clean up refinement stage

git-svn-id: https://svn.salilab.org/imp/trunk@16345 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Use correct C++ namespace syntax, as recent SWIGs get confused by the previous
syntax. Fixes issue #155.


git-svn-id: https://svn.salilab.org/imp/trunk@16347 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Rather than calling exit(), throw sensible exceptions.


git-svn-id: https://svn.salilab.org/imp/trunk@16348 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Fix typos.


git-svn-id: https://svn.salilab.org/imp/trunk@16349 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Fix typos.


git-svn-id: https://svn.salilab.org/imp/trunk@16350 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Set sensible defaults for max_clustering parameters.


git-svn-id: https://svn.salilab.org/imp/trunk@16351 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Add missing headers.


git-svn-id: https://svn.salilab.org/imp/trunk@16352 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Remove unnecessary import, which doesn't work with older Pythons.


git-svn-id: https://svn.salilab.org/imp/trunk@16353 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Remove unnecessary call, which doesn't work on older Pythons.


git-svn-id: https://svn.salilab.org/imp/trunk@16354 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Remove duplicate copy to fix symlink problems with _compat_python.


git-svn-id: https://svn.salilab.org/imp/trunk@16356 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
tweak history

git-svn-id: https://svn.salilab.org/imp/trunk@16357 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Simply include high-level RMF.h.


git-svn-id: https://svn.salilab.org/imp/trunk@16358 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
add regex for charles

git-svn-id: https://svn.salilab.org/imp/trunk@16359 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
sync RMF to 564afdbcbfd51cf422d35a5a7ad5717f1f6f6a1c

git-svn-id: https://svn.salilab.org/imp/trunk@16360 e91f8c7b-0e32-4433-a9ac-4502d39a4eab