Merge pull request #3406 from CyrusBiotechnology/delucasl/write_seqres
From @decarboxy at Cyrus:
optionally output SEQRES lines in PDB files
This PR extends the pdb outputter to produce SEQRES records.
This feature is off by default and can be turned on with -out:file:write_seqres_records
also added a test that exercises the feature. No integration test changes expected.
Merge pull request #3270 from RosettaCommons/smlewis/pdb_diagnostic_test_language
New language for the PDB diagnostic test, to make its results more interpretable to the community. Example run here: http://benchmark.graylab.jhu.edu/test/418571.
Merge pull request #2480 from RosettaCommons/JWLabonte/sugars/database
Carbohydrates: Ensuring that all sugars in the database have their anomeric forms also
This merge adds about 20 new .params files to the database, such that all current sugars have their anomeric forms present.
All unit tests pass; integration test changes expected in a few carbohydrate-related tests. Output change in c-term-conjugation test because of additional residue types being added.
Merge pull request #3234 from RosettaCommons/vmullig/shush_noisy_tests
Switch some unit tests from std::cout or TS_TRACE to proper tracers
Tests can't be muted unless they use tracers.
Merge pull request #3216 from RosettaCommons/vmullig/add_octahedral_metals
Add support for octahedrally-coordinated metals to the CrosslinkerMover and to the simple_cycpep_predict application
Merge pull request #3107 from RosettaCommons/roccomoretti/only_for_extras_dummy
Add dummy cc file for 'only_for_extras' build.
It appears the static build doesn't like an empty source list when an 'only_for_extras' library isn't active. Add a dummy source file which will be used for that purpose. Should fix the mac.clang.static.build.release test on the test server