commit 1295438cd4bd2be39c9dbbfab8db669ab62415ab Merge: ce262d3 8236a8b Date: Sat Dec 12 00:30:01 2020 -0500 Merge pull request #5135 from RosettaCommons/vmullig/update_docs1 Update documentation so that main repo points to current master of docs. This is to add the page on using VSCode with RosettaScripts (https://www.rosettacommons.org/docs/wiki/scripting_documentation/RosettaScripts/Using-RosettaScripts-with-VSCode). commit ce262d3634861f3c7e26e9a28ba22521591e3fbe Merge: d183d3a dd41a11 Date: Tue Dec 8 16:48:25 2020 -0600 Merge pull request #5122 from RosettaCommons/roccomoretti/fix_PoseRTS_get_variants Fix issue with PoseResidueTypeSet::get_all_types_with_variants_aa() It looks like that due to caching behavior, PoseResidueTypeSet::get_all_types_with_variants_aa() will "double up" the underlying residue types. It turns out that special casing this function isn't necessary, as the base class implementation effectively only uses the public interface which is properly overloaded. commit d183d3a67482f6c3e6b451a59783a50ef6445a12 Merge: 6c8a8f0 8492146 Date: Mon Dec 7 15:02:05 2020 -0500 Merge pull request #5121 from RosettaCommons/JackMaguire/InverseRotCst Updating inverse rotamer CCs commit 6c8a8f044a9959e155e55e15fd84294010a70049 Date: Thu Dec 3 09:51:28 2020 -0800 Make addVirtualResAsRoot add a residue to its own chain (#5116) I think that this is a reasonable change since it doesn't make sense to have the virtual root in the same chain grouping as the last residue of the pose that you are adding it too. the current implementation is annoying because if you're trying to make sure the pdb_info is is line with experimental data I use pose.chain_sequence(i) to get the polymeric entities, then each are aligned. Adding an X at the end can make this annoying. If this PR breaks a lot -- then I will figure out the corner case in my own code. * Make vrt residue on its own chain * update ssa test commit 0f25f47ae98dc403a3c8c9352777f738ce24a55f Merge: fac69dd ee78b8a Date: Wed Dec 2 09:02:52 2020 -0500 Merge pull request #5110: aleaverfay/bugfix_pepspec_anchor_at_term pepspec: copy coords instead of overwriting anchor This fixes a bug brought to me by Astghik Tsokolakyan who was getting a segfault from the count_pair code and saw that I had written count_pair. Astghik was using the pepspec application setting the pep_anchor to be the first residue in the peptide, but also extending the peptide 3 residues off both the N- and C-termini. The extension code works nicely building off the termini, but after the extension completes, it does some centroid modeling and switches back to fullatom where it calls "replace_residue" on the anchor residue to restore its rotamer. This is a problem when the anchor residue in the original pose was a termini residue and its a middle-of- the-chain residue after the extensions have been added. One solution is to not anchor from either termini, but that can't be the right solution as the app in its documentation says that you should be able to use a single residue for the anchor. The bug fix is to copy the coordinates that can be copied from the original residue into the new residue. commit fac69dd63b19b7d5dac246655b6c15158b98365e Merge: 22408fd 60dce76 Date: Tue Dec 1 20:40:56 2020 -0700 Merge pull request #5111 from RosettaCommons/sergey/residue-fix fixing update_ResidueType_enum_files script commit 22408fd82586485cbf19d8b54fbba04449961287 Merge: 3eaef2a ad2486e Date: Tue Dec 1 19:31:04 2020 -0500 Merge pull request #5108 from RosettaCommons/vmullig/update_energy_method_tracers Update tracer names for classes in core/energy_methods This is a follow-up PR to #5103 . That PR corrected the namespaces for files in `core/energy_methods`, but was not intended to alter output (so that I could confirm that there were no integration test changes). This replaces the tracer names with ones reflecting the new namespaces, which _will_ change a lot of integration tests (but trivially in each case). Note: The initial diff includes all the changes from PR #5103, since this is branched off of that branch. Once #5103 is merged, I will merge the latest master into this branch to make it clearer that the only changes are from commit d6df11b, only updating tracer names. - [x] PR #5103 must be merged before this PR. - [x] Update integration tests that selectively unmute tracers. commit 3eaef2aa50482bc20a543156c775ef4dd79ce8e3 Merge: d763ec9 223e154 Date: Tue Dec 1 15:03:03 2020 -0500 Merge pull request #5103 from RosettaCommons/vmullig/clean_up_namespaces_a_wee_bit Clean up the namespaces a bit. When energy methods were moved from core/scoring to core/energy_methods in order to split core.3 and create the current core.4, there was a need to finish the split quickly: linking the enormous core.3 library was taking too long and using too much memory for some people's systems, and the change needed to be in master before additional energy methods were added. Unfortunately, this meant that the energy methods retained their old namespace, breaking the convention of ensuring that directory structure and namespace match in Rosetta. This PR aims to clean this up, and to change the namespace for the energy methods that are in core/energy_methods from core::scoring to core::energy_methods. Note: in the interests of keeping the integration tests interpretable, this PR does not change tracer names. Pull request #5108 will subsequently update the tracer names. This PR must be merged before that one. For reviewers: Although this is a huge PR, it should only change namespaces. (The only other cases are a few places where I switched new to make_shared, and one or two places where I switched MyClass myobject = MyClass( params ) to MyClass myobject( params ).) Nothing in this PR should alter Rosetta function or output (but for possible trajectory changes that are hard to anticipate from mysterious things that the compiler does differently). commit d763ec9657e8bce5d12a4ac6d3b341151d14dfb9 Merge: 4d16533 952db3d Date: Mon Nov 30 20:37:59 2020 +0100 Merge pull request #5105 from RosettaCommons/teunhoevenaars/fix_mathvector_sum error corrected of a zero initialization without type commit 4d16533b169ca225b3207be5e540ba0f3bfdd711 Merge: 7207360 48a72c1 Date: Fri Nov 27 14:41:41 2020 -0500 Merge pull request #5104 from RosettaCommons/everyday847/additional_docs_update Bump docs commit 7207360ec306440c5329902f695ee4ce5ecc1abf Merge: 22b2560 4d3c7ca Date: Tue Nov 24 16:53:43 2020 -0500 Merge pull request #5097 from RosettaCommons/everyday847/update_farfar2_docs Updated docs submodule commit 22b25601504eb8a3794b8273d6c6ee459477ba7d Merge: 8ea9207 060d06d Date: Tue Nov 24 09:52:04 2020 -0500 Merge pull request #5096 from RosettaCommons/JackMaguire/InverseRotCst Unit test for side chain coord csts commit 8ea92071489cad5832b631b059563c14646f21b7 Merge: 8371582 18fde6e Date: Mon Nov 23 19:33:58 2020 -0500 Merge pull request #5019 from RosettaCommons/vmullig/c2_crosslinkers Add full support for 1,4-bis(bromomethyl)benzene to CrosslinkerMover and simple_cycpep_predict This pull request adds full support for 1,4-bis(bromomethyl)benzene to the `CrosslinkerMover` and to `simple_cycpep_predict`. When used with the `CrosslinkerMover`, this crosslinker can be used to link two L- or D-cysteine residues in either an asymmetric or C2-symmetric pose, or an L- and a D-cysteine residue in an S2-symmetric pose (all of which are symmetries matching the crosslinker itself). Tasks: - [x] Add symmetric params file. - [x] Add `CrosslinkerHelper` subclass for 1,4-bis(bromomethyl)benzene - [x] Copy from 1,3,5-tris(bromomethyl)benzene case. - [x] Update asymmetric case. - [x] Update symmetric case. - [x] Switch to using `CYS:SIDECHAIN_CONJUGATION` patch instead of `CYX`. `CYX` should eventually be deprecated. - [x] For 1,3,5-tris(bromomethyl)benzene, too. - [x] Check TBMB tests. - [x] `CrosslinkerMover` integration tests: - [x] C2 symmetry. - [x] S2 symmetry. - [x] No symmetry. - [x] Add to `simple_cycpep_predict`. - [x] Integration test. - [x] Check integration test. - [x] Beauty. - [x] Documentation. - [x] For `CrosslinkerMover`. - [x] For `simple_cycpep_predict`. - [x] Update to point at latest master for documentation submodule. Tests pass. Integration test changes are all expected: - simple_cycpep_predict_1_4_bbmb, crosslinkermover_1_4_bbmb_asymm, crosslinkermover_1_4_bbmb_c2_symmetry, and crosslinkermover_1_4_bbmb_s2_symm fail since they're newly added with this PR. - database_md5 is picking up the new params file. - simple_cycpep_predict_tbmb and threefoldlinkermover_tbmb_symmetric have small but expected trajectory changes resulting from the switch from CYX to CYS:Sidechain_Conjugation. Qualitatively, the output is the same. ![BBMB_render1](https://user-images.githubusercontent.com/4205776/95399812-0af8cb00-08d7-11eb-8b34-9953383ab1d7.png) commit 8371582c66a136c65464a989dc1d496e8ed4e1d8 Merge: 2f79fe5 22ba8ce Date: Fri Nov 20 19:07:44 2020 -0500 Merge pull request #5024 from RosettaCommons/JackMaguire/HYP Adding hydroxyproline to packer palette. This is some good ole fashion test driven development. I'm adding one line that breaks a test for @vmullig and @everyday847 to fix. The test I'm breaking is the ability for Rosetta to load hydroxyproline into a PackerPalette. ---------------- From @vmullig: So this was a bit more involved than I had anticipated. The status quo in Rosetta was that hydroxyproline was a patched version of proline, with name "PRO:pro_hydroxylated_case1", 3-letter code "HYP", and 1-letter code "P". We wanted to be able to specify "HYP" (and "DHYP") in a PackerPalette, but this would require that the base name is "HYP" -- the CustomBaseTypePackerPalette matches on base name, not on three-letter code. We don't currently have the ability for patches other than the chirality-inverting patches to change the base name, and the chirality-inverting patches create a new base type when they do so -- we have some hard-coded stuff that requires on-the-fly patched types to retain the same base name, and which assumes that all unique base names are represented in the set of base residue types that are created at Rosetta initialization. It is convenient to create hydroxyproline by patching proline (ensuring that we're copying the proline geometry and properties and whatnot), but inconvenient to expect the user to know that that is what we're doing internally -- he/she should be able to work with HYP, not PRO:pro_hydroxylated_case1, and to have the full freedom of manipulating an independent residue type, not a type variant. So ultimately, the only feasible solution was: - To generalize the logic for special patches that create new base types. - To modify the pro_hydroxylated_case1 and pro_hydroxylated_case2 patches so that they both create new base types. - To modify the PackerPalette so that it does not attempt to match on the hydroxyproline-specific variant types when setting up lists of designable types. This works now, and I've confirmed that we can design with HYP sand DHYP simply by adding them in the list of allowed types in a CustomBaseTypePackerPalette. It also should be relatively easy to apply this to the small number of other special cases in which we would want a patch to create a new base type. commit 2f79fe5935f67088cd12a493a0032acede58d5c0 Merge: 129854a 2099c8b Date: Fri Nov 20 08:16:01 2020 +0200 Merge pull request #5058 from RosettaCommons/ShiHoch/SeqprofConsensus Some code and logic cleanup in SeqprofConsensusOperation commit 129854aabf8593955616851862a194cad81a1a60 Merge: 3bcd921 74d55d8 Date: Thu Nov 19 21:31:46 2020 -0500 Merge pull request #5074 from RosettaCommons/JackMaguire/InverseRotCst Adding option to AddConstraintsToCurrentConformationMover for inverse rotamers Adding the inverse rotamer equivalent of "bb only": "sc_tip_only". It only adds constraints to atoms impacted by the final chi angle. commit 3bcd92163e2aa840bde3eef66441b1edb97c5759 Merge: 3506fbc 934a7cb Date: Thu Nov 19 21:31:34 2020 +0200 Merge pull request #5090 from RosettaCommons/ShiHoch/FilterScan Shi hoch/filter scan commit 3506fbc54ec477dff9a3069921e329b69013f9ff Merge: 6786e56 06abf5a Date: Thu Nov 19 13:07:02 2020 -0500 Merge pull request #5073 from RosettaCommons/bfrenz/interface-ddg-fixes From Brandon (who also approved the itests changes as correct): This PR fixes some issues for how multi residue mutations are read in to the refactored version of the ddg code. It also adds interface optimization to the wild type scoring. As a result the code has also been cleaned up and chunks of it have been moved into independent functions. commit 6786e56d524105a5908f56ee01e8d0eab84983a1 Merge: c6e07be 3876342 Date: Thu Nov 19 09:28:49 2020 -0800 Merge pull request #5089 from RosettaCommons/solberg/contact_ms_tweak tiny tweak; remove unnecessary sqrt commit c6e07becd845804d7e8fdb5ef7a91a9320b236db Merge: 98cd031 84991ad Date: Wed Nov 18 19:44:05 2020 -0500 Merge pull request #5076 from RosettaCommons/JackMaguire/SmallVector This is my humble attempt at getting boost::container::small_vector to be 1-indexed to be more of a drop-in replacement for utility::vector1. commit 98cd031561289279c34fb3f88cfdc65ab4de1298 Date: Wed Nov 18 17:19:20 2020 -0500 beautifying commit 513d3b7d0fed351056eb93e1b35e2581247789e2 Merge: 83d83e4 adb46dd Date: Wed Nov 18 08:46:44 2020 -0700 Merge pull request #5071 from RosettaCommons/bcov/ContactMSFlags ContactMS apolar_only and squared commit 83d83e41283ef44a6ae652f9450c57dc680ec32d Merge: 7f783a1 8416d10 Date: Tue Nov 17 08:47:38 2020 +0200 Merge pull request #5084 from RosettaCommons/ShiHoch/MinMover Multiple comma seperated jumps can never be parsed as int commit 7f783a1e0b877fe44149b23fce4d055c6dd45bcb Merge: 05396b0 19274cd Date: Mon Nov 16 16:41:19 2020 -0800 Merge pull request #5080 from RosettaCommons/dimaio/dna_dihedral_newmin_fixes Check for DNA in atoms_with_dof_derivs commit 05396b05d8bf56c518706b273522c012fa21c6df Date: Sat Nov 14 20:50:59 2020 -0700 triggering clean rebuild