commit 122f5c958a089e6b7f90d3663346c4d154affc09
Merge: c3272bc 6c1d2ea
Date: Sun May 24 16:08:11 2020 -0400
Merge pull request #4723 from RosettaCommons/everyday847/rna_cluster_show_n_clusters
rna_cluster: Show number of resulting clusters
commit c3272bc12863b00aeba752baebbd15e737e0b1b1
Merge: 29e67ca 2f155cb
Date: Wed May 20 18:57:50 2020 -0700
Merge pull request #4722 from RosettaCommons/BobbyLangan/remove-python-prints
Changing python print() to logging.info() in h5_fragment_store
commit 29e67ca8330a882f5d00e02cd2d73a9da34dbc85
Merge: cb360c5 614c1d3
Date: Wed May 20 16:43:14 2020 -0500
Merge pull request #4720 from RosettaCommons/epr_deer_clangtidy_fix
Minor quality edits to EPR code (clangtidy)
commit cb360c57ed4ba63d45678afba4bf6a39d8dd958d
Merge: 312d3c7 0ea51ef
Date: Wed May 20 11:59:13 2020 -0500
Merge pull request #4716 from RosettaCommons/roccomoretti/master_fixes
Handful of fixes to the integration tests.
There were some minor issue with various integration tests which were leading to test "breakage" in master on the test server. Address these.
commit 312d3c746a5d4176e15d348158d9d727630d1e3f
Merge: 9085d7a a4acdd6
Date: Tue May 19 17:08:20 2020 +0200
Merge pull request #4707 from RosettaCommons/teunhoevenaars/loopmodel_min_refiner_chi
fix set_chi bug in MinimizationRefiner
commit 9085d7abc1f4f3b1549cc313e9fd684f334e852f
Merge: e15db9d b0f8960
Date: Mon May 18 21:21:49 2020 -0400
Merge pull request #4711 from RosettaCommons/JackMaguire/Fix
Multistage XML bug
@jadolfbr caught this mistake in the MRS XML over the weekend. Lazy copy/pasting on my part. Thanks Jared!
commit e15db9dfea7768d56a9a2a7f9dc1becf64ed31c3
Date: Mon May 18 17:25:38 2020 -0400
beautifying
commit 64d08bbfc5fc178de317b17bbf520af6488f98d8
Merge: 3affa54 66d4dfd
Date: Mon May 18 13:26:56 2020 -0400
Merge pull request #4698 from RosettaCommons/vmullig/tweak_simple_cycpep_predict_sci_test_threshold
Tweak thresholds on simple_cycpep_predict scientific test a bit.
The recent weak to the Dunbrack libraries seems to have made simple_cycpep_predict a little bit slower (less than 10%). As such, the simple_cycpep_predict scientific test frequently fails just because it isn't sampling as much as expected. This PR relaxes the sampling threshold just a bit, since I think we'll just have to accept the slight slowdown.
commit 3affa540053198df7baa2f3c9897c5087a0cd88b
Merge: b32ceb6 d8c1760
Date: Sun May 17 16:56:12 2020 +0200
Merge pull request #4632 from RosettaCommons/lqtza/RAb_blast_filter_updates
RAb and SD Filter/Option Updates
commit b32ceb649fe213b8d4fc77e88b95f2a40e483ea5
Merge: fb07838 adb03dc
Date: Fri May 15 19:58:17 2020 -0600
Merge pull request #4705 from RosettaCommons/weitzner/pose-bindings-hotfix
Add missing `numpy` imports
commit fb07838599362f9b0a8d5a31747e975e1278f222
Merge: c522e9e 0864e0a
Date: Thu May 14 11:01:53 2020 -0700
Merge pull request #4683 from RosettaCommons/danpf/fix_es_int_test
update loop_grower_N_term_symm integration test
commit c522e9e9054813e62f9415bcc29478af67fee549
Merge: cf2ae46 990e9eb
Date: Thu May 14 10:55:54 2020 -0600
Merge pull request #4697 from RosettaCommons/revert-4687-klimaj/distributed_logging
Revert "Small fixes to pyrosetta.distributed logging" (was #4687)
commit cf2ae46593191e96766860a0d91785147963cc2e
Merge: e2350dd b99c010
Date: Thu May 14 10:15:25 2020 -0400
Merge pull request #4694 from RosettaCommons/JackMaguire/FixExtrasEverything
Fixing compiler errors in clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug
Thanks Rocco!
commit e2350dd0f620a514cedf97f6d552fd241d23ee8c
Merge: 6a0c751 6188aec
Date: Wed May 13 17:08:54 2020 -0400
Merge pull request #4696 from RosettaCommons/JackMaguire/FixOtherTests
Denoisifying the smart annealer integration test. This seems to work - thanks for the review Rocco!
commit 6a0c75187100c70045142d8f9c11c06ac075e244
Merge: 857e3b2 05fc762
Date: Wed May 13 11:19:16 2020 -0700
Merge pull request #4695 from RosettaCommons/dimaio/gcc74_fix
Fix maybe-uninitialized bug with gcc7.4
commit 857e3b25d1f08261336988c4bff4730ef1868a1e
Merge: 842c835 c167cd1
Date: Wed May 13 11:18:58 2020 -0400
Merge pull request #4692 from RosettaCommons/revert-4624-vmullig/threadsafe_approximate_buried_unsat_penalty
Revert "Make the ApproximateBuriedUnsatPenalty threadsafe" temporarily
Reverts #4624. This PR introduced a bug that I need to track down that's tripping a few people up. Sorry about that.
@bcov77
commit 842c83575a32447e39d9510ecf5a860ee93a0f64
Merge: 8187eb3 04b8635
Date: Wed May 13 08:18:39 2020 -0500
Merge pull request #4691 from RosettaCommons/roccomoretti/fix_rotamer_uninitialized
Fix uninitailized variable in StoredRotamerLibrarySpecification.
The uninitialized energy can cause issues if not set later.
commit 8187eb35f29b502e81a7fbd0504cb7a909856302
Merge: 3d2f430 90d6e00
Date: Tue May 12 19:00:41 2020 -0700
Merge pull request #4682 from RosettaCommons/dimaio/beta_fix_clone_atom
Fix a bug when using both beta and the -clone_atom command line input
commit 3d2f430d3e5df5bbc01730c44ddaf45299e738d0
Merge: c7ffa9b dadab29
Date: Mon May 11 18:56:48 2020 -0700
Merge pull request #4452 from RosettaCommons/danpf/align_pose_to_seqs
Align a pose pdb info to a sequence mover
commit c7ffa9bab949783bb5713c20daa32854eeab07c9
Merge: 4580c4e 638a430
Date: Mon May 11 17:56:45 2020 -0500
Merge pull request #3537 from RosettaCommons/alamo/deer_energy_method_pr
New energy method for using experimental DEER data
commit 4580c4ec5dfdb21f46bc80783ad61d1a785b72c6
Merge: b034548 6c122d2
Date: Mon May 11 15:48:58 2020 -0700
Merge pull request #4687 from RosettaCommons/klimaj/distributed_logging
Small fixes to pyrosetta.distributed logging
commit b0345481c5f904911af10e2950863bfde870dccd
Merge: 3cd5a75 33efdc5
Date: Mon May 11 16:25:33 2020 -0400
Merge pull request #4646 from RosettaCommons/yingyue0414-patch-add_kdn
Add Keto-Deoxy-Nonulonic/Keto-Deoxy-Octulonic acid acid to Database
commit 3cd5a75bd5255f81447c6ccbd9fd1d89308f861a
Merge: cf0cbbe c56ee12
Date: Mon May 11 10:58:33 2020 -0700
Merge pull request #4684 from RosettaCommons/yhsia/ddg_fix_3
Added threshold_min to ddgfilter. This allows the user to set a minimum ddG to the filter in addtion to the already existing threshold option that sets the maximum allowed value.
Added dump_pdbs option to ddg. When set to true, will dump the intermediate pdbs during the ddG run for debugging purposes.
commit cf0cbbe5d33b92a1809e756480479557e5029347
Merge: 8a1554f 8208215
Date: Sat May 9 11:35:06 2020 -0600
Merge pull request #4686 from RosettaCommons/benchmark
fixing make_fragments scientific test
commit 8a1554fa22aa63bbac3fb02697262f7737d8480c
Merge: 2fb5f3d 540e113
Date: Fri May 8 14:03:14 2020 -0500
Merge pull request #4680 from RosettaCommons/roccomoretti/params_out_spacing
Fix spacing in params file output.
The params file reader expects a fixed-column format for the atom names, but the current output is giving whitespace separated. This causes issues with CCD types, which don't have fixed-spacing atom names on read-in.
commit 2fb5f3dc016ab2d7172be880dc678922aabd5ec1
Merge: f98ad04 ac41e60
Date: Thu May 7 12:07:17 2020 -0400
Merge pull request #4681 from RosettaCommons/vmullig/clang_tidy_fix_47
Fix clang tidy warning: removing redundant "virtual" in functions marked "override".
commit f98ad046ef76418f1431e66d54e6074e2a0ec48c
Merge: e1fc962 1d4a7a8
Date: Wed May 6 13:59:29 2020 -0500
Merge pull request #4656 from RosettaCommons/roccomoretti/dunbrack_precision
Adjust Dunbrack library generation to address test server issues.
It looks like a fair part of the integration test instability on the test server may be due to differences in the Dunbrack rotamer library binary on different machines. (Potentially due to release/debug differences.)
A substantial portion of the difference in release/debug mode binary file generation is due to truncating the spline-fit derivatives to single precision. Changing that to double precision greatly reduces the numeric difference between debug-mode and release-mode generated Dunbrack binaries (at least on my machine).
To further prevent differences in compilation mode from altering integration test trajectories, the way the Dunbrack binaries are stored on the test server was altered, such that each compilation mode gets its own Dunbrack binary.
Both of these changes should hopefully greatly reduce the spurious integration test diffs we've been seeing on the test server.
The Dunbrack binary version has been increased to accommodate for the change in precision. This will result in regenerating the Dunbrack binary.
commit e1fc9625ff53a0f7f08b0a8da674b00ad9c0c94c
Date: Mon May 4 16:36:51 2020 -0400
beautifying
commit 3da2121be3808a720107365e912c5f57375f6b64
Merge: 7225dfe f921937
Date: Thu Apr 30 21:18:51 2020 -0600
Merge pull request #4676 from RosettaCommons/sergey/binder
fixing Conda install issues
commit 7225dfecb44495bd3e39713a43da330c666191fe
Merge: 8fe6b05 3cd53d9
Date: Thu Apr 30 14:30:52 2020 -0600
Merge pull request #4677 from RosettaCommons/weitzner/convert-xcode-project-generation-script-py2_3-compatible
Make Xcode project generation script py2/3 compatible
commit 8fe6b053cf035fd4880cb330512383860fcca715
Merge: fa1bddb cf901c1
Date: Wed Apr 29 16:30:47 2020 -0400
Merge pull request #4671 from RosettaCommons/kkappel1/autodrrafter_fixes
A few minor auto-DRRAFTER fixes.
commit fa1bddb50e8f61a84911fb47fbbff39cfa537015
Merge: 24657a3 ad8e5d1
Date: Tue Apr 28 22:13:03 2020 -0400
Merge pull request #4553 from RosettaCommons/yingyue0414-patch-aldohexofuranosyl
Add Aldohexofuranosyls to Database
commit 24657a3ea486fc9adceafe7fe31e4d51238883cc
Merge: 1bbb2f2 b4be55d
Date: Tue Apr 28 22:07:25 2020 -0400
Merge pull request #4609 from RosettaCommons/yingyue0414-patch-modified_aldohexofuranosyl
Add Modified Aldohexofuranoses to Database
commit 1bbb2f297449ecc43f97265e37fe9b0450f8fdec
Merge: 201351d 1fb9264
Date: Tue Apr 28 11:40:13 2020 -0400
Merge pull request #4439 from RosettaCommons/JackMaguire/MLAnnealer
Adding SmartAnnealer
This PR adds an annealer which uses TensorFlow to disqualify rotamers on the fly. I have preliminary data below that shows that dynamically decreasing sample space (either conservatively or aggressively) gives a better score as a function of time.
Thanks Rocco for the review!
commit 201351d25586d06f7de41353616299a9611524a6
Merge: dcaa903 07a4ce0
Date: Sun Apr 26 13:35:39 2020 -0500
Merge pull request #4664 from RosettaCommons/roccomoretti/fix_master_tidy
Fix issues with clang_tidy in master.
Fix recent breakage, fix issue with tests which are failing on master.
Also reorganize cppcheck test and add subtest parsing.
commit dcaa903c265a6a81a0984bd8815b1589319f31a2
Merge: a618f90 be22bec
Date: Sat Apr 25 15:31:23 2020 -0600
Merge pull request #4669 from RosettaCommons/sergey/pymol
fixing Python3 version of PyMOLRosettaServer.py
commit a618f907ae919c70768171923cf6bb1217faeee3
Merge: 37948c9 70cc88d
Date: Sat Apr 25 14:49:01 2020 -0400
Merge pull request #4624 from RosettaCommons/vmullig/threadsafe_approximate_buried_unsat_penalty
Make the ApproximateBuriedUnsatPenalty threadsafe
The ApproximateBuriedUnsatPenalty caches `symm_vs_self_asu_resnum1_`, `symm_vs_self_asu_resnum2_`, and `symm_vs_self_rotamer_count_` inside of itself for computing pairwise interactions in the context of a symmetric IG. This prevents threadsafe calculation, and is also generally unsafe: it means that the scoreterm accumulates state on repeated calls to `ApproximateBuriedUnsatPenalty::evaluate_rotamer_pair_energies()`, and assumes that the function calls from external code will proceed in a particular order. This PR has refactored this, which allows the `approximate_buried_unsat_penalty` scoreterm to be used with multi-threaded interaction graph precomputation.
commit 37948c9a20832786dd00c91375f52833f8a8b982
Merge: b60d946 93541dd
Date: Fri Apr 24 16:36:41 2020 -0400
Merge pull request #4665 from RosettaCommons/vmullig/fix_dorn_bug
Fix a symmetry bug with NCAAs.
The BACKBONE_AA option was not properly being mirrored by the D_AA patch. This affected the rama_prepro and p_aa_pp scoreterms for D-NCAAs.
This PR also updates some tests that were performing redundant tests of beta_nov15 (which is now our ref2015 default scoring function) to test whatever the current beta scorefunction is.
commit b60d946d9318afb78465fc3da9f02b21fd39ed30
Merge: 6ad331f 4bb7900
Date: Fri Apr 24 11:23:24 2020 -0500
Merge pull request #4653 from RosettaCommons/roccomoretti/clang_10_fixes
Fixes for compilation on Clang 10
Fix some issues detected by Clang 10 compilation.
commit 6ad331f4312bd97f19ff0323ee5ddfe9e9605ef7
Merge: 4b9d6bd 80fc90f
Date: Thu Apr 23 19:47:39 2020 -0400
Merge pull request #4650 from RosettaCommons/vmullig/internal_hbonds_metric
Add a simple metric (and a thin wrapper filter) that computes internal hydrogen bonds in a peptide.
This is something that I script over and over in RosettaScripts from the HbondsToResidue filter and some combining filters, producing a Frankenfilter that is both clunky from a user interface standpoint and inefficient from a computational standpoint. (It has to re-evaluate hydrogen bonds for every residue.) It's time I wrote a metric and a wrapper filter for this.
This is also something that currently requires me to update residue numbers in my script when a target changes (which is highly prone to user error), but which, with this pull request, will be doable with ResidueSelectors instead (which, if not idiot-proof, is at least idiot-resistant). For this reason, I'll put it in the `Modernize RosetttaScripts` project, too.
Tasks:
- [x] Add simple metric.
- [x] Getters and setters.
- [x] Remember that set_hbond_types() should throw if all types are set to false.
- [x] XSD function.
- [x] parse_my_tag().
- [x] calculate().
- [x] metric().
- [x] CitationManager fxns.
- [x] Documentation --> in RosettaCommons/documentation#41
- [x] Add filter that thinly wraps the metric.
- [x] Getters and setters.
- [x] XSD function.
- [x] parse_my_tag().
- [x] apply().
- [x] CitationManager fxns.
- [x] Documentation. --> in RosettaCommons/documentation#41
- [x] Unit test.
- [x] Integration test.
- [x] Beauty.
- [x] Make the filter's interface a thinner wrapper for the metric.
- [x] Fix cppcheck.
- [x] Fix serialization.
commit 4b9d6bd6a2ffda4a986a42988dd72c5a1cb7691e
Merge: 3e6396a 373f80c
Date: Thu Apr 23 03:23:14 2020 -0400
Merge pull request #4662 from RosettaCommons/vmullig/fix_typo_in_master
Fix typo that slipped into master
commit 3e6396a5f17abd70d2d40a618b21097e9ffed564
Merge: f46c65e d46d813
Date: Wed Apr 22 22:26:02 2020 -0400
Merge pull request #4658 from RosettaCommons/everyday847/fix_rna_idealize
A better RNA idealization mover
commit f46c65e989e7c66d05b8edcff0c5f982c2070160
Merge: bda922d d79d576
Date: Wed Apr 22 18:32:16 2020 -0400
Merge pull request #4433 from RosettaCommons/everyday847/general_monomer_sampler
Update the general monomer sampler
commit bda922dc72faacdd712a760c7a9fdc647bc048e8
Merge: dca16de 2f3928b
Date: Tue Apr 21 12:22:12 2020 -0700
Merge pull request #4655 from RosettaCommons/guangfeng/galiganddock_bugfix
Guangfeng/galiganddock bugfix
commit dca16dee188e61ea2bd2d7f75830a2b7fb905bc0
Merge: 43186e0 83e591b
Date: Tue Apr 21 14:24:07 2020 -0400
Merge pull request #4645 from RosettaCommons/yingyue0414-patch-neuraminic_acid
Add to4 / to7 / to9-Neuraminic acid to Database
commit 43186e059c1952f0e65fda4d473c5e39370eace4
Merge: abcf277 3ab50b4
Date: Mon Apr 20 11:25:11 2020 -0500
Merge pull request #4636 from RosettaCommons/roccomoretti/filter_value_metric
Add a SimpleMetric which wraps a Filter.
We're looking at converting the usage of Filters for calculating values to the SimpleMetric framework. In that conversion process, it would be really useful to have a RealMetric that's able to wrap a Filter, for backwards compatibility purposes. -- That is, if you have some framework which currently stores a filter and then uses the report_sm() functionality of that stored filter, you would want to convert it to store a RealMetric and use the value calculated by that real metric. But you also want to preserve backward compatibility in case people have old XMLs which are using and passing around Filters.
That's what the FilterValueMetric is for. It's just a RealMetric which can take an arbitrary Filter, call report_sm() on it, and use that value as if it was calculated by a RealMetric proper.
The intent is not to be used "earnestly", but mainly as a backward compatibility shim during the process of updating things to use the metrics framework.
commit abcf277dc47614f6d8f7c3327e8c0e0774bf00ee
Merge: 89feb59 d88b51d
Date: Thu Apr 16 11:01:53 2020 -0700
Merge pull request #4648 from RosettaCommons/dimaio/generic_inputter_fullatom
Let GenericJobInputter respect the in:file:fullatom flag
commit 89feb597bd8a91cbaa8820e9f1dacc18accecb1a
Merge: ecbee2f 1a40669
Date: Thu Apr 16 12:50:02 2020 -0400
Merge pull request #4524 from RosettaCommons/JackMaguire/auto_ig
This PR adds simple logic to prevent new users from spending a preventably-large amount of time precomputing 2-body energies.
commit ecbee2fe85fcbbcf4481daf13a21a5269bfa392d
Merge: 330299f ff5ab5d
Date: Wed Apr 15 17:46:16 2020 -0400
Merge pull request #4634 from RosettaCommons/mlnance/sugar/fix_sacch_seq_building
Fix Pose building from saccharide sequence
commit 330299f3325c1c3fe5e21e0373644778caab60e7
Merge: 50a65c5 814a7d8
Date: Tue Apr 14 13:48:44 2020 -0500
Merge pull request #2466 from RosettaCommons/roccomoretti/parse_tag_interface_change
Change the interface to parse_my_tags
This is the final merge in a series of merges to reduce the interface of parse_my_tag(). This PR removes the Pose parameter from the parse_my_tag() function on Movers and Filters, leaving it as `void parse_my_tag( utility::tag::TagCOP tag, basic::datacache::DataMap &)` (like most other RosettaScripts objects.).
The Movers map and Filters map parameters have been merged into the DataMap object, and the Pose parameter has been removed completely. -- In general, there's no reason to rely on the state of the Pose at parse time. There's no guarantee that the state of the Pose at parse time will match that at apply time. Instead, you should cache the information (residue selections, chain designations, etc.) and then evaluate it on the pose passed to apply. There are various objects which allow you to do this deferral more generally.
Correspondingly, APPLY_TO_POSE has been removed. An empty APPLY_TO_POSE section is fine, but any content in that section will result in an error. See https://www.rosettacommons.org/docs/latest/scripting_documentation/RosettaScripts/Updating-RosettaScripts for more information about how to convert an XML using APPLY_TO_POSE to something that will work with the new scheme.
commit 50a65c5a982c344c0331c652d79e1127212167f1
Merge: 454bc7c d6ce4d9
Date: Mon Apr 13 22:05:30 2020 -0400
Merge pull request #4639 from RosettaCommons/dig_param_io_fix
Dig.params and Rho.params IO_String & comments quick fix
commit 454bc7c6da604865b6bdd25e7ba4618add92d674
Merge: 5c06e14 d943016
Date: Mon Apr 13 15:56:04 2020 -0700
Merge pull request #4644 from RosettaCommons/guangfeng/galiganddock_bugfix
Guangfeng/galiganddock bugfix
commit 5c06e1405761a9f40cb4c219470fb1106067cc2a
Merge: 11cdcb4 b297420
Date: Mon Apr 13 15:43:29 2020 -0400
Merge pull request #4642 from RosettaCommons/vmullig/helical_bundle_predict_sequences
Add support to helical_bundle_predict for arbitrary heteropolymer building-blocks.
This is mainly an input issue. This PR lets you put in a sequence file containing a whitespace-separated list of residue type names in lieu of a FASTA file.
This pull request also updates the EnvPairPotential so that it properly handles D-amino acids.
commit 11cdcb4e0a1580f4d045916ab23cd2fee2b00d56
Merge: 76f4bd6 88f28cf
Date: Mon Apr 13 15:41:45 2020 -0400
Merge pull request #4641 from RosettaCommons/vmullig/add_centroid_ncaas
Add centroid params files for AIB, ORN, DAB, and DAP.
This adds centroid-mode params files for commonly-used noncanonicals, plus a unit test confirming that they work as expected.
commit 76f4bd6d8c8ead62524e662990ad3f9f1864a4a3
Merge: 1b9e841 7271516
Date: Mon Apr 13 13:24:25 2020 -0400
Merge pull request #4562 from RosettaCommons/mlnance/sugar/add_more_sugar_codes
Adding more "easy" sugar PDB codes from the ligand list of the ProCarb database
commit 1b9e8416beaf6b16e502d6322199d1e5c34b9df4
Merge: 3121c73 185dc0f
Date: Sat Apr 11 12:08:40 2020 -0400
Merge pull request #4628 from RosettaCommons/everyday847/FARFAR_ligand_flexibility
Ligand flexibility in FARFAR2
commit 3121c734db02d2b62dd1974dcb8daface3f50057
Merge: c1f98fe bda400b
Date: Fri Apr 10 09:29:24 2020 -0700
Merge pull request #4619 from RosettaCommons/dimaio/bbi_init_from_pdb
Two changes for design of crystal lattices:
* add the ability to supply a reference pose to BuildingBlockInterface
* add the ability to add named symmetric DOFs to TaskAwareSymmMinMover
commit c1f98fedd9d01a8545376c410de2b13c9a3d79b4
Merge: d6acfa4 eeaccf3
Date: Fri Apr 10 09:44:22 2020 -0600
Merge pull request #4631 from RosettaCommons/benchmark
Updating benchmark scripts so they can be run on Windows. Updating PyMOL mover, reducing max-packet-size lower bounds.
commit d6acfa4cdbcffc690c65edba9f11bfb135f3cd4a
Merge: 55e216a abaa99f
Date: Fri Apr 10 10:41:58 2020 -0400
python_cc_reader module to python3 (#4590)
Submodule update for the tools repository which includes a large structural change to the `python_cc_reader` module and its conversion to python3.
The directory structure for the `python_cc_reader` module is now as follows:
```
tools/
python_cc_reader/
python_cc_reader/
beauty/
code_improvement/
cpp_parser/
external/
inclusion_removal/
library_splitting/
tests/
utility/
```
The rationale for this dirname-within-dirname structure was given on this page:
https://docs.python-guide.org/writing/structure/
At the top level `python_cc_reader`directory live the user-level scripts such as `library_levels.py` and `beautify_changed_files_in_branch.py.` Within the lower level `python_cc_reader/python_cc_reader` directories live the modules that actually do all the heavy lifting.
These scripts are imported by a number of other scripts in the `tools` repository, and I have updated all of these scripts.
commit 55e216a0de8f80abd3deb83e58a4f5203d5c70b3
Merge: 8e488be b3a505d
Date: Wed Apr 8 15:49:54 2020 -0700
Merge pull request #4637 from RosettaCommons/guangfeng/galiganddock_bugfix
Guangfeng/galiganddock bugfix
commit 8e488be72878527022b5936a51d98f50964d9229
Merge: ea7d9db fee5abd
Date: Wed Apr 8 16:41:08 2020 -0500
Merge pull request #4316 from RosettaCommons/roccomoretti/mover_filter_map_remove
Remove Movers_map and Filters_map from the Mover/Filter parse_my_tag interface.
There's no actual reason to have a Movers_map and Filters_map separate from the DataMap we pass to parse_my_tag(), it's simply a historical artifact. Removing them (and placing their data into the DataMap) allows us to reduce the importance of Filters in RosettaScripts, and also will allow us to use Movers/Filters as parameters in setting up more complex ResidueSelectors, SimpleMetrics, etc.
This PR removes the Mover & Filters map from the main interface for parse_my_tag(), going from 5 parameters to 3.
This is merge one of a two part merge, where the second merge removes the pose parameter. That should hopefully be merged in shortly.
commit ea7d9db17e866ad533a88273dac9890745b2e005
Merge: 94006ef 162a8eb
Date: Wed Apr 8 13:58:32 2020 -0500
Merge pull request #4635 from RosettaCommons/roccomoretti/master_fixes
Fix some master tests.
The alpine build test seems to have issues with public virtual inheritance of VirtualBase - we can just remove that.
Also fix some unused usings issues with clang-tidy.
commit 94006ef4e50388a2bedb01571e7270544f78f486
Merge: f6d4e41 370f439
Date: Wed Apr 8 09:03:59 2020 -0500
Merge pull request #4611 from RosettaCommons/roccomoretti/database_md5
Add a database_md5 integration test.
Going off a suggestion by Sergey, have an integration test which dumps the MD5 hashes of all the database files. This should hopefully help us debug situations in the future where test server databases get 'dirty' with state.
commit f6d4e41e24da062dec9d0341d1d393f7baa995a9
Merge: bb21bba de1f6d2
Date: Tue Apr 7 16:20:21 2020 -0500
Merge pull request #4533 from RosettaCommons/roccomoretti/parse_input_refpose
Address using the input pose as a reference pose in parse_my_tag.
This PR deals with those Movers and Filters which purposely use the input pose as a reference structure. The approach I'm taking is to add the input pose to the DataMap, but in a fashion where it's (sort-of) treated like another reference pose - in fact, those Movers/Filters which use the input pose but can't already take a reference pose have been updated such that they can take a regular (SavePoseMover) reference pose.
Information about how to update things for the new scheme are documented in the "Updating RosettaScripts" page on the documentation wiki.
commit bb21bba4cb0efa42f53cb60a627ba2cb2844c4fa
Merge: 539de9d f589d3c
Date: Tue Apr 7 08:51:27 2020 -0400
Merge pull request #4603 from RosettaCommons/JackMaguire/tensorflow_manager_pr2
Second incremental merge of the TensorFlowManager
This PR adds the ability to evaluate multiple tensors at once, which is called a "multirun".
Main branch: #4362
First increment: #4545
commit 539de9d625e1c2c217d70ed6043ba83accbef830
Merge: 2ee2b10 d6d5746
Date: Mon Apr 6 20:49:27 2020 -0400
Merge pull request #4600 from RosettaCommons/jadolfbr/glycan_modeler_defaults
Update GlycanTreeModeler defaults to the best found during benchmarking
commit 2ee2b1086eeea048553049c49f0646f977ccd085
Merge: df640cc 11dc0a0
Date: Mon Apr 6 12:12:07 2020 -0400
Merge pull request #4601 from RosettaCommons/jadolfbr/fix_quench
Fix GlycanTreeModeler quench mode to pre-virtualize residues
This reduces bogus interactions of glycan trees that have yet to be modeled.
Also:
- Skip virtualization in ConvertRealToVirt mover if the residue is already virtualized.
- Remove an extra real to virtualize call in the modeler, which did nothing but very slightly increase run-time at each layer build.
@huxz
commit df640cc8d025d1ffcee83c2d8c1e713bf6619295
Date: Sat Apr 4 17:48:38 2020 -0400
beautifying
commit c6250cbdc7651a55cfb024456b3089e8f8d032fe
Merge: e50bad2 201468d
Date: Fri Apr 3 23:37:22 2020 -0400
Merge pull request #4622 from RosettaCommons/vmullig/tweak_atomicdepth
Small tweaks to AtomicDepth calculation
This makes the following small tweaks to the AtomicDepth calculation:
- When attempting to mutate residues to leucine, only mutate alpha-amino acids. (Would crash otherwise.)
- When attempting to mutate residues to leucine, do not mutate sidechain-connected residues. (Would crash otherwise.)
This code is used by the `approximate_buried_unsat_penalty` scoreterm. (I sadly have to admit that, unlike my `buried_unsatisfied_penalty`, the `approximate_buried_unsat_penalty` is quantum computer-ready, since it's pairwise-decomposable.)
commit e50bad21b6671765a0bec5671249eb6ffae4e9e3
Merge: 04e7737 25bd319
Date: Fri Apr 3 13:57:34 2020 -0400
Merge pull request #4602 from RosettaCommons/jadolfbr/sugar_bb_defaults
Change sugar_bb default and add intra_rep term if not present
- Change sugar_bb weights to .5, as this is ideal for both ref_2015 and beta. Turn on `fa_intra_rep_xover4` at 0.55 if not present when using `-include_sugars`.
- Generally recommend the beta/Rosetta-ICO ScoreFunction if intra_rep is off.
All three of these (sugar_bb .5, intra_rep, and generally -beta) improve decoy discrimination significantly when de-novo modeling sugars, or building sugars into density.
commit 04e7737efdc9866b3eaa1e928898eee03ef3b196
Merge: 2ee9dd0 d95c04b
Date: Fri Apr 3 13:31:26 2020 -0400
Merge pull request #4586 from RosettaCommons/jadolfbr/disulf
Ignore virtual residues in FullAtomDisulfideEnergy
If we have virtual residues on either side of a potential disulfide, ignore it. We already do this for REPONLY, we should do this for virtual residues as well, like other energy terms.
commit 2ee9dd06e1e994c8a1c3ced0f897b401396b5661
Merge: 9e261a3 09d753a
Date: Fri Apr 3 13:22:56 2020 -0400
Merge pull request #4616 from RosettaCommons/jadolfbr/fix_anchored_graft
Fix anchored graft mover for super short loops.
commit 9e261a38434f5f358bc470fc3d42a171591d4661
Date: Wed Apr 1 23:01:09 2020 -0400
beautifying
commit 18d66fe0101defde5a00609efbe61010b1898d34
Merge: 59f765b f83e3e6
Date: Wed Apr 1 19:42:31 2020 -0400
Merge pull request #4613 from RosettaCommons/vmullig/update_pymol_selection_metric
Making SelectedResiduesPyMOLMetric robust to PDB files that lack PDBInfo, and providing the option of outputting Rosetta residue numbering instead of PDB residue numbering.
The SelectedResiduesPyMOLMetric currently assumes that all poses have PDBInfo. This updates the metric to be compatible with poses that don't, and adds an option to allow a user to force Rosetta numbering as output instead of PDB numbering, if he or she so wishes.
commit 59f765b9c3b3b6d23cf6fbaa2addbfde48ab482b
Merge: 1409591 8fd7f73
Date: Wed Apr 1 17:45:25 2020 -0400
Merge pull request #4614 from RosettaCommons/SudhanshuShanker/sugarbb
bug in omega calculation
commit 14095910d909e6f151ed93585610a6969abea492
Merge: b170d43 5bd4ce8
Date: Wed Apr 1 16:27:14 2020 -0400
Merge pull request #4605 from RosettaCommons/everyday847/rna_cluster_origins
Add rna_cluster flag -numbered_pdb_output
commit b170d4392768aaca81fac9e5f24faddd689e8293
Merge: f764033 dfe72bf
Date: Tue Mar 31 17:39:29 2020 -0400
Merge pull request #4531 from RosettaCommons/yingyue0414-patch-ketopentofuranosyls
Add Ketopentofuranosyls to database
commit f7640332ba34df8fcc5166906b25e09b9a11f5ca
Merge: 8d689eb 0a061c3
Date: Tue Mar 31 12:46:16 2020 -0400
Merge pull request #4608 from RosettaCommons/yingyue0414-patch-quip_namefix
Quick Fix Quivonose Name
Quivonose is 6-deoxy-Glucose instead of 6-deoxy-Galactose (which is fucose)
The parameter files were all correct but the comments were not changed when converted from fucose.
For instance in to2-alpha-D-Quip
# ->2)-alpha-D-quinovpyranosyl [->2)-alpha-D-6-deoxygalactopyranosyl]
# ->2)-alpha-D-quinovpyranosyl [->2)-alpha-D-6-deoxyglucopyranosyl]
# Fucose is a common galactose variant
# Quinovose is a common glucose variant
commit 8d689ebd524607251379aa00080641adfd7ac7f8
Merge: 62affaa 62bf176
Date: Tue Mar 31 10:09:22 2020 -0600
Merge pull request #4432 from RosettaCommons/tlfobe/mm_atom_type_extra_params
added option for add_mm_atom_type_set_parameters, created util functi…
commit 62affaa769cc426debafb67aa4756cb9ffa4d4d4
Date: Mon Mar 30 11:57:10 2020 -0400
dummy
commit 7d21608dbe703c7de0b78308aaf639884aa5558e
Date: Mon Mar 30 11:52:24 2020 -0400
dummy
commit b04ed8b18645759b8ca4853111585ab446f393de
Date: Mon Mar 30 11:49:42 2020 -0400
initiating clean rebuild
commit c68d4d3c873fcfb720aa7b858eb089c371c32e10
Merge: 8d775ab 953889f
Date: Mon Mar 30 10:49:35 2020 -0500
Merge pull request #4587 from RosettaCommons/roccomoretti/submodule_relative
Convert .gitmodules to use relative paths.
Right now we're hard coding SSH paths for various submodules, which is annoying if people cloned main using https, especially now that we have submodules which are required for compilation.
It turns out, though, that Git can use relative paths for submodules, which allows the submodules to be cloned using the same method the main repo was.
commit 8d775abaddcd0fbff7e735f1dd62dfcf92dd3228
Merge: 895ea2e 8a4257c
Date: Mon Mar 30 07:59:28 2020 -0400
Merge pull request #4545 from RosettaCommons/JackMaguire/tensorflow_manager_pr1
First incremental merge of #4362
This PR includes the singleton machinery and functionality to evaluate simple networks. Networks with multiple inputs and parallel network evaluation will need to wait until a future PR.
commit 895ea2e50047d1b8c67a029eb6473c7f724dde66
Merge: 453a059 10b8f2b
Date: Fri Mar 27 11:33:27 2020 -0700
Merge pull request #4595 from RosettaCommons/revert-4594-revert-4585-bcov/longxing_bp_builder
Revert "Revert "FoldTreeFromMotif and TargetClashEnergy""
commit 453a059bd8d3d9613558f3bd8c505bf846c14fdc
Merge: fc32a14 fb1fc8f
Date: Fri Mar 27 10:46:01 2020 -0500
Merge pull request #4594 from RosettaCommons/revert-4585-bcov/longxing_bp_builder
Revert "FoldTreeFromMotif and TargetClashEnergy"
commit fc32a14e7600a6216cd6c6317e23d8a6263d2bd1
Merge: 4381331 c21822a
Date: Thu Mar 26 16:41:46 2020 -0500
Merge pull request #4591 from RosettaCommons/roccomoretti/quickfix_master
Quick fixes for master tests.
Recent commits of mine broke the clang tidy and xcode tests on the server. This PR should fix them.
commit 4381331245e3c2d1c96e3db53229965d4b173fa0
Merge: 8b85065 cfbfbaf
Date: Thu Mar 26 13:53:31 2020 -0700
Merge pull request #4585 from RosettaCommons/bcov/longxing_bp_builder
FoldTreeFromMotif and TargetClashEnergy
commit 8b850656abf3f89abf728f2b3ee9b1fc5491bcb0
Merge: 0840a91 d0561ce
Date: Thu Mar 26 11:55:23 2020 -0500
Merge pull request #4475 from RosettaCommons/roccomoretti/rename_ReferenceCount
Rename ReferenceCount class to VirtualBase.
The ReferenceCount class has been a misnomer for several years now. It's purpose is no longer related to owning pointers or referencing counting, but now is simply to serve two purposes. The first is to serve as a common base class in Rosetta (such that we can store a generic ReferenceCountOP and then typesafely dynamic_cast it back to the true class), and the second is to ensure that all of the classes in a polymorphic hierarchy (i.e. one where a base class pointer/reference can point to a derived type) have a virtual destructor.
commit 0840a913640fb154357316971a8f4b0903f2659d
Merge: 50aca2d 2ccfe5c
Date: Wed Mar 25 12:48:46 2020 -0600
Merge pull request #4582 from RosettaCommons/benchmark
fixing unicode issues in tutorial tests
commit 50aca2d75d2cbb958298a2f1ff49bc6023529463
Merge: 09a60b3 aeee6a0
Date: Wed Mar 25 11:52:12 2020 -0500
Merge pull request #4360 from RosettaCommons/roccomoretti/boost_submod
Update Boost to 1.71, convert to submodules.
The primary goal of this PR is to update Boost to a more recent version, but as a part of it it converts Boost from a "vendorized" (code-in-main repo) to a submodule system.
The Boost submodules should be auto-updated as part of the build process (the `update_submodules.sh` script), so it should (hopefully) be invisible to most people.
Here's how it's laid out: The existing source/external/boost_1_51_0/ directory is removed, and a new source/external/boost_submod/ directory is added. (And all build systems should be updated accordingly.) Within that subdirectory are direct links to the ~86 submodules of Boost that we're currently using (from https://github.com/boostorg/). (While Boost provides a "superproject" repository, we're not using that, and as such don't have to deal with nested submodules.) The submodules should be pointing a the 1.71.0 release tag version.
Most of the submodules are being taken directly from the Boost.org's GitHub page, but there are a few with Rosetta-specific changes we're hosting directly.
The layout of the submodules doesn't quite match the layout of the released boost directory, so there's a script which will symlink the contents of the submodules into the appropriate locations in source/external/boost_submod/boost/ (it prefers to symlink directories, but there are certain things it needs to symlink as files.). Those symlinks are committed into the main repo, and shouldn't need to be regenerated unless we update Boost.
commit 09a60b3463f948119620965d9e55574a3a142164
Merge: 84814a7 c430530
Date: Wed Mar 25 11:42:10 2020 -0500
Merge pull request #4515 from RosettaCommons/roccomoretti/defer_pose_from_parse_tag
More removal of pose usage in parse_my_tag()
There's a number of Movers, etc. which can simply have their Pose usage deferred from parse time to apply time. See the PR page for a list.
commit 84814a7f5ced15f9529c5c48ef7dd7fed8459a5e
Merge: 696e766 c768a05
Date: Tue Mar 24 22:54:57 2020 -0400
Merge pull request #4581 from RosettaCommons/vmullig/fix_integration_tutorials_test
Fix the tutorials integration tests
Some scripts needed to be updated for Python3.
commit 696e766ff0b7fd72dca31013b6f5bc1b6e3abb16
Merge: 5ca6dbe d2204f3
Date: Mon Mar 23 14:30:08 2020 -0500
Merge pull request #4577 from RosettaCommons/roccomoretti/repack_wo_ligand_fix
Fix RepackWithoutLigand
Amanda Loshbaugh discovered that the repack without ligand functionality was actually redesigning in some cases. This is due to the DetectProteinLigandInterface actually skipping the interface detection and just going with a default all design run in the abscence of an option. This is suboptimal, so change things such that we always detect the interface and never design in the repack without ligand case.
commit 5ca6dbe3c4948fec59b9acb1e2d6b13a5a4c1e33
Merge: 46379ff 9548c26
Date: Sun Mar 22 22:27:21 2020 -0400
Merge pull request #4579 from RosettaCommons/revert-4570-mlnance/sugar/fix_OMe_seq_on_read_in
Temporarily revert "Fixing pose building from saccharide sequence"
Reverts #4570
Pull request #4570 unfortunately caused a slowdown in pose read-in. Certain unit tests are now timing out (which may or may not be due to the pose read-in slowdown). Certain integration tests are also failing to run (e.g. test1_benchmark and dna_interface_design), which is likely one or more separate, unrelated problems. Since we don't know what all needs to be fixed, it's probably best to revert the whole pull request, fix the problems in a branch, then re-merge. This pull request therefore temporarily reverts pull request #4570 so that we can do that. @mlnance @JWLabonte @roccomoretti @everyday847
commit 46379fffa8623add712450ef3d4ba1f0b430fc8c
Merge: 87e2ba4 04bbce7
Date: Sun Mar 22 11:41:45 2020 -0600
Merge pull request #4578 from RosettaCommons/sergey/binder
enabling bindings for `core::scoring::sc::MolecularSurfaceCalculator` and `core::scoring::sc::ShapeComplementarityCalculator` classed in distributed build
commit 87e2ba4f5f5d022837ad3142badc3e14cddc0849
Merge: 1e92956 357d5d9
Date: Sat Mar 21 09:34:34 2020 -0700
Merge pull request #4574 from RosettaCommons/bcov/ShuffleFile
ShuffleFileDistributor random without replacement
commit 1e92956afe2a8bacfefbabb5fce74a232e3631e7
Merge: 251b706 8f880a1
Date: Thu Mar 19 14:15:00 2020 -0400
Merge pull request #4570 from RosettaCommons/mlnance/sugar/fix_OMe_seq_on_read_in
Fixing pose building from saccharide sequence
commit 251b706572874110d0473ace018b1908e0492128
Merge: 2cd1eb2 2ff01d1
Date: Thu Mar 19 10:37:40 2020 -0700
Merge pull request #4575 from RosettaCommons/dimaio/galigdock_freeze_res_option
Adding a new option to GALigandDock, frozen_scs, that lock user-specified sidechains in-place. This allows auto-sidechains to be applied, but certain sidechains to remain frozen.
commit 2cd1eb2f340d7138098ebc0e0c1d1859f02fd48a
Merge: 827dd76 afca7b2
Date: Wed Mar 18 23:03:25 2020 -0400
Merge pull request #3209 from RosettaCommons/ssrb19/SymDock_relax
SymDock with motif dock score
commit 827dd760fe16e0e1dbaa9bfd4175b1ad67168e5a
Merge: 31040c3 ffc3fd3
Date: Wed Mar 18 22:17:54 2020 -0400
Merge pull request #4573 from CyrusBiotechnology/smlewis/FTHhybridize-opt-error
HybridizeFoldTreeDynamic move error handling nearer to error
commit 31040c33608d1c57dbdfc3d7eafe7d5ee8e3c3a4
Merge: b2b5bdb 695e047
Date: Tue Mar 17 17:24:13 2020 -0400
Merge pull request #4558 from RosettaCommons/JackMaguire/AutoBool
AutoBool type for XML
This PR adds the ability for your xml tag to have a boolean attribute with an auto option:
Note this does not touch the xsct_rosetta_bool options at all. This creates a new xsct_rosetta_autobool. The new type is currently not used by anything so no behavior is expected to change.
Thanks for the reviews everyone!
commit b2b5bdb67c8c62111759d6d8bfb56c6886506af2
Merge: b4ba962 86d38cd
Date: Mon Mar 16 17:23:04 2020 -0600
Merge pull request #4568 from RosettaCommons/benchmark
fixing integration tests
commit b4ba962eced5467f5a3ce16d980c4fef8d644226
Merge: e78b99d 4003dca
Date: Mon Mar 16 10:37:03 2020 -0700
Merge pull request #4559 from RosettaCommons/danpf/fix_parallel_write
fix parallel.py binary write errors
commit e78b99da7cd29377569e22c0197518f21cace5dd
Merge: 3c9b793 0377ce2
Date: Sun Mar 15 15:21:04 2020 -0600
Merge pull request #4565 from RosettaCommons/benchmark
updating Binder prefix path calculation during PyRosetta build
commit 3c9b79350531121661392add201ed467bcc14872
Merge: ea7147e be93067
Date: Sat Mar 14 13:49:26 2020 -0600
Merge pull request #4563 from RosettaCommons/benchmark
Benchmark scripts refactoring
commit ea7147e9d9e18114e6c579013c8bac6c82433f49
Merge: 8565822 6bf1ff8
Date: Sat Mar 14 07:43:04 2020 -0400
Merge pull request #4564 from RosettaCommons/mlnance/speed_up_find_best_match
Don't look for best `rsd_type` match if there is only one option
commit 856582283dc66773697b3dca9d664f3e812c9983
Merge: ce6f14f acafd5b
Date: Fri Mar 13 14:34:55 2020 -0700
Merge pull request #4554 from RosettaCommons/yhsia/ddg_fix_3
add integration test for ddG in symmetry mode