Tidy up and make callable from MultiFit application.


git-svn-id: https://svn.salilab.org/imp/trunk@16130 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
--version now also shows program name.


git-svn-id: https://svn.salilab.org/imp/trunk@16131 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Top-level integrative docking application; parse and check command line options.


git-svn-id: https://svn.salilab.org/imp/trunk@16132 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Do PatchDock docking.


git-svn-id: https://svn.salilab.org/imp/trunk@16133 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Update for new show() output.


git-svn-id: https://svn.salilab.org/imp/trunk@16135 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Raise proper exception.


git-svn-id: https://svn.salilab.org/imp/trunk@16136 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
gperftools is now optionally linked into base, not benchmark.


git-svn-id: https://svn.salilab.org/imp/trunk@16137 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Complete docking step.


git-svn-id: https://svn.salilab.org/imp/trunk@16138 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Remove unused functions.


git-svn-id: https://svn.salilab.org/imp/trunk@16140 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
fix test tfailures

git-svn-id: https://svn.salilab.org/imp/trunk@16141 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Test AlignmentParams() class.


git-svn-id: https://svn.salilab.org/imp/trunk@16142 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Replace libTAU parameter file parsing code with boost::property_tree, and
use more-or-less-standard INI file format. Removes dependency of IMP.multifit
on libTAU.


git-svn-id: https://svn.salilab.org/imp/trunk@16143 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Use ini file format.


git-svn-id: https://svn.salilab.org/imp/trunk@16144 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
check for SetVersionString so that we don't try to use old versions of gflags that we don't (perhaps yet) support

git-svn-id: https://svn.salilab.org/imp/trunk@16145 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
define deprecation macro when not gcc or clang

git-svn-id: https://svn.salilab.org/imp/trunk@16146 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
clean up includes

git-svn-id: https://svn.salilab.org/imp/trunk@16147 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
fix include path

git-svn-id: https://svn.salilab.org/imp/trunk@16148 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
add missing semicolons

git-svn-id: https://svn.salilab.org/imp/trunk@16149 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
push people away from not very useful macro

git-svn-id: https://svn.salilab.org/imp/trunk@16150 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
add missing include

git-svn-id: https://svn.salilab.org/imp/trunk@16151 e91f8c7b-0e32-4433-a9ac-4502d39a4eab