more missing #includes

git-svn-id: https://svn.salilab.org/imp/trunk@16157 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
more missing #includes

git-svn-id: https://svn.salilab.org/imp/trunk@16158 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
more missing #includes

git-svn-id: https://svn.salilab.org/imp/trunk@16159 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
more missing #includes

git-svn-id: https://svn.salilab.org/imp/trunk@16160 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Score transformations against experimental data.


git-svn-id: https://svn.salilab.org/imp/trunk@16161 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Filter and combine scores returned from experimenal methods.


git-svn-id: https://svn.salilab.org/imp/trunk@16162 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Cluster transforms with PatchDock.


git-svn-id: https://svn.salilab.org/imp/trunk@16164 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Do FiberDock refinement; add download URLs to program help.


git-svn-id: https://svn.salilab.org/imp/trunk@16165 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Final scoring: recompute z-scores for new set.


git-svn-id: https://svn.salilab.org/imp/trunk@16167 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Combine final scores and write results file.


git-svn-id: https://svn.salilab.org/imp/trunk@16168 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
'combine' combines z-scores, so extract z-score, not raw score, when only
using a single score.


git-svn-id: https://svn.salilab.org/imp/trunk@16169 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Set sensible default.


git-svn-id: https://svn.salilab.org/imp/trunk@16170 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Reverse z-scores for EM3D and CXMS.


git-svn-id: https://svn.salilab.org/imp/trunk@16171 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
Fix naming of SAXS receptor/ligand.


git-svn-id: https://svn.salilab.org/imp/trunk@16172 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
move test of base log functionality into base

git-svn-id: https://svn.salilab.org/imp/trunk@16174 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
remove standards checks for protected

git-svn-id: https://svn.salilab.org/imp/trunk@16175 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
don't call do_show in object show

git-svn-id: https://svn.salilab.org/imp/trunk@16176 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
turn on wrapping of protected methods in swig

git-svn-id: https://svn.salilab.org/imp/trunk@16177 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
forgot to remove a file

git-svn-id: https://svn.salilab.org/imp/trunk@16178 e91f8c7b-0e32-4433-a9ac-4502d39a4eab
use swig's native handling of protected methods, not the macro

This simplifies code, makes it easier to read and fixes issues with the doxygen docs becoming separated from the method name by the protection line

git-svn-id: https://svn.salilab.org/imp/trunk@16179 e91f8c7b-0e32-4433-a9ac-4502d39a4eab