Adding clang-3.4 to scons config files. This should fix linux.clang unit tests.

• Summary

Carbohydrates: added centroid files to database This push also reorganizes the centroid residue_types and patches directories to match those of the fa_standard set. fa_standard files for sugars have been copied over so that some initial tests can be run in centroid mode for sugars. ---------------------------------------- Unit test status: Pass Integration test status: No changes

• Summary

First commit of some symmetry testing code. Only added new apps files, no changes expected.

• Summary

Undo commit c1879dfc262b90ca0c6f5e476407b5fc71befff6, which contained broken nonsense as a result of a misguided attempt to remove map::at cals from SequenceAnnotation.cc where there were none. : (

• Summary

Remove map::at from SequenceAnnotation.

• Summary

Remove map::at() calls in AbscriptMover.

• Summary

Merge bugfixes with trunk.

• Summary

Carbohydrates: Refactored glycosidic torsion getters/setters This push corrects bugs in Pose::phi(), psi(), and omega(), and the cor- responding setters for carbohydrates. Previously, they did not function prop- erly in some cases, such as at branches. I have removed as many uses of strings as I could to improve code efficiency. I expanded unit tests for sugars. ---------------------------------------- Unit test status: Pass Integration test status: No changes expected

• Summary

Fixing build

• Summary

Re-enabling SpanFileIO unit test - previous error seems to be a stochastic error unresolved for now

• Summary

Make fold and dock moves parsable in RosettaScripts

• Summary

Fixing extras=python under clang

• Summary

Modify symmetry code to handle symmetries in which torsion changes can propagate to downstream monomers. No integration test changes.

• Summary

Adding try/catch block to fix app_exception_handling test.

• Summary

fix initialization of variables so that they do not depend on order -- caused SWM/SWA tests to crash

• Summary

getting rid of unused variables that triggered failure of debug build.

• Summary

Legend: