commit d2d9f90b8cbcacfd7a1f69aefa5de610b100e8a9 Merge: d6f83ca 2f328c2 Date: Fri Jun 19 14:33:13 2020 -0500 Merge pull request #4797 from RosettaCommons/roccomoretti/address_unit_release Fix the release-mode version of the EPRSpinLabelTest unit test Convert an exact comparison of a real to a delta comparison. commit d6f83ca3920e8b037fac7bc8c15f186d3c008b5b Merge: cd6074b 7256944 Date: Thu Jun 18 23:14:10 2020 -0700 Merge pull request #4784 from RosettaCommons/everyday847/better_FMI_debugging A few extra .trace output statements for debugging FullModelInfo problems commit cd6074b877b1790ad7cc2da6b5d2b99c8dd8d9ee Merge: 151dc13 7d62ad1 Date: Wed Jun 17 17:13:42 2020 -0400 Merge pull request #3470 from RosettaCommons/JWLabonte/sugars/database2 ResidueTypes: Modifying patch system to allow for multiple aliases per atom This merge allows one to add multiple atom aliases from a patch file, which previously was only possible from a .params file. It further adds more aliases to a few sugars, which will help Rosetta load in a few obscure sugars from the PDB that currently fail because of atom naming. This merge also fixes an error in H-placement on acetyl groups that are not trans. commit 151dc13e850c8d3fdb91c994ad1721d8b193e15b Merge: 330e8d9 d37d22a Date: Tue Jun 16 15:36:08 2020 -0400 Merge pull request #4495 from RosettaCommons/yingyue0414-Add-tetroseandtriose-to-database Complete .params files for triose and tetrose residues in database commit 330e8d96378d24aeb32e50eb9bd2718b8b810376 Merge: a94262c b1867a0 Date: Sat Jun 13 00:44:31 2020 -0400 Merge pull request #4148 from RosettaCommons/JWLabonte/PDB_IO/HETATM_records PDB IO: Correcting how HETATM records are decided This merge corrects how Rosetta decides between writing a PDB ATOM record and writing a HETATM record. Historically, Rosetta saved LIGAND ResidueTypes with HETATM and POLYMER ResidueTypes with ATM. This was in conflict with how the records are defined by the PDB, which is that only canonical AAs and NAs get ATOM records; all other types of residues should receive HETATM. See issue #3509 for further details/discussion. All unit tests pass. 98 integration tests give expected changes with a multiplicity of .pdb output lines changing from ATOM to HETATM. commit a94262c3892228e2a27aa28e4e01e86cd3ab1871 Merge: 2d03adb 4de1916 Date: Thu Jun 11 15:06:16 2020 -0500 Merge pull request #4774 from RosettaCommons/roccomoretti/sf_weighted_sum Don't spend time multiplying by zero with linmem_ig. Performance analysis of a fixbb run of 1qys with the -linmem_ig flag indicates we were spending ~20% of the time doing EMapVector::dot() calls to multiply the edge scores by the weights. Given that most of the weights are typically zero, we can improve runtime by only multiplying through by the nonzero terms. This requires us to pre-calculate and store the non-zero terms for the ScoreFunction, but that turns out to be relatively straightforward. This PR adds a ScoreFunction::weighted_sum() method, which does the dot product between an EMap and the weights of the ScoreFunction, but only iterates over the non-zero terms. I then use that for the "hot" function in the OnTheFlyInteractionGraph. commit 2d03adbcd8df6eafe19c6a80221ae46f5c96153d Merge: 3c2b921 8cd002e Date: Thu Jun 11 15:04:55 2020 -0400 Merge pull request #4693 from RosettaCommons/revert-4692-revert-4624-vmullig/threadsafe_approximate_buried_unsat_penalty Re-merge "Make the ApproximateBuriedUnsatPenalty threadsafe". (Reverts RosettaCommons/main#4692). This re-merges the thread-safety fixes to the ApproximateBuriedUnsatPenalty. Tasks: - [x] Figure out what's causing the bug and fix it. --> A spurious pair of runtime_asserts have now been removed. Note: this diff (https://github.com/RosettaCommons/main/pull/4693/commits/d6dd51482bc8e7d857263381317db30f544b5c6d) shows the only changes from pull request #4624 (for which this is a reversion of the reversion). commit 3c2b9218275f8fc8c1da9911ecff390908cc3bc6 Merge: 55987dc 26d3508 Date: Wed Jun 10 20:43:22 2020 -0400 Merge pull request #4770 from RosettaCommons/smlewis/remove_blacklist_in_PDBdiagnostic Smlewis/remove blacklist in pdbdiagnostic Per a good idea I saw on the internet, renaming "blacklist" to a more neutral "blocklist" within the PDB diagnostic test. Will alter only that test itself. commit 55987dc6c44a57e6e509128702d35c449e6bafac Merge: 74a68c0 2307538 Date: Tue Jun 9 18:39:10 2020 -0400 Merge pull request #4191 from RosettaCommons/JWLabonte/sugars/database Carbohydrates: Expanding recognized GLYCAM codes This merge introduces updated and expanded GLYCAM 3-letter codes for input from AMBER, following the documentation provided here: http://glycam.org/docs/forcefield/glycam-naming-2/ @mszegedy and @thieker, this may be of interest to you. This PR is a response to issue #3546 and a continuation of work begun in PR #3544. commit 74a68c0b700ed0ab751f3130c33d211e07030b36 Merge: f07b967 63ff253 Date: Tue Jun 9 18:35:30 2020 -0400 Merge pull request #4457 from RosettaCommons/JWLabonte/PTMs/cofactors Coenzymes: Adding SAM and S-adenosyl homocysteine to the database This merge adds .params files for SAM and its demethylated version. It also adds an integration test for the loading of cofactors in our list. This merge also fixes a bug that caused the sugar_bb scoring term to crash when ligands were involved. commit f07b96794c9915d7c7d5f74a59dcb00ee5f5d673 Merge: 034d375 f511a17 Date: Mon Jun 8 14:10:01 2020 -0400 Merge pull request #4773 from RosettaCommons/vmullig/skip_submodule_update_with_nover_option Two small tweaks to scons build system This pull request: - Alters the behaviour of the --nover flag, so that in addition to skipping the versioning script, it skips the submodule update script. This saves time on slower filesystems during rapid rounds of development and compilation, if the developer knows that these submodules do not need to be updated. - Updates the help that one sees with `./scons.py --help` to: - Add examples for mpi, serialization, and cxx11thread builds. - Add the recommended default compilation command to build vanilla Rosetta for production runs. - Clarifies that `-j` accelerates _builds_ and not _Rosetta execution_, while `extras=mpi` or `extras=cxx11thread` can accelerate _Rosetta execution_ and not _builds_. - Adds the `--nover` flag to the help. commit 034d375f314dfa770be58e3f1fe26cb85fc8a739 Merge: 6dbf2f11 1ad2f05 Date: Sat Jun 6 23:53:34 2020 -0400 Merge pull request #4576 from CyrusBiotechnology/smlewis-propose-hybridize-fix potential patch for running hybridize with other polymers (NAs) commit 6dbf2f116f9d3b22621a8e9bc95d3bfed0f15f33 Merge: d9d4d5d a3b79a1 Date: Sat Jun 6 10:55:39 2020 -0600 Merge pull request #4751 from RosettaCommons/sergey/f2 Updating release scripts. Adding releases for PyMOL-Rosetta scripts. Adding PyRosetta Wheel releases. commit d9d4d5dd3fd516db1ad41b302d147ca0ccd78abd Date: Fri Jun 5 18:06:54 2020 -0400 beautifying commit 0d6f90a8cb9fa0567ca76bb71ee93bfe73340c70 Merge: f795386 30899e2 Date: Thu Jun 4 19:12:24 2020 -0500 Merge pull request #4746 from RosettaCommons/roccomoretti/icc_fix Fix ICC test on test server ICC 19 is having issues with the boost::accumulator usage, possibly due to the boost update. I'm not quite sure why it's having the issue, but we can work around it by removing the usage. commit f7953865680fdb7fa1527b1f459711c8e7ed9aa7 Merge: 3445b81 e74ba43 Date: Thu Jun 4 08:45:46 2020 -0700 Merge pull request #4721 from RosettaCommons/dpaoliello/ndarrayallmerged Update ndarray and Eigen3 externals commit 3445b81a95f953743d508146308aeb752956dcc2 Date: Wed Jun 3 10:51:48 2020 -0700 Fix subelement xml for AlignPDBInfoToSequences (#4763) When I had written the xml interface for APTS I wasn't aware that subelements had to be defined in parse my tag. This was silly, but hopefully this PR fixes that. (previously this Target interface would fail at the XML schema validation check) commit 0da2b218d7dc4d118f6fd94051a4e31306907dc5 Merge: 0dd5fba 2b4749b Date: Tue Jun 2 12:47:49 2020 -0500 Merge pull request #4760 from RosettaCommons/toadlover/fix_restrict_to_DNA_interface Toadlover/fix restrict to dna interface commit 0dd5fba50532c803f0bc9fc1297163b4d29633c2 Merge: 979cdee 3da2e1a Date: Tue Jun 2 08:25:48 2020 -0500 Merge pull request #4758 from RosettaCommons/roccomoretti/master_fixes Quick fixes to master Some issues in master that were easy fixes - beautification, removing a using,and being clear about namespace. commit 979cdeee29cb6414412f199c33885a364b7ccfbb Merge: 1007cfa f2fe6da Date: Sun May 31 16:06:04 2020 -0400 Merge pull request #4750 from RosettaCommons/JackMaguire/Fix Modernizing code templates with implicit copy constructors and unpublished module boilerplate for the citation manager commit 1007cfa03a098c7a723dcba88f269e22ba943c30 Merge: 9c2ed72 7009d51 Date: Fri May 29 13:22:53 2020 -0700 Merge pull request #4735 from RosettaCommons/hahnbeom/gadock_repro fixing GAdock to reproduce original behavior commit 9c2ed7261a0b664c3d7df6230f8bfd52001e1e20 Merge: b74224e 8e37bf4 Date: Fri May 29 12:08:32 2020 -0700 Merge pull request #4743 from CyrusBiotechnology/bfrenz/wildtype-opt Added option to refine the wild type structure when running Cartesian DDG with new refactored code. commit b74224ed075660d35d7fb1eee4c32f2a29d64200 Date: Fri May 29 09:13:01 2020 -0700 remove 'script_file_specified_' from fastrelax (#4747) This option was unused in FastRelax and throughout rosetta -- therefore it was removed. commit 54e4f9e8ae04845cbaeb9e72fdb9ed2b60bff264 Merge: 235c3e7 883eeac Date: Fri May 29 18:10:04 2020 +0200 Merge pull request #4737 from RosettaCommons/lqtza/fix_ab_graft_sci_b Fix broke ab scientific benchmark due to bad flag commit 235c3e71b2bf3776e18d22d940878fdb288d0fb3 Merge: 336a25e 41e3761 Date: Fri May 29 10:22:29 2020 -0500 Merge pull request #4732 from RosettaCommons/roccomoretti/cached_type_fix Fix CachableDataType name map. There's been some recent additions to the Pose's CacheableDataType. The issue is that the enum->name map wasn't updated along with it. Curiously, though there's a check for this, it doesn't seem to be exercised by any of the integration or unit tests. Add a unit test which will catch this situation in the future, and fix the current lack of enum->string mapping for the three entries which are lacking it. commit 336a25efade5b558de64e9de1aa0ad3a23a994a4 Merge: 22f5f7e 4eb3a6b Date: Thu May 28 12:51:15 2020 -0600 Merge pull request #4744 from RosettaCommons/sergey/f updating `scons` `setup_platforms.py` script so it exit immediately if specified compiler could not be found commit 22f5f7e4a7d392fe0bd18cddde8c1de96a4014e9 Merge: fb2d871 8db00ec Date: Thu May 28 10:20:20 2020 -0700 Merge pull request #4745 from RosettaCommons/dimaio/cartmd_relaxscript Fix error in setting cartesianMD temperature using relax scriptfile commit fb2d87106711aad8798c867641b4c2bfc9835bec Date: Wed May 27 19:07:18 2020 -0700 #4736 - rm deprecated build flag from cmake (-ffor-scope) It would appear this -ffor-scope was deprecated in 8.1 according to: https://gcc.gnu.org/onlinedocs/gcc-8.1.0/gcc/Deprecated-Features.html#Deprecated-Features so this should fix most of the cmake/ninja warnings. commit ea704a00977180e144acac19c3264f060ea0ee03 Merge: 0df0399 41fe3c0 Date: Wed May 27 14:45:18 2020 -0400 Merge pull request #4718 from RosettaCommons/JackMaguire/ResidueIters c++11 range-for support for residue ids commit 0df0399627424fbc75a5f4c9ae23c44b85293899 Merge: e5f9e99 aea1cb1 Date: Tue May 26 15:33:30 2020 -0700 Merge pull request #4699 from RosettaCommons/revert-4697-revert-4687-klimaj/distributed_logging Revert "Revert "Small fixes to pyrosetta.distributed logging"" commit e5f9e998efdb2d32cd79891c49675476f0d28b63 Merge: 122f5c9 ffb141a Date: Mon May 25 19:34:11 2020 -0400 Merge pull request #4689 from RosettaCommons/everyday847/reimagine_rna getting RNA protocols off their island