update RMF to 65c38c243eecfc06aae1baabaa5d1aeee46bfeca

git-svn-id: https://svn.salilab.org/imp/trunk@16479 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Update README with some better instructions

git-svn-id: https://svn.salilab.org/imp/trunk@16480 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Adding SecondaryStructureResidue decorator and a psipred reader

git-svn-id: https://svn.salilab.org/imp/trunk@16482 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
changing match_score to rmsd instead of correlation

git-svn-id: https://svn.salilab.org/imp/trunk@16483 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
adding SecondaryStructureResidues to AnchorsData and some functions to query them

git-svn-id: https://svn.salilab.org/imp/trunk@16484 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
adding some include files

git-svn-id: https://svn.salilab.org/imp/trunk@16486 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
added setup_secondary_structure function to AnchorsData which creates default SSRs for every anchor point

git-svn-id: https://svn.salilab.org/imp/trunk@16487 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
update docs upon suggestions from riccardo

git-svn-id: https://svn.salilab.org/imp/trunk@16489 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
add script to create an alias of a module with a different name

git-svn-id: https://svn.salilab.org/imp/trunk@16490 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
suppress build prefix on doxygen files too

git-svn-id: https://svn.salilab.org/imp/trunk@16491 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
merge compatibility into base as we kept having to treat compatibility specially, and it doesn't do very much

git-svn-id: https://svn.salilab.org/imp/trunk@16492 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
require a repository argument to build in-source too

git-svn-id: https://svn.salilab.org/imp/trunk@16493 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
clean up empty module directory as git-svn doesn't

git-svn-id: https://svn.salilab.org/imp/trunk@16494 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Actually, the file is called standards_exceptions.


git-svn-id: https://svn.salilab.org/imp/trunk@16495 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Fix case: exit is not the same as Exit.


git-svn-id: https://svn.salilab.org/imp/trunk@16497 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Fix RPM build.


git-svn-id: https://svn.salilab.org/imp/trunk@16498 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
move some kernel teste to base

git-svn-id: https://svn.salilab.org/imp/trunk@16500 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
remove unused file

git-svn-id: https://svn.salilab.org/imp/trunk@16501 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
move example configs into a place where doxygen will find them

git-svn-id: https://svn.salilab.org/imp/trunk@16502 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
minor cleanups of types and use of get_squared() in algebra

git-svn-id: https://svn.salilab.org/imp/trunk@16503 e91f8c7b-0e32-4433-a9ac-4502d39a4eab