Carbohydrates: adding missing file for Lewisx to i. test system

• Summary

Fix -jd2:ntrials behavior According to all the documentation, the -ntrials value should be reset for each nstruct. That is, if you FAIL_RETRY on every attempt, a setting of -nstruct 6 -jd2:ntrials 5 should run through 30 attempts for each input structure. Previously, the ntrials was shared between all nstructs for all input structures, so a -nstruct 6 -jd2:ntrials 5 with a constant FAIL_RETRY would do just 10 attempts, 5 for *_0001, and 1 each for *_0002 through *_0006. This commit changes it to the intended behavior.

• Summary

Updating unit tests script so it add used command-line's in to the logs

• Summary

Attempt to fix performance build. The performance build uses gcc 4.1, which isn't all that C++11 aware. This means things like std::map.at(), which work fine for recent gccs, don't work on the performance build.

• Summary

Adding a new pilot app (symmetric grafting)

• Summary

Reducing timeout value for integration.debug tests to 17 minutes

• Summary

Fix some remaining warnings under gcc 4.8 On my machine with gcc 4.8 only 5 warnings remain, regarding either RNA enums or aa_mpr, all of which I believe are being addressed by others. Also, tweaks to the cmake warnings-as-errors setup, again to better match scons builds.

• Summary

Fix unused-local-typedefs warnings GCC 4.8 added a class of warnings for in-function typedefs which are defined but never used. This commit clears them up, cleaning up compile output for those of us using GCC 4.8.

• Summary

Fix debug mode scaffold_matcher integration test. Protocol was attempting to add backbone stub constraints across polymeric bonds which weren't polymeric. Add checks which will keep this from happening. scaffold_matcher integration test changes expected, as it was previously using uninitilized memory for backbone stubs.

• Summary

Cmake build fixes. Turn off enum-compare-as-error (like scons builds). Also, remove -w from release build, as that inhibits the warnings-as-errors settings.

• Summary

Try to fix performance build by removing std::map.at()

• Summary

Attempt to fix header only build.

• Summary

Merging master into my local branch (which itself is an attempted fix of library levels)

• Summary

Cherrypick Frank's changes to RotamerTrials unit test This should fix the mac.clang.unit test results on the server.

• Summary

Warnings Removal: attempt to fix static build

• Summary

Fix library levels and debug app_exception_handling tests. Remove unneeded header in protocols/ncbb/oop/OopCreatorMover.hh to fix library levels. Change application specific -sasa flag to -sasatest to avoid conflicting with the Rosetta-wide -sasa option group. This fixes the debug-mode app_exception_handling test.

• Summary

Legend: