Move experimental-data-specific command line options into the Scorer subclasses.


git-svn-id: https://svn.salilab.org/imp/trunk@16181 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Add a test of the entire protocol.


git-svn-id: https://svn.salilab.org/imp/trunk@16182 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
get all files by default

git-svn-id: https://svn.salilab.org/imp/trunk@16183 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
match parameters in the file and the code

git-svn-id: https://svn.salilab.org/imp/trunk@16185 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Remove unnecessary prefixes.


git-svn-id: https://svn.salilab.org/imp/trunk@16186 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Pull responsitibility for setting up the build dir out of scons into a python script

- this makes scons faster as the dependency graph is smaller and scons depenency graph algos suck
- is more accurate as the dependencies weren't handled right with regards to symlinks/headers and preprocessing
- is much simpler as we have one script that sets (most) things up
- will make it easy to use cmake or some other build system

git-svn-id: https://svn.salilab.org/imp/trunk@16187 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
fix minor doc bugs

git-svn-id: https://svn.salilab.org/imp/trunk@16188 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
fix includes

git-svn-id: https://svn.salilab.org/imp/trunk@16189 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
improve restraint docs

git-svn-id: https://svn.salilab.org/imp/trunk@16190 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
move examples to single files and follow the doxygen example scheme

This remove a level of processing needed in the scons scripts

git-svn-id: https://svn.salilab.org/imp/trunk@16191 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
fix \relates hack

git-svn-id: https://svn.salilab.org/imp/trunk@16192 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
pull module overview stuff out into doxygen file

git-svn-id: https://svn.salilab.org/imp/trunk@16193 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
remove mentions of FailureHandler as it is not used

git-svn-id: https://svn.salilab.org/imp/trunk@16194 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
add README.md

git-svn-id: https://svn.salilab.org/imp/trunk@16195 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
add forgotten file

git-svn-id: https://svn.salilab.org/imp/trunk@16196 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
don't mark do_show as override

git-svn-id: https://svn.salilab.org/imp/trunk@16197 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
add missing header

git-svn-id: https://svn.salilab.org/imp/trunk@16198 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
remove local module in example system

git-svn-id: https://svn.salilab.org/imp/trunk@16199 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
make things work when building out of source

git-svn-id: https://svn.salilab.org/imp/trunk@16200 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
remove bad character

git-svn-id: https://svn.salilab.org/imp/trunk@16201 e91f8c7b-0e32-4433-a9ac-4502d39a4eab