commit 3cad483ccac973741499159e12989a7143bf79de Merge: fdd9e71 f0a1059 Date: Tue Mar 28 21:36:45 2017 -0700 Merge pull request #2143 from RosettaCommons/vmullig/tweak_genkic Decrease verbosity of GenKIC backbone_bin filter The backbone_bin GeneralizedKICFilter is a bit too verbose. Switching its output to the debug tracer. Cosmetic changes expected to the genkic_bin_setting integration test. commit fdd9e71c3a71b1bbd5e9e6f21327432d10df240c Merge: ac8ea95 492bf42 Date: Mon Mar 27 11:09:48 2017 -0400 Merge pull request #2123 from RosettaCommons/guffysl/residue_type_constraint_generator Guffysl/residue type constraint generator commit ac8ea95e95ae26fe410686d06808883dacb37711 Merge: f99bee9 014545f Date: Sun Mar 26 17:00:38 2017 -0700 Merge pull request #2137 from RosettaCommons/everyday847/run_until_finished Run stepwise Monte Carlo until finished commit f99bee9b076596a6dd064610ac20bb7cf4671b35 Merge: 1b8e520 2e7c454 Date: Sun Mar 26 07:38:51 2017 -0700 Merge pull request #2139 from RosettaCommons/rhiju/6D_loop_close_tests integration tests for generating and using 6D loop_close potentials commit 1b8e520de684695fdf9ed74a7fd7b901f98b36a5 Merge: 79b3ffd f906c5e Date: Sat Mar 25 13:17:45 2017 -0700 Merge pull request #2124 from RosettaCommons/rhiju/rna_denovo_master_mover Rhiju/rna denovo master mover all test changes are cosmetic due to change in Tracer name. commit 79b3ffd9eb2cd07e5167de59f37a6055e3c43056 Merge: af8783e 1bcf09b Date: Sat Mar 25 14:02:57 2017 -0500 Merge pull request #2130 from RosettaCommons/roccomoretti/split_by_selection Add utility functions for jump/residue selection correspondence. One utility function ( core::kinematics::jump_which_partitions() ) to test if a jump splits a pose according to a defined set of residues. Another function ( core::kinematics::get_foldtree_which_partitions() ) to (minimally) rearrange a FoldTree such that a single jump does split the pose. commit af8783e9df3ef0bd8430fd9e4f60c57ff70e4439 Merge: 7375bd5 e8d0b68 Date: Fri Mar 24 16:58:21 2017 -0600 Merge pull request #2126 from RosettaCommons/benchmark Adding test suite descriptions commit 7375bd563197b7eafb1efed7737366035e64afbc Merge: ab13853 3f43c15 Date: Fri Mar 24 22:43:07 2017 +0100 JumpDownstreamSelector bug fix So, for a FoldTree such as: FOLD_TREE EDGE 1 115 -1 EDGE 1 116 1 EDGE 116 221 -1, a call like: ResidueSelectorCOP jump( new JumpDownstreamSelector( 1 ) ); ResidueRanges ranges( jump->apply( pose ) ); will create a ResidueRanges[1] of 116-220, missing the last residue of the chain. This change should solve this issue. commit ab138539acf40cd6e70fbda2ba59e9dcce59610d Merge: 6b2a876 fa8175e Date: Fri Mar 24 12:00:13 2017 -0700 Merge pull request #2131 from RosettaCommons/dimaio/etable_bug_nblist_autoupdate Fix a small bug in etable when nblist_autoupdate is used. commit 6b2a8762a0952510ffb67161fce4c8cf60762b5f Merge: a6eb814 94bea0a Date: Fri Mar 24 02:52:41 2017 -0700 Merge pull request #2132 from RosettaCommons/vmullig/fix_aib Fix AIB structure prediction for BOINC. I missed a few MAL->AIB renamings in the database patches. commit a6eb814c15b0711422412555c0b0d7255aaea192 Merge: a87cdcb 35d2032 Date: Thu Mar 23 09:26:50 2017 -0700 Merge pull request #2121 from RosettaCommons/rhiju/reorganize_rna_denovo reorganize directory/namespace structure for rna_denovo/farna test changes are cosmetic. commit a87cdcbe9ff94dbc08ac545d54d019e047b09d34 Date: Wed Mar 22 14:34:00 2017 -0500 Fix integration test ignore list We don't want to compare any lines with "TIME_STAMP" on them. commit 8a96f86dc7ef2da0a7f81d790e3e7c1b968638bb Merge: 7a2d4e6 80c8c98 Date: Tue Mar 21 09:06:07 2017 -0500 Merge pull request #2120 from RosettaCommons/roccomoretti/chain_fix2 Chain numbers and letters and jumps, oh my! In Rosetta there's several ways of specifying a "chain": chain numbers (chain ID), chain letters, and jump numbers. These are not interchangeable. In general, there is *NOT* a 1:1 correspondence between chain numbers, chain letters or jump numbers, unless the pose has been specifically set up as such. To help reduce confusion, add documentation to (new function) Pose::num_chains() which describes the various options, and explicitly points out they may be different. Also add pointers to that documentation from various places where the distinction is relevant, or where a naive person might find a function that works with "chains" and might need clarification as to the distinction. Fix a number of utility functions in core/pose/util.hh which work with chain numbers/letters/jumps so that they're more robust to poses where the correspondence is not 1:1, and unit test them with a funky pose. Bonus: I've added C++11 move constructors and initialization list constructors to utility::vector1/0/L, so creating vector1s with defined contents is easy: utility::vector1 single_digit_primes{2,3,5,7}; commit 7a2d4e6693896aae8b2adb3df31189c64e17f195 Merge: 1770014 493a0f8 Date: Tue Mar 21 09:05:13 2017 -0500 Merge pull request #2115 from RosettaCommons/roccomoretti/tracer_annotation Update formatting for error conditions Several changes to improve diagnostic messages in the (rare) event of Rosetta failure. * Have the Fatal/Error/Warning tracers automatically label the output level with "[ FATAL ]"/"[ ERROR ]"/"[ WARNING ]" respectively * Consistency allows for easy grepping/noticeability of errors or warnings. * It also makes it easier to change how we tag tracers if people don't like "[ FATAL ]"/"[ ERROR ]"/"[ WARNING ]" * Many tracer output statements have been updated such that 1. We don't double-print the Error/Warning tags 2. Tracer statements which say they're warnings/errors actually go out on warning/error priority * runtime_assert() and debug_assert() output has been reformatted to be a bit more user friendly * e.g. We now indicate that the condition printed has failed, rather than implying that the condition is an error in itself. * `assert(false)` is not a good way to end the program, as it provides absolutely no information about what the failure was. Fix all the `*_assert(false)` instances I can find with something like `utility_exit_with_message()`. * Replace most of the plain C++ `assert`s with Rosetta `debug_assert`s, as that gives more information. (e.g. the backtrace on platforms which support it.) Lots of cosmetic changes in integration tests expected. commit 1770014c148a700be7681ee03eec4975f5976bfd Merge: ac6fa1b 7e25dc1 Date: Tue Mar 21 04:13:47 2017 -0700 Merge pull request #2087 from RosettaCommons/vmullig/fix_silent_read_issue_2 Incremental merge for fixing the silent file read issues This is an initial merge of the changes in pull request #1955. It fixes the silent file read issues, but not the write issues. See that pull request for full details. A handful of integration tests show cosmetic changes because the silent file reader is a bit more verbose with badly-formatted silent files, but no test changes of substance are observed. This should make silent file read much more resilient to the mysterious silent file write errors. Merging. commit ac6fa1beb57c70914b419b2e07450f1add8b81f4 Merge: 971219c d8cf5c8 Date: Mon Mar 20 10:41:05 2017 -0700 Merge pull request #2118 from RosettaCommons/dimaio/beta16_fix_tors_corr Fixing a few errors with -beta_nov16. Since these are bugfixes, I am making this change the behavior of beta_nov16 rather than add a new flag. This will trigger rebuilding of Dunbrack binaries. commit 971219cdc4c1fe119197c7eaae2700656880a12c Merge: 8e033be cb7950f Date: Sun Mar 19 21:58:51 2017 -0700 Merge pull request #2117 from RosettaCommons/vmullig/fix_bluegene_cyclopsorine_failure Correcting Blue Gene failure due to silly mistake in sarcosine Ramachandran maps. @jcminerlanl , if you're using the sarcosine Ramachandran maps after our discussion today, you should pull the latest master after I merge this in. I found a silly mistake. commit 8e033be0e76daa35a38987b5cbf4f7552dd5133d Merge: f990831 b794081 Date: Sat Mar 18 17:13:42 2017 -0500 Merge pull request #2119 from RosettaCommons/roccomoretti/beta_validate Add beta and beta_nov16 to the Dunbrack database validation tests. commit f990831328ddc5a63aa39ddccb5bd556e3db3b17 Merge: 28c1185 5d31ec6 Date: Fri Mar 17 10:33:06 2017 -0700 Merge pull request #2103 from RosettaCommons/hahnbeom/cart_bonded_bugfix Bug fixes cart_bonded commit 28c11856a035afcc5300b1a597d22830462daad6 Merge: 6d76726 308290a Date: Thu Mar 16 21:54:09 2017 -0500 Merge pull request #2114 from RosettaCommons/jadolfbr/ab_design_updates RosettaAntibodyDesign updates This PR changes and adds a number of things to the RAbD protocol and framework: - 1) Add a new cmd-line option `-primary_cdrs`. This sets the CDRs to be used for the outer cycle. Very useful if you want to graft-design a specific CDR, such as H3 and allow neighboring CDRs to sequence design, but you are primarily interested in sampling H3. - 2) **Simplifies the protocol.** You can now use `-graft_design_cdrs`, `-seq_design_cdrs`, and `-mintype` to run the whole protocol. If you want specifics, you can use the CDR instruction file. This makes a design run as simple as: `antibody_designer.macosclangrelease -s my_ab.pdb -graft_design_cdrs H3 -seq_design_cdrs H1 H2 -primary_cdrs H3 -light_chain lambda` - 3) Sets outer_cycle_rounds to 25. This is a much more reasonable number, but requires 4x as many decoys. Runtime for pack is ~ 2 minutes/decoy, while using _min_ as the mintype (_pack/min/pack/min_) is about 10 minutes/decoy. - 4) Make _min_ the default as this has been shown to work pretty well and take significantly less time than using the full relax flexbb design protocol. Make this do min/pack/min/pack instead of a single min/pack and then requiring users to set the inner_cycle_rounds to 2. - 5) Make the default to min_neighbors as we did in the benchmarking. These are reasonable defaults ``` L1 MinProtocol Min_Neighbors L2 L3 L2 MinProtocol Min_Neighbors L1 L3 MinProtocol Min_Neighbors L1 H3 H1 MinProtocol Min_Neighbors H2 H3 H2 MinProtocol Min_Neighbors H1 H3 MinProtocol Min_Neighbors L1 L3 ``` - 6) Add a new option for disabling certain amino acids, `-disallow_aa` which takes a list of either one or 3 letter codes. Enable this option to be set Per-CDR in the instruction file. - 7) **Add resfile support.** Nothing hacky, only there to further limit which residues are packed/designed, and can further limit residue types for design. - 8) **Add viewer support.** Enabled by extras=graphics and adding `-antibody:design:view` to the command line. - 9) Require the `-light_chain` option to be given and use it to limit grafts/sequence profiles for clusters. - 10) Make the default to design nothing. Require the user to give designing CDRs either through the command-line or through the CDR Instruction file. - 11) **Better Memory Management.** Make the previous default where we cache all the CDRs we will be grafting to be the option `-high_mem_mode`. This is off by default as if you do denovo design on an antibody with this option, you will need ~3-4 GB/process. So now we have an option `-cdr_set_cache_limit`, which we use as a cutoff at 300. This means that after we have cached 300 CDRs, we stop caching and then, load them on-the-fly if we need them. This actually has the benefit of making the setup phase much quicker, as we would never use all the CDRs we cache in a single process anyway. Perhaps with JD3 or threading, we can do this better eventually. - 12) Make the `-global_atom_pair_scoring` option True so that the atom_pair_cst score is used throughout the protocol - which can then act as a filter. - 13) Remove a bunch of experimental options to simplify what actual options we are using. commit 6d7672612cfc1b466cc39d1e2286343a4ba1b250 Merge: f6f13d7 b8b5df3 Date: Thu Mar 16 18:10:13 2017 -0700 Merge pull request #2113 from RosettaCommons/rhiju/rna_denovo2017_stage1 Rhiju/rna denovo2017 stage1 • test changes are for `rna_denovo` command lines. Some are cosmetic. Others occur after numerous fragment insertions and appear to be due to numerical instabilities. commit f6f13d701802fd47a9a4791780e0388f0ff6881e Merge: 4d94207 b325a04 Date: Thu Mar 16 15:58:05 2017 -0400 Merge pull request #2112 from RosettaCommons/aleaverfay/beautify_Mar2017 Aleaverfay/beautify mar2017 We resolved at the recent WRC meeting that we would be beautifying the code on a per-pull-request basis, with a test that will fail if any of your source files have not been beautified. To get that working, master will have to be beautified again. To that end, I've updated the beautifier to handle some aspects of C++ that it couldn't before (lambda functions with semicolons, macros that can't be followed with a semicolon; namespace aliasing) so that now all of master beautifies. This is a pre-beautification version of master that fixes things that needed fixin' so that the beautifier will work on it. I'll perform the actual beautification once Sergey has the testing server ready to run the new test. commit 4d94207a8978f677287aa9412ae8ec81e7950dbb Merge: e16824f 550ade8 Date: Thu Mar 16 10:26:19 2017 -0500 Merge pull request #2109 from RosettaCommons/roccomoretti/feature_errors Add additional error reporting to poorly parsed FeatureReporter tags. commit e16824fac7a7239d7459c1810a6aec4f5fdf53fa Merge: d3e29dd 6e1f53b Date: Wed Mar 15 09:24:13 2017 -0400 Merge pull request #1972 from RosettaCommons/aleaverfay/offrot_w_lkball Per-residue setup-for-scoring Residue contains a datacache similar to Conformation's and Pose's datacaches, but the only way the datacache can be updated is through setup_for_packing, when you have constructed a RotamerSet object. In the off-rotamer packer, you do not have a pre-calculated set of rotamers and so this function cannot be used. This has the unfortunate consequence of making LK_Ball inaccessible to the off-rotamer packer. The new interface for energy methods proposed in this PR would allow them the opportunity to indicate "yes, I need a per-residue setup-for-scoring opportunity" and then for those EMs to be given write access to the per-residue data cache, without getting write access to the Residues themselves. - [x] rename "requires_a_setup_for_scoring_opportunity" to "requires_a_setup_for_scoring_during_minimization_opportunity" in all existing 2BEMs - [x] create a new "requires_a_setup_for_scoring_during_regular_scoring_opportunity" function in EM base class - [x] create a new (overloaded) "setup_for_scoring_for_residue" function that passes in a Residue's datacache. Add accessors for this datacache to Conformation. - [x] Add calls to "setup_for_scoring_for_residue" to ScoreFunction and the off-rotamer packer. - [x] Update LK_BallEnergy to use this new interface It may very well be that EnergyMethod::update_residue_for_packing could be replaced by this new interface. commit d3e29ddfa500ca42062487776fab6b077ca24de0 Merge: 42fedd8 e5a6d33 Date: Tue Mar 14 11:25:56 2017 -0400 Merge pull request #2097 from RosettaCommons/JWLabonte/BackboneMover ShearMover: fixing bug in ShearMover If `ShearMover` tries to shear a peptide following a cis bond, it actually twists it. This merge will fix that. (It also turns off shear moving for sugars for now.) 15 integration tests change, because moves that were previously made are no longer allowed. All other tests pass. commit 42fedd8f71c1d04151e125f04cc4b4538c9808f5 Merge: 10d97b8 d0750fa Date: Tue Mar 14 08:15:47 2017 -0400 Merge pull request #2110 from RosettaCommons/lqtza/floppytail_com_in_ordered_region_only Addition of FloppyTail-related PyRosetta scripts and minor changes commit 10d97b8f5cc4a0265992f57944eaf450f66f7730 Merge: 33e71d5 a63664d Date: Mon Mar 13 16:36:13 2017 -0500 Merge pull request #2101 from RosettaCommons/jadolfbr/fix_quench Fix GlycanTreeIntegration test Fix backward-direction quench-mode GlycanTreeRelax. Split the 3 tests into separate integration tests. Speed them up by removing the final optimization step. commit 33e71d50908555c9dfb210c62f1745c5687e18bb Merge: a9aac0f 8e9b65c Date: Mon Mar 13 08:48:05 2017 +0100 LabelPoseFromResidueSelectorMover and SplitAndMixPoseMover SplitAndMixPoseMover. By default extracts all the pieces of a pose as selected through a ResidueSelector but it also allows to then mix the order in which the new pose contains the different pieces. Furthermore it allows to merge pieces coming from different chains into one chain. Because it comes from a ResidueSelector the pieces are, logically disconnected. thus, it produces a multi-chain pose or a pose with chain breaks. Rewrites the PDBInfo. LabelPoseFromResidueSelector. Adds or removes labels on residues selected through a ResidueSelector. Thought to work in combination with ResiduePDBInfoHasLabel. commit a9aac0fdfaf5c1781a0723304aaad3730017545c Merge: f9670be c88273c Date: Mon Mar 13 00:18:02 2017 -0700 Merge pull request #2106 from RosettaCommons/vmullig/fix_aib_patching Fixing NtermProteinFull patch case for AIB (which still said MAL). This is a pretty small change. No unit or integration test changes expected. commit f9670bee3d6ed52c7802844096af9b5d3a2f9b3b Merge: d32bfad ca44625 Date: Fri Mar 10 20:28:01 2017 -0800 Merge pull request #2104 from RosettaCommons/yhsia/symdofmover_bugs msc SymDofMover XMLSchema fixes commit d32bfad6b2d9026f2e592c8d95e3959063014982 Merge: cb85c27 6b1f2b9 Date: Fri Mar 10 15:20:31 2017 -0800 Merge pull request #2102 from RosettaCommons/yhsia/symdofmover_uniform Yhsia/symdofmover uniform commit cb85c27479de76d61789c1bf513060ac9c424521 Merge: 1a87dff 50be32d Date: Fri Mar 10 13:05:53 2017 -0600 Merge pull request #2095 from RosettaCommons/havranek/virt_coord Havranek/virt coord commit 1a87dffaddea82b7ad3c3d5c69847df497ada29a Merge: 332c1e0 3168905 Date: Fri Mar 10 11:29:09 2017 -0600 Merge pull request #2083 from RosettaCommons/roccomoretti/no_color_log_file Add suppression flag to CSI Sequence printing. Rosetta printing color highlighting of tracer output is nice ... if you're on a terminal which supports it. If you're redirecting to a log file, or on a terminal without support, it can produce rather ugly control code sequences in the display (e.g. '^[[0m') There's some existing autodetection logic to catch when you're redirecting a file, but it's not always foolproof. This pull request reorganizes things and adds a new option `-out:no_color` which suppressed the printing of the CSI sequence codes. Additionally, the `-out::mpi_tracer_to_file` option also toggles the same CSI suppression setting, to suppress the control code printing in the MPI logs, even when the main output is still directed to the terminal. As an added benefit, I've removed some now-unused logic from tracer output, which should greatly speed up printing to tracers. One catch is that, due to the static initialization order fiasco, I needed to convert the utility::CSI_* entries from static objects to functions which return the appropriate objects. MPI integration tests expected to change, as control codes are now being suppressed. commit 332c1e0bb66d6a1b2f85101d8732dbda753d1246 Merge: 3e2ccce 6907857 Date: Fri Mar 10 05:44:40 2017 -0800 Merge pull request #2096 from RosettaCommons/vmullig/fix_bluegene_issues Fix compilation on Blue Gene / clang. commit 3e2ccce690a1279a54a7af32f08bb2e5de10a1ee Merge: 9319fc3 4571e1a Date: Thu Mar 9 13:26:38 2017 -0600 Merge pull request #2086 from RosettaCommons/jadolfbr/glycan_relax2 Glycan Relax - Version 2 his PR adds a new protocol for modeling glycans, GycanTreeRelax. This protocol models glycan trees from the root of the glycan trees out to the foliage using virtual residues to model outward. This protocol significantly decreases the energy of final de-novo modeled glycans and fixes many of the pathologies associated with the original version when used on every residue, especially the roots. If you are modeling glycans, this is the protocol you want to use. @raemisch @JWLabonte @dwkulp Add integration test for this protocol. Other integration test changes are cosmetic from increased debugging output with debug tracer for MoverContainer. Here is the general description: Brief === A protocol for optimizing glycan trees using GlycanRelax from the base of the tree out to the leaves. Works by making all other residues virtual except the ones it is working on (current Layer). GENERAL ALGORITHM ================== We start at the roots, and make all other glycan residues virtual. We first model towards the leaves and this is considered the forward direction. GlycanRelax is used for the actual modeling, we only model a layer at a time, until we reach the tips. If more than one round is set, the protocol will move backwards on the next round, from the leafs to the roots. A third round will involve relaxation again in the forward direction. So we go forward, back, forward, etc. for how ever many rounds you set. QUECHING ========= By default, we model all glycans simultaneously. First, all glycan roots (the start of the tree), and slowly unvirtualize all glycan residues, while only modeling each layer. Alternatively, we can choose a particular glycan tree, run the algorithm, and then choose another glycan tree randomly until all glycan trees have been optimized. Here, we call this quenching. GLYCAN LAYERS ============= Draw a tree on a paper. We start with the beginning N residues, and work our way out towards the leaves. Layers are defined by the glycan residue distance to the rooot. This enables branching residues to be considered the same layer conceptually and computationally, and allows them to be modeled together. **--LAYER SIZE--** The distance that make up a layer. If we have a distance of 2, we first model all glycans that are equal to or less than 2 residue distance to the root. We then slide this layer up. So we take all residues that have a distance between 3 and 1, and so on. **--WINDOW SIZE--** The layers are slid down throught the tree of the glycan. The window size represents the overlap in the layers. A window size of 1, means that the last residue (or residues of layer 1) from the last modeling effort, will be used again as part of the next layer. A window size of 0, means that no residues will be re-modeled. Typically, we would want at least a window size of 1. commit 9319fc350a0900b5acd9ea4721c1c088cd46f11d Merge: 33968e4 10d84d4 Date: Thu Mar 9 20:08:40 2017 +0100 Merge pull request #2094 from RosettaCommons/jaumebonet/rmsdfromselector TrueResidueSelectorCreator is now included in the init.cc and, thus, is accessible through RS with the tag. Several functions in core/select/residue_selector/util.cc to evaluate ResidueSubsets. RmsdFromResidueSelectorFilter allows to apply ResidueSelectors to both the pose and the reference_pose (loaded through the SavePoseMover). commit 33968e473adc558a16a54606084d0a676eda87e9 Merge: 18ca39d edb2659 Date: Wed Mar 8 22:38:20 2017 -0800 Merge pull request #2093 from RosettaCommons/everyday847/restore_proper_alignment_numbers Align to the modified local reference pose if applicable commit 18ca39d8fa65ab5cfd743eb59bd7039870372535 Merge: 45c5a9e 7935856 Date: Wed Mar 8 12:33:12 2017 -0700 Merge pull request #2089 from RosettaCommons/sergey/binder Adding PyRosetta apps commit 45c5a9e6b9b62fa0dcd231259e9f9809909051f7 Merge: 4400a7f 763d901 Date: Wed Mar 8 06:45:14 2017 +0100 Merge pull request #2088 from RosettaCommons/jaumebonet/constraintutils Changes in SecondaryStructureSelector and AtomPairConstraint with new non-default behaviour. Added SegmentedAtomPairConstraint and ReleaseConstraintFromResidueMover. commit 4400a7f7110dc47374e4c3fb834ff2a4c411f909 Merge: 98c1849 78301d3 Date: Tue Mar 7 18:19:17 2017 -0800 Merge pull request #2090 from RosettaCommons/hahnbeom/beta_nov16_bugfix2 fixing incorrect behavior of FastDesign scheduling commit 98c1849e857dc025783cddc5c3d5de5e4654b5f6 Merge: 8b2a418 bfe0d1c Date: Tue Mar 7 17:45:16 2017 -0600 Merge pull request #2084 from RosettaCommons/jadolfbr/gl_virts_glycans Virtual + Glycan residue updates to the OpenGL viewer This PR adds an option group for the OpenGL viewer and some options and changes in default behavior (`-viewer:`). - `-viewer:show_virtual_residues bool` (Default true ). Changing this to false will not show virts. By default, they are shown as white. If there is consensus on NOT showing them by default, I'm totally fine with that too. This just maintains the way usual way. - `-viewer:single_glycan_color bool` (Default true ). We now show glycans as a single color by default. Like a blue/purple ish with near-white side chains. Uses @rhiju 's way of showing non-protein residues, just changes the colors for them and the side chains. Looks decent and is very easy to see for many glycans on a single protein. Change this to False to see them as rainbow or chain-based. I would have colored them per-tree, but the functions only get residues and not the full pose (for some completely unknown reason actually). commit 8b2a4188ed0379f68e81fa83f3c742e305a4fc7c Merge: 4422420 c314b8c Date: Tue Mar 7 17:44:37 2017 -0600 Merge pull request #2082 from RosettaCommons/jadolfbr/gl_compile Make compilation of graphics mode work on mac. Adds a line in basic.settings to warn of the deprecated GLUT on mac os instead of crashing for graphics-mode only builds. commit 44224209bdb150ef31814b9a988c78c970aa942f Date: Mon Mar 6 17:52:04 2017 -0800 Small tweak to bettercluster pilot app. commit 67d30361e4bdfa62ad051f850233ce37205935eb Date: Mon Mar 6 16:48:50 2017 -0800 Beautifying master. It hasn't been beautified in some time. Please be sure to use Andrew's new beautify_changed_files_in_branch.py script to beautify your branch before merging into master from this point onward. (It's a very fast script -- it just takes a few seconds.) commit ffb98a7e9006fd365dc3961731fe01766c5243a5 Merge: 261926c 5b8d35e Date: Mon Mar 6 16:37:06 2017 -0800 Merge pull request #2074 from RosettaCommons/vmullig/fix_christine_nmethylation_issue Make the UnsatSelector compatible with symmetry Christine Kang reported an issue in trying to N-methylate peptides with symmetry. It turns out that the problem isn't with the N-methylation code, but with the UnsatSelector, which was being used to select positions in which the amide proton isn't involved in a hydrogen bond. This pull request aims to make the UnsatSelector compatible with symmetry. While I'm at it, I'm adding serialization support for the UnsatSelector, too. Tasks: - [x] Make the UnsatSelector symmetry-compatible. - [x] Make the UnsatSelector serializable. - [x] Beauty. While I'm at it: - [x] Modify FastRelax so that the scorefunction is made symmetric or asymmetric to match the pose. It's silly to ask the user to keep declaring separate symmetric or asymmetric scorefunctions -- it's just one more barrier to learning Rosetta. - [x] Do the same with FastDesign. commit 261926c784b8ab373904dea04526a6777c2db8ae Merge: 7b4d80c 52a7faf Date: Mon Mar 6 16:30:53 2017 -0800 Merge pull request #2078 from RosettaCommons/vmullig/refactor_xsd_functions_a_wee_bit Expose useful XSD-parsing functions in utility, and add a few more I'm cherry-picking some Rosetta changes from my GUI branch. Note that none of this makes Rosetta aware of the GUI in any way -- these are just utility functions that make it easier for the GUI to get information from the RosettaScripts XSD about the interfaces for movers, filters, etc. It makes sense for them to live in Rosetta since many different pieces of UI and non-UI code may want to use them. commit 7b4d80ca8070495e6f8b5886afddaf6bcbc659b1 Merge: b2f83cd 3c07a59 Date: Mon Mar 6 17:35:39 2017 -0600 Merge pull request #2085 from RosettaCommons/roccomoretti/cmake_nan_inf Update CMake for NaN/Inf issues. Pull Request #1737 fixed the scons build system for proper Inf/NaN handling, but the CMake subsystem was overlooked. This pull request fixes the issue, by adding the proper exclusion flags to the CMake build systems. commit b2f83cd96cebc40c0a36eda463b5d8177a1a0546 Date: Fri Mar 3 03:26:04 2017 -0800 Shushing an integration test that's producing spurious differences. It need not output the core.init tracer. commit e03ee5705ad09eaf641650c0542bbefaefb60c92 Merge: 91c33f3 9036c54 Date: Sun Mar 5 10:48:56 2017 -0800 Merge pull request #2081 from RosettaCommons/rhiju/better_loop_close Rhiju/better loop close Tests that change are expected -- restoring `thermal_sampler` and changes in FARFAR/rna_denovo. commit 91c33f395c4ecad0ef97c65708b3256c4436863b Merge: 8744492 e194189 Date: Sat Mar 4 16:39:32 2017 -0800 Merge pull request #2064 from RosettaCommons/hahnbeom/beta_nov16_bugfix beta_nov16, fixing minor bugs & adding support to FastDesign scheduling commit 8744492f87335bc050c4959d7ed6005dc30e0765 Merge: f1167c2 89aa6a2 Date: Sat Mar 4 16:05:26 2017 -0600 Merge pull request #2072 from RosettaCommons/roccomoretti/rs_include_fix Attempt to fix behavior of read_in_and_recursively_replace_includes() Brian Weitzner observed that RosettaScripts was **SLOW** with very large XMLs. He identified read_in_and_recursively_replace_includes() as the holdup. The previous version was using a rather sub-optimal algorithm, with a bunch of wasted effort. This PR changes the algorithm used to a more efficient one. Instead of exponential-ish behavior with XML file size, we now have linear-ish behavior. commit f1167c2825b095742dc1453caf901acbaa798276 Merge: 6ba1038 83c11e9 Date: Sat Mar 4 12:17:47 2017 -0600 Merge pull request #2080 from RosettaCommons/roccomoretti/ReturnSidechainMover_fix Update ReturnSidechainMover to be less sensitive An external user was having issues with ReturnSidechainMover and patched residue types (like phosphorylated tyrosine) due to centroid/full atom residue type name mismatches. Don't error out if the sequence doesn't match -- Output a warning message instead. (This also prints better diagnostics, to help track down the issue.) commit 6ba1038adf1acb7b90d731f6ad823c82efeca1d2 Merge: 859996e 8824e8a Date: Sat Mar 4 12:17:05 2017 -0600 Merge pull request #2079 from RosettaCommons/roccomoretti/with_message Adjust output printing for utility_exit() Just utility_exit()-ing without a message is very user unfriendly. Fix a few instances of that, and also bump tracer priority for other locations. commit 859996e724828ccd2ca890c6439d2d00ddb1e9ff Merge: 99719e7 391cf55 Date: Fri Mar 3 10:02:41 2017 -0600 Merge pull request #2070 from RosettaCommons/revert-2069-revert-2029-roccomoretti/ubsan_fixes Revert "Revert "Fix integration.ubsan"" Re-instate the ubsan fixes of PR #2029 that were reverted by PR #2069 due to build issues. commit 99719e7a32129022d69dce66a1a96f4f3b931802 Merge: deadab0 a3e731a Date: Fri Mar 3 06:33:00 2017 -0800 Merge pull request #2061 from RosettaCommons/rhiju/on_the_fly_cubic_interpolation On-the-fly cubic interpolation All tests pass (except ones that were broken, and a new one to test cubic-interpolated 6D loop_close). commit deadab0a8f4391652fbb3f2a481d5092b118d72b Date: Fri Mar 3 05:48:52 2017 -0800 Argh. Sorry; problems are endless. commit d9f06d44dc87b0ff3463fec5c5567802a371689d Date: Fri Mar 3 01:45:59 2017 -0800 Whoops -- broke PyRosetta unit tests with an undefined function that I should have removed completely. Apologies! commit 39c5c937f1b0757729b8fc8e012a29adc5fd17c0 Merge: d042c3e 3d1e394 Date: Thu Mar 2 19:02:03 2017 -0800 Merge pull request #2076 from RosettaCommons/everyday847/fix_unit_tests Fixed unit test -- sorry! commit d042c3ed10342496dcd0f6f5a480686e0060d003 Date: Thu Mar 2 10:13:23 2017 -0600 Fix two integration test issues. 1) The integration test ignore_list wasn't set up with MPI in mind - this fixes that oversight (MPI adds additional characters between the tracer name and the output) 2) Fix the currently broken header_using_check integration test, and add a README.txt to help future people know what's going on with the test. commit 537c047bf8a7e3f75d7db07f87f91b2fde08174e Merge: c272876 1d18079 Date: Thu Mar 2 09:55:53 2017 -0500 Merge pull request #2035 from RosettaCommons/aleaverfay/movemaps_from_residue_selectors This PR will introduce a new MoveMapFactory class that is more-or-less equivalent to a TaskFactory: It will construct a MoveMap (equiv: PackerTask) just ahead of MoveMap use given a Pose It holds instructions (equiv TaskOperations) for specifying the MoveMap behavior using ResidueSelectors and (new!) JumpSelectors This will add a MoveMapFactoryDataLoader and a JumpSelectorDataLoader into RosettaScripts to define new top-level elements. The MoveMapFactory begs for an additional TorsionSelector or DOF_Selector mechanism for selecting DOFs that are otherwise inaccessible. That'll go on a to-do list for now. Perhaps with the MoveMapFactory and with ResidueSelectors, we have enough justification for sweeping through existing Movers and Filters in an XRW trying to get them using this friendlier interface for controlling behavior, as proposed at WRC by @cdbahl commit c27287613e2d540d40a42562bf74fd9e73ba5cd8 Date: Wed Mar 1 19:32:57 2017 -0500 Reverting 59313 commit 0dc358090012a19997ec03c46f2b93265bf27e2f Merge: a1fcd40 38fba35 Date: Wed Mar 1 16:27:12 2017 -0800 Merge pull request #2058 from RosettaCommons/everyday847/only_beta_changes Just the beta sampler changes commit a1fcd4072f3f99c3dd512b0ef3c691bc39313343 Merge: 4933371 9c5f505 Date: Wed Mar 1 16:19:40 2017 -0800 Merge pull request #2068 from RosettaCommons/everyday847/swa_accelerations Make SWA faster in two ways commit 4933371295292b55a76c44ca27ebd76e4e348034 Date: Wed Mar 1 18:51:22 2017 -0500 Intentionally breaking one of the unit tests to re-test Testing Server 'Broke Something!' notifications. This commit will be reverted shortly. commit def8d5c97f4152f026d4e2a764a64ac4be01faac Merge: c5b7d57 0c9b8e7 Date: Wed Mar 1 13:07:18 2017 -0700 Merge pull request #2062 from RosettaCommons/sergey/binder PyRosetta, various Binder improvements. commit c5b7d577d5f148cf0e25f381b566eee914f33f51 Merge: e99fb99 e54bd16 Date: Wed Mar 1 14:00:58 2017 -0600 Merge pull request #2069 from RosettaCommons/revert-2029-roccomoretti/ubsan_fixes Revert "Fix integration.ubsan" Reverts RosettaCommons/main#2029 Caused major build issues. Reverting until things are fixed. commit e99fb9990e21b06747616f3923857165e23d98a6 Merge: af6fa34 6b91c66 Date: Wed Mar 1 12:06:11 2017 -0600 Merge pull request #2029 from RosettaCommons/roccomoretti/ubsan_fixes Fix a few issues which were causing issues in the integration.ubsan tests: * There's a bug in boost::format that invokes undefined behavior: https://svn.boost.org/trac/boost/ticket/11632 * There was some uninitialized variables in GlycanRelaxMover * For the thermal_sampler integration test, the params_ variable of RECCES_Mover isn't getting set. I don't know enough about this to say where it should be getting set - instead I just added checks such that similar oversights will be much more visible. The thermal_sampler integration test is now on perma-failure until the issue is addressed. commit af6fa34f866a39547d8267f8a6cc63486a78c821 Merge: 99781a8 5daf010 Date: Wed Mar 1 06:29:35 2017 -0800 Merge pull request #2067 from RosettaCommons/vmullig/tp1_integration_test Add integration test for protocol used in upcoming paper. I'm not 100% sure that everything used is already covered by tests; nor am I sure that the integration of the components will continue to work in the future. Tasks: - Add the protocol (used to design threefold-symmetric peptide 60mers with threefold-symmetric crosslinkers). - Strip it down so that it runs in ~1 min but still tests the essential workflow. commit 99781a84f0b6fa3adb1bf8ecaf1abe9fb248088f Merge: c24669b 31c01c4 Date: Wed Mar 1 09:06:41 2017 +0200 Merge pull request #2057 from RosettaCommons/fix_Splice_integration_tests Fix splice integration tests commit c24669b7f592c0dc91533fff8a9630fe8a7b0302 Date: Wed Mar 1 07:56:08 2017 +0100 Update observers commit 06d9af1d8bb30c6dd8bf3c27f68394633fbd07d3 Date: Wed Mar 1 07:55:56 2017 +0100 Update observers commit c45d5d0050b3ed89527a239ebde3a5fc31d5128b Date: Wed Mar 1 07:55:44 2017 +0100 Update observers commit 5ab7be5fa3245e76ab6df3e44d4dd8971e2312ae Date: Wed Mar 1 07:55:33 2017 +0100 Update observers commit 610c5a3e06290ce1a491f461f6ef3fa731da7e18 Date: Wed Mar 1 07:54:42 2017 +0100 Update observers commit 79375851ce402ce2332077cad720b32c87e26015 Date: Wed Mar 1 07:54:28 2017 +0100 Update observers commit 3cbb061a37aa717f74f38c3eeb6fa10fedc1471f Date: Wed Mar 1 07:54:16 2017 +0100 Update observers commit 0acca5147f783be8182edc1708f33f275857c06d Date: Wed Mar 1 07:54:03 2017 +0100 Update observers commit 1123baa1f7a268a75fb17c03ed78b537d84a04aa Date: Wed Mar 1 07:53:23 2017 +0100 Update observers commit b91a1f82a31146cd04c8c081a698c9a8e0563a67 Date: Wed Mar 1 07:53:12 2017 +0100 Update observers commit db23a96d548bdcc3824527b8ad09f93c702b660e Date: Wed Mar 1 07:52:58 2017 +0100 Update observers commit fb20dabde5ef57cd83263c3b3137e7ef15c03a17 Date: Wed Mar 1 07:52:39 2017 +0100 Update observers commit 2b2648a9aafad419eec062a86834b2f2932e5274 Date: Wed Mar 1 07:52:01 2017 +0100 Update observers commit 1582f80754794b0942ff648b7cd71bf642550de1 Date: Wed Mar 1 07:51:34 2017 +0100 Update observers commit 8121e59fab2fe3a552011da94ff1121903a55b49 Date: Wed Mar 1 07:50:45 2017 +0100 Update observers commit 5ba712b29c362329aedad4d9eb0dec438816f4fe Merge: 6949f76 12e3840 Date: Tue Feb 28 19:54:55 2017 -0800 Merge pull request #2059 from RosettaCommons/kylebarlow/ddg_backrub Fixing XMLSchemaAttribute in SwitchChainOrderMover commit 6949f76929141b47a97adf7c31b95d45ea60b34a Date: Tue Feb 28 18:53:05 2017 -0500 For now removing code_duplication test until licensing issues resolved commit f688eadce14ec789ee7738935bf88aa1b3abdde0 Merge: 0de31e0 f77095c Date: Tue Feb 28 08:14:42 2017 -0800 Merge pull request #2054 from RosettaCommons/everyday847/misc_util Miscellaneous updates that ended up in the beta samplers commit 0de31e0c679f7678213240e9a746d591ca018c77 Merge: 6c09d19 d5d010f Date: Mon Feb 27 12:41:58 2017 -0800 Merge pull request #2049 from RosettaCommons/jadolfbr/skip_loading CYD backwards compatibility Replace CYD with CYS:disulfide in the name_map of ResidueTypeSet for backwards compatibility of features databases (among others). commit 6c09d19fca1366167830f555272b875ce7750d6a Merge: 9889db9 eabd7ef Date: Mon Feb 27 12:17:50 2017 -0800 merge from master. commit 9889db9d542282ec045950812874be5585f02569 Date: Mon Feb 27 11:39:00 2017 -0800 making Andy the observer for the ERRASER test which keeps timing out