f720639631795449d403eff7fbd3374
Author: Robert McGibbon <rmcgibbo@gmail.com>
Date:   Fri Jun 28 18:37:17 2013 -0700

    change rmsds_to_reference() to just rmsds_to()

commit 8dfec6c6897cf35a7d8232efcfffef17570cdb92
Author: Robert McGibbon <rmcgibbo@gmail.com>
Date:   Fri Jun 28 18:33:47 2013 -0700

    remove the old rmsd code

commit 673ef8aa01dfd32a05dd72acbdf921cb966c42be
Author: Robert McGibbon <rmcgibbo@gmail.com>
Date:   Fri Jun 28 18:25:14 2013 -0700

    renamed some stuff

commit a77ed45296954951bc4e7508158db519c1ebb410
Author: Robert McGibbon <rmcgibbo@gmail.com>
Date:   Fri Jun 28 18:09:13 2013 -0700

    fixed critical bug in wrapper code

commit d2ba7674c6b567e2bd1ea5c57b04ac4fc0a9b7a0
Author: Robert McGibbon <rmcgibbo@gmail.com>
Date:   Fri Jun 28 17:07:22 2013 -0700

    little stuff. started removing code from the old rmsd

commit 7178994def00ba697022f0e2e7e1def577f3bbe4
Author: Robert McGibbon <rmcgibbo@gmail.com>
Date:   Fri Jun 28 17:01:25 2013 -0700

    added the half-working rmsd code from Imran's new IRMSD