undo accident shrinkage of the IMP caused by the new Mac tendency to save files automatically

git-svn-id: https://svn.salilab.org/imp/trunk@16297 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
just use boost.programoptions instead of gflags

it is easy enough to implement what we need and it removes a dependency. It also makes the api c++ class rather than macros, which is nice.

git-svn-id: https://svn.salilab.org/imp/trunk@16299 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
add missing #include

git-svn-id: https://svn.salilab.org/imp/trunk@16300 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Suppress warnings

git-svn-id: https://svn.salilab.org/imp/trunk@16301 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
fix arg call

git-svn-id: https://svn.salilab.org/imp/trunk@16302 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
more benchmark fixes

git-svn-id: https://svn.salilab.org/imp/trunk@16303 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
allow construction of selection from ParticlesTemp

git-svn-id: https://svn.salilab.org/imp/trunk@16304 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Mostly fix bug where optimized particles that are not scored wouldn't get updated

This address #154, but doesn't entirely satisfactorily resolve it. Perhaps need to make all access to particles be checked for the particle being up to date (and all containers too....)

git-svn-id: https://svn.salilab.org/imp/trunk@16305 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
add flag to print out version and build info

git-svn-id: https://svn.salilab.org/imp/trunk@16306 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
fix preproc symbol name

git-svn-id: https://svn.salilab.org/imp/trunk@16307 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
make sure to quote arguments

git-svn-id: https://svn.salilab.org/imp/trunk@16308 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
always build config.hs as scons somehow gets the dependencies wrong when scanning some cpp files and doesn't build them in time

git-svn-id: https://svn.salilab.org/imp/trunk@16309 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
make sure to create directories

git-svn-id: https://svn.salilab.org/imp/trunk@16310 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
nightly branch update
add missing #incldue

git-svn-id: https://svn.salilab.org/imp/trunk@16312 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
add missing #include

git-svn-id: https://svn.salilab.org/imp/trunk@16313 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
add test of overloaded methods with particles

git-svn-id: https://svn.salilab.org/imp/trunk@16314 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
remove useless swig directives

git-svn-id: https://svn.salilab.org/imp/trunk@16315 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
clean up atom::Selection

git-svn-id: https://svn.salilab.org/imp/trunk@16316 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
allow computation of rmsd on selection, closing #111

git-svn-id: https://svn.salilab.org/imp/trunk@16317 e91f8c7b-0e32-4433-a9ac-4502d39a4eab