commit 3ba1aaa69637d143d3e7a0497fe9e99a2b65f1eb Date: Mon Sep 7 10:55:02 2020 -0700 Lift uses of `make_shared` that cause MSVC to crash into their own functions (#4966) Issue Details: When `make_shared` is used via a using declaration as a default parameter value, it causes MSVC to crash (see https://developercommunity.visualstudio.com/content/problem/1170468/ice-when-using-make-shared-via-a-using-declaration.html). Fix Details: Move the use of `make_shared` from the default parameter value into a function, then call that function as the default parameter value. commit ca4e36ec389cf20302b9960f63ad354ffb347a0b Date: Sun Sep 6 10:27:27 2020 -0700 Use WinSock2 for `PyMOLMover` (#4958) Issue Details: `PyMOLMover` uses a number of network APIs that either weren't being included for the Windows build, or were included via legacy winsock. Fix Details: Include the WinSock2 headers where these APIs are required. commit 77f2f6a7d2dbf641530679b9845389822bc90b14 Date: Fri Sep 4 14:41:15 2020 -0700 Use `utility::file` in `FragmentScoreFilter` instead of OS-specific APIs (#4956) * Add Win32 implementation of directory manipulation in `FragmentScoreFilter` Issue Details: `FragmentScoreFilter` uses Linux/Mac OS specific headers/APIs to change the current directory and create a new directory. Fix Details: When building for Windows, include the relevant Win32 headers and use the Win32 APIs. * Use utility::file in FragmentScoreFilter instead of OS-specific APIs * beautifying commit e3f2a694e904afc871714bc1b0d9ff7927cc664c Merge: b63268d 1c6e067 Date: Thu Sep 3 21:32:28 2020 -0400 Merge pull request #4941 from RosettaCommons/vmullig/tag_getOption_for_bool_strings Try to address cases in which a developer has provided a default value for a boolean as a string in parse_my_tag(). This code compiles correctly, but doesn't do what one expects: ```c++ bool myoption = tag->getOption( "myoption", "false" ); ``` The developer _expects_ that if the user doesn't specify the option "myoption", it will default to `false`. Unfortunately, the string literal `"false"` is sent to the `Tag::getOption( std::string const &, bool const )` function as a `char*`, which can be cast automatically to a bool. Any non-`nullptr` value gets interpreted as `true`, however, so the default is set to `true`. The general solution (since even if we fix all the instances currently in the codebase, this will creep back in) is to implement `Tag::getOption( std::string const &, char const * )`, which parses and interprets the default string and converts it to a `bool`. This PR does this. Thank you to @danielzaidman for bringing this issue to light! commit b63268d858e35ed5198893af10aebe360c092333 Merge: 9a9ece8 4207961 Date: Thu Sep 3 18:41:07 2020 +0300 Merge pull request #4937 from RosettaCommons/danielzaidman/AlignChain_BugFix Fix a bug in AlignChainMover commit 9a9ece8d82a2137ea4ef951acd9b32dc0cbc3b0e Merge: 27a914c c0e5e45 Date: Wed Sep 2 13:13:24 2020 -0700 Merge pull request #4957 from RosettaCommons/dpaoliello/UseSSizeTMacro Use `platform::SSize` typedef commit 27a914c50d04d05d8c3a34406f4a2ba946bbabd4 Merge: 7649530 7c516d7 Date: Wed Sep 2 13:02:21 2020 -0700 Merge pull request #4949 from RosettaCommons/dpaoliello/AddIncludes Add includes needed to use STL Containers (e.g., vector) when building with MSVC commit 76495305b35946413116bd01b345bf2c26279eab Merge: bb46fb1 60ea57f Date: Wed Sep 2 13:01:20 2020 -0700 Merge pull request #4952 from RosettaCommons/dpaoliello/RemovePStream Remove uses of the POSIX-only `pstream` header commit bb46fb1208e96955094a68de76a2001f01f4e9fb Merge: 0e2d829 15efd27 Date: Wed Sep 2 12:49:49 2020 -0700 Merge pull request #4953 from RosettaCommons/dpaoliello/FixRandom Fix the Windows build for `init_random_generator.cc` commit 0e2d8299d0c32423298b998f0ff93c29f0833bde Merge: 258b2c8 bf1b0b1 Date: Wed Sep 2 12:38:38 2020 -0700 Merge pull request #4954 from RosettaCommons/dpaoliello/MathDefines Define `_USE_MATH_DEFINES` before `cmath` is indirectly included. commit 258b2c8b99ef37f835706b0785c48dc7e4789a29 Merge: e692634 ec5330f Date: Wed Sep 2 12:27:25 2020 -0700 Merge pull request #4959 from RosettaCommons/dpaoliello/UnDefDelete Undef `DELETE` to avoid the Win32 define conflicting with an enum value commit e6926340fbc124173b5a26c4a8dec35cfc0a2bdb Merge: 9361ca1 07f1036 Date: Wed Sep 2 12:27:08 2020 -0700 Merge pull request #4955 from RosettaCommons/dpaoliello/UseSizeOf Ensure that `size_of` is brought in from base type commit 9361ca16545c90d79a7fa05e052d92e10a320e85 Merge: 35b3a5c 6c0b36b Date: Wed Sep 2 12:00:22 2020 -0700 Merge pull request #4960 from RosettaCommons/dpaoliello/QualifyUint Fully-qualify uses of `core::uint` commit 35b3a5cfadfc22354d034ad55367a6bc82b119b4 Merge: e425e8d ee47d19 Date: Wed Sep 2 14:17:22 2020 -0400 Merge pull request #4856 from RosettaCommons/vmullig/move_cavity_volume_from_devel_to_protocols Move CavityVolumeFilter from devel to protocols The `CavityVolumeFilter` was used in Silva _et al._ (2019.) De novo design of potent and selective mimics of IL-2 and IL-15. _Nature_ 565: 186–191, but the scripts in the supplement can not be run, and by extension the work that the paper describes is not reproducible, if this remains in devel. At least one person has been asking about this on the Rosetta forums. Tasks: - [x] Move this filter to protocols from devel. - [x] Move supporting class, the `CavityCalculator`, to protocols from devel. - [x] Add citation info. I'm going to count this as an unpublished module since Tom wasn't on the paper in which it first appeared, and it wasn't really described in that paper, and Tom might want to write a paper describing this. Also: - [x] Update the tools submodule to point at the latest master for the tools repo. commit e425e8dc9297bfba3c5232af0a2a254307a5d00f Merge: db0d3bb 15e56cc Date: Wed Sep 2 11:05:46 2020 -0700 Merge pull request #4947 from RosettaCommons/ckrivacic/FragmentScoreFilter_fixes Ability to report averages of all fragments at all positions commit db0d3bbf09db1de22b67e8be32e541ef7eb1db4f Merge: e15b51d e184bc3 Date: Wed Sep 2 10:43:46 2020 -0700 Merge pull request #4963 from RosettaCommons/dpaoliello/GitAttr Add `.gitattributes` files to indicate symlinks that are directories commit e15b51d526812c60750d4aa8d29d2c42125353e3 Merge: 1ef2cc0 4fa64f4 Date: Wed Sep 2 10:28:55 2020 -0700 Merge pull request #4967 from RosettaCommons/dpaoliello/RemoveHeaders Remove unneeded, or missing, headers commit 1ef2cc05f91a28e8312111941058f85e724a734f Merge: 842d147 6b283d1 Date: Wed Sep 2 10:14:32 2020 -0700 Merge pull request #4961 from RosettaCommons/dpaoliello/UniformInit Use uniform initialization syntax to avoid MSVC parsing issue commit 842d147e4b980dcc831a9289c628eb8cd0e00805 Merge: 82a7b73 35cd185 Date: Tue Sep 1 15:22:28 2020 -0700 Merge pull request #4950 from RosettaCommons/dpaoliello/MatchTypes Use the `Size` type instead of the underlying type commit 82a7b7366b307cb8b61cc3f517e2528f14c3837a Merge: a837745 86ed0c7 Date: Tue Sep 1 16:12:30 2020 -0500 Merge pull request #4946 from RosettaCommons/shannontsmith/isc_bugfix Seeing major score changes in interface scores after PR #4928. Althou… commit a837745ba39b710fdef74e89eb4c9f732e88288f Merge: a2ca817 f1e9e69 Date: Mon Aug 31 10:28:23 2020 -0700 Merge pull request #4944 from RosettaCommons/guangfeng/galiganddock_bugfix GALigandDock bugfix commit a2ca81716dedad471fc54f30420363ba99e873a7 Merge: fd1c8ce e5d7190 Date: Mon Aug 31 12:12:29 2020 -0500 Merge pull request #4942 from RosettaCommons/roccomoretti/header_fixups Some header/namespace fixups. There's some forward headers we didn't have that we probably should have. (Most notably, core/chemical/rings/RingConfomer.fwd.hh which was called out specifically by the code in places.) Also, there was some "AUTO USING NS" stuff that is mostly pointless at this point -- we should either include the header or delete the using that was requiring it. I also deleted a editor temporary file. commit fd1c8ced991b69b754b632e54343720a59e87137 Merge: 2014331 f9ce52a Date: Sun Aug 30 11:28:06 2020 -0500 Merge pull request #4939 from RosettaCommons/roccomoretti/filenotfoundfix Fix bug in FileNotFound error. We were putting the source file name in the error message, not the name of the missing data file. commit 2014331df5b18178afa9cb0ed3cba9d9a70db24e Merge: 29e957c 689897a Date: Sat Aug 29 14:44:48 2020 -0400 Merge pull request #4940 from RosettaCommons/vmullig/fix_hbond_counting_in_simple_cycpep_predict Fix hydrogen bond reporting at the end of simple_cycpep_predict. I managed to break this in pull request #4702 by forgetting that my hydrogen bond counts were no longer negative numbers. This also adds a unit test confirming that another piece of needed functionality functions (though it turned out not to be the culprit). commit 29e957c2d093ca1e1877b2d5cadbc95af5ec5ec1 Merge: 24d644b a4719f7 Date: Sat Aug 29 00:39:03 2020 -0700 Merge pull request #4936 from RosettaCommons/everyday847/hotfixes_rna RNA + build hotfixes commit 24d644b24f244cb64fbb1b59b0684e6340e3f9d7 Merge: 4e8093c f7f2be4 Date: Fri Aug 28 12:13:50 2020 -0500 Merge pull request #4938 from RosettaCommons/roccomoretti/grid_cache_size Fix issue with memory usage in ligand docking. There's been a number of reports of ligand docking eating up memory. Most of these can be fixed by setting -max_grid_cache_size I don't think there's a reason not to have this set to a finite value, so I'm making that change to the default. Additionally, I think the memory growth is in part due to a fix I added a while back which adds the grid center to the lookup hash string. Because the ligand center moves during docking, when the InterfaceCalculator goes to calculate final grid scores, it creates a new (used-only-once) grid set. What we can do is allow the GridManager to pull out a grid which is "close enough", which should pick up the original grid in many cases and thus not cause a grid regeneration and associate memory bloat/cache churn. commit 4e8093c5fb149988e5741ac4660d80c90a3952a6 Merge: 0f276b0 3b2c655 Date: Fri Aug 28 17:04:14 2020 +0300 Merge pull request #4930 from RosettaCommons/danielzaidman/rosetta fix the overwrite option of molfile_to_params.py commit 0f276b0b73b85f4f8caaaa8da9ac5fb78f1793ad Date: Thu Aug 27 20:40:38 2020 -0400 beautifying commit 066b054d27507cfb7c8db23f40dad5655e78bb7a Merge: 09a361a b047b93 Date: Thu Aug 27 15:39:45 2020 -0700 Merge pull request #4927 from RosettaCommons/revert-4926-revert-4897-dpaoliello/noreturn Re-merge "Use the C++11 `[[ noreturn ]]` attribute" commit 09a361a3e807874384e1b92d4e64394383121454 Merge: 973e179 890d498 Date: Thu Aug 27 11:41:11 2020 -0500 Merge pull request #4929 from RosettaCommons/roccomoretti/no_ascii_options Try to give better feedback with non-ASCII options. An error that comes up semi-regularly is where someone uses an en-dash instead of a hyphen in Rosetta options. (Certain Word processors like autoconverting things.) Adjust option parsing to try to better highlight cases where this may be happening. Additionally, we can handle dos/unix file ending issues in option files by broadening the meaning of 'whitespace'. commit 973e17960fef37e50a4e4e02741c561fc4305dcc Date: Wed Aug 26 11:42:08 2020 -0700 reduce nbr_radius to something reasonable for DNA params (#4933) It would appear dna has had its NBR_RADIUS set to 1000 for a very long time. This isn't super scientific (I just used the calculated radius of GUA from molfile_to_params.py) for all of them (+0.1) Perhaps in the future it might be smart to remake them in-case something else is wrong, but frank says that he has some DNA fixes #4871 and that these params seem to work well for him in that branch so its likely that only the NBR_RADIUS needs to be updated danpf 2020-08-26 NBR WAS set to 1000.0, I set it to the value molfile_to_params.py set for GUA on a single PDB + 0.1 it is possible this could be improved, but this seems good enough for now as it is no longer 1000.0. commit 2a4a430c0cd913e8fb06e82bc8e2f0468b32d50d Merge: e84e4bf 9ab5747 Date: Mon Aug 24 16:13:53 2020 -0400 Merge pull request #4923 from RosettaCommons/JackMaguire/AtomicDistanceResSelector Adding residue selector interface to AtomicDistanceFilter commit e84e4bf1607ba0d7896c281ad4f36fcf9c96b7c7 Merge: d889a7a 3dac436 Date: Mon Aug 24 14:20:49 2020 -0400 Merge pull request #4920 from RosettaCommons/rahelf/docking Rahelf/docking commit d889a7a46f3bef1331aa1b66fd9abdbf43aedad9 Merge: f204525 c4b9b51 Date: Mon Aug 24 14:06:39 2020 -0400 Merge pull request #4835 from RosettaCommons/jonpliu-patch-5 Carbohydrates: adding fluoro sugars to the database. All tests passed. commit f204525bcd2897b7c620f58fa098598be19dd893 Merge: 6dedbd4 45ad8c6 Date: Sat Aug 22 18:14:04 2020 -0400 Merge pull request #4912 from RosettaCommons/everyday847/rnabph Bug fix to RNA_BasePairHandler commit 6dedbd4c240c738acaeac4698f33c74f6dd74076 Merge: 4a652cd 7f80f8d Date: Sat Aug 22 17:41:05 2020 -0400 Merge pull request #4928 from RosettaCommons/vmullig/tidy_up_clang_tidy_warnings Removing unused values flagged by clang-tidy. Note that the operator() called here has no side-effects; its ONLY effect is to return a value that's never used, so it's safe to delete it. Additional notes added by Rocco: Looking at the code and #4890, it looks like the removal is fine. The computation that was previously done with these variables has been moved to the output_interface_deltas(). Presuming the component energies sum to the total scores, then the transformation should be valid. (As the difference of the sums of the components should be equal to the sums of the differences in components.) ... Well, with the caveat that you're either not using the normalization function, or that the normalization function is a linear (not affine) scaling, and the sum of normalized components is equal to the normalized sum of components. -- But looking through the current options for normalization factors, that's the case. (And the normalization option isn't used much, anyway.) commit 4a652cde8e205e64e2e4c7947b2c18b072e43ebd Merge: c33099f d90e3af Date: Fri Aug 21 19:12:45 2020 -0400 Merge pull request #4926 from RosettaCommons/revert-4897-dpaoliello/noreturn Revert "Use the C++11 `[[ noreturn ]]` attribute" Reverts #4897 This merge broke compilation. Reverting temporarily until this can be fixed. commit c33099fa17c5a72b14fae2ef6d2367871026ffea Merge: 26e100a adde71c Date: Fri Aug 21 11:45:30 2020 -0700 Merge pull request #4897 from RosettaCommons/dpaoliello/noreturn Use the C++11 `[[ noreturn ]]` attribute commit 26e100a2fbe40d4bfb539294f836fbc130d66fb4 Merge: bd10f67 f96b41c Date: Fri Aug 21 14:16:31 2020 -0400 Merge pull request #4859 from RosettaCommons/vmullig/handle_disulfides_in_mutate_residue Allow the MutateResidue mover to break disulfide bonds automatically. It's a bit silly to have the MutateResidue mover leave a pose in an unstable, un-scorable state with a "dangling" disulfide partner (which still expects to be bonded to something) if you try to mutate a disulfide-bonded cysteine. This PR ensures that the mover automatically removes the disulfide partner's DISULFIDE variant type when it makes the mutation. There is an option to restore the old behaviour in the rare cases in which a user might want that, but it's clearly marked as not recommended. commit bd10f6718d6cee42941b6ee590a0d285cb646f09 Date: Fri Aug 21 11:34:58 2020 -0400 beautifying commit 9aeafcf593b0dc03a6ce3bd0da77dc544d23634d Merge: bdb4711 cec0ee8 Date: Thu Aug 20 17:52:24 2020 -0400 Merge pull request #4592 from RosettaCommons/vmullig/add_cys_sidechain_conjugation_patch Adding CYS:SidechainConjugation patch. It's a bit silly that we still have CYX for sidechain conjugation to cysteine. This adds a CYS:SidechainConjugation patch. For now, I won't remove CYX, since it's probably needed for backwards-compatibility with a lot of things. commit bdb47115f211a7ed4135632659b7e55eca57f237 Merge: 5851053 daf05a9 Date: Thu Aug 20 16:38:01 2020 -0500 Merge pull request #4890 from RosettaCommons/BrennicaMarlow/InterfaceScore_Mem Brennica marlow/InterfaceScore_Mem commit 58510536310bebeb71d85d4a35d72796215ab83a Merge: 2f54d0d 432ddfd Date: Wed Aug 19 12:27:40 2020 -0400 Merge pull request #4915 from RosettaCommons/JackMaguire/SingleResSelect Adding residue selector interface for DeclareBond mover This PR: - Allows DeclareBond to take a residue selector instead of a raw resid - asserts that the residue selector accounts for exactly one residue - Inserts this new usage into some integration tests commit 2f54d0dfac311a6b28e52a08a8ff70613dc7c919 Merge: c344406 89ef276 Date: Wed Aug 19 08:57:04 2020 -0400 Merge pull request #4884 from RosettaCommons/JackMaguire/Wcomma Adding -Wcomma to clang build commit c344406e496d686cb8bff38dceed67c07a1f3b7f Merge: 3255af5 7ab543c Date: Wed Aug 19 08:55:42 2020 -0400 Merge pull request #4889 from RosettaCommons/JackMaguire/ParsedProtocolUtil Making MoverFilterPair more user-friendly commit 3255af5c99bbb3d56b2c528aaefa15a66c554a21 Merge: 25ba96a a65f07f Date: Tue Aug 18 21:05:05 2020 -0400 Merge pull request #4786 from RosettaCommons/vmullig/cycpep_predict_hbonds_update Switch simple_cycpep_predict to use the PeptideInternalHbondsFilter This is a simple PR to switch the simple_cycpep_predict application over to using the PeptideInternalHbondsFilter, which should reduce computational cost a bit. commit 25ba96a9eb536bc05635448c893175f35cf630e2 Merge: f54c775 d9eacc7 Date: Tue Aug 18 18:03:47 2020 -0500 Merge pull request #4914 from RosettaCommons/jadolfbr/timing_profile_bug Fix bug in TimingProfileMetric copy constructor. This makes the copy constructor not copy over the construction time. This was a major bug identified by @francesc45 where the time would be additive and not per-nstruct due to the use of copy constructors in RS. commit f54c775ccf8c7885504249ef26d6cd50da5bc49f Merge: 2bea095 a9bec8f Date: Mon Aug 17 17:59:29 2020 -0700 Merge pull request #4792 from RosettaCommons/dimaio/beta_ref_weights Update reference weights to exclude stability data in fitting commit 2bea095bd4ad8a28008972510970448807532637 Merge: fbb973d 2eb9837 Date: Mon Aug 17 17:29:07 2020 -0400 Merge pull request #4905 from RosettaCommons/GAndrianov/minimize_ppi_jump_all Adding jump_all feature commit fbb973da9f6e6f1674ed53bc1245921a93612e2b Merge: a69d51d 68845c0 Date: Mon Aug 17 13:33:01 2020 -0400 Merge pull request #4911 from CyrusBiotechnology/smlewis/yifan_hybridize_bugfix Bugfix @yfsong found in ligands in hybridize. commit a69d51d4b89e70701e22c8c95b6c13df85a3f23c Date: Sat Aug 15 17:06:06 2020 -0400 Possible fix to stochastic failure in HRFDyamicsEnergyTests (#4910) The one thing that I can see is that there's no check that the data read from each line of the initialization file can actually be interpreted as an int and a float (which the code expects). If this fails, the int and the float _should_ be set to 0 and 0.0, respectively, under the cxx11 standard, but earlier standards left the container variables unchanged. I'm wondering if that's what we're seeing here, resulting in stochastic behaviour since the int and the float are uninitialized. I'm adding a check that the line was properly parsed, and taking out the blank line in the config file. I don't know that this will fix the stochastic failure, but it can't hurt. Tasks: - [x] Add the check. - [x] Confirm that the unit test now fails consistently due to the blank line. - [x] Remove the blank line in the config file. - [x] Ensure that test passes. * Remove blank line in test. * Update tools repo to point at latest master. commit 42d5263340532011c1fa010277e8cb5501ed2a18 Merge: 2b8e850 212f87b Date: Fri Aug 14 22:51:40 2020 -0700 Merge pull request #4900 from RosettaCommons/normal_mode_mpm_clean Make NormalModeRelaxMover able to pass outputs to a MultiplePoseMover commit 2b8e8504e568f321cf0190194c3f01964627e33f Merge: c4f1b64 7c73372 Date: Fri Aug 14 16:28:59 2020 -0700 Merge pull request #4896 from RosettaCommons/dpaoliello/UseNonFwdHeader Ensure the non-forward declaration headers are included for types used in standard library containers commit c4f1b641850673adc387705ea245c15467d72b57 Merge: ead5552 76df2a2 Date: Fri Aug 14 15:55:37 2020 -0600 Merge pull request #4906 from RosettaCommons/sergey/binder PyRosetta update. Enabling binding generation for `numeric.rotation_axis_angle` function. commit ead55520943ed0a4f72d5ad5bd03460ceb462233 Merge: 3057698 e3cb113 Date: Fri Aug 14 10:28:31 2020 -0700 Merge pull request #4894 from RosettaCommons/dpaoliello/STLHeaders Windows build: include additional standard library headers commit 3057698131c299a6db987b3b95c1681f9e87549f Merge: 88fdd63 c6325a7 Date: Fri Aug 14 12:37:32 2020 -0400 Merge pull request #4904 from RosettaCommons/JackMaguire/ParsedProtocolUtil_cherry Tracking the number of filters passed in ParsedProtocol Thanks for the review, Jared! commit 88fdd6366dc64142258074c612cda89fc6caa6b6 Merge: b94bdb1 a010b9b Date: Fri Aug 14 08:32:42 2020 -0400 Merge pull request #4907 from RosettaCommons/JackMaguire/fix_notebook Fixing Notebook test that I broke commit b94bdb1f6b567f39555515f10b490cfa3e62cbef Merge: 57f2d5e 8cf4927 Date: Thu Aug 13 17:45:54 2020 -0500 Merge pull request #4667 from RosettaCommons/jadolfbr/parser_logic Enable Residue Selector logic across RosettaScripts This PR does one main thing, it allows most classes to use selector logic through their `selector=` option in a tag. It does this through using the logic in `parse_residue_selector` and `get_residue_selector` after checking if the selector exists in the DataMap first. (I was going to roll my own parsing logic/etc. before @ajasja pointed me to use the already-present logic - so thank you @ajasja for that - saved a lot of time!) A lot of selectors have been updated to use the util - I was frankly shocked at how much pure copy-paste happened in getting selectors. **This functionality has been extensively tested, has a unit test, and we have a few bonuses.** 1) You no longer need to use `!` and can use the actual word not. Why not eh? (courtesy goes to @ajasja for this) 2) You no longer have to have everything caps. 3) A disulfide container crash has been properly wrapped in an exit instead of a vector segfault 4) The `SelectedResiduesPyMOLMetric` now uses the custom type IN the selection. I Should have done that a long time ago. 5) Logic works when doing `selectors=` for each selector in between commas I hope this will be as beneficial to everyone as it has to me the past week. My 150 lines of selectors have been cut to only a select important few. **The caveat to this is as follows**: I tried to find all the classes where selectors were being pulled straight from the `DataMap` (which, honestly, I didn't know people actually did when I started this) and fixed as many as I could through a few searches. I may have missed some. Due to the inconsistent use of the `residue_selector` name and inconsistencies when using multiple selectors, I cannot envision a way to test this exhaustively. If you have ideas, please let me know! commit 57f2d5e07da60ae59daa4094349f73ef77988b3c Merge: 90215e1 061f3f3 Date: Tue Aug 11 09:58:07 2020 -0700 Merge pull request #4899 from RosettaCommons/dpaoliello/RenameAttributeMacros Rename attribute macros commit 90215e1b08e510d1d1f4b85c1a3bcd37599d3d2b Merge: a24f8de 4ac122b Date: Mon Aug 10 09:34:11 2020 -0700 Merge pull request #4895 from RosettaCommons/dpaoliello/MatchDefinition Change `look_up` to match the type of the `tensor_index` variables it is initialized with commit a24f8dee2cd4bcccb5f45e6243ab583fd9c42385 Merge: 634d561 c855ddb Date: Fri Aug 7 12:53:59 2020 -0700 Merge pull request #4893 from RosettaCommons/dpaoliello/RemoveDeadFile Remove bad symlink commit 634d561ce7f69fbb70d29722b75c43936ed28d26 Merge: 896032c 600a3f0 Date: Fri Aug 7 14:40:16 2020 -0400 Merge pull request #4873 from RosettaCommons/jonpliu-patch-6 Carbohydrates: adding phosphorylated sugars to the database commit 896032cb307c3d942c68aef65734f90594fa59fe Merge: 0856065 5e0428d Date: Mon Aug 3 08:34:39 2020 -0700 Merge pull request #4885 from RosettaCommons/bcov/ClangTidy Fixed a clang tidy issue in CacheableResRotPairFloatMap.cc commit 08560650bd70bbbb7840a2d75c9e8b60f88b8546 Merge: f5c8f29 59bcdea Date: Mon Aug 3 11:12:56 2020 -0400 Merge pull request #4881 from CyrusBiotechnology/smlewis/fix_disulfidizer_detection_copybranch DisulfidizeMover fails when you have disulfide sets like [(3, 21), (10, 24), (20, 29)] in the input because it erroneously pairs 20-21. See this comment from the middle of the code: //this check alone determines if two residues are bonded to each other, (and their presence in the set means they are disulfide bonded in general), but as written this does not work properly with vicinal reisudes polymer bonded to each other, but not disulfide bonded to each other. commit f5c8f292035ff44264547ab6c8b254f51724fccc Merge: 1b17f26 5a83a8a Date: Fri Jul 31 17:33:54 2020 -0700 Merge pull request #4690 from RosettaCommons/bcov/approx_upgrades2 approximate_buried_unsat_penalty upgrades commit 1b17f26a5290e07e07f07f7a7722ae3c5ec87324 Merge: 34b2a46 21e8d1c Date: Fri Jul 31 10:12:05 2020 -0500 Merge pull request #4880 from RosettaCommons/sarahbiehn/hrf_bug_fix Bug fix: adding missing option_values in EnergyMethodOptions.cc commit 34b2a46cfee6502ddb75a3ee7fdcc5478d961cb2 Merge: dfbee7a 5bab015 Date: Thu Jul 30 10:43:04 2020 -0500 Merge pull request #4877 from RosettaCommons/roccomoretti/fix_master_tests Fix zeromq test and some other tests. commit dfbee7af523706bcc047f748854137066d90eebd Merge: 7dbc20d 626ffe5 Date: Mon Jul 27 13:55:50 2020 -0500 Merge pull request #4846 from RosettaCommons/roccomoretti/calculator_sm Convert the CalculatorFilter to a CalculatorMetric In light of the push to move from Filters to SimpleMetrics for value calculation, this PR adds a new RealMetric, the CalculatorMetric, which can take other RealMetrics and compute a value with them. This is very similar in intent and function to the CalculatorFilter. (In fact, the CalculatorFilter was re-implemented in terms of the CalculatorMetric, using the FilterValueMetric as a bridge.) Also, because I could, you can now define the metrics being used for variables "in-line" under the CalculatorMetric tag. (The name parameter is not optional in this case.) commit 7dbc20d1b2d94e5f7be18787d5fd51eccd7098b9 Merge: 949ade4 b1d389d Date: Mon Jul 27 14:31:14 2020 -0400 Merge pull request #4840 from RosettaCommons/sarahbiehn/hrf_dynamics Rosetta script nma_relax.xml and score term hrf_dynamics commit 949ade4c6b4b882bb694b01bd73a3ec7227f6fd6 Merge: 4756f8a d0bff30 Date: Mon Jul 27 13:11:12 2020 -0500 Merge pull request #4832 from RosettaCommons/roccomoretti/deboost De-Boostification C++11 introduced a fair number of constructs and standard library features which make pre-C++11 Boost library functionality redundant. (Primarily by elevating various Boost library features to standard library features.) On a bit of a whim, I went through the Rosetta codebase and converted a number of Boost usages to their C++11 equivalents. The hope is that be refocusing the usage on the standard library versions, the code will be easier to approach by new people. There are a few places where I didn't convert the existing usage, in part because the boost version has a feature which the std version doesn't. I tried to leave notes as to the rationale. This merge also doesn't convert unordered_map and unordered_sets, due to slight behavioral differences between them. commit 4756f8ab7940542c5945d4601890688964af00a2 Merge: 451a301 f8b873a Date: Fri Jul 24 21:46:56 2020 -0400 Merge pull request #4876 from RosettaCommons/smlewis/remove_inappropriate_comment remove inappropriate comment commit 451a3019d88dd81de37ddd3287a441ef29e7cbe3 Merge: 49768c7 c25bd79 Date: Thu Jul 23 16:50:07 2020 -0500 Merge pull request #4860 from RosettaCommons/jadolfbr/strongt Add default constructor for StrongType to allow use in maps. Thanks to @JackMaguire for the constructor fix here! - Add default constructor to StrongType to allow use in maps - Add a const ref operator to allow more common functionality - Add decrement operators - Add note that +/- operators are implicit commit 49768c722bb77f2604577213aa6f8e319a3f734c Merge: bdbdc16 7afcd55 Date: Thu Jul 23 12:09:02 2020 -0700 Merge pull request #4863 from RosettaCommons/dimaio/denovo_bugfix Fix a bug in denovo density that arises when a fragment contains all … commit bdbdc16e45a0b7d41d51e5b7c04ea25ef82a69c1 Merge: ab8a146 5ecc784 Date: Tue Jul 21 10:51:02 2020 -0400 Merge pull request #4734 from RosettaCommons/MentenAI/PeptideStubMover Adding Residue Labels From The PeptideStubMover commit ab8a1461ccd0c42eb605f0d949c9a481845548ed Merge: 59f52f9 8494953 Date: Sat Jul 18 16:22:46 2020 -0600 Merge pull request #4857 from RosettaCommons/sergey/f Adding support for `extras` in scientific tests commit 59f52f9adf470b994c5a3a611fb4c9af94c4bb61 Merge: 886e404 a7465a0 Date: Wed Jul 15 21:20:59 2020 -0400 Merge pull request #4853 from RosettaCommons/JackMaguire/HBondMetricXML Fixing HbondMetric XML Interface commit 886e40432568875a572cbeec19d0b4242c5076c5 Merge: 6a9ffca 94dea75 Date: Wed Jul 15 18:55:38 2020 -0400 Merge pull request #4769 from RosettaCommons/vmullig/peptide_pnear_vs_ic_scitest Add a scientific test for the correlation between peptide computed PNear and experimentally-measured IC50. The rigidity of a peptide macrocycle is a determinant of binding affinity. When peptides are optimized for favourable interactions with a target, computed PNear (or DeltaG_folding) values correlate well with experimentally-measured IC50 values. This correlation has improved as the Rosetta energy function has improved, from a vague correlation with talaris2013 and talaris2014 to a pretty good correlation that actually predicts rank order with ref2015. (This is likely due to the practice of training against physics-based fluid simulations used for ref2015.) It would be good to ensure that this trend continues for future versions of the energy function, so I'm adding a scientific test. commit 6a9ffca35846c85866838ae8a232fae7d23462e5 Merge: b90fa2e 0798c39 Date: Wed Jul 15 15:45:10 2020 -0400 Merge pull request #4847 from RosettaCommons/vmullig/fix_clang_tidy_une_fois_de_plus Fix clang-tidy tests. A few more little issues have crept in. One, the failure to mark AddResidueCouplingConstraint::clone() as virtual or override, probably really is a minor bug. commit b90fa2e009b74e121d812cbd289b8808d2556528 Merge: 43e678f be0334e Date: Wed Jul 15 10:18:59 2020 -0600 Merge pull request #4790 from RosettaCommons/tlfobe/add_atoms_flag Adding `-add_atom_types` flag commit 43e678f19df4de04e12023de26e49876ef47b614 Merge: 6c72cc8 257c147 Date: Sun Jul 12 21:53:52 2020 -0600 Merge pull request #4843 from RosettaCommons/benchmark - fixing scientific tests Python environment deployment on Mac - fixing Symmetry tutorial - updating unit tests timeout for core:ContactOrderEnergy_Tests and core:RotamerSetsTests test suites commit 6c72cc81148950c3f71aef68afb7f56087e89ad8 Merge: ac22212 7169cc0 Date: Sat Jul 11 11:01:16 2020 -0500 Merge pull request #4834 from RosettaCommons/roccomoretti/iosfwd Convert stream header usage to iosfwd As the templated stream headers can be rather bulky, the C++ standard library provides an iosfwd header to forward declare many of the classes & objects which are provided by them. By using the iosfwd header instead of something like iostream in the hh files, we can possibly simplify & speed up compiles, by not forcing the compiler to include/compile the stream headers when they're not needed. Most of this was an automated replacement of includes in header files, followed by a "will it compile" fixup. There were some movement of functions to cc files, and some conversions of izstream and ozstream to plain std::istream and std::ostream in function signatures. (You can pass an ozstream to a std::ostream reference.) commit ac222123629b7524dc7c03f83cde778d77e75a3d Merge: f4caaa1 65fb740 Date: Fri Jul 10 18:14:56 2020 -0400 Merge pull request #4844 from RosettaCommons/vmullig/update_vscode_git_settings Minor tweaks to versioning of .vscode configuration files We don't really need anything in the .vscode directory to be under version control except for `.vscode/c_cpp_properties.json`. Spurious warnings about changed files pop up whenever new file extensions are opened with VSCode, since the `.vscode/settings.json` file gets auto-extended whenever this happens. This pull request: - Removes redundant lines in the .gitignore file (but keeps the .vscode directory listed, removing only a redundant listing). - Removes `.vscode/settings.json` from version control (since this file seems to auto-configure itself well). - Adds `.vscode/settings.json.template`, just in case we do need to restore the settings file for any reason. - Keeps `.vscode/c_cpp_properties.json` under version control (since this contains Rosetta-specific setup, specifying that we use the cxx11 standard, that the external directories should be included, and that PTR_STD should be defined). commit f4caaa18f6e475b301c45aa33ccf7cabca07da6d Date: Fri Jul 10 14:47:30 2020 -0700 Add residue level control to the AlignPDBInfoToSequences mover (#4826) This pr enables the ability to set pdb info residue numbering that is more complicated than simply starting at 1 Included are unit tests and integration tests that utilize this new functionality. % source/src/core/sequence/Aligner.cc -> Alter pointer error to throw instead of hard exiting. commit fadbc97020c60ce40f86339f40c498d1a72b4755 Merge: 1971176 cb3ac28 Date: Fri Jul 10 12:37:48 2020 -0500 Merge pull request #4798 from RosettaCommons/roccomoretti/index_selector_reverse_message Add warning message regarding the Index selector's reverse option. Potentially counter-intuitively, the reverse option of the Index selector doesn't invert the selection, but instead invokes a count-from-end behavior. Attempt to catch instances where users misuse this option, and print appropriate warning messages. (Particularly in cases with PDB numbering, where the count-from-end behavior doesn't really make sense). commit 1971176c65345379f8c89dca44dababb180459f1 Merge: 115bf01 d404d3f Date: Thu Jul 9 13:32:47 2020 -0700 Merge pull request #4842 from RosettaCommons/dimaio/update_fasol_pilotapp Updating a pilot app used in dualOptE commit 115bf0175a43d5a2d22764566521e7cbc00d9b99 Merge: 35db91c 4fc7e3d Date: Thu Jul 9 16:03:33 2020 -0400 Merge pull request #4791 from RosettaCommons/vmullig/rename_within_HierarchicalHybridJDApplication Replace "emperor"/"master"/"slave" within HierarchicalHybridJDApplication, which some people found objectionable. I'm still not a fan of making an major effort to avoid _analogies_ to slavery when the tech industry and the University of Washington still make use of _actual_ slavery in the form of forced prison labour (i.e. I think we're just making institutions look virtuous that don't deserve to be made to look virtuous, which engage in a practice that's banned in most developed nations), but maybe once we've made this code change we can talk about something more concrete that we can do that actually helps to close the 13th Amendment loophole and to end slavery in the U.S. TODO: - [x] Change "emperor"/"master"/"slave" to "director"/"manager"/"worker". - [x] Carefully check the integration tests. (Everything will change, but make sure nothing breaks.) - [x] Update documentation --> see RosettaCommons/documentation#42 - [x] Check scientific tests --> they failed. - [x] Update scientific tests. - [x] Re-check scientific tests --> they passed. - [x] Update `threads_per_slave` option. - [x] Beauty. - [x] Note that pull request #4761 must be merged before this one. commit 35db91cc14bc55e64442f9a26c1aa543a83bdf2a Merge: 48afcb4 47d7c39 Date: Thu Jul 9 11:19:27 2020 -0500 Merge pull request #4766 from RosettaCommons/roccomoretti/vtune_1 Some simple efficiency tweaks. I was playing around with the Intel VTune Profiler (on relax runs), and noticed a few "high spots" which could be addressed without too much restructuring. Mainly these were in reducing the number of memory allocations, though there were a few runtime-related issues. I don't think there's substantial performance improvements here, but I think all of the changes fall into the category of "not worse", either in runtime or comprehensibility. commit 48afcb40ec3ee668a3960b489e4a7bea0c7c6487 Merge: 3515247 ede28c7 Date: Thu Jul 9 11:44:18 2020 -0400 Merge pull request #4768 from RosettaCommons/vmullig/multithreaded_frag_picker Remove support for Boost::thread (in favour of cxx11thread) Since switching to C++11, there hasn't really been a reason to use Boost::thread instead std::thread, and we don't really want two threading frameworks that we have to test. Indeed, the Boost::thread build seems to have bitrotted. This PR removes support for this, and adds a cxx11thread test for the fragment picker. Task: - [x] Add back missing .vscode file so that VSCode works "out of the box". - [x] Remove Boost::thread support from fragment picker. - [x] Remove Boost::thread build. - [x] Switch other apps that use Boost::thread to use std::thread instead. - [x] Integration test for fragment picker with threads. - [x] Update documentation. --> No updates needed. It seems that the Boost::thread build was undocumented. - [x] Fix single-threaded case. - [x] Add documentation for multithreaded fragment picking. - [x] Beauty. Also: - [x] This pull request updates the tools submodule to point at the latest master. commit 35152472413b5f59ebf2a8ffae2bc88875c8bfb8 Merge: 8ecab77 14e58ed Date: Wed Jul 8 11:47:10 2020 -0700 Merge pull request #4839 from RosettaCommons/guangfeng/galigdock_genparams GALigandDock mol2genparams python scripts update. 1. Added a function to rename atom names in mol2 files in order to fix duplicated atom names issue; 2. There is an issue that sometimes NH-CR in (C=O)-NH-CR is incorrectly assigned as a conjugated bond type. In some cases, e.g. APAJIL from CSD, NH-C=O is conjugated but NH-CR is not. To fix this issue, the dihedral angle of the input structure is used as a second check, if the angle (current range is from 40 to 140 degrees) is clearly not planar don't assign it as a conjugated bond.