adding try/catch block to the pilot app pad_helices

• Summary

Merge pull request #2551 from RosettaCommons/everyday847/pocket_grid Break up large files into more sensible units ^ This will be absolutely the first pass of MANY; notably, I split out some too-aggressive changes to PocketGrid that had functional effects, and there are SO MANY files that I could do this to. Ultimately, this just involved creating 3 new subclasses of specific pose utils.

• Summary

Big oops! Disabling out the failing unit test in TestAutoDetectGlycanConnections.cxxtest.hh meant there were no non-failing tests! CxxTest got grumpy :'-(

• Summary

Disabling Jared's unit test until he gets back from vaction

• Summary

Merge pull request #2625 from RosettaCommons/sergey/f Refactoring integration.compare(...) so it always marking test as 'script failed' when .test_did_not_run.log or .test_got_timeout_kill.log files present in test output

• Summary

Merge pull request #2624 from RosettaCommons/everyday847/working_native_Fix Working native fix Integration test failures are due to an inexplicably early merge base chosen for the comparison in re: CONECT record output. If you look at my code diff, that's just not affected by these four lines of code.

• Summary

Merge pull request #2626 from RosettaCommons/JackMaguire/fix_mpi_unit_tests Fix MPIWorkPoolJobDistributor Unit Tests

• Summary

Merge pull request #2569 from RosettaCommons/aleaverfay/spades_performance_bugfix Moving forward with a non-inner-loop-disrupting Spades implementation Spades introduced a read into the options system in the inner-inner-innermost loop, looking at the options system billions of times. This is slow, yes, but it also disproportionately slowed down the multithreaded build. The goal that spades is seeking is to have water not desolvate. That's actually easier to implement by adjusting the LK parameters of a new atom type used only by water: "OW". When the Spades flags are on the command line, OW's LK_DGFREE and LK_VOLUME are set to 0. This commit removes billions upon billions of read accesses into the options system -- but I understand from @jklai that there are others that ought to be removed. In particular, the reads in inline_atom_pair_energy.hh really need to be removed. Be warned: if previously you looked for the atom whose atom-type was "OH" in a water residue, that atom's type is now "OW" There are a lot of cosmetic integration test changes caused by the addition of a new atom type. There are two integration test changes where a full-atom pose is being scored by the centroid "vdw" term, and the addition of a new fullatom atom type causes this centroid score to change. These are weird tests. There are two trajectory changes for the hydrate protocol that I can explain quite easily: before, the fa_sol term was turned off for water scoring, but now water derivatives. Oops! Now fa_sol is off for both scoring and derivatives.

• Summary

Adding two missing semi-colons to help the beautifier

• Summary

Merge pull request #2621 from RosettaCommons/xingjiepan/loop_hash_kic Xingjiepan/loop hash kic

• Summary

Merge pull request #2616 from RosettaCommons/roccomoretti/skip_compile_benchmark Add '--skip-compile' option to the benchmark.py script. This allows you to skip the compilation phase of the benchmark.py script if you already have things compiled locally.

• Summary

adding a pilot app that does helical bundle heptad repeat stitching

• Summary

Merge pull request #2611 from RosettaCommons/sboyken/mchbnet_updates2 Sboyken/mchbnet updates2 (resubmission)

• Summary

Merge pull request #2595 from RosettaCommons/aleaverfay/pdb_conect_performance_bugfix JD3 bottleneck / PDB output taking too long Attempting to fix a pretty serious performance bug in PDB writing that spent O(N^2) time trying to determine the CONECT records. This impacts JD3 protocols quite heavily in that it creates a bottleneck on node 0 when outputting the results from other nodes. Fixing a few bugs in the way CONECT records were written out at the end of PDBs. For this reason, lots of integration tests change, but not coordinates of structures written out -- only the record of which atoms are bonded to which other atoms.

• Summary

Fixed the text rendering code in the R@h graphics app.

• Summary

Merge pull request #2620 from RosettaCommons/JackMaguire/improved_jd3_archiving Archiving Refactor for JD3's MPIWorkPoolJobDistributor

• Summary

Legend: