Merge pull request #945 from RosettaCommons/jadolfbr/simple_threader Jadolfbr/simple threader Adds a SimpleThreadingMover to Rosetta and RosettaScripts in simple_moves. This mover is exactly what the name suggests. Thread a sequence from start_position onto a pose. Sequence is 'threaded' together and packed. Optionally pack neighbors using loop machinery. If '-' is in the sequence will skip those positions. Example with neighbor packing: ``` <ROSETTASCRIPTS> <MOVERS> <SimpleThreadingMover name=threader start_position=24L thread_sequence=TGTGT--GTGT pack_neighbors=1 neighbor_dis=6 pack_rounds=5/> </MOVERS> <PROTOCOLS> <Add mover_name=threader/> </PROTOCOLS> </ROSETTASCRIPTS> ``` https://www.rosettacommons.org/docs/wiki/scripting_documentation/RosettaScripts/Movers/movers_pages/SimpleThreadingMover

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Merge pull request #1121 from RosettaCommons/vmullig/fix_irm_again Trying to fix the inverse_rotamer_remodel integration test. This was broken by a combination of recent XRW-related changes to PDB output. Attempting a simple fix.

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Merge pull request #1125 from RosettaCommons/everyday847/beta_util 1. Adds a toy app for evaluating a few 3_14 helices and point mutations vs. a target. 2. Fixes a bug with annotated_sequence that would totally screw up creating noncanonical poses from sequence--it would create them by jumps every time. 3. Messes around with my macrocycles pilot app a bit. 4. Integration tests for macrocycles app, since it is compiled by default. 5. Activates metapatches for residues other than just the peptoid 101, as they were meant to be!

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Merge pull request #1123 from RosettaCommons/nmarze/SnugDockTest SnugDock integration test updates: -Updating SnugDock integration test to include ensemble dock -Making snugdock app public -SnugDock integration test changes are expected -All other integration test changes appear to be existing minor numeric instabilities

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Merge pull request #1122 from RosettaCommons/roccomoretti/branch_distances_public Move batch_distances application to public. Application was used in the publication doi:10.1073/pnas.1202485109, so should be public. (We had a request on the forums.) This application already has an integration test.

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Merge pull request #1120 from RosettaCommons/vmullig/tweak_etable Splitting some of the changes from pull request #1093 Pull request #1093 (which aims to make RamaPrePro work with cyclic geometry and noncanonicals) revealed problems with cyclic geometry and the etable energies which I also fixed in that branch. It also produces a few more integration test changes than I had anticipated. I'm cherry-picking some of the changes from that pull request into a separate pull request so that I can pinpoint which changes are causing which integration test changes. This pull request: Tweaks the logic for the etable energies to ensure that cyclic geometry is handled properly. If I've done things properly, the only integration tests that change should be the ones that involve cyclic geometry. Test changes look good (only cyclic geometry and noncanonical connections show changes). Merging.

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Merge pull request #1119 from RosettaCommons/revert-1053-everyday847/remove_extra_pcs Revert "Removed old versions of pseudocontact shift code no longer in use as of 2010"

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Merge pull request #1118 from RosettaCommons/everyday847/fix_metalloprotein_valgrind Fix valgrind error identified by Rocco in metalloprotein setup

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Merge pull request #1117 from RosettaCommons/jadolfbr/sugars/debug_pdb_info Fix Simple Glycosylation test 2 This is attempt number two to fix this integration test. Attempt 1 uncovered deeper bugs in setting dihedrals from the LinkageConformer data for residues with > 1 omega (ASN-glycan linkage), which I missed when I merged before. The unit tests are now expanded for N glycan omega angles and tested

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Merge pull request #1108 from RosettaCommons/phbradley/dna_scoring Phbradley/dna scoring: add new energy methods, potentials, and database files to support a few dna-specific energy terms. Part I of a series of a couple of commits. Integration changes were observed locally and on the test server, but they appear to be entirely due to the addition of several new score types in the ScoreType.hh enum.

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Merge pull request #1103 from RosettaCommons/roccomoretti/rotamer_max Rework proton chi expansion With the new PDB components, there are some ligands which have an insane number of proton chis. (15+). Even at a very small level of proton chi sampling (60, -60, 180), the proton chi rotamer variants themselves absolutely kill packing and take up huge amounts of memory. (3^19 equates to greater than one billion proton chi combinations.) To fix this, I've instituted a scheme where the proton chi expansions are randomly subsampled, if they exceed a pre-specified limit. This should be set high enough that it won't affect anything that isn't currently bogged down due to proton chi expansion. We also had a large amount redundancy in the proton chi expansion code. I've centralized some of this, but there's still opportunities for further consolidation.

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Added RRM dinucleotide pair utilities

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Merge pull request #1114 from RosettaCommons/jadolfbr/sugars/debug_pdb_info Fix simple_glycosylation Integration Test Fix crash of simple_glycosylation in debug mode. Fix release mode simple_glycosylation test stochastic changes.

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Merge pull request #1110 from RosettaCommons/vmullig/fix_lei_app Turning on one of Lei's pilot apps. This pilot app is used, and should be compiled by default so that compilation can be tested. Its main() function has everything in a try/catch block, so it should be good to go, but I'll run it on the test server first. Correction: there were some owning pointer issues that were preventing compilation on Mac/clang. I've fixed these, now.

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Merge pull request #1107 from RosettaCommons/vmullig/rmstest Adding integration test for the fit_helixparams app in a case that was producing bad geometry and bad fits prior to my corrections to the RMS machinery. I want the problem to STAY fixed. The fit_helixparms_rms integration test should produce a PDB file in which every mainchain atom (except the carbonyl oxygen) has a copper atom that overlays perfectly on it. Distorted geometry or imperfect copper atom placement is a sign that something has gone wrong. Small changes to the coordinates that do NOT distort the geometry or affect the placement of copper atoms relative to backbone atoms are acceptable. There is a README.txt file that explains this in the integration test directory. I'll also add the expected output to the expected_results directory.

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Added auto detection of jupyter via env var.

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