Rosetta 2014.17.56722 Date: 2014-05-08 Branched off commit: 316151a0577b39ec9ebb8dac7e2d4a1f06104b58 Tail state commit: dd3c77b06879e83faa378c55a2d6498f427e25e1 Previous version: 2014.16.56682 Previous branched off commit: 5587a8cb28a727eebd118e7e8e264171e1c5bcef Previous tail state commit: 5b8e80680ca9434c5d5c7d7f632c2f400a88dacf Release notes ============= NEWS: NEWS: This push introduces lipids into Rosetta. NEWS: [DETAILED DESCRIPTION OF CHANGE] NEWS: NEWS: COMMIT LOG ========== commit 316151a0577b39ec9ebb8dac7e2d4a1f06104b58 weekly release: stripping DONOTRELEASE-wrapped code commit 5fe71bd3f71bf40b407e254206e5c6a302e361c3 Compile fix for gcc 4.6.3 with warnings-as-errors; there is a pseudo-uninitizalized variable in a pilot app that makes that compiler grumpy, and was holding up the release script. Also added copyright header and vi-emacs settings header to that file. No test changes expected, as pilot app has no integration test. commit 1e931356568b6e96a6db26e08c55252263956a65 Minor bug fix. Compiled on windows but not linux. commit fb854dfb8401193ebc5ffd4455c8f6584dd8fb35 Minor modification to previous bug fix suggested by Seth Cooper. commit 4e50258fe516f011c5915235fb0377c692607557 I accidentally removed the boost_1_55_0 directory when pushing fixes for the windows build. So sorry for that. I'm adding it back as a quick fix since I don't know how to properly revert a commit on the master and I want to make sure things are back to normal as soon as possible for everyone. commit 62b3a4f0f9d3af3322118f1933c9ace0cfb92d7f Updates for windows port. commit a7e92941690a0dcfd2077e583d7f2072910dd1ad Merge branch 'master' of github.com:RosettaCommons/main commit c7d648b7b259166808e44d612a4a86171136069e Fix for access violations in the WIN32 BOINC build. No tests run; changes only affect WIN32 platform. commit bd939a8e254e759b33104db720c2b535c0994f05 add options to have PyMolObserver only update on energy on conformation changes. Options: -update_pymol_on_energy_changes_only -update_pymol_on_conformation_changes_only These should be passed along with usual show_simulation_in_pymol option. Note that by updating on energy changes only, pose length changes will not occasionally cause a segfault which sometimes happens when the observer kicks in and shouldn commit b3a6a45f885c7d0b8d82b4681d61d3c9b483e9b3 move changes from graft_optimizations branch commit 6c9e9221a1b208dab36727c9e50d91bf9df723de Fix a warning I was getting in antibody/metrics.hh due to an uninizialized templated struct. Fixed by making a default constructor that initializes templated members to 0, this should be fine as it seems usage of this struct is templating to primitives (eg. core::Real) commit 9556aabcf30cc76e8f8ac9097e699165090d0a17 Changing build settings for phenix builds. Updating option.py which fails on some python versions. commit b8dc1234f8490b9e473a5568474dce85060aa3cc Fixing gcc build which gives an error from the double-->float conversion in the center of an array initializer list in Frank's cryst_design.cc application. commit 55fc9c7c3c0a98df3737cad22bdb4c139eab565f [minor update of SandwichFeatures] - typo corrected (@overviewprotein_tools/scripts/clean_pdb_new.py) [integration tests comment] - should not change commit 7ce53d96f15cc3041ead43190efa91e060559697 [minor update of SandwichFeatures] - added a new column 'average distance between (two) sheets via central residues in edge strands' (prints until 1 floating point like 6.4) - added a new column 'minimum distance between (two) sheets via central residues in edge strands' (prints until 1 floating point like 6.4) - debugged for a case when strands are < 3 for topology identification like in '1A21' - default of exclude_sandwich_that_has_near_backbone_atoms_between_sheets_ = 'false' - default of exclude_sandwich_that_is_linked_w_same_direction_strand_ = 'false' [integration tests comment] - should not change other than features and features_database_schema (if any) commit a0e31b53fe372971095b6b68bc1a6c45865f1b4d pull from remote commit 90e112d82c92cdb1991e21b44ebc20563eabc018 Bugfix for -missing_dens_to_jump commit 1bade8a8653d8671a28dec42e6a358f3a9b2a7ca small bugfix for -missing_dens_to_jump commit 8acc4b7c4a0441b3aca90f3897a51f7da15216a9 Now fixing clang build. commit 8f120701d8dcd4ced23474ee3d10dcc0904932c1 updates to pilot apps commit 617ab5278f9f47b25b5303638b3f950350453770 Fixing gcc build (wasn't an error on my machine). Also fixing NetChargeFilter to test build. commit 001941a705f8292d89ff9bb24d18795963ca8061 expansion_rounds default set to 12 commit 80dfee0f1e9bd0350a3ba4ca747621557ac0a8e6 expansion_rounds as a new option commit 8392d1b2ad95db9dc17b4592c6e34197c3f47097 MultiplePoseMover additions: task operations import support, Filter pose selector, filter status passing from sub-protocol. Merge from luki-mbi/rosetta_scripts. Unit test status: All Pass Intergration test status: All Pass commit 154b9bd7d2048e716d465523524484b1b52a0b5a Updates to pilot app. commit 208b479192a17144c3596e24f890186dfcf35a47 bugfix to pilot_app commit 4660b21d1360bd4f6e317caa83ee5c97ec93e9e8 NetCharge filter now accepts task operations. Designable residues in the task operations are used to select the residues over which to count the net charge. no test changes expected. see wiki for details. commit 89cfb3bd849a07dae62cbdcfcc93619ec71bf0fe Remove continue_selection() for now, some want to always run all filters to report values. commit 080305ab3edaab83ef7830d136265256c4392364 remove unimplemented copy constructor to fix pyrosetta build commit efb19b0da35f5bf5abc85b521f8c98de329ce35d Remove autogenerated options files which were (re)added to the repository. commit fa2d9b6656f0967bb63afc9e17c44c24d4b4b563 Merge with head. commit 82108fc1131092332756a5d66fd0731ad3c240cb Updated the boinc build to work without the BOINC_GRAPHICS pre-compiler directive (for the android boinc build). commit 0709f610b1b18b0075f569e4db2099f4d973a97b fix more warnings that only showed up on gcc build commit a4f5a6be5c6b1ec5ae8dd5966a193d9608686539 Fixed a small bug in the boinc app. commit e5ae0051d8dca6da27763a495da58c9eeeb306a2 fix another warning, remove options files that were re-added commit 162d4f173cb1d8ccb46f453f24b8b9873d8e85f3 fix a warning that broke the build commit 3acd4509f1423da6690ac476ed7adc8a3e1aed11 Merge branch 'master' of github.com:RosettaCommons/main Conflicts: source/src/protocols/ligand_docking/MinimizeBackbone.cc commit da625a62612b32f8c2f7069fd68bae8ee882bbc8 Updates for windows port. commit e1534cc36cddcd47151c33da4d687c55714e3050 Add AntibodyFeatures reporter and R scripts, update InterfaceFeatures and R scripts, update AntibodyInfo and cdr clusters NEWS: ==Antibody== - closest North-Dunbrack CDR cluster now prints in AntibodyInfo show method - have Antibody metrics Sasa calculations use SasaCalculator2 (which means default radii is now correctly reduce like InterfaceAnalyzerMover) - add check for peptide bond C-N lengths in AntibodyInfo to check for missing cdr density or poorly closed loops. This check is default true and can be turned off using the option -antibody:check_cdr_chainbreaks false. - add optional AntibodyInfo check for wonky peptide bond geometries in cdrs. This check is default false and can be enabled using the option -antibody:check_cdr_pep_bond_geom true. The function that is called has been added to loops/util and checks the deviations from the dunbrack/karplus Conformation Dependent Library values within some user-controlled cutoff value. ==Features== - Add AntibodyFeatures reporter + many R scripts for analysis - Update InterfaceFeatures reporter (add a few more columns), reorganize R scripts and add a few more ==Bugs== -debug missing enums of some rare cdr clusters -debug some antibody metrics via testing with thousands of antibodies ---------------------------------------- Unit test status: Pass Integration test status: Antibody integration tests will change - both cosmetically and any reporting Sasa metrics *SnugDock integration test updated to not check CN peptide bond. There is a 2.56 A C-N bond at 31 H. commit 9137eb5ec484d4e18a73e2804a68776333c29bff change snugdock integration test to ignore chainbreak commit 666f1fa33e77e36f18e8b5b982a8b7d5396544dc TaskAwareCsts is now able to constrain residues to a particular residue of choice rather than to the first residue in the constrained segment. In multi-chain poses it makes sense to put the anchor positions at the source and sink of the minimized jump degree of freedom. This way minimization along the jump dof is not affected by the chain constraints; only bb minimization is affected. See wiki for details. No test changes expected. commit 1b088af26a3a12815333bc9d70ea09e9a93fd938 Resolving ambiguous constructor for PyRosetta build. commit c261c60c9bbbfb9d68b8f007382dfe8866c116f5 Removing pilot apps from compilation. commit 724328c6a867d104d402e01df6715b9f3d0f9864 Another instance of an include file that needs to be commented out. commit 08edbd8c43f45cd59374a25780e9149ec3824e56 Commenting out include line that causes compile failure on test server. commit 950def574553a439c631406a8a6478e398ba1598 Adding svm-based helical end cap scoring. Also adds a new feature reporter, and this changes this integration test. commit 590f5d7efc106f516de1c0a62a6d8b73b505fb34 Adding svm-based helical Ncap scoring. Also adds a new features reporter. The features reporter integration test changed due to the new reporter. commit b2a4976b913adf9fe8286e61cbd5abf597f8d274 Adding a mode to AddChainBreak. Flag remove=true (dflt false) will remove the specified chainbreak rather than adding it. No test changes expected. commit 1379be0246b1e02247f23f9c3708e42729fa1ab2 SetAtomTree does some trivial testing that the foldtree is kosher right at parse time commit 1eba62051a502a71c084668517795923054a78c4 Fixing some compilation bugs on Windows platform commit 83d50bca7e013d61138a39ce69612b354c348e2d Adding context normalization to CppType_Complex. Various build fixes. commit b115b5bb59e8591171480e2d99d87113c96a724d add residue foreignkey to abfeatures residue table and struct foreignkey to interface features residue table commit 0ed4059b66d985b6499064298a1aa932c47d2ef2 SetAtomTree can now read a fold tree from an external file. Useful in cases where the fold tree is sticky and not quite general... no test changes expected commit 3e4f19220ecb8557d7a7fb02cf1cda4cc3003448 Created all the known elements as enums. Work with them in a similar way as AA enum Added unit test for the enum All other files edited were to get compile to work on my system (Werror resolutions) commit 44bbf2d59074c719cb889ca170619d2429751997 Create enums for elements commit bf4c43a2fde4e73c4b23093f86df791f8928a725 Adding helix ncap scoring with an svm. commit 999e68f039f0241941ef3cf4fa69d898cd38e5a8 Minor changes to Splice.cc. Should not casue integartion test changes commit fda95ccdf25f24152c7d5a6050d14b3f29962945 Minor changes to Splice.cc. Should not casue integartion test changes commit fbfe26748caaedddc555143ba4a9a217595f2788 Disable continue_selection() for now -- needs better implementation. commit 91329073caf35081af2e5f6b35a4e59562f9b73f Adding pose selector debugging info, stop for AND logical operator to avoid unnecessary evaluation of further statements for a given pose. commit 18c8f876b37dd36eecd27132318a8d399546a7a7 Adding Filter PoseSelector to use an exsting RosettaScripts filter as a pose selector in the MultiplePoseMover. commit 37592607bf7f0d888d4a92a7a2402084cff8764d trying to remove another undefined function to get pyrosetta to compile. commit 32b4783d56374e79ee0da014a09745fcb0c76580 mininterfacesum added commit 15f33b6f101b471c6d4c3401fd50445c56dcf2e2 Adding unit test for taskoperations imports. commit c4f8d9c4741342ac35a4f91f4a105dd7d1b13573 Restoring legacy protocol resume support, that can be enabled with the resume_support=true option on the PROTOCOLS tag. Off by default. commit 6193d3a4f6ba0df9dc060157930e0b61427c6e1b restoring library levels. commit 28be522d4574cb48ee0f663262ac6509b7ff19cf Adding support for importing of task operations in IMPORT tag in the RosettaScriptsParser. commit d182d38b333bbd75b333eec23a8d5e06b937a10e removing another undefined function to restore PyRosetta build commit 2af025e5f3796ee315ba002c384cd2b8d46455ff MulipleOutputWrapper: Detect and pass on mover status; do several attempts to obtain a pose before failing. commit 6bdefb58d492c693636ccda68763d1b599dc1288 Update to current master. commit 2a7be35a623c4835b3b38ee292bfbe5aeb2e15c0 fix merge commit bd28178fe55e004af7fa5e3a22faae2808b0e0d7 Refactoring function UpperEdgeGraph::add_edge and making it return 'void’ instead of returning 'Edge' reference commit 8b5042480838ac667acc14b73715b26c2f349c82 PyRosetta, fixing some compilation bugs on Windows commit 86b54474e874f21db56094a7798e08ad22412c19 removing undefined functions to restore PyRosetta build commit 31b8cc5d17d95bfb63e1abe9d24592ced301079c Merging my pilot app with the trunk commit 2c0df1cc5e1518ce1c5ea78570d331815eaa9cdd my call_mover pilot app uses -nstruct option commit 3ee83d73f48e20ed8e24df514f5558ae9bb375c8 Fix typos in performance benchmark readme commit 56b377ae2d58cd90815c41a904a38629ed6ccf38 Fix typos in performance benchmark readme commit 99e9cedaf680153bb77b0495b518263232e1f6ff merge cryst_design.cc changes to master commit 3d493ea79c967c6ac366f430695b5caeae629fc0 more options and cluster functionality commit 31a81b7bfe60e2c7ed5fb4d45a6e6a3e5ab30dcd Bug fixes: 1) Max pose selection count in TopNByProperty pose selector. 2) MultiplePoseMover: Drop poses for which sub-protocol failed (via mover status). Unit tests: Pass. commit ad591b9f10b2cbc8f20bd94988099a5f8806e7e2 merge master into ab features commit 2f1ff135d303d7bb32095baca35d8570daa1eca7 cryst_gen: support for O,T + small bugfix commit 901f93b2830efb39a51fc3a39be547cbb97e7b66 Fixing warning that broke the build under gcc 4.7.2 I added a cast in StructureFeatures::write_schema_to_db from uint32 to SSize to avoid 'comparison between signed and unsigned integer' warning commit f363f8ab2d3984583b0c8b4998dbd351477ab39f Merging vmullig/metals into master. This fixes some bugs in automatic metal setup and in handling noncanonical amino acids templated on canonicals. --All canonical l-amino acids are now metalbinding, since the backbone carbonyl coordinates metals in some structures. --Some bugs in src/core/util/metalloproteins_util.cc have been fixed. --An assertion failure in debug mode in metalloproteins_util.cc has been fixed. --An assertion failure in debug mode with templated noncanonicals has been fixed. --BPY.params has been tweaked to avoid a (benign) assert failure. Unit test status: All Pass Integration test status: 1 changed test: The carbohydrates integration test shows cosmetic changes (since it outputs loaded residue type properties, including whether the types are metalbinding or not). modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/ALA.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/ARG.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/ASN.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/ASP.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/CYD.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/CYS.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/CYV.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/CYZ.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/GLN.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/GLU.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/GLY.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/HIS.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/HIS_D.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/ILE.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/LEU.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/LYS.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/MET.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/PHE.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/PRO.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/SER.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/THR.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/TRP.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/TYR.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/VAL.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_binding_ncaa/BPY.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/CA.params modified: source/src/apps/pilot/vmullig/test_metalloproteins.cc modified: source/src/core/import_pose/import_pose.cc modified: source/src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibrary.tmpl.hh modified: source/src/core/util/metalloproteins_util.cc commit 3d5aced49db87f7ccfe21f4ad52c052764712697 # [ONE LINE DESCRIPTION OF CHANGE] # NEWS: [DETAILED DESCRIPTION OF CHANGE] # ---------------------------------------- # Unit test status: [Pass/Fail/Not Run] # Integration test status: [Number of changed tests / Not Run] # [NAME_OF_CHANGED_TEST_1]: explanation of change explanation of change ... # explanation of change, cont'd. # [NAME_OF_CHANGED_TEST_2]: explanation of change #+BugFix [BUG_NUMBER] [LINK_TO_BUG] # Uncomment and fill in the line above to indicate this commit # fixes a known bug. # On branch vmullig/metals # Changes to be committed: # (use "git reset HEAD ..." to unstage) # # modified: database/chemical/residue_type_sets/fa_standard/patches.txt # new file: database/chemical/residue_type_sets/fa_standard/patches/carbohydrates/5-acetylation.txt # modified: database/chemical/residue_type_sets/fa_standard/residue_types.txt # new file: database/chemical/residue_type_sets/fa_standard/residue_types/carbohydrates/to6-beta-D-Galp.params # # Untracked files: # (use "git add ..." to include in what will be committed) # # tests/integration/ref.log # # It took 3.48 seconds to enumerate untracked files. 'status -uno' # may speed it up, but you have to be careful not to forget to add # new files yourself (see 'git help status'). commit 93c7a67ae8950812bc4fb1d715e6f517efc5131d Tweaking BPY.params to avoid setting off a (fairly harmless) assertion failure in debug mode. commit 4a99517cd432cf6f663670420ea6304f89ba2c3d Reverting last change. commit 52944e7322974bc3ccd3b55c8017d31ee8fac5fb Trying to debug an assertion failure in Residue.cc with the BPY noncanonical. commit 21f11caf01beeb179a0f0689568c6de6097abc4f Assertion error in RotamericSingleResidueDunbrackLibrary.tmpl.hh fixed, I think. commit 893402a861a2713e33e3e4fc0f170771f6dc6918 Removing unused var in test_metalloproteins.cc commit d722e072b5b62e1a6db8ff581e4d1be0850f7e1c Removing debug output from metalloproteins_util.cc. commit 9b52ec859efc449fdc9766457ec0d734d717382a Tweaking metalloproteins_util.cc to try to solve a crash problem that appeared with the structure of human sPLA2 (3u8h). commit b93c42710254eb61b15a55e8e768b0782dca065d Fixed a little mistake that Will and Jeremy pointed out: I was using the distance multiplier where I should have been using the angle multiplier in the setup for automatic metal constraints. commit 7e3c93d88aef985127b61e5be88b84692654de14 Tweaking CA.params. commit 0454c118aedc02ab755a6ef0f14fb613291644b4 Fixed a possible bug in metalloproteins_util.cc, I think. Maybe. Possibly. commit fde8f73373bc574c8fd85226bc1007a1f025470f Tweaking metalloproteins_util.cc to fix an assert error in debug mode. commit 5a9a22435f370489a3a2c07b9eb50f8ee774153e Updating BPY.params: the backbone oxygen can bind metals, too. commit 16eba61b267c5819e5d7cbd413fa4bac3520b14b Updating l-amino acid params files. Backbone carbonyl can bind metals. commit 49c01a1515d28984cdb036b816a400dd898d8920 Fixing some build problem on Windows commit 6dac15a0653d5ca5916ebe9e1e57f75e91db3265 Merging my pilot apps with trunk commit f3d5caecf45e0811c2b0ed72e37fc4fe2dad7a15 my call_mover demo (pilot app) parses some standard options for I/O commit 69f60e514cf78b2a04a88bc72909bc1c87c0164c Merging cryst generator code with master commit f1ba7680a55e1ba91ea2c63037d0772b69b577a7 More fixes to cryst generator commit a1ab2aa5a3e82afa699861c71834c795427e1e2c Check in pilot app for crystal generators commit f693e713813e8020d3a60ab63dbc73a2eb002097 restore unit tests involving BinarySilentStruct after my last checkin commit 41d82a0076333b9941d9ec1a141f2464c349c52d (part of fix) removing highly illegal dependency of ObjexxFCL on utility (due to change of assert to runtime_assert, which was useful for debugging but not critical). commit 008a7c9bc8eae11bb8b237b6dc550cbe6811c755 To use this protocol via BOINC the random number has to be moved outside the class in order for the BOINC build to initialze it otherwise a null pointer will be generated and the protocol will crash commit 8914363277f256b3e20d8205881b614aa6b39420 removing highly illegal dependency of ObjexxFCL on utility (due to change of assert to runtime_assert, which was useful for debugging but not critical). commit b16aa9dd9f44592ddce8698f01021c9b97b6dcd8 Remove autogenerated options files which were added back in Also, update xcode/make_project.py to (re)generate options automatically. commit c099724ec1a08434b21e922b275afd1ab4a26dfb fix to builds after merge with rhiju/swm_general. commit 41be622af580213867aa6d3af54186c2ed2c1f3f Fixing some builds commit e82fdae596e8afaf31cc69cbc6c42f2212aa8979 Refactoring utility::vector* classes to use platform SSize and Size instead of size_t and ssize_t. This should simplify PyRosetta cross compilation. Fixing some bugs in Windows build. commit dd329a745266d85b4d0734b8320823635d5e4f39 Updates that implement stepwise monte carlo for proteins, on the way to unified SWM implementation for RNA/protein complexes (from rhiju/swm_general branch). Several additional fixes, including restoration of swa_rna_gagu_17 and swa_rna_gagu_20 integration tests, and addition of some swm_protein integration tests. Checked integration tests -- besides changes in RNA, SWA, and SWM tests, some cosmetic changes due to change in fa_standard patches and addition of TAUTOMER propery to HIS_D residue type. On my mac I also see a late change in an antibody test, which seems like a floating point deviation. commit a78377bd10b201fd5a3731ffb1d23757a2ea1984 fixes needed to restore integration tests; and to run gdb with 'catch throw'. commit b477e80dfba8988eb87ad8a70cd64573c2df0b85 restoring patches needed for integration tests (which I had temporarily removed to speed up residue type set load in for most apps). soon will implement functionality where each app can register additional patches, and will make these optional again. commit 724675bdefdbd865a2870bfe86ec4b1634dc7595 Another bugfix for cryst docking commit 9aaaa641ee51fa4da439f2a3fbea44e463b2f939 updated default values for cb/n/o commit ebe2f08af302a639cd032093b19a88fa77a1ff21 added interface_sigwidth option commit 13e5702b3764f1e691868e90a3f292426d0b0ff2 restoring graphics build after war(of the warnings) atrocity commited by sarel. commit 4ebdc0f8a69fe2489f298f42c60bee33ee5fb6cc restoring graphics build after war(of the warnings) atrocity commited by sarel; also had an interrupted merge -- am trying to restore now. commit 128d71db62ad07cff87cf99ad3eca6f191d0d85d restoring graphics build after war(of the warnings) atrocity commited by sarel. commit c3dbcec03482746beaf521a6cf05476484dbfed7 Removing some of "using namespace X" from headers. Fixing Windows build. commit 4894659ef3122440fd2c23c4a792f72580cc37d5 added options to remodel, psipred prediction commit 562b8df33cb6d516edce74a68af92101c2e35495 added options to remodel, psipred prediction commit f36f73e3c4dca93cecbc7e6f71d9adab69721aef Added options to Remodel, psipredfilter, per residue sasa commit feb38469e0622d748de1b91c6229f28388a7576c updated Remodel, added features to SSPredictionFilter and PsiPred, and TotalSasaFilter commit 4e4e250886ed1fde888af97db35965f999605e52 Merge branch 'master' into rhiju/swm_general commit 9c8d216244905b2fc0bd256dc53b5c13af60a068 fixing conflicts with master and getting all apps to compile in branch rhiju/swm_general commit 7f238cc71e7c2d78721666f2dbf679f19c6541a8 Remove unused/meaningless version comments from fa_standard residue_types commit c26b1c3750425022eba2986a97b8f99ba8991c48 Remove a debugging line. Will fix the swa tests commit 3582f718b86a9f5dfeda01a37bd80a91acaf2448 Bugfixes to cryst_design commit 06100c637fd8f491963667152f367ea8bed08bf2 Fix swa_rna_main for terminal residues. commit af79dcf20c901ef3bde7702eeed36af618df8f37 Fix the swa_rna_main app for terminal residue rebuilding commit dc924c8423f19b5fad7c75a6b45ea06f55d0d429 getting rid of or updating some apps to work with reorganized directories. commit 83f5c18e84db3314c3cf358e6ebb144a7a21e0ef adding an explicit flag to link to libstdc++. this seems totally gratuitous, I know, but for some reason is necessary on a cluster I have that just updated its gcc. commit 75dedb629b81c7ab6ef76472a8bfd0aa54687c1f Merge branch 'master' of github.com:RosettaCommons/main commit 523567a9da88e087171e8f1c0d67738661466f66 replacing a TERRIBLE HACK message with an explanation of what needs to be fixed. Thanks Vikram & Alex for the suggestion. commit ee467e8e569ccd8a4f238841afa2cac7e750d058 Fix swa_rna_erraser test. commit e0d3fd32f1b9c0b0b0c689f788872851a1925a7b Fix the swa_rna_erraser test. commit 298e17292d758aff1c84eeba1352e1f4ab584c51 Fix element loading with ResourceManager. This should make the file_list_locator and residue_data_resource integration test work appropriately again. Also fix some database files which were missing the elements line. commit 08370b90d0256ce4a563dab629a083ae5c74933b Fix the erraser_minimizer app. Fix a bug in ICY rna residue type. commit 5d1cee95db545b44cd76658cab0c8727eb235154 Revert chanes on residue type lists commit 23624e5b678811a7c0b5b47ba379f762f1179507 Fix the erraser_minimizer commit 0cfb1eb8d7283aebd2a980111726a4cb50549d0c Updating benchmark/integration.py script so it remove all bin/* symlinks before building. This should prevent deleted executable from being reused in integration tests. Thanks to Rocco for suggesting this idea! commit 9e9d86c121036f58bc39fd8a8d6c9127f24d15e3 Merge branch 'master' into fcchou/turner commit a88301cdde973644494c862e0100525955c232b7 Restoring correct functionality of core/scoring/sc/MolecularSurfaceCalculator::AddAtom on Windows platform. Fixing some compilation errors when compiling with MSVC. commit f3f5f378a5edd3c67b4084f83aa8cbaca7c495a4 Updating PyMOL Mover. Adding pymol_name functions. commit ac9be9584d0e7650774f0b4456ae117d24aa8284 sigwidth fix commit fb4f575d973e63d5fb68df06bfbe4c61cecfe8aa Exiting with exception now gives non-zero exit codes Change the standard try/catch block such that exceptions cause the program to exit with a non-zero exit code. As a consequence, (properly written) integration tests will now correctly show when program exits cleanly, or when it errors out. Update app_exception_handling to test that applications exit with non-zero error codes when passed bogus options. I somewhat arbitrarily picked "-1" as a general "something wrong's happening here, what it is ain't exactly clear" code. This can certainly be changed if anyone is so inclined. (One possibility is to embed the exit code to use in the exception itself, in case we want to use it to pass signals up the chain.) Also, fix some dos-mode line endings issues. ** Integration test changes expected: app_exception_handling - different command file. jrelax - was erroring out with a bad option. Now fixed. The following integration tests have errors, and should now continue to fail until those errors are fixed: swa_rna_gagu_20_append_floating_base_by_jump swa_rna_gagu_17_append_floating_base swa_rna_erraser erraser_minimize swm_nickedhelix commit ee39bb9f728e11aba9f0a1c3ba4917c777f5619d Minor updates commit 70fd510e9a573a85eb4d462d5d42218d46944bad Scoping to current class is apparently not uneccessary "Considered an error by many compilers", absolutely required by others commit facd5dddbfcb3af308d784d61e9e56ee04431e48 [minor update of SandwichFeatures] - exclude H for number_of_RK_in_sw - default min_sheet_angle_by_four_term_cen_res (defined by 3 middle residues in each edge strand)= '25' since during repopulated de novo design of 3_1L9N, '27.2' of min_sheet_angle was observed for ideal-looking decoy - added a destructor - more int than Size to reduce Xcode warnings - restored accidently deleted 'do not face' phrases where appropriate [integration tests comment] - should not change other than features and features_database_schema (if any) commit 55b2b64494f2c76ecb9c2fc511f66be1e234662a Fix ccpcheck errors Ran cppcheck 1.49 on all *.cc and *.hh files in src/ using --suppress=stlOutOfBounds (as cppcheck is confused by vector1's) No test changes observed locally. Did not touch anything in src/apps/pilot, but addressed everything else: * Memory allocated with new[] needs to be freed with delete [] src/basic/gpu/GPU.cc src/core/io/serialization/serialize_pose.hh src/core/scoring/sc/ShapeComplementarityCalculator.cc src/numeric/geometry/hashing/xyzStripeHash.cc * Add freeing of memory in alternate code paths src/core/scoring/electron_density/ElectronDensity.cc * Address possible memory leak with realloc src/utility/libsvm/Svm.cc * Fix deletion from vector while iterating over it src/protocols/forge/build/SegmentInsert.cc src/protocols/forge/build/SegmentRebuild.cc * Fix use of the wrong object in iteration src/protocols/docking/DockingHighResLegacy.cc * Division by zero issues src/protocols/simple_moves/TailsScoreMover.cc * cppcheck says scoping to current class is "unnecessary and considered an error by many compilers" src/core/pack/interaction_graph/DoubleLazyInteractionGraph.hh src/core/pack/interaction_graph/LazyInteractionGraph.hh src/core/pack/interaction_graph/LinearMemoryInteractionGraph.hh src/python/bindings/src/utility/_utility__by_hand_beginning.cc * Spurious parenthesis and missing curly braces (some of these files might not be compiling) src/core/chemical/sdf/ctab_parser.cc src/devel/path_rover/pathrover.cc src/devel/path_rover/pathrover.hh src/devel/simple_options/test.hh src/devel/simple_options/working/test.hh src/protocols/noesy_assign/Assignment.hh src/protocols/noesy_assign/CyanaModule.cc * Random code that has been ifdef'ed out for over 6 years - I think it's safe to say we don't need it anymore src/protocols/jobdist/JobDistributors.cc commit b65d51027bff4fef9ba644f02769f542115712f2 Splice log changes. Expect log changes in splice integrations tests. commit dd3d98955cbffe6bb8ed08afe371cc4eb833ca9f ConstraintSetMover previously deleted the current constraints from the pose and imposed the newly read ones on it. This behaviour is sometimes undesired. I addd a flag, defaulting to false, named add_constraints, which instead of overriding the previous constraints adds new ones. See wiki for details; no test changes expected. commit fafd915bb839853072b4b35a66bd20e1d5630f40 merge onto a commit to fix layer design Merge branch 'master' of github.com:RosettaCommons/main commit 55276852e91d6d2199c601183ed23a276bce3538 Fixed bug in layer design. Previously if you ask for layer LLHHHLHHH you are getting layer LHHHLHHHX a shift of 1. This error causes helix capping residues to be shifted by one, the inability to get proline at the start of a helix along with other potential wonkiness. See example below: protocols.flxbb.LayerDesignOperation: secstruct is:LHHHHHHHHLHHHHHHHHHLHHHHHHHHHLHHHHHHHHHLHHHHHHHHHLHHHHHHHHHLHHHHHHHHHLHHHHHHHHHLHHHHHHHHHL protocols.toolbox.SelectResiduesByLayer: pore_radius : 2 protocols.toolbox.SelectResiduesByLayer: core ( E, L, H ): 20 20 20 protocols.toolbox.SelectResiduesByLayer: surface (E, L, H ): 40 40 40 protocols.flxbb.LayerDesignOperation: --------------------------------------- protocols.flxbb.LayerDesignOperation: Residue 1 protocols.flxbb.LayerDesignOperation: ss=H Sasa=146.46 >This should have started with ss=L protocols.flxbb.LayerDesignOperation: basic layer = Nterm protocols.flxbb.LayerDesignOperation: restricting aminoacid to repacking protocols.flxbb.LayerDesignOperation: Active layers: none protocols.flxbb.LayerDesignOperation: --------------------------------------- I expected integration test changes but didn't see any. commit 921161394f931503706e19c2b3b98d478412ff70 Fix warnings issues seen on gcc4.4 but not gcc4.8 commit 788768f2542e57769201a6b775ccd5490dbd4c10 Address debug mode integration failures. In which I promote assert()s to runtime_assert()s to make long-standing errors more noticable. Also, reenable compilation of an application that somehow got disabled. Integration test changes expected for those tests currently failing in debug mode. commit 069a1237a7b7634f5c769df5f922f584f53b1d77 Splice will now respect segment information even if sequence profiles are not set. Cosmetic log changes in the 3 splice integration tests commit b43efb75a3939aabc7a7c46158e6cf8bd905c066 PoseComment output clarifications. No test changes expected commit 5fe8072d3d84abfc46385291fcbb8e308156fa9b cryst_design.cc with options added commit 8d82e5e01c7fb859dc5c475d97263283722a798a Fixing some of the build errors on Win64 platform commit f8ac9c971834e3da8b3c945ae16826e714f39166 FastDesign now prints a very useful table of the task factory commit 30c7c5d82340a80e9ddef779a54a09f1438c6655 Fix valgrind error on ResidueType unit tests. nbr_atom_ was being left uninitialized under non-params file construction, resulting in bad memory access under the unit tests. Add a consistent initialization value, and appropriate checking. commit 7baa23db080108dafcdf7e5d0dabd5b64da8c3b2 fix early crash from erraser_minimizer in graphics viewer commit 019a766f2d35a6593240b70ab57e0033f98ea985 If given a blueprint, SecondaryStructureFilter now scans the strand pairing and determines whether it is possible for all "E" residues to be paired. For these residues, DSSP will always return "L" because there is no hydrogen bonding. The wanted ss string is modified by converting unpaired residues to "h" (which means L or E). This does not change the behavior if a ss string is specified, or if a complete blueprint with 100% paired strands is specified. This change allows checking the secondary structure of partially-built sheets, which was not previously possible. commit 253dbc8b4ec0738ec9a86d3aaa43949c8a10062e DesignBySecondaryStructure now correctly eliminates ligands from the DSSP string commit dcf00773c89fb52b2ab2235a0a01c5af767cb58f real removal of old alternative to StepWiseSampleAndScreen in protein SWA. commit de56a36952311c666135b4a4ce734f2a69773ebd conversion of StepWiseProteinResidueSampler to use SampleAndScreen. No integration test changes -- cool! commit cbd07211aa891e445b5ced02df63ab56fd3f36d8 deprecating old PoseFilter in favor of new StepWiseScreener class. Initial refactoring needed for converting protein modeling to StepWiseSampleAndScreen framework, though that is not default yet. commit bc9306f0b995de12813ccab3fff41653471e3423 Detect connectivity for crystal docking now works. Scores returned now correctly represent the weakest interface in the lattice. commit 67288358812f2ed62e3a69ff0165e37141b8c383 Refactoring StepWiseProteinPacker into StepWiseProteinMultiPosePacker (which handles iteration through a sampler) and StepWiseProteinPacker (which retains core functionalities, incl. prepacking) commit 0c5e45258ab998e4344c5cf0f9b78a8e5b994320 Carbohydrates & Lipids: updating centroid database files commit 623f81da6bc8ebe28563292a0f87f0649861ff36 Fixing header-only build commit 2426df96c02279a4fedb62728c223f6515cd582d moving calc_rms into FullModelParameters as it does not change during the run, and simplified number of variables held in StepWiseProteinModeler. commit 53577e0db3b3f878f73ef7afffc5bc185b38ae29 In SWA/SWM for proteins, remove full_model_info setting/resetting which is now longer needed, as we no longer pass through silent structs. Found an interesting issue in which PDBInfo became obsolete for a pose (despite being accurate) during fixup_residue_type_variants, now fixed. commit d4c7fb5dc1a8f0104d403ff499ec0079b676c140 deprecate silent structs from StepWiseProteinPoseMinimizer commit 46b754f3dcc033204db1959356dfd08d1cf9de18 deprecate silent structs from StepWiseProteinPacker commit 7836228b78f619ec7e908068a30dc1cd87d34374 deprecation of stepwise_pose_setup as an alignment tool in protein SWA. I do not remember the use case for this, and in any case, we have new superposition tools to handle this now. commit 49ca9b17cf5a816e9f55a1683784b1512c8ca424 getting rid of unnecessary extra silent struct outputted in -preminimize runs from SWM commit 7454097329f3c9b2ca9b9d9471e56544594016e0 fixing StepWiseProteinPoseMinimizer to not output any poses that were not minimized. commit eed5845479a0a9ee00e06f2f60160774b6619129 factoring Protein sampling/clustering out into a ResidueSampler -- preparation for merging with RNA by creating an exactly parallel structure. Changing StepWiseClusterer to be pose-based (rather than silent-struct based) for simplicity and easier transition to sample-and-screen framework for eventual merging with RNA. commit 76d149a0f1d4f64e9dfc5bd79cc0f385061f612b Make RandomGenerator default & copy constructors private. You must provide a magic number when constructing a RandomGenerator. Also, each RandomGenerator must have a unique magic number, so copies are a no-no. Praise/blame go to Per, who got me looking at the issue. (Unfortunately, this doesn't fix his problem.) No test changes expected, as no one was really violating these rules. commit f96ec53aff2a575fbe2a4eaf1bad81d4cabee9a0 Fix GasteigerAtomTyper unit tests. The source of the problem was a *reference* to a COP that was being passed around. While the underlying object was still existing, the COP object itself was getting deleted, resulting in bad memory access. This expressed itself (intermittantly) on Mac but not Linux due to differences in how the memory was being handled, and if the referenced memory was reused or not. commit a3b14bc052035ee236c76b8aee7835b495a31285 Removing ‘using namespace std’ from some of the protocols .hh files commit 6797ab4d551711a5af710767b2246376c94844da For some reason, my clang version will not compile these files without the extra include(core/io/silent/ProteinSilentStruct.tmpl.hh) for files: test/core/io/silent/protein_silent.cxxtest.hh test/protocols/jumping/JumpSetup.cxxtest.hh commit 469c1cc69f279b5787607dbcc5613d260f396407 Deletion of old StepWisePoseSampleGenerator. commit f0a201dc435f54997be471d80784580c24fa74cc GenericMonteCarlo can now write a progress_file with information on each step, its accept/reject status, the filter value and the pose sequence. no test changes expected commit 4389289be6bed69eac1fc619d57d48c44125915f Fixed bug in splice that caused it to disrespect delta length cutoff when iterate disabled. Changed get_disulf integration, so that it does not rely on the template to get the rigid body orientation of pose (this was the cause of a very rare error). Cleaned out some comments in RBOutMover. commit c6e1a5ba15afa4edf06bbdf283042b4dd44fdf3b Generic MC now explicitly states Reject if a move fails. Cosmetic integration test changes expected in MC tests commit 40383f1c059752e578a6a35aa6c097797cdd1953 reducing verbosity of RelativePoseFilter and adding verbosity to PoseCommentFilter. no test changes expected commit bbf9d1bc8f92e5c86f4a2cd5b53c225c97c41104 fixing a bug in RBIn: if the current entry exceeds the number of entries in the database it now rewinds to the start of the database instead of crashing. commit 66a2fe469276d353af66dbb35f4b00f7fa1656f1 PyRosetta. Adding debug environment script. Updating incremental build logic. commit 3bdade7a01a2587be1ab80f5bb3c81ed3964cc61 Check for lbfgs_armijo_nonmonotone minimizer in nonideal minimization Nonideal minimization with other minimization methods can be painfully slow. Detect if people are using other methods, and warn if that's the case. commit 9b1ab4518b5dd23adc12f25e9d6da5fde94e9692 Removing ‘using namespace’ from some of .hh files commit 1c339865fe8d8b36ea876dd3714e03dfa33bd1dc Add additional error handling to matcher The matcher can run into a segmentation fault if the atom names in the constraints file don't exist in the residue being matched. commit a27776013cc54a43c7d933789cd1f0e7c5de1ec5 PoseCommment can now search through all the pose comments without knowing the key. no test changes expected. See documentation page for details commit 0ba62f65d26e0b0dbc4b62b8c33b4fee46818b18 Adding PoseCommentFilter which can help control execution flow in RosettaScripts by probing the pose's comments. Once the RosettaScripts wiki is back online we'll explain how to work with this. No test changes expected. commit 7211bdb2321913eae3260e0937463c8c18867ff1 RBIn and RBOut can now work directly with a previous defined foldtree rather than figuring out what the correct jump should be. No test changes expected. commit 4a4b4bb2ed400c5b6266ac29efc42ebebe690753 Fixing a bug with symmdock when dof bounds are given commit 9c8c5962cd3f7b62396eb40ae32fdd379ece93fc Rosetta is now FAT! NEWS: This push introduces lipids into Rosetta. In addition, it adds MM atom types to all carbohydrates and introduces the MAINCHAIN_ATOMS field for topology (.params) files. Full details described below: * Two lipids have been added to the database -- the common fatty acid, linoleic acid, and the amino lipid "head group", sphingosine. This permits me to begin testing glycolipids in addition to glycopeptides, oligosaccharide ligands, and polysaccharides. You can read details of implementation decisions I made regarding lipids here: database/chemical/residue_type_sets/fa_standard/residue_types/lipids/README.txt * To load the 2 lipid ResidueTypes, use the -include_lipids flag. * I have added a glycolipid, galactosylceramide (GalCer) to the integration test system (tested with the carbohydrates). * A LIPID property has been added to ResdidueType with an appropriate private datum and getter. * The default main chain designation has been restored to what it used to be a few months ago, i.e., Rosetta will, by default, search for the shortest path from the LOWER_TERMINUS to the UPPER_TERMINUS. For any ResdidueType where this is not correct, one can specify the main chain explicitly in the topology file using the MAINCHAIN_ATOMS field, for example: MAINCHAIN_ATOMS C1 C2 C3 C4 C5 C6 O6 * I improved debug output in several places, providing warnings where there were easy ways to lead to silent seg faults from bad .params files. * I added show() methods to both Residue and ResidueType, providing superior information for either debugging purposes when introducing new ResdidueTypes or using PyRosetta interactively. * I performed some minor code refactoring to break up obnoxiously long stretches of code in residue_io.cc. * Added correct designations of main-chain, backbone, and side-chain atoms to all carbohydrate and lipid .params files. * Expanded, corrected, and clarified documentation/comments in ResidueType.cc and residue_io.cc; in particular, I clarified the distinctions between main chain and backbone atoms. (Also moved some comment blocks into the Doxygen- correct location in the file.) * Added MM atom types to all carbohydrate and lipid .params files. * Made some other minor tweaks to carbohydrate patch files to improve accuracy of scoring and nomenclature. * Fixed severe bug in internal carbohydrate code regarding alignment of virtual atoms. ---------------------------------------- Unit test status: Pass Integration test status: 8 tests changed rings, carbohydrates: expected hbs_design, oop_create, oop_design, oop_dock_design, scaffold_matcher: from spelling error corrected in output loop_creation: missing fold tree output in one line (I have no idea what this is about; please let me know if this seems to be a problem.) commit ffe26c57e7c389ad9d245045e898272c3e0c6cad merging commit 854d972712e8160cd85f2b289d4104a0079e8f11 Fix matcher error catching issue commit 91aa4f7337b4398417156110dec443a78ffccb83 Carbohydrates: adding 1st glycolipid to integration tests commit 683bf609cc72498f305fb84472c576256e740872 Carbohydrates: bug fix in aligning virtual atoms commit bb43686d119053db43ca0b8d708c33c8d35ade20 Lipids: adding -include_lipids to options system commit 86731ed5a53e3a37e7cb3cd27d2a8ec045f30fd9 ResdidueType: removed debuging output and added a warning tracer to AtomICoor for when the index is wrong in CONN records commit b262ba9afb56ed99c0ccfcb2520bca20c713a3e2 Added function header to Splice.hh file commit d830f02c0bae9eda1f7f9270674a38cafcef5d49 Added function header to Splice.hh file commit bb63d26fda37411c006046f9fb0a6ff7ca128cf3 more fixes to crystal design commit e3c03639efd96b02cee389a2f2065ad77d28d7f0 Adding motif incorporation and bigfix for LoopMover_Backrub. 1. New application for incorporating motifs into flexible loops. 2. Fixed bug in LoopMover_Backrub that prevented proper use of stored scorefunctions that were provided to the constructor. 3. Saw integration test changes in: match_1n91 inverse_rotamer_remodel match_6cpa cstfile_to_theozyme_pdb commit 8e67c55e446bc154d3bd32198ca8a9731c19147c Adding application for motif incorporation. Fixing a bug in LoopMover_Backrb.cc that prevents correct usage of stored score functions. commit cc22f4f7cecb6b4c46ab86bf4942a071d3adf007 Minor correction to Splice.cc. Change will cause log changes to all splice* integration tests commit 898522520495bda233538092fd8e1814e69ac44b Minor correction to Splice.cc. Change will cause log changes to all splice* integration tests commit d35cac07c501282d319e3d95765cd8cb9aa92ee7 Lipids: wrong CONN id in .params file commit 83d361aa35e65dd8d0708c5b8d5604a34a628387 Renaming core::scoring::interface namespace to core::scoring::interface_. This should solve problem when namaspace clash with ‘interface’ keyword when compiled with GCC-4.8. commit d515cb6a1b3a83964eb4f7e619694da1526c8c33 Fixing PyRosetta build commit 2715c93a5df216f772f24872f7ade1a8e2be461f Fixing some build errors on Cygwin platform commit 28cce757a80b729f7f9425b4440ae838f4000d90 Adding missing namespace specification to boost function_template commit 5371a5f00d19915e30c371f0c380348531d8a490 Fixing Clang build commit 0a413f7d25f3ca030aace8eeb413b70ec22c7157 Updating version script call in windows build route commit 85d4e1c8c77f607dcbe31489560f34e215db526e Another couple bugfixes to cryst dock. Working for all spacegroups now. commit 84ca032967c80af98e5f2f7724893aef3323fbb9 Adding a public app for motif incorporation. Also, fixing a bug in LoopMover_Backruc.cc that prevented the correct use of score functions provided to the constructor. commit 0f424085d1aca65bbd651a79bf1951f40ad496dc Another bugfix for cryst_design. All spacegroups but F4132 working. commit 57391a0c00db3e96da282def8808f4432258880e A bunch of bugfixes to crystal_dock commit 294e664098a86391fc52b21ea3d49081d586d854 Minor fixes to Splice.cc Can handle multiple seqeunces when adding seqeunce constraint to pose Expect Integration changes to splice_out, splice_in and splice_seq_const commit 314140344d6d94cf4561c11de59285e1c39a7c23 Debug: adding tracer output to Conformation to figure out why Rosetta won't link my residue connections commit cf574b45bf8aa2713e0d2e160fe71d97d4d5d828 deleted missed debug couts commit 3e6d39566a0b0b0666bc9a6c529ef2ac44a5c759 Carbohydrates: adding 1st glycolipid to integration tests commit 3a0191c690f8d74f8b32bf6182fc0af83e39d27d Carbohydrates: adding MM atom types to N and NAc patch files commit e4784566a9e2c60808528b97d82b42e558eecc60 Carbohydrates: upper termini for sugars now called non-reducing end, instead of upper terminus commit 514eed4f8fd20fbe02533ba5e575b8dbfa0a649e Lipids: fixes to the 2 lipid database files commit e3f930bd88fa861e5da498b70dbeef485931ea1f Carbohydrates: fixed mistakes in assigning bb atoms commit 510e88b28f825f937658fb321550e91008cc11c9 Carbohydrates: added MM atom types to 8-a-Neup commit 2e5d61ddb0fb6ca5491b7ef83be46681c3c604c8 Carbohydrates: added main-chain and side-chain designations to 8-a-Neup and cleaned topology file formatting commit c888412564ae2ea70f2b46e1f53f10d2eededd18 Carbohydrates: added MM atom types to 6-a-D-Glcp commit db24d8eb153d0d1ce127a45a35a03153dc4dff34 Carbohydrates: added MM atom types to 5-b-D-Psip commit cb960a14e70d1b67ea53e4f86fd9f0f18ce28431 Carbohydrates: added main-chain and side-chain designations to 5-b-D-Psip and cleaned topology file formatting commit 3a9ba7e43ad648e3dfe86ced052e362c10a8bfe7 Carbohydrates: added MM atom types to 4-b-D-Glcp commit f73478a7922d7e22ae64bb342b8e2046a8d4a914 Carbohydrates: added main-chain and side-chain designations to 4-b-D-Glcp and cleaned topology file formatting commit ef1a0cfcd1128d8b28ab99b9c6dbe6e425c82661 Carbohydrates: added main-chain and side-chain designations to 4-b-D-Galp and cleaned topology file formatting commit e443eb7f32b1b1c042a6d75798083b7302f92b62 Carbohydrates: added main-chain and side-chain designations to 4-a-L-Fucp and cleaned topology file formatting commit ff540bfc45d94b8e7d2e94e54c43ac3b4488ce3a Carbohydrates: added main-chain and side-chain designations to 4-a-D-Glcp and cleaned topology file formatting commit 39d6aa58d6cdf999de96f722bf57abff937e1f16 ResidueType: refactored main-chain atoms designation code; previous version failed to work because atoms had not been ordered properly yet? commit 172abcf3e7401f95f83a8fb4b74c16ccd2c9f0dc Fix handling of ligands when using DSSP with SSPrediction filter commit e854dfa997831d104056a1dd1a616cae504321bb Fix handling of ligands with DSSP by SSPrediction filter commit 9b34b32b8778756e482d3acc71de86318e3c2455 Carbohydrates: pilot app tweaks commit bd594bcb4dd80dbe43257f4bcbfd7affe4ebc852 ResidueType: declared and defined show() method for Residue commit 2a92bcd78ad72e429eb0cf9d65f6036b7ac824e0 ResidueType: defined operator<<() and show() method for ResidueType commit 88a06444c47acaa7a70d182aa163969ee7394566 ResidueType: declared operator<<() and show() method for ResidueType commit 2747b81f4626b7469feb2eff34a7ae845f13ebb8 ResidueType: moved around comments to correct usage for Doxygen commit 5db9ae5f9ee2b927b11a43a66d5c0276dbcf4898 Carbohydrates: added main-chain and side-chain designations to 6-a-D-Glcp and cleaned topology file formatting commit 35ee94ee17c75f55e08d6f1e0d5fc3542578a8f3 Carbohydrates: added MM atom types to 3-b-D-Manp commit b441dad5e8d43dc37b2dd2d8d5e371d6ec60b16f Carbohydrates: added main-chain and side-chain designations to 3-b-D-Manp and cleaned topology file formatting commit ad5971555c5caa2a5ae4b672c714d7b059894025 Carbohydrates: added MM atom types to 3-a-D-Manp commit 2d090f0de2f6d436901902ad102f141d0f11de2b New Integration test for LayerDesign Task Includes a ligand and a short pack-only run. commit 30fd8728eac12528c5a5c48c6bda6bbcde164314 Carbohydrates: added main-chain and side-chain designations to 3-a-D-Manp and cleaned topology file formatting commit 7e679c082821cc1eb39d797da714be94169606bf ResidueType: :( removed helpful warning from residue_io, because it will not work before finalize() commit 241316b196a7757240459e0e74e2e35dbfc2f7b6 Carbohydrates: added MM atom types to 3-a-D-Glcp commit 7fb28e34174dbba9a3b61a33b4c506e29fc812f8 bug fix commit df7502322f5febc74a0321582534088dcdb28e21 severe bug fix commit d983336937c90430770146a13dcdd249742e6ae6 Carbohydrates: added main-chain and side-chain designations to 3-a-D-Glcp and cleaned topology file formatting commit 37b47c9faf435fe065e55f9e7eab4ee9bbac4c12 Carbohydrates: added MM atom types to 2-a-D-Manp commit 287bd318d14328bf6f5e6896679d19f816fc8821 Carbohydrates: added main-chain and side-chain designations to 2-alpha-D-Manp and cleaned topology file formatting commit c9b57fe3e7173249272bdd2afdeabecc384b51bc bug fix commit 902a78aa6e89bd0ad52af70834615e4c091d9d7f Merging my copy of the master commit a82b7a5b2c2a790a5954e248b64a5695d2df147b logic fix commit 4b2d7e77c3c8864143c58f78dfef52806474f373 Lipids: added new main-chain designations to lipid topology files commit 65f489dedd0132969dac91bef84686038cfa852c ResidueType: refactored to move some code into a subroutine commit 8f1f395b4c5454926c575d43ddf54b60e1dea6f7 ResidueType: improved debug output regarding main-chain designations commit dc6977a3ade710b440298528f72e16c3539e4ced Residue Type: removed default main chain definition code and restored old default commit 761ed80b6bac9f015acbb2f8b30cf057b90bf8b5 Residue Type: adding ability to set list of main-chain atoms from a topology file commit 7ddc29c2a54ccd2e8d947cdd7e70df628f6d5e70 Lipids: adding is_lipid_ datum to ResidueType with getter commit 59bc5b449485372afa0b9c70532e79210d4fac16 Lipids: corrected designation of variants commit b1a7f31930a6f679ecfafc249afee29e185aa1e1 Lipids: adding glycolipid PDB test file commit b660dbf49d4cc2f957aec2d55ff5835166ea3f54 LayerDesign fix to allow ligand-containing pdbs to run Original layerdesign didn't work on ligands. Our old fix added "L" to the ddsp secstruct string for each ligand molecule. Rocco's recent, better, fix, puts a " " for each ligand, which broke our old, hacky and un-integration-tested fix. This commit gits rid of the hacky fix and works with Rocco's fix. All Unit tests pass and integration tests pass. We should still make a LayerDesign integration test. commit 330fd2d67cb71df3d4192acd1c241158a377622c Adding git-branch prefix to observer emails commit e58f27b2f9cc30f1497f14a80d5a6d2b20b1c602 Merging my copy of the master (just one bug fix) with the trunk commit ceebb8b299013744742dbdb7ac1938b4a9464c01 Fixing a bug in SecondaryStructure class ObjexxFCL::FArray1D_float confidence_ was not initialized which resulted in segmentaiton fault commit 691c3da197c6bb9dbc898be95d353a721aff3235 Fix Performance benchmark Adjusting performance benchmark to account for metal ion changes Vikram recently checked in. Interesting note: if a non-polymeric residue exists by name in the PDB, but doesn't have any appropriately named atoms, it will be built, but fill missing coordinates will never succeed. Better error checking of this is probably necessary. commit 2f233e796e1245820c7a4176a1ae81d482cb3078 Pulling in master updates. commit 442b5deec3354bc323d0c8a7cc4b457cddde2fe8 Lipids: need to tell params file that it is a branch point or lower terminus, etc. commit 5f747a3c4b9ad1d336045d3cb92b9bca5b4d346f Porting integration tests observers from svn_users.py to /observers files commit 331efc5d6b60abd3e93608769dbf079ed07ac3fb bug fix in sphingosine.params commit 5cc068714220c5c27d0ceb643c917401118081b9 Lipids: 2 new types added to list commit 3ce07c9f97ffa6ffa24e7679bb22005d311fb92d Lipids: adding linoleic acid to the database commit 0675475ac90656f7b02199dcc8e752b4840bcc30 Lipids: adding 1st lipid (sphingosine) to the database commit fa50b53165cdc6caff4775e9c0318e53bba84f38 Benchmark scripts. Refactoring how exclude files are handled in regression tests (i.e. store them but do not compare). Adding example observers files. commit cadeb9f34d91223be8a779543e7265dbe30b8f0a Pulling in new changes hoping the warnings go away. commit b5e89a9b0e495953159d58352e7aa44bd3a4ddc8 PyRosetta. Fixing build script error when running on Python-2.6. commit 1ccd1e0a40244600e4c91b97e58ba2cb9d733b3d Revert "Revert "Fix issues with Gasteiger atom typing"" This reverts commit b1603f390f31c154481f5b0a4fc58c208c1cc2a6, restoring cab6655af046ce82e656c1c35b9fda7c7cc9fa33 I could not get the test server changes to recapitulate locally -- more tellingly, the reversion did not see the inverse of the observed test changes. Moreover, it looks like other commits from the same time period also showed similar test changes, indicating an issue with the tests. I don't see any test changes locally with this commit, aside from the added unit tests, and the standard numeric instabilities. commit ac450c4b2742f710a8e028c683d1bfb7fea44148 Revert "Revert "Fix issues with Gasteiger atom typing"" This reverts commit b1603f390f31c154481f5b0a4fc58c208c1cc2a6, restoring cab6655af046ce82e656c1c35b9fda7c7cc9fa33 I could not get the test server changes to recapitulate locally -- more tellingly, the reversion did not see the inverse of the observed test changes. Moreover, it looks like other commits from the same time period also showed similar test changes, indicating an issue with the tests. I don't see any test changes locally with this commit, aside from the added unit tests, and some cosmetic tracer issues. commit 56aa4744442fca1e8dfcfc3917b4006f5fa3b6bd Adding pilot apps to pilot/nmarze. Nothing used by unit/integration tests was changed. commit 20c3d5a40b074bc28ac3c5fd95703e62ea1a9e45 adding pilot apps to pilot/nmarze commit 9575fbc5e48a62f7ed288e74e49ae5a79f3069bd PyRosetta, debug build: Adding link to toolbox. commit 5508b89f602905b2bb59af2486cdaacd9182fb5a fixing broken pyrosetta build commit dfe26f3d5ae1f29dfaedd62e89e04e8d74c14e88 Commenting out guilty methods for breaking pyrosetta build - hopefully we fix it this time' commit d2da8843eeb724218c389df3f186d13786b1e55a merging (small) changes with the current state of the trunk commit aa9b03aa180eb173b88c79a52f8b9141513fb9d7 Fixing some -Werror=maybe-uninitialized errors that make gcc 4.7.2 fail to compile commit 04342abe772db26cdc974ed6748fbef23850a1ae Updating include guards again. HOpefully this fixes the pyrosetta build commit f776b8411b2778a4dc969ea6fc30cdd429c10f0e Updating include guards in Membrane FA Potential class. THis should hopefully fix the pyrosetta build commit 3b042be46e994d0a8b941229012e84dcdad8e7f1 Merge branch 'master' of github.com:RosettaCommons/main commit 0035faf29cdf52a6b3106c7bb87e887dfaa1d636 Added a new mover (ResidueTypeConstraintMover) that assigns a ResidueTypeConstraint to a pose (All I did is just making a simple mover using Sarel's ResidueTypeConstraint) [integration tests comment] - should not change any integration test commit 5cb0cdb59416e14afe9862a7956685445f4ae68d Quick fix commit d544ed2cd56074a60ad0bda1ddcc71938b9b2949 Fix low-hanging gotos Fix gotos that were simple replacements of break/continue/do-while/etc. The gotos that are remaining are either multi-level breaks, other more complex flow control, or in files I didn't bother to touch. (I didn't bother with the multitude in apps/pilot/, as many of those are in "private" applications, and some numeric/ files, as those look to be straight transliterations of external code.) All tests pass on my machine. commit e08b130d8f0c266d09446ab0749fe1280b6e41c8 A simple pilot app demonstrates how to use movers commit 3f55c95210c4e42365424beb8260104b8849bdbc fixing warning/error which should also fix the build commit 642bada287cd92103ff60c5e88b845fbf4d293bd a pilot app reads a binary PsiBlast ckeckpoint to test the new functionality commit f49e45a461c183ba14a8aa456a09024f9ec72da8 Rosetta can now read binary CHK files produced by PsiBlast (holding sequence profiles) This alleviates the need for producing flat-text *.checkpoint files, as has been done my nnmake -in::file:binary_chk option added, used by the fragpicker commit 43d205397ff0f95a3647c7a041ae49a4022b275d Fixing the build on Mac with clang >= 5.0 It compiles nicely by clang 5.0 and gcc. commit 256d031132854b0d1ad74e9729530764b29bae4b Merging my branch for fragment picker stuff with the changes introduced to the master commit c0fc69f6aa1775a41edb088fe9332102f738270c Logmessage added to RotamerLibrary.cc prints the random file name generated commit 361cb64479ec3f7945877a9a0a9e640c2fd07944 Fixing unittest for mac build, lower tolerence commit e7bde0e286f05ddb2186cb083b79afe4cc58a2cb Updating Centroid Rotamer (cenrot) Model 1. reweight pair and pair_ang by env dependency 2. refined rotamer cluster, new cenrot dunbrack lib 3. cbeta term for cenrot 4. bigger vdw radii for minimizing 5. updating unit test 6. minor bug fixing for compiling others: Adding more parameters for cart_bonded term Hack in CartesianMinimizerMap, use RB1 to mark single atom vdw term can load more than one atom_vdw.txt Unit test all passed 53 ingegration test changes found 12 of them due to the cart_bonded term or new cenrot weights file FAIL nonideal_rtmin FAIL mr_protocols FAIL hybridization FAIL fold_cst_new FAIL metalloprotein_abrelax FAIL abinitio FAIL splice_seq_constraint FAIL repack_with_elec_dens FAIL minimize_with_elec_dens FAIL features_database_schema FAIL symmetry_multicomponent 2 of them just failed as ref (missing weights file?) FAIL splice_out FAIL splice_in others are minor numeric changes due to adding new cenrot_cbeta term commit 8d815fe8f2c600c5a3382a2b82e3c398057b3593 Fixing clang 5.0 build on mac commit 57b37e738cb7f75bb38d1de685f401fc69cc6653 Merging my branch for fragment picker stuff with the changes introduced to the master commit 30a68df78c8eec5b85dfc9dda29222d558000a7a Fixing debug build commit 5b68e79e91553ddcf25ec318f45cb33731514eb2 Fixing score naming bug in abinitio code commit b90f3350c18b4cd2c1909a4584302c9f3d8eccd4 Removing erroneously typed character to fix the build commit c608eb59ebad9bdd67b79c67d8f16bc8073f721a This should fix all of the newline erros that were added. If it does not resolve the issue, I will revert. Sorry about this commit d778d29851fabc460b7999e01fca9f5ce4be77df Updating Centroid Rotamer (cenrot) Model 1. reweight pair and pair_ang by env dependency 2. refined rotamer cluster, new cenrot dunbrack lib 3. cbeta term for cenrot 4. bigger vdw radii for minimizing 5. updating unit test 6. minor bug fixing for compiling commit a5bd0d0ea6fb7d062e2fbd695cbe029a1acd8b04 Adding missing newline that broke the build commit c3a35b4807a8ebc8f7db0f1134365fb53b8dc074 RosettaMembrane Framework Update - Library Reorganization News: The membrane framework code is now split accross three namespaces. Below is the new organization: core/conformation/membrane: Includes all code involved in defining a membrane protein. Includes: - Spanning Topology - Lipids Accessibility - Membrane Info object in conformation core/membrane: Includes all code required for making and working with a memrbane protein at the core level. Includes: - All resource manager classes - All geometry definition classes - Membrane protein factory protocols/membrane: Top level interface for creating a membrane protein. Includes: - Membrane Unit test mover (mover for unit/integration testing) - Create Membrane Pose Mover (simple mover with Rosetta Scripts hook) This commit should fix the library level build. library_levels.py passes in master. Unit Test Status: All pass on Linux GCC Integration Test Status: None expected, other than currently failing tests Added: 3/21/14 commit 321926fffaced9d84b8b8b23aa85586955dccfaa Merge branch 'rfalford12/mpframework_devel' commit 89b45008072d803f8f86808b56065932bef4d65e Removing util script in preparation for master merge commit 962667ff931b7a288eb4c6a79fba59221dfbe0ba Debugging namespacing changes in unit tests - everything up to date commit d09a6840ea516794ec2726254d48f8ab9a4545ff Debugging the regular build one more time - off to battle the unit tests commit 858dc46519b59de5324d544799aff5a18e0c96ec Removing an unecessary old namespace and continuing to debug commit 2dad4d28a7e8a695c3fae9771f6a38d04f2f0a97 remvoing framework headers from membrane potential class - not quite ready for those yet commit c6c062c0d802ef9967bed85cd5a5168307f2103a Resolving more merge conflicts in membrane protential that clearly breaks the build commit a72b1c8922a66fcc616124c416ed6a3e7cf51354 Resolving merge conflicts in pull commit 1c5426ac26e1807bf8694637199f6a274e3334f2 Fixing bug in protein silent struct commit a10214bccd1e5203596db754e440d6dc0eb7e894 Updating protocols level unit tests to include namespacing updates commit f35160c2675a4698dc26c6a17b47c02f3ecf7aea Getting rid of old legacy membrane protein loader commit 037dcb4a53d136dc70a5f3e066b39ddf33addd38 Renamespacing core unit test and fixing core.test.settings file to organize correctly with a mirrired src structure commit 094170791d2dc3cb70f5ae2ab9a258a9848fffbb Resolving namespacing issues in the geometry unit testing suites ' commit e9d6de10575256bc3c0cdd8dfd3905e4906dc3ac Moving the membrane info unit test to the correct namespace commit 084fc255f1db3593568c6d161c5dbae896b83c7c Fixing small bugs and typos - resolving the rest of the core 3 build commit 4ca1e29f188ad191f3c1631c32975dbf944f3306 Updating movers in protocols to match the new namespacing - stil needs to update the unit tests commit 6811d562a9a0d078125b9aa44634c7daf906b519 Fixing namespacing errors in util geom commit 78fc47de24e6d02329f4f25c944728e67e8f71c1 Updating the embedding factory to use the new namespacing scheme commit 240e1f02d5d79ec73291ae09844fcddffc0eee54 updating namespacing in membrane protein factory commit fe76ee19575eb745cc20542687e7751c87a34fe7 Updating IO classes in membrane core 3 to include the correct conformation based namespacing for its dependencies commit 5484f2c7415013756270d948bdaa292c24d71d8b Adding newly namespaced core 2 membrane framework files commit 7636b44302818e1ee525d8d125c9d02692d85a46 Quick debugging - internal build of core 2 resolved commit 97547ce1d154b4be9b7bda06a452a3a8041811dc Fixing internal core 2 namespacing - will try to build up to core 2 with 3 level mp namespacing commit 5cb6219da8e1cdbdff061db6bcbc807d66018994 Moving to 3rd level namespacing in conformation ' commit 609ce9cc80e32c88f3ce924aede2e5ebf2a66b1a Moving util directory to core conformation as it lives in the conf membrane layer commit e074f39ab20fb2a6e36cc297b79121883250bafb Reorganizing the membrane library structure to obey the 2nd level library rule commit 22f67a8918e07c904d848b60fa642aa10d743aed Fixing compiling warnings and errors commit a4e0a892daf57fb50c10fb72e47f9d06784a1d01 Comment out the KIC unit tests. These are my tests, and for some reason they're failing on mac and not linux. I'll debug this issue once I get access to a mac, but in the meantime I'm just going to turn them off. commit 15b89c0727bac1952d8c1c177a9858832c5b6adb Merging my branch with the new code from master commit 97ae5e9cf9ab34328697ee2bcc5f127b1280fd85 [minor update of SandwichFeatures] - further differentiation of automatic generation of resfile like surface-heading residues at core strands - more int than Size to reduce Xcode warnings - better tracers [integration tests comment] - should not change other than features and features_database_schema (if any) commit 2f39c218831edacdfeb5ffd83fb8c7a8720bc111 Fixing quick typos to resolve the mac build in XCode commit 1a737bd081b417d5dacab4c59a6533bb3e6dba00 Removing EOL warnings from MembranePotential classes and adding annotated scoring files for membrane fa potential commit c20b425805c650bbbc91efde26e20dabf6f8656f Adding annotated and documented versions of Membrane Potential classes commit f082900f5db24a7426e055390e645f1e80c48a26 Adding membrane scorefunction integration test commit 387fe2f4dc18f047f0b8d081b9b9b07c2e5e1f30 Quick cosmetic changes commit fa89ee72af6cd244e287a3af6beb0268a1664dfb Adding scripts for env, pair, pair_ang commit 07b3d751f94b74f6debc8d79b74abb7eb7c8a279 Updating scripts for calculating cenrot dunbrack lib commit eaa611524c3f293739d029e10a1c455a75aac14a Merge of ninja master with rosetta remote master commit f1fa96684a7dc016127eda1bbc38298d54bcf93b merging with master; some files were required to remove commit fb38bf53b5b2bac6b7bb5734d725f7dfff0c36e1 This update should fix the pyRosetta build. Library level stil broken - that fix is in progress commit b85ad2c17f35d48d0ead563bd111ec9404db7bb1 Rosetta learned how to read binary files holding sequence profiles produced by PsiBlast This is used by fragment picker; a new option added commit b679892860ecfcf71aaac334ae939f6ae4847936 Merge branch 'master' of github.com:RosettaCommons/main commit bc18043a22bb847c6162ad712fe6bb5ac12b07f8 This change should fix the pyRosetta build commit 1b729950997e00339def547d3a89308181b3bc71 Fixing io library level conflicts commit 273e3dda7bc42d0b265ee988d003b388464e9c30 Fix build If you don't want people to call your default constructor (for example, you're storing a data member by reference) all you need to do is declare the constructor as private, and then omit the definition. This will prevent the compiler from automatically making a default constructor. Additionally, src/basic/options/options.py was adjusted to allow the older version of Python on the performace benchmark computer to work. commit 18cc6bf5c7421d21aaedb6e99f22c1714f5922ca Adding annotated scoring files commit 93992ccbc4c92847ddb9069dee9b9ab13218cd82 Adding unit test util script to main source directory in the devel branch (will need to un add this when you push to master) and scoring integration test commit 53314b0cba0ff5c96f15f39ebfbb5e1d081c3795 Merging ninja master with remote master branch commit 5da41df62cccddd8fb3f018824ed3c154bfdee6e RosettaMembrane Framework Updates Updated: 3/20/14 Updates: New MembraneInfo Object - Replaces previous MembraneConformation subclass - Contains placeholders for lowres and highres scoring members - Includes new corresponding unit test - Removed all previous MembraneConformation code + tests Unit Tests: All Pass on Linux GCC Integration Tests: No changes expected, other than the ones that sometimes currently have trouble commit f70c4f82fcffc70e27ff001d7cfab588208ee9cf Adding back some pilot apps I commented out of the build due to a previous linking issue commit e32c14f2a4b49725f653438a7ef1fbdf95bae395 Merge branch 'master' of github.com:RosettaCommons/main commit 968842a202da4d4643a83414e400efad3c4ce582 I should really compile before pushing and work in my own branch. Intense shame. Sorry again! commit 8f1f44f0f977dba34c4bdc18765d6218ac3de94e Unintentionally commited a piece of non-working code. This fixes that... Sorry. commit 82e6f0785ca4c518cf34712cdafda8808b2c2b50 getting NativeClient to compile commit 0e7fde1c8d68310f1deb7e15e4580e426f870aa0 getting nativeclient to compile commit f172b0ec9eb85d325c624c5bf667c03bc176770d GPSRosetta: New functions to score Pseudocontact Shift (PCS) data generated from multiple metal binding tags/centers. NEWS: [DETAILED DESCRIPTION OF CHANGE] The distance restraints are implemented in a manner analogous to finding locations uisng GPS satellites. The current implementation is directed via usage of a broker file and can be used to setup atmost 4 different tags. GPSRosetta is an extension to previously implemented PCSRosetta which uses PCS data Ref: PCSRosetta: C Schmitz et.al. J Mol Biol. Mar 9, 2012; 416(5): 668–677 GPSRosetta: Yagi H et.al Structure, 2013, 21(6):883-890 Unit test status: [Pass] commit b8f68adb4e845b007c02314a0593d313737a9795 removed option keys tracking commit 43339425ddd1204b8b992e5e0573e6b4ec49d9aa GPSRosetta: New functions to score Pseudocontact Shift (PCS) data generated from multiple metal binding tags/centers. The distance restraints are implemented in a manner analogous to finding locations uisng GPS satellites. The current implementation is directed via usage of a broker file and can be used to setup atmost 4 different tags. GPSRosetta is an extension to previously implemented PCSRosetta which uses PCS data from only a single metal center. Ref: PCSRosetta: C Schmitz et.al. J Mol Biol. Mar 9, 2012; 416(5): 668–677 GPSRosetta: Yagi H et.al Structure, 2013, 21(6):883-890 commit eb16d5c77919f6d80981e5f27df059eefcb9a979 Merge branch 'master' of github.com:RosettaCommons/main commit 327e15e8b2cdce1e2aa149779d429a50d15fc5cb PCS Scoring with multiple Tags: New scoring functions which can score PCS data with atleast 4 different tag sites are added commit b392937ff820a7caaffab0fd8f52b97cfb7d4a4a Fixing clang build (tested with 3.5-1ubuntu1). Attempt #2. commit 5a457e857002bf2b971665c7ec65528b4d3a60a0 Fixing clang build (tested with 3.5-1ubuntu1). commit 39fbf2a1bea06e634773c8eb904389c09cf9b137 Merging local and remote master branches commit b27bf47336fc4549c1c0748681fc5973a73e011e Adding MultiplePoseMover and MultipleOutputWrapper (merging branch luki-mbi/rosetta_scripts). NEWS: The MultiplePoseMover allows a multi-step "distribute and collect" protocol to be implemented in a single RosettaScript. First, it collects all poses from the previous mover in the protocol. Next, poses are selected from the complete set using Pose Selectors, some of which use Pose Property Reporters. The sub-protocol, if any, is then run on all selected poses. Poses for which the protocol succeeds are output to another mover for further processing, or to the Job Distributor for output to persistent storage. This mover can also be used to "branch out" without any selection criteria (i.e. generate many diversified poses) or purely as a selector to trim down the set of poses based on some criteria. MultipleOutputWrapper is a simple wrapper that will execute the mover or ROSETTASCRIPTS protocol it wraps to generate additional output poses from the original pose. This commit disabled RosettaScripts resume support, since it's interfering and needs a better implementation. Unit test status: Pass All test pass except SpanFileIOTests, which fails to run on my machine (Linux, gcc 4.8.2) with: core.test: src/ObjexxFCL/DynamicIndexRange.hh:103: ObjexxFCL::DynamicIndexRange::DynamicIndexRange(int): Assertion `legal_static()' failed. Integration test status: 37 test changes (all cosmetic) Cosmetic changes are expected in the following tests due to the clean-up of empty protocol reports. Additionally, there's a new message about deprecation of the tag in favor of . Enzrevert_xml add_job_pair_data dock_with_hotspot_place_simultaneously favor_native_residue grid_scores_features hotspot_graft hts_io hybridization inverse_rotamer_remodel kinemage_grid_output ligand_dock_grid ligand_dock_script ligand_motif_design ligand_water_docking loop_creation make_symmdef_file nonideal_rtmin place_simultaneously posttranslationalmod_io ppk rosetta_scripts_setup rotamer_probability rs_flexbbmoves rs_loophash score12_docking score_only_silence splice_in splice_out splice_seq_constraint startfrom_file symmetry_data_resource The JD2 now outputs additional poses generated by a mover, thus the following test now produces multiple PDBs: rs_loophash The pose tag is now at the end of the PDB file name (for clarity), hence some output file name changes in: AnchoredDesign antibody_designer broker_membrane docking_prepack jd2test surface_docking commit df74783160e50ce52b964c73496c4c628d01f1b6 Benchmark scripts. Adding ‘ignore’ file list. This should break all regression tests. commit 8e6d3410c21b5ca77ef01cc960726c5ebc6a4877 Merge branch 'centroid_rotamer' of github.com:RosettaCommons/main into centroid_rotamer commit 2e4a76a22e9e2664245e1426673e2bfd63d8bd81 Increasing VDW radii of hydrophobic side-chain (detected by fa_rep) Minor changes in cenrot-relax weights commit cf4f7f21549f1c364cb8eee5027dc8cce34d1316 Adding new min.txt for vdw, clashing energy E>10, guided by FA-relax commit 274b36ff0e296330d69c010fe00922c4a885e109 Downweighting hb/pair terms in cartmin, increasing vdw parameters commit aa379f4e77311c8f98057820696034e6d210b863 Adding new score weights and load from code commit 0c61b1030ef2d6fa7bf2e67e157b1c8ca212c737 Adding new code for scan over packed residue pair. Adding new min vdw radii. commit efef0edc738928525ddbab7800aff90a92674bb4 Adding GDTTM to output commit bdfff6839e0b18a959bbf2cc5318a3fd5d8ed895 Addming bigger vdw radii for min cenrot, now AtomVDW can load alternative vdw params commit 2667b44177be3d6d88f193e354829b86e257cd07 Adding option for min mover commit d2fab5bb47c5ffd87bc935a01d072ee0a5bfdf28 fixing output silent file header commit e573939cc17ff81daeee86ec61b30f496c4a9c90 Adding more options for cenrot_jd2 commit 3e3013e6b0cb9bfa5023e688faaf5f55ffe9e5b8 Merge remote-tracking branch 'origin/master' into centroid_rotamer commit a4d62e4ec20a570cbeba62274f87e4f55b8b81be Commented out a few TRs in scoring per Andrew's request for performance reasons commit b272bba56acaa119a74b1869f1425f9ab444b3f0 fix even more warnings turned error in mpi-build commit 76ef438ed684eb833607dad693699cd2476d487a fix even more warnings in mpi-build commit 9388d00b91c6121de38ceb76b12da786bda843c3 fix more mpi-warnings commit 16446a2ec15b6099a9ebd04989fab3957df5a6f3 fix more warnings in MPI build commit 3ef3016b6af5aa0fe64831bf7cf14bdac4a4eba6 fix warnings in MPI build commit 09d3c38c5c071152bf164873190b1a887952e0c2 The applications in chemically conjugated docking will now complain if a file is passed to in:file:s, rather than complaining and exiting whatever you do. So, one of the key characteristics of the UBQ applications is that they accept two input PDB files via two different flags (GTPasepdb and UBQpdb) and do not use in:file:s/in:file:silent/in:file:list at all because they're used internally. One issue is that the apps apparently checked for whether those in:file flags were being used by the .active() method, which appears to be true in a painful number of cases these days (perhaps that changed since the apps were originally developed, but it seems that for at least one of them, .active() is true even if it appears nowhere in your command line. Changing to .user() adequately resolves the issue. commit 092677185780331f3014a8c84d6763b1ae9f08b7 Error message for using in:file:s improperly recommended using the -GTPase_pdb flag rather than -GTPasepdb (which exists) commit c4cd23627ecd734235ddf6216164c60f31025658 The chemically conjugated docking applications all required .active() to be .user() in order to run So, the ubiquitin docking applications use special input PDB flags because they involve two co-equal structures and use in:file:s etc. internally. In order to die if in:file:s, :l, or :silent were being used, the app was quitting if [flag].active() (which was always true, so it would quit) instead of [flag].user(). commit 0cd73f4579aa2d72fe554dde4bd6a1640afb0f4d Warnings Removal: removing reorder warnings from new membrane code to fix builds commit fc4c2bf2ced0d6a87c77677d4dac3926d047e4be WARNINGS WAR Z: Reorder warnings are now errors. Reorder warnings are bizzare; they happen when you initialize private data in a constructor in a different order than they are listed in the header file. I think this is a performance issue.... Besides removing the large number of reorder warnings, I also removed a mis- cellany of other warning types, though these are not yet errors, because there still remain a few hard-to-fix ones in each category. There are also a hundred or so unused variables out there still. Some notes: * The test server is full of bunk when it reports the same 10 errors over and over. Andrew Leaver-Fay's supposed unused parameter in the MMTDriver test was fixed, (else it wouldn't build, and it does). Likewise, Jared Adolf- Bryfogle's sign-compares have been fixed. Does anyone know how to get a fresh report of warnings? Something is not quite right. * Thank you for your patience in clearing some of these sneaky warnings. Thanks especially to those of you who recently fixed builds from errors-née- warnings that you may not even have added. * While removing warnings, I found some significant bugs in code; this is why we want to make warnings errors. Among them: - l. 441 of scoring/contraints/until.cc had if (start_res <= residues[x] >= end_res) which I changed to if ((start_res <= residues[x]) && (residues[x] <= end_res)) One can make such an expression in Python but not C++. (Also, that ex- pression did not make mathematical sense either.) - I left a comment note at l. 2534 of protocols/pockets/PocketGrid.cc; there were 3 lines of code that didn't really do anything, which looks like it is probably a bug and was intended to do something with an offset. Could someone take a look at this? * protocols/relax/AtomCoordinateCstMover.cc had some really complicated if statements that were throwing warnings because of confusing &&s and ||s; I tried to fix this, but could someone please double-check that I did not mess up the logic of the conditionals? thanks * likewise the confusing conditionals at l. 1179 of PocketGrid.cc ---------------------------------------- Unit test status: Pass Integration test status: 1 change, which may have come from my changes to AtomCoordinateCstMover -- looks to be minor numerical changes commit 3c4712c20d7be20e06876413b5699eb4a26cdc06 fixing an integration test output diff commit 4992ebdfe843adf68f6dd4902dfb24c958d926de Warnings Removal: last reorder warnings removed commit 4712188439a7248fb6c0d40895c789cdf9c36737 Fix the unit_test and pilot_apps_all builds. commit d0aa1016f6de3f9a773e656241d1ca70ae9fb20c Merge branch 'kalekundert/devel' of github.com:RosettaCommons/main into devel commit 43e3bba0c76479ea45a71efeb3f1ab2a0f43108d Fix compiler warnings that just became errors! commit 3bf9a17554c3f457e79a77dbdd85b388730bb304 Add some missing unit test input files. commit 0935b10e7bdd37bab2c085b84b19d32ac313c0b9 Warnings Removal: - 20 commit 7e03c25495b2abda761d02d35d15ad5735698d60 merge master into master - fix unit test build commit cdc3f107504e43aac52b9f320fe207ac5d2e4fcd fix unit tests I broke commit a7863107a182b9f7c402d1b1180734c9290783f0 Fix the performance of the refactored KIC code. The performance of the refactored KIC code never matched the performance of the original KIC code. This was due to an error in the way the fold tree was being configured. The problem is now fixed, but the architecture is no longer as clean as I would like it to be. I hope to push another commit which cleans up the architecture in light of the fold tree bug (and a few other things) in the next day or so. commit 313686ff238cda6214055bb5e3a95ac208c47007 Merge branch 'master' into devel commit 1eacf4f0729ce7328abf26433a7515545d5889a2 Updating unit tests script json output. Setting log as empty string for passed tests. commit b055d08dc486efe1679b435a96d784acb53e1b09 First part of sasa refactoring First part of sasa refactoring This is part one of the attempt to fix issues concerning values reported by the sasa functions in sasa.hh. https://carbon.structbio.vanderbilt.edu/mantisbt/view.php?id=323 [New namespace core/scoring/sasa] -All general functions for Legrand sasa from the old files have been moved (for now) into sasa/util. These general functions have been renamed, for example get_sasa to get_legrand_sasa, etc. -Sasa now has an abstract base class, sasa/SasaMethod; Code computing sasa has been integrated into a class LeGrandSasa. -General oo interface to sasa calculations is a new class called sasa/SasaCalc. This has been designed to limit incorrect uses of sasa radii in the future, but the methods can be used by themselves. Note that the factory class for different types of sasa methods is still basic and still needs to be finished. -metrics/simple_calculators/SasaCalculator2 has been added for the purpose of eventually replacing the old SasaCalculator. It has the same interface as the old one, with more values such as hydrophobic sasa, and relative hydrophobic sasas. This calculator uses SasaCalc for its calculation -sasa radii for the new calculator uses -sasa:sasa_radius instead of the old option as a new set of options are included for SasaCalc. [general changes] -SASA_RADIUS has been changed to SASA_RADIUS_LEGACY -SasaCalculator has been changed to SasaCalculatorLegacy [InterfaceAnalyzerMover] -IAM has been updated to use SasaCalculator2 using the default settings of LJ radii and all-atom-calculations. These can be changed back to the old values using the options -sasa:use_legacy_behavior and -sasa:include_hydrogens_explicitly false [current sasa using code] sasa files in core/scoring are still there for now and remain pretty much untouched. All code besides IAM have not been changed to use the new code. This will be a slow transition with both ways coexisting for some time. Next update will have code using functions in the sasa files to use equivalent renamed functions in util. These functions will use the new classes for their computation to limit code duplication. After that, files will be changed to use the new code and defaults on a case by case basis or however we decide on at minicon. [options for SasaCalc - usable by SasaCalculator2/SasaCalc/IAM] Copying options from options_rosetta.py for those that are interested: -sasa:method : LeGrand : The method used to calculate sasa. More will hopefully be added in the future.' -sasa:include_hydrogens_explicitly : true : Include hydrogens explicitly in the calculation. Explicit vs implicit calculations use different radii sets. These default sets can be controlled via cmd line. Historically, calculations included hydrogens implicitly. But its 2014 and we have hydrogens on our molecules. Some protocols may overwrite this setting to their needs. -sasa:probe_radius : 1.4 : Probe radius used by SasaCalc. Default is radius of water -sasa:include_probe_radius_in_atom_radii : true : This is typically done in calculation of SASA, and in fact is one of the defining features of SASA. Turn this off to calculate the SurfaceArea instead. -sasa:include_only_C_S_in_hsasa : true : Include only carbon or sulfer in hsasa calculation. This is typical. Only revert to false if excluding polar atoms by charge or everything will be counted as hydrophobic. Note hydrogens are dealt with automatically. -sasa:exclude_polar_atoms_by_charge_in_hsasa : false : Polar carbons and other atoms maybe should not be included in hydrophobic hSASA - though historically they were. Set this to false to get historic hsasa. -sasa:polar_charge_cutoff : .4 : Charge cutoff (abs value) to use on heavy atoms if excluding hydrophobic atoms from hSASA calculation by charge. The default is optimized for protein atom types (which excludes only carbonyl and carboxyl carbons. By default only carbon and sulfer are excluded.) -sasa:implicit_hydrogen_radii_set : chothia : The radii set to use when including hydrogens implicitly instead of explicitly. chothia=naccess. Acceptable values: 'chothia', 'naccess','legacy' (reduce does not work yet) -sasa:explicit_hydrogen_radii_set : LJ : The radii set to use when including hydrogens explicitly. -sasa:use_legacy_behavior : false : Use Legacy radii with all atom SASA calculation. This is a bit wrong as were double counting any hydrogens with radii that were optimized for a scorefunction that is no longer used. ---------------------------------------- Unit test status: Not Run Integration test status: 11 changed features and fold_and_dock changed due to atomtype extra parameter namechange of SASA_RADIUS to SASA_RADIUS_LEGACY all others that fail are using IAM in some way. Any reported values of SASA are changed as expected (by around ~10-15%). deltaUnsatHbond values reported are also changed - however, these -should- be more correct as the hydrogen sasa is now increased instead of being a part of the large heavy atom radii from the legacy radii set. commit deb691ae61047a4fc5f2d921379caf175d21c65b Warnings Removal: ~5 more commit c146dc0ee42dc131b0e14616c0eec6316ea03115 Merge branch 'master' into devel commit 0b6bb4b96ca655e4bf71a674234550cdd7e7d648 Warnings Removal: removed ~5 more warnings commit 4a63441dd04fe3ddb0465e46ce12f086942c2be4 Fix debug mode remodel integration tests. In Conformation::delete_residue_range_slow() setup_atom_tree() is called before the LengthEvent is fired, but after the residues are deleted. setup_atom_tree() can fire an XYZEvent as it updates residue torsions. For the remodel integration test, the PyMolObserver acts on the GeneralEvent, after the XYZEvent, so it sees an outdated PdbInfo object, as the PdbInfoObserver hasn't acted on the length event yet. Update Conformation::delete_residue_slow() and Conformation::delete_residue_range_slow() such that the length event fires before setup_atom_tree() is called. Additions to the unit tests to confirm event ordering. No integration test changes expected - only PyMol displayed info is changed. commit d7c4f778e98fd6b836bd29299d2356a120e635cc Warnings Removal: removed ~5 more warnings commit aff894287408f1970e42c268c6d98bf1b449bc28 Merge branch 'master' of github.com:RosettaCommons/main commit 404cc4ba8915876692dd6cb8ca3ec1735ce9a6b6 Commenting out failed span file loader test for now to fix ut in server commit c647cc776adf46b5158644a89088750d19eb688f Fixing library levels build commit fe3f2bb500a3536a404f10c7fa520f6dc4124611 Fixing header only build commit fd0d17ede956d2c04f15875f6643675c5b5e6d9d Fix debug mode remodel integration tests. In Conformation::delete_residue_range_slow() setup_atom_tree() is called before the LengthEvent is fired, but after the residues are deleted. Setup_atom_tree() can fire an XYZEvent as it updates residue torsions. For the remodel integration test, the PyMolObserver acts on the GeneralEvent, after the XYZEvent, so it sees an outdated PdbInfo object, as the PdbInfoObserver hasn't acted on the length event yet. Update Conformation::delete_residue_slow() and Conformation::delete_residue_range_slow() such that the length event fires before setup_atom_tree() is called. Additions to the unit tests to confirm event ordering. No integration test changes expected - only PyMol displayed info is changed. commit e5993a23b8a579ee70ad1485598a8a6b1c4140bc Warnings Removal: removed about 5 more warnings commit 9388ad7abb96f73fd06205b0f4ae16ae3ba4e523 Warnings Removal: removed about 15 reorder warnings as well as other types and set reorder warning to be an error commit 8f68e7334cbe5dad75fe768f8d15ce086ba4d582 Merge remote-tracking branch 'origin/master' into devel Conflicts: source/cmake/build_unit/CMakeLists.txt commit 8275bdf568d48b2ff4c4ec323b89d956e4d1bcc3 manually add sasa optionkeys commit 00fe0c5d19a0e21b8f4c10fcf848f9d1cc34d780 Tweak my pilot apps and analysis scripts. commit 8e3fdc589b255d821a24209c63cea3d037bbe3f6 add warning to sasa.hh commit 78ab9fa679c1b0fd273d867c145fe139e448968f RosettaMembrane: Membrane Protein Framework This push includes the code for supporting conformation of membrane proteins in Rosetta. All of this code was written by Rebecca Alford withh help from Julia Koehler Leman and Brian Weitzner (all Gray Lab). Additions: ============= New classes for storing membrane protein topology (SpanningTopology) New classes for storing membrane protien lipid accessibility ada (LipidAccData) New Classes for storing membrane protein and membrane associated chain embeddings Factory for calculating membrane embeddings in combination Support multiple chain embeddings and topologies Support multiple membrane chains in poses Membrane protein kinematics + conformation (membrane specific fold tree) Factory for loading membrane proteins (standalone for now, hopefully via JD2 soon) Fully reosurce manager supported code Resource Loaders: SpanFile, LipoFile, EmbedSearchParams, EmbedDef, MembraneProtein New Unit Tests: ============= EmbedDefIOTests EmbedDefLoaderTests EmbedSearchParamsOptionsTests EmbedSearchParamsLoaderTests EmbedSearchParamsIOTests LipsFileIOTests LipoFileLoaderTest SpanFileIOTests SpanFileLoaderTests LoadAllResourcesTest GeometryUtilTest MembraneResiduesTest EmbeddingFactoryTest MembraneConformationTest MembraneProteinFactoryTest New Integration Tests: ============= mpframework_integration.cc Test Server Status: ============= Unit Test Status: All Pass Integration Test Status: All Pass commit 2e47b34c053055cca55e33e0f3a6903dd732711a Adg changes to support error handling commit 73be8da5709f3b4c9936e21bf964884b9b0decc6 Fix debug-mode antibody_legacy integration test Antibody loop detection was using outdated neighbor graphs. Changed to update neighbor graph before use. Release mode antibody_legacy integration test change expected, as the neighbor graph being used has changed. commit 7fd92ba1837c2b18706241b811802ee14533a153 Merge branch 'master' of github.com:RosettaCommons/main commit 706e3adcad878a8e6be38a2a162dba30052deb44 merge master into sasa_refactor branch. commit 2c8ae5db7b3467ef81e4552eba96b9a0741e1452 Adding modified pilot apps to exclude database checking app for mp residues commit 66418a3d36b6523c0f9a91874d4daac697cfc31b regenerate options. have IAM pass around references to vectors, not the vectors themselves commit 931146e137e7c5d2da215062eaedbdfd151676a5 pulling from master commit f48820024507b14dc6c7a88de00235f50d3b0b97 Editing the XML-name of the NeighborhoodResidueSelector to "Neighborhood" from "Neighbor" which is less clear. commit 7d007230b22b133856c15a1ca1a2483c6ce914eb # [ONE LINE DESCRIPTION OF CHANGE] # NEWS: [DETAILED DESCRIPTION OF CHANGE] # ---------------------------------------- # Unit test status: [Pass/Fail/Not Run] # Integration test status: [Number of changed tests / Not Run] # [NAME_OF_CHANGED_TEST_1]: explanation of change explanation of change ... # explanation of change, cont'd. # [NAME_OF_CHANGED_TEST_2]: explanation of change #+BugFix [BUG_NUMBER] [LINK_TO_BUG] # Uncomment and fill in the line above to indicate this commit # fixes a known bug. commit f1656fc6d92358bcb98262ed9d883cb2bed26da3 Merge branch 'rfalford12/mpframework_master' commit eb47ea00798af6b7ace4392677a48e66b19f121b Changing an invocation of an option's "active" to "user" so that the protocol can run commit b5d5e78790f9079ca9d154d9c4dbab23760adcfb Warnings Removal: attempting to fix clang release and Mac gcc debug builds Can anyone explain why the isystem directive was ignored in the Mac gcc build? See: http://benchmark.graylab.jhu.edu/test/4439 The error was from an unused parameter in boost, even though boost is set as a system directory. For now, I just removed the warning as error for mac gcc. commit 5f777f5faa5e349c7e105bbee11498b7f36dff69 Warnings Removal: attempting to fix clang release and Mac gcc debug builds Can anyone explain why the isystem directive was ignored in the Mac gcc build? See: http://benchmark.graylab.jhu.edu/test/4439 The error was from an unused parameter in boost, even though boost is set as a system directory. For now, I just removed the warning as error for mac gcc. commit 3e8faec74738e18010d59fa83acb263711cefa7a debug explicit hydrogen sasa option and change defaults to keep carbonyl and carboxyl carbons in hydrophobic sasa calculation for now. commit 68299e99085a34a2772258971fbffe597c8f3a44 Removing mpframework integration from the test system for now commit 25c7bcecbbb7e2e3403352c8743d44939aa67728 Changing mpframework integration command file commit 605822a92ef8e4189a2658f95c706256d2312edd Adding missing copy files to protocol.test.settings for mp code commit ab2253331c487c09f716f6bc70906422b7f5757e pulling from master commit 75b700949aef76a4d6f3ba0de2042dd4853579ed adding NMer stuff to database/sequence and automated database path stuff to NMer score methods commit d20d9c18658ed03b98d7709e968db586cd7cacb9 Added unit test file copying back to core.test.settings - no idea how it got deleted commit ebe893c983b102fcd8f94b6c035d26f5c9fb4ab7 Merge branch 'kalekundert/devel' of github.com:RosettaCommons/main into devel commit 3bc65871712a2c45a3c0cff4fc2168f4310fcdab Setup chainbreak scoring with the KIC fold tree. commit 03f31f4be196a94064fee7a5391dee62e7640778 Merge branch 'kalekundert/devel' of github.com:RosettaCommons/main into devel commit 3558ec9b43a930318788ce8507a46df3fa7dbad2 Add PdbLogger to LoopRelaxMover It's currently commented out, but this will just make it easier to quickly turn on in the future. commit 299998b80f02c2a5f7f7c729afb102ecb5171bba Add KicMover.setup() This method is used to make sure the fold tree is setup at the right stage in the loop modeling process. commit e8a0ac624d7a9782e96a672782b6783e8b2c5170 merging in master commit d7f1884a4500b1c2608d3d886fa4d702fdaba8fd WARNINGS WAR Z: unused parameters now counted as errors This push removes ~150 unused parameters from function definitions and turns on the Wunused-parameter warning as an error. Notes: * This one is set as an error only in the debug builds. This is because some people like to use parameters solely for testing purposes in asserts. * Rocco, I attempted to change the cmake files by mirroring what you did in your last push. Let me know if I made a mistake. * If you get the unused-parameter error when compiling, it is the easiest one to remove. Simply delete the variable name from the fuction definition. ---------------------------------------- Unit test status: Pass Integration test status: No changes commit 79dfa449613fa57bff40e04cda43b1bad3ee8de4 Warnings Removal: set release mode to ignore unused-parameter warnings, as they are often used in asserts in debug mode commit 976d8552c4d56f73f8e512d6a209e07496a3547c Warnings Removal: now treat unused-parameters as errors commit 9186dbe7deb51d18cecf54b924a2ce89f2d79326 Warnings Removal: removed ~140 Clang unused-parameter warnings commit 8cd12c41efe5d0c6ebb69098991265df000f92cc Update default CMAKE builds to have the sign-compare as error This avoids the situation where things compile fine on your local machine with CMAKE, but dies on the test server. commit 4013ff52f6c778a0a068df90d0e4c2f94cd0b7c0 debug hphobic sasa in sasacalc commit e88bf69356fce3ac2a00dab52aa5ae94c96f3eb1 Warnings Removal: set release mode to ignore unused-parameter warnings, as they are often used in asserts in debug mode commit bd70b57465c624920834a632fc26484567618005 Bug fix for gcc build commit 9843f2bdcf1d6f67218ba60e358ecf64e3393803 Warnings Removal: now treat unused-parameters as errors commit 5cb096ff18179450b597f2dad785d49894471966 merge master into sasa_refactor branch. fix conflict in RSparser commit 1c22170d15a6bbc49ad67da5f76d658cf48cf939 add legacy option in sasacalc to help debug commit bb880e045007286cd4b99bd9c6c15d8c875939ec Warnings Removal: removed ~140 Clang unused-parameter warnings commit c5d0348ca515f45e5ddd383d5116302ae1ea0f44 # [ONE LINE DESCRIPTION OF CHANGE] # NEWS: [DETAILED DESCRIPTION OF CHANGE] # ---------------------------------------- # Unit test status: [Pass/Fail/Not Run] # Integration test status: [Number of changed tests / Not Run] # [NAME_OF_CHANGED_TEST_1]: explanation of change explanation of change ... # explanation of change, cont'd. # [NAME_OF_CHANGED_TEST_2]: explanation of change #+BugFix [BUG_NUMBER] [LINK_TO_BUG] # Uncomment and fill in the line above to indicate this commit # fixes a known bug. # On branch FotW/Weverything # Your branch is ahead of 'origin/FotW/Weverything' by 2 commits. # # Changes not staged for commit: # (use "git add ..." to update what will be committed) # (use "git checkout -- ..." to discard changes in working directory) # # modified: source/src/core/scoring/methods/SWM_RMSD_Energy.cc # modified: source/src/devel/sewing/FourHelixGraph.cc # modified: source/src/devel/sewing/ThreeHelixRepeatGraph.cc # modified: source/src/protocols/canonical_sampling/MultiTempTrialCounter.cc # modified: source/src/protocols/electron_density/BfactorFittingMover.cc # modified: source/src/protocols/pockets/PocketExemplarMultifunc.cc # modified: source/src/protocols/stepwise/enumerate/rna/screener/StepWiseRNA_BaseCentroidScreener.cc # # Untracked files: # (use "git add ..." to include in what will be committed) # # .directory commit 9248fd3b2409a73a281014dd8e684bccf6e7c60a Warnings Removal: removing 2 warnings from a unit test to fix gcc unit test build on testing server commit bf0ce7d3b5a59f650ca3702862f01a46ae4d5e7d # [ONE LINE DESCRIPTION OF CHANGE] # NEWS: [DETAILED DESCRIPTION OF CHANGE] # ---------------------------------------- # Unit test status: [Pass/Fail/Not Run] # Integration test status: [Number of changed tests / Not Run] # [NAME_OF_CHANGED_TEST_1]: explanation of change explanation of change ... # explanation of change, cont'd. # [NAME_OF_CHANGED_TEST_2]: explanation of change #+BugFix [BUG_NUMBER] [LINK_TO_BUG] # Uncomment and fill in the line above to indicate this commit # fixes a known bug. # On branch FotW/Weverything # Your branch and 'origin/FotW/Weverything' have diverged, # and have 1 and 1 different commit each, respectively. # # Changes not staged for commit: # (use "git add ..." to update what will be committed) # (use "git checkout -- ..." to discard changes in working directory) # # modified: source/src/core/scoring/methods/SWM_RMSD_Energy.cc # modified: source/src/devel/sewing/FourHelixGraph.cc # modified: source/src/devel/sewing/ThreeHelixRepeatGraph.cc # modified: source/src/protocols/canonical_sampling/MultiTempTrialCounter.cc # modified: source/src/protocols/electron_density/BfactorFittingMover.cc # modified: source/src/protocols/pockets/PocketExemplarMultifunc.cc # modified: source/src/protocols/stepwise/enumerate/rna/screener/StepWiseRNA_BaseCentroidScreener.cc # # Untracked files: # (use "git add ..." to include in what will be committed) # # .directory commit e8e47b79b59d4f29761d29658007e64c9dc3b44a Warnings Removal: removed two warnings from one of Jared's tests (This should fix the broken build on Macs.) commit e5a07e337baadf4a4b30d202ab38eb160f3f1470 Warnings Removal: removed two warnings from one of Jared's tests commit 949df90952063da67854b1be5bf341416d863e26 Warnings Removal: fixed Scons so it won't report warnings from external/cxxtest -- thanks, Rocco commit b7e4a1bbba974b3a58d918a4f31698455a6dbc53 debug hSASA commit 6a6c76e9d253e143cd22c2b881e14df82679fa39 begin debugging SasaCalc commit a1d984cf2f3a333dc34b3fb5036f471c49e81039 change sasacalc use in IAM to sasacalc2 commit 1124da43d1b63746e81faef84cd1c68e2bf06780 Updating integration command commit d1a765441153b6c4a556fdf04d6cf133eaccae3b Return the low energy structure for loop modeling. This is as opposed to just returning the endpoint of the simulation, which might be much higher in energy than the lowest energy structure found. commit 9bcedbd00f41c14addde574ec7feec42060f534b Comment on why a custom fold tree is useful. commit 49dcd54b11155af8b1ecbb0c33e3b99977717fd0 Merge branch 'kalekundert/devel' of github.com:RosettaCommons/main into devel commit ab9c8e6c6173bac6cf8d5208b543d887e18248af Switch back to using a custom fold tree with KIC. commit d66f1867b745e259db6b5f44208faa1162520b67 Merge with origin/kalekundert/devel. commit 1c98641b960ba7bf5760a01817c897c4ccd3fe38 Tweak the pdb preprocessing script. commit 283283bf0befed3f4846ca45418734510ea8d659 Add fold-tree unit tests for KIC. commit b1882e48b41acd6183fc7902bc5e4dc16dcb3407 Merge with /origin/kalekundert/devel commit e41da251ba4ff38e49649352a4d70d3c27856e34 Make numpy_cache use a large blob type. I also added a check for numpy arrays that are too big to cache in `helpers.py', so that the scripts will crash gracefully if I ever use data that's too big in the future. commit e233b947d3877bce89db25b02f38ddc36b5effae Update the options system for refine_kic_refactor. commit c3a3c664576b186aca2ef6cfe42a6d328d7c4b8a Use refine_kic_refactor instead of refine_kic_v2. Just a quick bug fix. commit 209dc99240b924a25e1c78294c22a19fefd5cdc2 Merge with origin/cmake/one_script commit b385ced62ab6bc9393cef8b86f39e4ee61918aae Rearrange when the cmake modules are included. commit a56d43dff095392c51e19cb8ea0dcc218d2cdb48 Merge with origin/cmake/one_script commit c1f55e129508da8529015b546471f9eca4b10731 Prevent useful cmake files from being ignored. commit f155b2cba95c6e3674bb53be88c53f0d4cd9d3a0 Merge with origin/cmake/one-script commit f2f2e1b2e112d05b2ad64fa35fee43f40a18d016 Add some files I forgot about. commit 771659799dc20dfd6183ccc9aa63aaa33c915e77 Merge with origin/kalekundert/devel commit 1c3edcd096ab0815bba5d552d9374ce5c7e74aa5 Make native_ensemble compatible with MySQL. commit 3d5b9e78e4cd016103996f2d0aec62cf55ba14b2 Add a branch option to make_new_build. This makes it possible to create builds that are specific to the current branch, which makes it easier to work with several branches at once. commit f3429c79dd174ad556853adb1c0d18ff20bd4eb7 Create a unified cmake build script. commit d84f50376d9f5b7f5adc161cb02a120259c2fbae Add a branch option to make_new_build. This makes it possible to create builds that are specific to the current branch, which makes it easier to work with several branches at once. commit 4710e8b54fccb4d3f97cd5e999ef3bbe5dc9b922 remote master pull commit 3ab3777a02a5fc10ddf70a92d5f8b866da737e1b fleshing out InsertionSiteTestMover to relax pose after intitial insertion and do a bunch of analytics. also adding an rms utility that allows comparison of poses of different lengths via a sequence mapping. no test changes on my machine commit cf94e97fa1f1e37ebc847ee8327accc7f7ef3cc1 Move partial_thread app to public Application is needed for the published RosettaCM protocol. commit 03cb359e8f9767e98a87b6519baddf1e46f55fe6 Tweak native_ensemble analysis scripts for MySQL. commit 91b286e047dd85d900865aab73dc332e99064296 Create a unified cmake build script. commit 17340089b543f39914d06c0c3dc272fe3a6a47d6 PyRosetta. Moving and renaming python version of protocols.jd2.DockDesignParser to protocols.rosetta_scripts.RosettaScriptsParser. commit be376b21ec2d31131a6f8c00fe32019cbc3f94c0 merge master into master right before about to push commit 0428435f7d3be58e53362840416887bd9e0d6b6d fix -interface parse_my_tag in IAM. more state bug fixes" commit 1e4b2b7a48c7e4b50ea21789761bcd467550aa37 fix remaining inconsistencies commit b41c0e6d1ba82bc9f3b0e0dd4ad414d104b83622 PyRosetta: changed version number of init() commit cc9655d013f457cc6f1e5cf11e32fd7096ccc97b Modified the displayed version number on init() commit 8da5dae083462b38a1af61979c1cfbaf0b881940 skip calculation of IAM data if no interface is detected commit 73be45c653dbe686dbdf3104b88e2dc6d9806e4e make sure to skip calculations if no interface is detected. commit 67b9ae7694c77a684509767f166425471e483db1 PyRosetta. Commenting out code related to DockDesignParser until I figure out what happened to that class in C++. commit 94301380c76299498d5e0c9d17a6db807fad1b27 remove overwrite of jump in IAM commit b1cbab41b8b221193db2b6dfedec3b8028183bf2 Carbohydrates: parameters for fucose and new int. tests This push introduces a miscellany of sugary things: * Virtual atoms now align properly. * There is an integration test for CarbohydrateInfo.show() output. * Old carbohydrates integration test renamed to rings, since that's what it really was testing. CarbohydrateInfo.show() tests named carbohydrates. * CarbohydrateInfo.show() is no longer unit tested. (See above.) * Fucose has been added to the database. This sugar residue is very important in real-world cases. * MMAtomTypes were added to several sugars for testing purposes. mm_std runs, but it returns NaN for 2 of the scoring terms. * A .pdb file for Lewisx was added to the testing system. ---------------------------------------- Unit test status: Pass Integration test status: 19 changes carbohydrates: expected rings: expected hts_io: did not run in ref or new swa_rna_gaga_O4_clustering: looks to be unstable all the others: output change as a result of my uncommenting the OS MMAtomType commit 086cdb29092e35aee1865c5a037d0b4251ab0ffb Carbohydrates: parameters for fucose and new int. tests This push introduces a miscellany of sugary things: * Virtual atoms now align properly. * There is an integration test for CarbohydrateInfo.show() output. * Old carbohydrates integration test renamed to rings, since that's what it really was testing. CarbohydrateInfo.show() tests named carbohydrates. * CarbohydrateInfo.show() is no longer unit tested. (See above.) * Fucose has been added to the database. This sugar residue is very important in real-world cases. * MMAtomTypes were added to several sugars for testing purposes. mm_std runs, but it returns NaN for 2 of the scoring terms. * A .pdb file for Lewisx was added to the testing system. ---------------------------------------- Unit test status: Pass Integration test status: 19 changes carbohydrates: expected rings: expected hts_io: did not run in ref or new swa_rna_gaga_O4_clustering: looks to be unstable all the others: output change as a result of my uncommenting the OS MMAtomType commit 1c4d90f87dac707258ff95248b4f8554de6c0bbc fix bug in IAM where it was saving state on data for > 1 output nstruct. Thanks to David Nannemann for identifying and helping to fix the bug. commit 40c63daaaa8ee18220d00841640e8cbb1d19b3d1 reinit for each job and input in both IAM and IAM app wrapper commit 62f25a47f4fbfe6fc7b8f380633b1e03d1d3b1a3 Carbohydrates: restoring pilot app to integration testing version commit d8abd45abc85371d3e2be9d87758b03cd2d0fe3e Carbohydrates: adding 3-branch.txt to patch system commit bcc5f0bf19082d5ad5e81770b6f5327f18c64ef6 Carbohydrates: added Lewisx .pdb file to testing system commit cbea5c8981bd44145089fd8b5531ff7a753a4b7c Carbohydrates: .params file bug fixes commit cd7ec60a6057cf55cea0349dbd4910dbbe8ca94b helix cooperativity bugfix - mismatching enum types commit 7493a3660490b0071e8dcf548a6d7763dd9fa5bd Benchmark2, adding score and library levels tests. commit ed7097ead0fcfa914c43216907958a4be8c42521 Dummy commit to trigger test server run commit 4e5dedabf30ec7864c4ade4806e0c243d20eebf6 Adjusting defaults for ‘extras’ option in score test commit c4ef957469cff95a8e31c5e86218e5657c7ce988 Restoring documentation index.html that was accidentally got removed with handwritten docs. Relocating it in to src/ to reduce source dir clutter. commit dbe63e995d478dd6187d8c05ef1cc5af12bc5e55 Fixing score tests for case when “extras” option was specified commit ae4f2f8a9bb49ede26d06ac9f205fe187a98d6aa Forgot a header. commit f821ccd2d7def35f87ba0d7d4826b55d2022a9a2 Carbohydrates: added mm atoms types to Gal and added Fuc commit 417a7fa7a1d69f847a14762f84232ba4ebf311f9 Carbohydrates: adding Fuc to accepted abbreviation list in database commit bc7c328829cd6206ef952fb8b39fb22a2eb213bd Carbohydrates: removed unit test that is now tested more appropriately with an integration test commit fdfbdce6d04fc6f8e1019b912ad5a8d381fabd01 Update doxygen for missing doc directory Remove doc directory from Doxygen setup files. Add in new mainpages, tailored to code-based usage. commit cbf7e8201a1b0578bc92a158c993a2a6775b33ea Change update_options for missing doc directory. Place the autogenerated options lists in src/basic/options/instead. Also regenerate options. commit 0d1e2c6e454102b9c68ff994d1ca674f8b510616 Update native_ensemble to support MPI. Some of the analysis scripts also had to be updated to support some of the additional information I'm now outputting (i.e. temperature). commit 65c087f6376ac64580480ce33f64b675a03797e5 Fix lingering bugs in canonical_sampling. commit 7c0674e4dfdcc5e873df8ec21f8390d822a969a7 Merge branch 'master' into benchmark commit 9529b057d9d41b36c9ba6101c7db64469316c379 Benchmark Score test: adding missing database flag commit e234b57c86607be61735e3f24e1fa4b6bc83d90b Removing hand-written doxygen documentation from the source code. All future documentation should be written to the gollum wiki. commit 43215ac05b2bba9c3fda1233996fd37001d7253a explicitly reinit needed InterfaceAnalyzerMover values as some protocols may use multiple applies commit c614d886493670655297baa5390150aaecc60a06 Carbohydrates: new sugars integration test commit 8cc5797f37f8af5967f28e19748bf38f00c158a8 fix IAM saving state for some data when used with app interface. commit 4610162706d556652a0c21479e8dfa5de179a437 Adding score function fingerprint test commit 47f13948cef3eb85de28e7569fa8b0f12a477632 Adding library levels tests commit e221c6fa1d45d70dc95d5e5547b0ff9dfb6d002d PyRosetta. Fixing build, increasing boost max function arity to 32. Adding bindings for Rosetta sqlite3 classes. commit 8642b33e9e5b96ccfef809a7bf662ce7a538c874 Carbohydrates: uncommented code for aligning OY and HOY virtual atoms in lower sugar termini; new main chain definitions seem to have fixed the old virtual atom tree bug; woo commit 71f86ec287e7e4a7fde067b2215f76a50d179e0b Merge branch 'origin/kalekundert/devel' into devel commit 6d80cc7fa85a68e655f0e1060b6a4103d5ba5bbc Rename ParallelTempering to MpiParallelTempering. Did the same thing for the HamiltonianExchange class. This is a prelude to making a serial version of the ParallelTempering algorithm. commit 7622649400eb3433a38a42e5051e6e46cf7d0bf6 First attempt to fix the pilot_app builds. I commented out the entry in pilot_apps.src.settings.all for the pilot app that wasn't compiling. commit 9615c4a1d8fb6660af5d9198e1db0706afdf3732 Fix another warning. commit c3239ca677f9eb94ed5c5030e2eaa4b779fdf798 Merge with origin/kalekundert/devel commit fc85ae86cfece0e1f2bdd157afc334581b487f0e Fix some more warnings. commit 12d300f7becdd4203870a82ba142d0e2b9454b68 Merge with origin/master commit 23574cf364aade03375bfa8969157ee91924e8ee Fix some warnings. commit ddbff17ecdcb5bfdd445318ac7426912b067aaa6 First attempt to fix build. commit 39540cfbf3bc9b04238cc941087295a06d0fc1fe Fixing the header build commit ed4aad89a85c4ca831c32039147d1e494ce4e1a0 trying to fix header only build commit 7bd3e07f9ad8db09b2637d23e3d7199ebad575ec Document and clean protocols::canonical_sampling. This commit adds thorough API documentation for most of the classes in protocols::canonical_sampling. Some modest refactoring was also done, but for the most part changes were kept inside the namespace. The biggest change outside the namespace is that MonteCarlo now holds a TrialCounterOP instead of a TrialCounter. This makes it possible to plug different TrialCounter subclasses into MonteCarlo. The metropolis_hastings integration test is expected to change because some additional move statistics are now reported. No other changes expected. commit 708f0f5f7b80bbeff9ef8b2d385118166074fb0f Add more documentation to canonical_sampling. commit 28e45a076d9d8f177883c2e127ba2a7fcbddcb4e Modified readme slightly for test commit 773dce5dbc1ee638d3fe83abab55db08a3d7cb27 Carbohydrates: debugging mm_std results commit aee64d176efd365fc3eb00bdadbb39ce5587d170 Merge branch 'master' into devel commit 3ca839896105c43a45ca1c3ff39fc677c01430b4 Make the MonteCarlo TrialCounter swappable. This commit also adds MultiTempTrialCounter, which derives from TrialCounter and is capable of simultaneously keeping statistics for many different temperature replicas. This counter can be simply plugged into the MonteCarlo class and used in the canonical_sampling framework. commit fff062a39bc365c4039b09418eaec8d5e837fcde This is joint work from Rocco and Steven. Lots of this code is ported from the Biochemical Library (BCL) made in Jens Meilers lab. Adding 100+ element types to Rosetta. Removed molar_mass and molecular_mass from all files and replaced it with mass() (really, that was just confusing) Removed fa_standard string from files loading element types and replaced it with "default" string (there really isnt a difference between centroid/fa elements. an element is an element) That being said, you can still add your own element types, if you have a burning desire Added new information to elements, vdw radii, electronic configuration, mass, group, period, element number Moved elements object onto the Atom data object added operator= and destructor to Atom class Added gasteiger atom types and atom typing to Rosetta Added methods to determine gasteiger atom types and atom typing to Rosetta Added gasteiger atom types to Atoms (default is set to null) ResidueType modified to hold new atom type information (default to null) Added extra information onto Bonds.hh to help determine gasetieger atom types Unit tests were modified to account for the new mass() function (really, only one place used it, which is our lab) Unit tests modified to call element_set("default") All unit tests pass Integration tests fail (I refuse to commit anything that wont change the integration tests change...I have a track record to keep): swa_rna_gagu_05_clustering (this changes when you touch residuetype) pH_mode (cosemetic changes) fold_and_dock (reports the new elements) molfile_to_params (added formal charge, cosmetic change) commit 0bfcac16d9f2157c04563e4181b3def0894f6108 Final fixes commit 1afeee04ba8ea2e53818588f467e32fce612484f pull commit dd84627ae131b7aeaed27ae9d47450bc12e82860 Replacing fa_standard with default for element types. commit 365f3499ea28055e6e28fc1ffe2271bd3f1c1989 merge master commit a8de77453542f79bf5ec6a703ba62f999e5587e2 added use_sidechain_neighbors commit 0d7ee8ba15ae3912e83fca786b28fc7353c51861 Changed the RigidBody transformation in xyzTransform to correctly center the coordinate systen on the origin before performing rotations. commit 8584e6b1e40f7850eee0c3b780cd3a7890c200eb Changed the RigidBody transformation in xyzTransform to correctly center the coordinate systen on the origin before performing rotations. Added ResiduePDBInfoLacksLabelCreator class definition to ResFilterCreators.hh to fix a declaration error. commit 0e3d2b5e62e8c678742563051477906c400388df Tweak the native_ensemble app. commit 99cbc04107579e392134c4d1d86f2b5b23bce3ad Comment on TrajectoryRecorder.update_after_boltzmann commit 69d105049efc109c61e15e7f11a45112aa58b26d merged in master after adding use_sidechain_burial to layerdesign commit d93fa922773453856f0f82f11ad1e642e03d2883 added use_sidechain_neighbors flag for LayerDesign commit 534d975c357b036a2d6d28e76bd05b4b9125b90d fxinging duplicated code commit 12ad3008fcc87447a6aee19160b6fa1c11cb3602 merge with master commit 35b57dabdb8296adea8b3cdb5a01d033beec2ce5 replacing all instances of element_set("fa_standard") with element_set("default") replacing all instances of moleclar_mass and molar_mass with mass() commit 7c0d8f4f084ed93020c9471a48cfa79e4dae0308 Fixing compilation issue commit a8ad4a8f51d68a9fbae7f54504c1fee36a9bb097 forgot to pull commit f8b6443887b7a1ded01686dfd3c063cb49f0c023 initial checkin of all changes made as per discussion with Rocco. No idea if it compiles or not commit f6bc2567ec1408f5e4d07d2c6abcdf81c338c44e small chagnes to unit tests to reflect the changes in molecular mass commit 399a5f30903eb33de152de67b62351c36249203c spelling errors...fuck commit b37c6847c8ca38cb03862c31cfff068d60b01718 Fixing unit test build by commenting out tracer stament in ring_detection. Changing protocols/md/CartesianMD.cc:243 so that mass look up is based up on the element type from Atom.hh commit 7bc491b38adbbcd4937c2ced6ca3c59d1f71f49c fixing typo and build error commit 2cf97ec8a6cfea15d58fce7cc47f1d03e5257acd Adding an element class to the constructor of atom. Elements are now accessed through the atom class commit f4b15f2370cfbab6fa87f63c60f3937a561c3dce cleaning up some comments from residue io commit f96690bf7f88fc09eb2715c6b1b465f00783fc16 Merging with master commit 4273d9c16ad04ea8aab5afddcc9cc630c9dceda2 I accidently erased shadow atoms from residue io. adding them back in commit d59e3b13d32b8a788e279f7ad5ac826b8553d5f2 fixing dependencies when using an owning pointer as private member data commit 13fe34ecf9ac81fa1cfcd57b12a0a5301f112113 Carbohydrates: turning unit test back on commit 7f1e0c7b5fe74bcc3901830212312a63a5dc2059 Small and Shear moves should skip rama check for residue types that have aa_unk Unit test status: [Pass] Integration test status: [Pass] commit edb20d55211d5b0d3f2adf28ad5caf5ed47b1562 Carbohydrates: adding virtual atoms to Neu to remove unfound DoF complaints commit aafc28b8d77c85ec5d5378a1bcbc505bc91365ee Merging density mover bugfixes commit bf086e7b67e960696f93d56a7c2193f42d65e2da Bugifxes to some of the density movers commit 88d589ab6ffef85040a2e76414892dfa6b89a0fa fix unit test compile commit 509221d83a77aacd77f29e35295603d50cb8fb7e Eclipse: adding style sheet commit 9a988a476e1c308c0458fb02931a49f72b8b5d88 adding unit test fixes commit a7eb45534d5ae4e19dabe1a741aba2efcd62b2f2 adding the actual directory and files for gasteiger atom types! commit 83cad2787b77e0e6c5cf81d0c29ac5ed9db4d6b2 editing file to include gasteiger commit db200f34e36c844f0662be8b790f6eb704cf8e42 renaming unit tests from bcl to gasteiger commit d0d4501de927efa5d7c88e83780c2ccc0594e219 Merge with master! commit a3fbab3a7d68085564575417418b89e135867990 Final file changes of bcl to gasteiger commit d2d01ce70e5b28cf135386143cf9c4bbcc38917c Fixing PyRosetta build. Removing declarations for undefined functions. Removing redundant const for returning VD values. Adjusting PyRosetta build script to pass ‘VD const &’ by value. commit 1ffcff4da7b2823c8e468d55148fe19672a03d15 Various documentation updates. Formatting fixes for doxygen documentation. Also, transition some overview documentation files from the Rosetta3.4 release which never got commited to trunk. These changes are in anticipation of the upcoming doxygen->wiki conversion. commit bdaa3fd499982ff687c1f659ebb4b35d17a97a64 Update score types doc for talaris2013 commit ec97120a9f433d8d69086b82917846373c858ac4 Add documentation from the Rosetta3.4 release This is documentation that Eran(?) put together for the 3.3 and 3.4 releases, which never made it back into trunk. Add them to master now, in anticipation of the upcoming doxygen->wiki conversion. commit 0ef95cda6844147421250b75d216e7d55af9e4d4 incremental push, just to make sure everything is in before going home commit ab0198d020a69dee4e2a733d4083df9b27547309 Refactoring bcl element so that it is now the main element file for Rosetta fixed pilot app so that it works with the new scheme commit d2ed558cf34bc128df656e03102f9b672a587a04 ResidueType: redefining main chain for all bu NAs commit 13d4ceba25b6f96489fcae593a7866b49dfd43f1 ResidueType: NAs use old shortest path method for main chain; all else now use .params def commit 2faf9dfb7f78b2753e6d5b842bb0b665c66036d0 Pulling most recent version of master in balej/testing. commit 7abe7d0bafa3d79f39d819d10f931578a874f10a Move protocols::jd2::DockDesignParser to protocols::rosetta_scripts::RosettaScriptsParser for clarity. Cosmetic changes to tracer names in integration tests expected. commit 86fe88e9f778d6f80ccd280ce160d442c9b095d1 Move protocols::jd2::DockDesignParser to protocols::rosetta_scripts::RosettaScripts parser for clarity. Cosmetic changes to tracer names in integration test expected. commit e105b3405ac5f7cedc66b1819e5fd22725462901 Pulling changes from origin/master into balej/testing branch. commit e9e44c2c7f961823cd84be1139b95dd583eca710 Try #2 to make version.py not dependent on Rosetta directory being called main I shouldn't have tested the first version in a directory called main... Still no test changes expected commit c2cf9083e5dcb357cbf558edeef9bfde84e389fb Removed get_resnum_to_subunit_component function from core/conformation/symmetry and moved functionality to core/pose/symmetry to fix error from symmetry_multicomponent integration tests on cases with TER in the middle of a chain in the input pdb. commit bc4692869cef0c9d119a2ca1f11b150419c8b5ec Lots of changes to ResidueType, see below. All unit tests pass. Integration tests fail in release mode, but not in debug. If your test fails and you are concerned, email me or the list. Changes to ResidueType atom data: Primary data in ResidueType such as: atom_base_ abase2_ chi_atoms_ nu_atoms_ mainchain_atoms_ nbr_atom_ actcoord_atoms_ cut_bond_neighbor_ atom_shadowed_ are now changed to contain vertex descriptors (VD). This means that during atom ordering, they do not have to be re-ordered (VDs are always up to date!). The data types that store this information are now a mix of maps and vectors. Because data lookup in maps is slow and the fact that Rosetta relies heavily on accessing this data based on an atom index, I have created cached versions of this data. The cached data is now generated after setup_atom_ordering has been called (see below). Changes to finalize(): finaliaze() no longer needs to create an old2new mapping. See following function changes for reasons why. Changes to setup_atom_ordering(): These changes are made to remove the need for having the delete_atom_ vector which keeps track of the deleted atoms. Since deleted atoms are removed from the graph, we can just iterate over the graph to create the atom ordering. Also, force_bb_ now contains the vertex descriptors that define the back bone. Because some new heavy atoms are added and removed by patching we need to reorder the atoms. The atoms are reordered with the backbone atoms coming first, sidechain atoms second, and finaly hydrogens last. The graph is iterated over, where bb atoms are defined by the force_bb_ map. If a hydrogen is encountered, it is pushed into the hydrogen vector. If the backbone is not found in the force_bb_ map, then the atom is a side chain atom, if not a hydrogen. During this process, the attached_H_end and attached_H_begin vectors are filled out. In order to keep the bb hydrogen atoms first in the hydrogen vector, only the heavy sidechain atoms are assigned to the sidechain vector while bb hydorgens atoms are pushed into the hydrogen vectors. After the bb and sidechain vectors are assigned, the sidechains are iterated over and their hydrogens are pushed into the hydrogen vector. Finally, the ordered_atoms_ vector is filled out with the bb atoms, sidechain, and hydrogen atoms. reorder_primary_data(): Now named generate_cached_data() Because all the primary data is based on VDs of varying data structures and Rosetta relies on atom index to access data, the reorder_primary_data has been changed to generate cached data for quick lookup. So, things like atom_base_, now become cached_atom_base_ and the function atom_base(index) now looks up data like so: cached_atom_base_[index]. AtomICoor, OrbitalICoor, and ResidueConnections: New private member data which stores the VD was added for these classes. Previously, they had relied on atom index for lookup in residuetype. Now, the functions that assign the atom index are now assigning those based on the vertex descriptor, because VDs do not change, however, the atom index does (the whole reason why we had old2new). chemical/Atom.hh: Previously, Atom.hh was a somewhat undefined class that contained things like atom indices, bonded atoms, atom bases, abase2, etc, etc. I have tried to unify what Atom.hh actually is. In doing so, I have tried to keep a separation of the "atom" and the "residue". This means that I moved the bonde atoms, atom bases, etch etc out of Atom.hh into ResidueType. Atom.hh now contains information about the actual atom, such as is it a hydrogen, the atom index, so forth so on. This allows for things that are set in ResidueType to rely on the actual atom and moves away from just having one atom type set. Eventually for ligands, we would like to have different atom types, but these atom types should share certain features such as whether or not its a polar hydrogen, aromatic hydrogen, etc, because the Rosetta scorefunction looks at these things. Atom.hh is still a somewhat experimental class and will probably have things added/removed from it. commit ca647de84a0a4038f085980171bcd4988fbfa694 Removed need for Rosetta's top-level directory to be called main for versioning to work This brings back versioning capability to we heathens who stray from the orthodoxy of "main" May our souls find peace Cherry-picked from my dev branch commit 2e5d086 No test changes expected commit dc94a230b9b29180b7738ce6f54f3f65eada1f41 Lots of changes to ResidueType, seen below. The comments in ResidueType have been changed to reflect these changes. Most important are the changes to setup_atom_ordering() and reorder_primary_data(), which is no longer called. All unit tests pass. Lots of integration test changes in release mode. However, if these tests are ran in debug mode, they are not changed. If an integration test changes that you are worried about, email me or the list(I have tried to catch all the test changes that were not expected.) Changes to ResidueType atom data: Primary data in ResidueType such as: atom_base_ abase2_ chi_atoms_ nu_atoms_ mainchain_atoms_ nbr_atom_ actcoord_atoms_ cut_bond_neighbor_ atom_shadowed_ are now changed to contain vertex descriptors (VD). This means that during atom ordering, they do not have to be re-ordered (VDs are always up to date!). The data types that store this information are now a mix of maps and vectors. Because data lookup in maps is slow and the fact that Rosetta relies heavily on accessing this data based on an atom index, I have created cached versions of this data. The cached data is now generated after setup_atom_ordering has been called (see below). Changes to finalize(): finaliaze() no longer needs to create an old2new mapping. See following function changes for reasons why. Changes to setup_atom_ordering(): These changes are made to remove the need for having the delete_atom_ vector which keeps track of the deleted atoms. Since deleted atoms are removed from the graph, we can just iterate over the graph to create the atom ordering. Also, force_bb_ now contains the vertex descriptors that define the back bone. Because some new heavy atoms are added and removed by patching we need to reorder the atoms. The atoms are reordered with the backbone atoms coming first, sidechain atoms second, and finaly hydrogens last. The graph is iterated over, where bb atoms are defined by the force_bb_ map. If a hydrogen is encountered, it is pushed into the hydrogen vector. If the backbone is not found in the force_bb_ map, then the atom is a side chain atom, if not a hydrogen. During this process, the attached_H_end and attached_H_begin vectors are filled out. In order to keep the bb hydrogen atoms first in the hydrogen vector, only the heavy sidechain atoms are assigned to the sidechain vector while bb hydorgens atoms are pushed into the hydrogen vectors. After the bb and sidechain vectors are assigned, the sidechains are iterated over and their hydrogens are pushed into the hydrogen vector. Finally, the ordered_atoms_ vector is filled out with the bb atoms, sidechain, and hydrogen atoms. reorder_primary_data(): Now named generate_atom_indices() Because all the primary data is based on VDs of varying data structures and Rosetta relies on atom index to access data, the reorder_primary_data has been changed to generate cached data for quick lookup. So, things like atom_base_, now become cached_atom_base_ and the function atom_base(index) now looks up data like so: cached_atom_base_[index]. AtomICoor, OrbitalICoor, and ResidueConnections: New private member data which stores the VD was added for these classes. Previously, they had relied on atom index for lookup in residuetype. Now, the functions that assign the atom index are now assigning those based on the vertex descriptor, because VDs do not change, however, the atom index does (the whole reason why we had old2new). chemical/Atom.hh: Previously, Atom.hh was a somewhat undefined class that contained things like atom indices, bonded atoms, atom bases, abase2, etc, etc. I have tried to unify what Atom.hh actually is. In doing so, I have tried to keep a separation of the "atom" and the "residue". This means that I moved the bonde atoms, atom bases, etch etc out of Atom.hh into ResidueType. Atom.hh now contains information about the actual atom, such as is it a hydrogen, the atom index, so forth so on. This allows for things that are set in ResidueType to rely on the actual atom and moves away from just having one atom type set. Eventually for ligands, we would like to have different atom types, but these atom types should share certain features such as whether or not its a polar hydrogen, aromatic hydrogen, etc, because the Rosetta scorefunction looks at these things. Atom.hh is still a somewhat experimental class and will probably have things added/removed from it.Changes to ResidueType atom data: commit ae937fbdf48f2536beb5f66665d77b1f2c2c7175 lots of residuetype changes! commit a6f09039d772d86ee04f8b2ceb0aac25b1901e96 renaming cached_* to *_indices. Try to fix indentation problem. Add comments commit 5432e78624663d522c6aa5c060839e418f4bf119 comment and variable name fix for clarity commit 7a3b6599a2c73c904539a285432498f49024572d added another HBS dihedral constraint For some reason, it takes a bit of persuasion to ensure that the HBS atom HYH remains anti to the hydrogens on CZH. Not a big deal, but maybe helpful to codify. commit 954e90a657077d209d0e56bc56b0d7e359821b23 added another dihedral constraint to HBS commit cff9508fbc7d7fe0fb993840c0187a9740a31d8f Added symmetry utility functions and removed from matdes/util, removed matdes/util and RestrictToNonZeroSASA because not longer needed, and incorporated updates to SymDofMover (including from Will Sheffler) and associated in:file:t option. commit 23df0f8dec322f7af37fd71b42e44ed7af82426f bug fix commit 01e024d8a5a64de18c6c166dc7a338914c2738d3 Revert "Modify the O4 type in RNA such that it cannot form hbond" This reverts commit 1a628ef59bcc62e5abfdfa89c1ae47dcd41a11b7. commit b40f8d548f9123e064c908d74312dbaeebcf1106 ResidueType: changing way main chain is defined for carbohydrates as test commit 17e4007926869522826ca8e6f6c474f2dc83d847 Updates on RNA atomtype of O4' such that it does not form hbond. Modification on cluster.cc. Merge branch 'fcchou/devel' commit d992765b10cba5537024ee878bd6d68d12e72c7e Make cluster.cc codes better follows the options semantics commit d4bbd0d67be14dbbbcf656475ef2e71b31ee60fa helix cooperativity - scale hbond_sr_bb weight according to length of helix commit bea819390be7578dff241db2164b87aeb388620e Updated translate_ligand function in Transform.cc to include a random initial rotation from 0-360 degrees in addition to the specified initial translation for sake of benchmarking commit 1fa8c78d7a40249bbe87ed1ebae68d89120144ff added the task operation DatabaseThread commit ffac35da3cdabd22084509fbcc4433a7e97c6d0e added TR for final sequence before threading commit 4adf423c43c450e3e025fc39356be6c002391c70 PyRosetta. Disabling wrapping of protocols::neighbor::Neighborhood (function pointer in constructor). This should fix PyRosetta ScientificLinux build. commit b4e45ace0eb6e25a88160f19580e38a7630b660f Turn off warnings on external headers. Add SYSTEM directive to CMAKE files for external/ directory include headers so that gcc & clang ignore warnings in those headers. Also add external/include/ directory to the scons changes made by Doug & Matt (4efc2437 & d669c1a8) such that non-boost headers (e.g. Eigen) no longer pop up warnings. Changes compile on my system. Hopefully there'll be no test server issues, as 4efc2437 & d669c1a8 should have troubleshot all of them. commit dea7756c76601d5b1bb5440a2439708dc659efad housekeeping and debug TR messages removal after the task operation works commit 3d4c5b4183dc093ae70f28409a45915bf25697a2 fetched master commit fb0bb3f916b1be76827b6032aec68242f0faef26 fixed bug in DisulfideEntropyFilter for when one disulfide is entirely contained in another commit 1b2051ad4c7ca9057fb8419280fbacd96d193a95 Benchmark2. Updating integration script, adding command lines for compilation and test-running to the logs. Increasing test timeouts for debug run. commit 4cafd9c1786bb41622c0406c2ae9092bbef67e27 change orbitals to orbitals_talaris2013 in Toolkit commit b99cfb7829bb5a623e98f26dc77dadedb397ea21 more bug fixes commit d1fdb9b72bcfb41983ab57db98e4edb7055da930 fixes commit a54de30e0dafdab28716d832c48da0aed02123d1 troubleshooting commit 9526c06daf465439a3296da06581b1c8953d68d1 Merge branch 'justinrporter/silentstruct' Implement a generalized SilentStruct::fill_struct. The new SilentStruct::fill_struct method provides a bit of functionality that seems to be used in all Protein and RNA silent struct formats. I integrated it into both Protein silent structs, but not into the RNA ones because the behavior is *ever so slightly* different, and didn't want to mess anything up, but it should be mostly safe. There is a very small change in trace-level output. Now both Protien and BinaryProtein SilentStructs announce at tr.Trace that they're loading energies. Integration test changes expected: 2 fold_and_dock : trivial output changes (like three lines, announcing energy loading) ThreadingInputter : trivial output changes (like three lines, announcing energy loading) Unit test broken : 0 commit d73b18f9cfbafc5f889795d2046ef08acd38aca9 Merge branch 'assaf' of github.com:RosettaCommons/main into assaf pull before push commit 4075dfdb8b2a4ba761d53a220c0e09cf5305b460 add ifs to the apply commit ec66c2f63c2e91c3660abc804d4c00f3e1f33980 Implement a generalized SilentStruct::fill_struct. The new SilentStruct::fill_struct method provides a bit of functionality that seems to be used in all Protein and RNA silent struct formats. I integrated it into both Protein silent structs, but not into the RNA ones because the behavior is *ever so slightly* different, and didn't want to mess anything up, but it should be mostly safe. commit f6a146e4a647a1ad2f4c4dcae39f3847e45ebec0 updates to antibody design and cdr cluster -Fix bug in cis/trans identification of cdr clusters where cis prolines were 1 residue off. This stemmed from Rosetta using different definition of phi than used in paper (i vs i-1). -Add cmd line option to override instruction file settings to automatically design a set of cdrs (-design_cdrs L1 L2 etc). -Change interface and neighbor distance cutoffs for ab_design to a better optimum. ########################### Integration Tests: antibody_designer should change commit ed46ea3a6ea4ae38ea187f928b7d43270fa31df4 [minor update of SandwichFeatures] - report beta-sheet capping info - debugged for cases that there are 0 electrostatic interactions - removed a warning unknow:0 src/protocols/features/strand_assembly/SandwichFeatures.cc:7041: warning: converting to core::Real [integration tests comment] - should not change other than features and features_database_schema (if any) commit 7b4ccdecc261362866505ca73aed241701db4a75 Adding new docking initial perturbation method: Ellipsoidal Randomization -New class: EllipsoidalRandomizationMover -Additions to unit test: DockingTest -Minor modifications to: DockingInitialPerturbation PCA.hh -No new integration test failures commit 273873a60d384d8609c6eb80fde936e35d6cd22c Adding new docking initial perturbation method: Ellipsoidal Randomization -New class: EllipsoidalRandomizationMover -Additions to unit test: DockingTest -Minor modifications to: DockingInitialPerturbation PCA.hh -No new integration test failures commit 6083daccbda846dea0d4743008fe318ea40fa81f Adding new docking initial perturbation method: Ellipsoidal Randomization -New class: EllipsoidalRandomizationMover -Additions to unit test: DockingTest -Minor modifications to: DockingInitialPerturbation PCA.hh -No new integration test failures commit bc71c31002decd764298816a4e0a4aa72f0b63d9 fix bug in RmsdFilter to allow superimpose or not when specifying two spans commit fcdfba4d383538520b2bbd68dfc7d0e84e27c8e1 commit source/src/pilot_apps.src.settings.all to avoid git merge error again commit eef96d2e8814c594d737e6a73f4e73c4d0ac18da commit source/src/pilot_apps.src.settings.all to avoid git merge error commit e066dae02f24742c55d7ad1972a4a94c1c294a53 adding integration test for terminal phosphate optimization for RNA commit 8abd3a795f45d5c4627a53bf6d3520e76c2c2359 turning on automatic optimization of terminal phosphates for stepwise monte carlo and assembly of RNA. This marks a merge from my branch rhiju/swm_phosphates commit 62e45e8de66131279efb3fba0185cebc6e3ac63a setting sampler_perform_phosphate_pack to true for stepwise monte carlo and assembly. commit 50076c264a50fccfbe0caaa1c0e47e7d0ba17a1a Merge branch 'rhiju/swm_phosphate' of github.com:RosettaCommons/main into rhiju/swm_phosphate commit 3f8fc1e7c449c5735289c39ccca1f9a5b94955c4 getting rid of some unnecessary verbiage commit f46ca078692eb2c604f6bd84f93fd0b8e6eef21e Merge branch 'master' into rhiju/swm_phosphate commit bfdc8182f6d77ba21d54bc76da5a43cf27d3f11f make sure bulges get build in -rebuild_bulge_mode commit 40a7b358d505973333228a33826aa023d954fd01 deleting unneeded stuff commit 98a0536744dbd92ccff3ed9f8f4cb606d7d08ad4 edited TR massages and default values commit 7d25735a6e89b545a64fa118412a4df9054e39d1 removed "design_residues" commit ecb93c1e35e3d6096dcdfb6a22c8719a0e36b999 changed the name in the creator file commit a4a0e22bd840ccf6afb344865bc112ac7c265b87 start and end res function defs commit 9d87c0aec2aa2a2b434a2350bf36625491f54457 removing target sequence commit 1a82738681c8306b86c9bc7e9b26adcd302ade9b # [ONE LINE DESCRIPTION OF CHANGE] # NEWS: [DETAILED DESCRIPTION OF CHANGE] # ---------------------------------------- # Unit test status: [Pass/Fail/Not Run] # Integration test status: [Number of changed tests / Not Run] # [NAME_OF_CHANGED_TEST_1]: explanation of change explanation of change ... # explanation of change, cont'd. # [NAME_OF_CHANGED_TEST_2]: explanation of change #+BugFix [BUG_NUMBER] [LINK_TO_BUG] # Uncomment and fill in the line above to indicate this commit # fixes a known bug. # On branch assaf # Your branch and 'origin/assaf' have diverged, # and have 1 and 1 different commit each, respectively. # (use "git pull" to merge the remote branch into yours) # # Changes to be committed: # (use "git reset HEAD ..." to unstage) # # modified: source/src/protocols.3.src.settings # modified: source/xcode/Rosetta.xcodeproj/xcshareddata/xcschemes/external.xcscheme # # Untracked files: # (use "git add ..." to include in what will be committed) # # source/compile.log # source/errors commit 5a27b62a081f1772467356a92711559c72e30167 linking problem commit 9eb66e22af87b2a600dfe7ffab88d627fdbc9fe4 Various cleanups to the Doxygen in the doc/ directory commit 6767d047dff65834e49aa55eb34660f12256ddd9 Carbohydrates: pilot app changes to debug commit d4a27a16f76bd9a244b1aab90b5c763f9a777463 merging in master commit 31182cf6e8c58e453256ecb9f0aef57740658011 daily commit 02bd3fa47a68d6ac9e5e2e928519924da49e406a author name commit e93fd8beb5b62f3f6ab44fd4c27b02183971db15 working copy - compiling commit 0c16cdbc84c2e7b3794d522ee37d943152728c75 wrote the apply commit 805e19c2e5dd14993ef58bda43bf06c09029d0e7 compile fixes commit cd38ecb810216050a44d9617b3e748a3ad0f50fa designable and leave as is functions commit d4061fc9014aeb4951dc9674daae4a97715f9e2a daily commit 521e11e27621800daf758f229ff1a136698740d3 daily update. changed the delta function to incorporate an exit commit 444eb727fb027db39699ca1ce6c0c152154b333a daily commit e762e45c296427bb39ac2479bff19a54d7db4f22 added the creator and fwd files commit bdda5b6cb2e25d577ae95138bbe85cbcc9d4a44f added the decleration files commit 03ab7a6e774dc9b50afe3ae62c5b9f36802cce3a not me commit 1d0b4e034093e600be9e62d2efca73e196fa19b8 added new databasethread.cc and .hh commit e9d2e175861d2b05937ab1b16b814caab1b5dc00 Commit to origin: new Etable search/creating logic. commit 1602379699c5ed3de7a091554e77e07c6434e4e6 Merge branch 'hahnbeom/patchs' commit 55828e1379378cdd9129add1d78906a4bf79a263 just merge Merge branch 'master' of github.com:RosettaCommons/main commit 7866eb15926d833fbef9d20b8b9126bde8f09639 debug commit 9ea550a0e1ddf24a86f555b5c2be29d814898ac7 debug commit 1190a3811e9081490488fb133b409f9eb2a60e22 Fix broken int tests (pH_mode test diff expected) commit 8360b202592cda376519787929b6fd192466ea26 Fix broken int tests (pH_mode test diff expected) commit 9e76ae8f68d7a868b2f3abec92d853db3b148179 Etable new logic working, before merge commit f8a82bdceedaeb83232a2990546bd5c0b8df55a8 Updating pH_protocol commit d02d51a1ef373cca58e093c0ba78a0138bbb68cf Updating pH_protocol and pH_mode integration test. commit 2d33bbc17045aa1c1922925bea5ba1d396700d55 Updating pH_mode integration test flags commit ab260ee083e350bda49cc3f6db94adf2e2e3f7bf Add markdown documentation output to update_options.sh. commit 9374a6c1df0d81903b33911e97375956b367e4ed Added new features reporter to compute RMSDs without superimposition. The reporter is named ProteinRMSDNoSuperpositionFeatures and is basically a clone of ProteinRMSDFeatures, but calls RMSD functions that don't superimpose. Currently, the all_atom_rmsd column in this reporter and the original ProteinRMSDFeatures actually computes heavy atom RMSD. A bug report (319) has been filed. Cherry picked from commit aff397f in kylebarlow/designmixer ---------------------------------------- Unit test status: Pass Integration test status: 2 diffs ligand_dock_script: unstable features_database_schema: changes to include new table from new reporter commit bd7cdf2bd271914cbd444c6b6a6bc9a1b70b1928 pkas.txt header changes to aid script parsing commit a415b694c3ec7ceb517aa485b761a70cb8ef8db2 Added new features reporter to compute RMSD with superimposition. The reporter is named ProteinRMSDNoSuperpositionFeatures and is basically a clone of ProteinRMSDFeatures, but calls RMSD functions that don't superimpose. Currently, the all_atom_rmsd column in this reporter and the original ProteinRMSDFeatures actually computes heavy atom RMSD. A bug report has been filed. Cherry picked from commit aff397f in kylebarlow/designmixer commit 93b57cdafd64bd4c11d4d1c758a2f7df9e06d3f6 Merge remote-tracking branch 'origin/master' into kylebarlow/general_dev commit b55c14f88ed03515b00ba850bef9e1a6f06df02a Dummy commit to trigger test server run. Integration test changes: rna_design commit 73f94d21ec597528648ad46018b9e22d6a0d6dfa Adding missing pdb commit 4e449b447c997bc9860dfded164d9b620e3bf14d More changes to B factor fitting, mainly to speed convergence commit 442e0e614e2646f7757e2cde72b9b4faf347f1b7 Merging update a071b84..0bfe8b4 before pushing commit 42acdf76e9c976189e3e05d08875eaf0305fe2c5 Added packing:ignore_ligand_chi option to use read-in conformers only without generating additional ones based on chi angles commit 0bfe8b47f5c619bac5de223cb1f2c140d2afefd6 Adding some additional check foldtree lines to make sure my fold tree is a valid foldtree before I go to set it into the pose commit 9d988c2da5d255213589a0167202ee1b8fb52803 Moving pdb to get a pilot app to run commit cb05399f944396a56a719a4cf632e0f0c8c3923c Adding file to get my pilot app to run commit 95da9b8a475d02b606408526e0ebd1e92b0d3d48 Adding new app to build settings commit a30306c40386256899bc3d1c37062d75570c0d4a Adding membrane foldtree app to my pilot apps commit f910ba0b34ef7eb541ab6d7c6d81f5ae9493eb76 Adding back xcode project template - now tracked by remote commit d131a92ad70b2594e87a76aa743d64fc1aeb3b56 Commiting local changes to xcode.py commit aa89e161e241f26e8909c1eb543351ddc0453337 updates to density tools app commit 143b86a67d963aead0e2e0a2a698cc516fbd427c Bugfixes to realspace B factor fitting; a few new analysis functions in electrondensity commit 1df78bc099267908f51ed67a0ba69ac5fa5ad44d remove unused include in InterfaceFeatures to fix library level build commit 6c7ee7b0fae3f5476a7037cf68403f45acbfe4d1 InterfaceAnalyzerMover updates, bugfixes; add InterfaceFeatures reporter and basic R scripts IAM Bugfixes: *IAM now includes hbonding energies in per-residue information and variables calculated using per residue information. This will show in the integration tests *detect_disulfides is now called for the separated pose, so that if any disulfides exist at the complexed interface, they are fixed upon separation. Otherwise you see energies of > 3x10^6 on each cysteine for the separated pose if it started as a disulfide. A more elegent solution to this for only the interface residues will be forthcoming. *Resfile function has been commented out to avoid confusion. Although you could set one in IAM, it didn't actually do anything. *Abort IAM directly after interface has been detected. No residues, no point in continueing. IAM Updates/Additions: *New multi-chain constructor for interfaces, ex L_H can be used via code/RS/app with -interface option. This with associated code enables analysis of the interface between any chain in multichain poses; for example only the L_H in an LH_A interface.This required that all energy calculations in IAM are now done on a per-residue basis, so chains can be excluded. Any excluded chains are moved away at twice the distance of the separated interface used for calculations. *Data computed by IAM is now held by two structs: InterfaceData and PerResidueInterfaceData. Some of the variables held in these structs are new. They can be accessed via get_all_data() and get_all_per_residue_data() IAM functions. Many variables use the new enum, InterfaceRegion, consisting of side1, side2, and total in order to get more information *Much of IAM has been refactored and reordered. Most functions and variables now have docstrings. Public functions that should have been private are now private. InterfaceFeatures: *Consists of most data from IAM in 3 tables: interfaces, interface_sides, interface_residues. More data will be added over the next few months. Default constructor will find all interfaces in the pose and calculate data for each of them. Interface can optionally be set via code or RS. Still need to update the wiki, but RS accepts options: interface, interfaces (separated by any of these: ,~+*&|;), scorefxn, pack_separated, pack_together, dSASA_cutoff (where interface data below this value will not be reported - default 100), and compute_packstat. *R scripts interface_composition, interface_energies, interface_dSASA, interface_residues, and interface_overall_metrics have been added to features test. These report basic interface data by sample source and most by interface as well. These will be expanded heavily over the next few months with more scripts and plots to be added. ---------------------------------------- Unit test status: Pass Integration test status: *All integration tests that use IAM will change cosmetically. In addition, all values that used per-residue energies before will change (per_residue_energy_int, side1_score, side2_score, side1_normalized, side2_normalized, complex_normalized), as these were missing hydrogen bond energies. This is now fixed via energy method option. commit ecd360e5eaedf8f2617f04c7c123876613b4bddf compiled and tested interface features. all unit test and integration tests pass or as expected commit a58beff0e005f04e006952a670696edf01989b07 PyRosetta. Fixing bug in Vector1 function that prevent it to create boolean vectors. Thanks to Javier for pointing this out! commit a071b8451e50272ab811c69c6307661ee1716f17 Bugfix in seqprofconsensus treatment of chain2 commit a1ce6b21085c912e27859d42af458f4b200431a0 Few tweaks to make pH_protocol ROSIE-ready commit 1d8888291aeeb5beb6e54276678f58de687ed909 merging master and patchs Merge branch 'hahnbeom/patchs' Conflicts: source/src/basic/options/keys/OptionKeys.cc.gen0.hh source/src/basic/options/keys/OptionKeys.cc.gen1.hh source/src/basic/options/keys/OptionKeys.cc.gen2.hh source/src/basic/options/keys/OptionKeys.cc.gen3.hh source/src/basic/options/option.cc.gen.hh source/src/core/scoring/etable/EtableOptions.cc source/src/protocols/relax/FastRelax.cc source/src/protocols/relax/RelaxProtocolBase.cc commit a7623e9381565be65247327f255f532400284650 current modifications update on Etable, relax Merge branch 'master' of github.com:RosettaCommons/main Conflicts: source/src/basic/options/keys/OptionKeys.cc.gen0.hh source/src/basic/options/keys/OptionKeys.cc.gen1.hh source/src/basic/options/keys/OptionKeys.cc.gen2.hh source/src/basic/options/keys/OptionKeys.cc.gen3.hh source/src/basic/options/option.cc.gen.hh source/src/protocols/relax/RelaxProtocolBase.cc commit e9ff4016b84f6e2e92cf11985b9b17d90589eea9 current version save commit 556f6f2f59866f2def52fc87a9badb369e59d5a6 [minor update of SandwichFeatures] - deal all nitrogens of ARG as terminal_polar_atoms when counting_electrostatic_interactions - report electrostatic interactions in 3 conditions: strand-surface, strand-core, and any secondary_structure - identification of N-O bridge becomes more accurate by correcting a minor mistake [integration tests comment] - should not change other than features and features_database_schema (if any) commit ba4a290fd74822aeab9da704bc2dad9fe4bbdc3f Few pKa prot additions for ROSIE commit 4da066bb2e6d3b3b73f53ffa9b2bf01d4dab9384 merge master into interface_features branch commit eeeb14273498f7c4898f6720b34579c03fbe04f9 remove use_stupid_foldtree_format from options and kinematics/Edge. From the comments it looks like it was only supposed to be there for a few weeks, not a few years... commit a284323d494f0eba3185e9864be986b6ecda7b9a screening job files can now store ligand starting positions no test changes expected commit 5757a1750435e0b9853de798321e9d5b0c892d24 general fix bug in IAM where interface disulfides were being stretched instead of cleaved upon separation commit 78597f4d1b0bd60fa18566439037d9d0c2f9b968 I’m a dork and put the start xyz data parser in the wrong place commit a185e9d49bf15d6f13561782cc894f77a474285f Adding ShapeGrid scoring grid This is an initital implimentation of a ligand scoring grid built using a spherical knowledge based potential. following integration test changes expected ligand_dock_script hts_io kinemage_grid_output ligand_dock_grid commit 37fd5b40e359f859889d320ffded458cec02293f [minor update of SandwichFeatures] - removed 1 simple warning - identify electrostatic_interactions by number_of_attractions, number_of_repulsions, salt_bridge,C_C_bridge,N_O_bridge and longer_range_ion_pair [integration tests comment] should not change other than features and features_database_schema (if any) commit 3a18d120b77bd19f7baaa324ee54d449d474152e Fixing PyRosetta build commit f6532d953f538089714520265eba9e381ef648c7 Enabling PyAsserts in debug mode. Refactoring FoldTree PyAsserts. commit aff5135d71c4455b1cb0b6ce47b6a9d4ede42699 adding histogram data to go with shapegrid commit a12e8f912ef823b9b515af0efc5a28b023670a3d adding the smoothing function back in commit 8a227c21530896b9e4f4293dc11a48f535cc0a68 found a bug in rendergridstokinemage commit 3f5c768233beb60a3dbf4f099b9ca6f6afd23c6f lets try the average commit 957d506157ad0c37a61ef8fda2d63e5d59babf46 lets try removing the smoothing function entirely commit 4c55420bb0b5d060d53c61ef07b4a6fceb8f12eb regenerated tables lead to more tweaks commit 86495069df7e596415210f361c0b70bc87ca5d16 instead of worst score compute sum commit c453b6a8a562f9f3b6af59a5406bbacfb21b0009 smoothing function tweaks commit 30538e55fa1e83e5dd20ea824551b24e84dc1da5 add overall interface residue plots, add more plots, remove energy outliers for all energy-based plots commit 358ea0754df9fb2204b08cc22d460403192781b1 forgot a - sign commit a97142070b184495cad08595e6e1a52eaab42e7c PEMDAS commit 1c2601c2dc23ee0f60b5ba6203a4a0de268ded72 im a dork. Fixing smoothing function commit f1b5a52eb530f49b617ef8ce5127b897f7feb106 Merge remote-tracking branch 'origin/master' commit ec851c7305dfea5ac7e4a8e865f33c58757b52da SeqprofConsensus will now be sensitive to chain. commit 9efb6711c0f3df82524b262d47cc4d0349ad5717 SwitchChainOrderMover now copies comments to new pose if "pdb_comments_true" flag is set to true. Should not casue integration test changes. commit d7eaac65526c56915ed283a4eefd80f853af92d3 SwitchChainOrderMover now copies comments to new pose if "pdb_comments_true" flag is set to true. Sould not casue INtegration test changes. commit b22878c6a04a49afdb251a08de316dcc91f0fbeb Code reorganization, help functions, and a little change in outputted verbiage for stepwise monte carlo & assembly of RNA. Great happiness from this refactoring. Changes to SWA and SWM ntegration tests have been vetted -- most are due to name changes of tracers. commit 5a26254ad77e1b1c70e167bfec6d0ab27c256c05 setting -allow_internal_hinge_moves and -allow_split_off to be true by default. they appear to both be very good at enhancing sampling of GAGUA pentaloop commit dc33062552c6a6f54d02612dd1b1aa3fe7164e83 pepScore and pepScore_noref variables initialized to 0.0 commit 0f79f11ba97560e58def532daa62214114c27c48 Fixed minor but in Splice. No Integration changes expected commit 143e4e0e687365329cb35cc1107abd26b191ef75 add more interface plots commit a9e871f17717cc996f5e80177548d385e8689386 restoring AtrRepScreener behavior for sample_both_sugar_base_rotamer -- just virtualize ribose of extra sample res not the whole thing (which may lead to no screening at all, since every pose will have the extra base stuck to something) commit dc42f90b8ebbd9101b6f3dcf36bbe7005c4bf8c7 found fix to variant type addition s-- should not copy back working_pose back into pose, just its conformation, or that can clone other data like other_pose() which can confuse external routines, in this case RNA_DeleteMover. commit ba63700742a54e7ea889eeaa68b7af4462d34e62 sample_both_base_sugar_rotamer was not getting passed into screener before its setup. That explains the error in the screener. Duh. commit 49d5e9543e6a6b5842114b8e09748ad258cc9147 trying to fix a potential virtualization mistake in case of atr/rep screening for sample_both_base_sugar_rotamer commit 2cff8013a2f5a2231cca95368470a80e6d017976 for StepWiseMonteCarlo, new option -allow_split_off which is like -allow_from_scratch, but does not try to instantiate dinucleotides from scratch. Instead it allows pieces that nucleate onto fixed domains (but are not themselves fixed) to be sliced off and remain as an other pose. This was happening by accident in some early GAGUA runs and led to the native; now turn it on in a controlled manner. commit 70c6da8d9343c12b5c82e4e8bc211b98382382a8 trying to fix a potential virtualization mistake in case of atr/rep screening for sample_both_base_sugar_rotamer commit a2f42a52f5fc6b99ceee845c0338b0605df83a0e trying to fix a potential virtualization mistake in case of atr/rep screening for sample_both_base_sugar_rotamer commit 17be250fab3b65d60d806025d7219a5373754924 [minor update of SandwichFeatures] - report avg_b_factor of each component in sandwich into database - count number of electrostatic interactions only with residues whose beta-carbon is defined with less location uncertainty [integration tests comment] should not change other than features (if any) commit 3bcbf87bbd0e51f5471cd87d03be4f4b770a32ed merging update to integration tests commit 1e40644ee1d0ad27666e33ce07cdb91a56d5409b explicit instructions to not minimize virtual phosphates for RNA in stepwise stuff. This is not general, and in fact may have no effect on minimization... lets see commit 8461d667d4c548f2f9678173fee55121f4079d07 needed to update flag for SWM design integration test commit 61efbca33b3ae7de94d9473687a4dbb1c9624d64 fixing up spacing in core/scoring/rna commit 6303af0e790be59dd77d661efc9ce103f59a303f fixing up namespaces in stepwise::rna::suite and stepwise::rna::sugar commit 1391853db41a76d6fb95338ce15a9cf0febce6c6 oops, moving StepWiseRNA_ResidueSampler out of rna/suite/ subdirectory. Its a master wrapper that can call stuff in rna/suite/ or snra/rigid_body. commit d32869bea6a978ea88c7d432204714ea0acdf2b0 creating MoverForPoseList class to help structure some of the core movers for stepwise enumeration, which take in lists of poses. commit 8e6a1ccd5bb56450d75f954f1129a5e04741991a adding comments at top of StepWiseMonteCarlo mover files. Restoring arvind constraint parameters for near-native runs. commit dcb675021e9a0cb41f3fc8e6819d54cbc8ab9497 renaming StandardResidueSampler to ClassicResidueSampler. commit 3f92cd9aab8104a8f740e52d6434935ff7adef39 reorganization of where RNA applications sit in apps/public/ -- they are not all in rna/ anymore, but spread out based on functionality (design/, farna/, rna_util/, stepwise/enumerate/rna/, stepwise/monte_carlo/rna/) commit df0d24e03c0ee30bb37f87d2a0955f96e4239e51 More re-organization for SWA/SWM on RNA. Moving samplers into suite/ and rigid_body/ commit bad5614d9a755da7fbe8dc9db18b4ab87d2e7a9c Moving VirtualSugar stuff into stepwise/enumerate/rna/sugar. Moving some older monte_carlo pilot apps to legacy. commit b7dde4c575d69f219bf7cfdd12a52f611112fb3c In StepWise MonteCarlo, adding -allow_internal_hinge_moves to allow resampling of internal suites. I think this is needed for GAGUA. commit f158b92e5021a1201a09b0a034f18b21152692ec again, fixing boundary case where sample_both_sugar_base_rotamers was activated in stepwise monte carlo commit 41be18e94cc11b4f325bfd1faeca5b3999a8c438 allowing a pose witha single virtual residue to be used as a "blank" pose in StepWiseMonteCarlo -- needed for testing runs starting from scratch. commit 69ba93ed8c572328bd975a6a7631a06d2c7052d3 getting rid of older movemap setup function; now using allow_insert object (perhaps not a great idea). at least integration tests do not change. commit 0911e9c061d3d7c167a63595094b7fc959c3dcd6 bug fix to rebuild_bulge_mode, silly overwrite with sample_both_base_sugar_rotamer option, oops. commit 6f074030675eb7c77bdf359b9c9ce895c72b91ca allow visualization of bulge getting closed during virtual sugar sampling commit 4860a7f3edf2eeafa9088a415b530322182d3b20 minor bug fix to building RNA dinucleotides from scratch -- should minimize all commit 29cadec1f58c8425309703ef974e1ab992e492dc some more output from RNA_TorsionPotential if verbose is set to true. commit c246504f1fb6ccf265050b4ade744cf7b2708345 restoring integration tests that were checking options were .active() -- now check if .user() commit c8d4434ae135783209dab57e3cf90c6426ececd9 testing removal of copy_copy in movemap setup for SWM and SWA commit 7b833ef8260090124be6efcfed1edfd78dc8bb98 oops was being too aggressive with sample_both_sugar_base_rotamer. commit 5b19f96901e9575f7d0a1e5ae395470993ae8f6f allow from_scratch even if dinucleotide is adjacent to instantiated residue. commit 5f8c551e06dc15f6c607adaada0a4a35bab6022e ah, missing setup of closed_cutpoint_distal. esoteric boundary case but caught in modeling loop 1 of j5/5 hinge of P4-P6 domain. commit f45935dcefa05af537e74812351fea9090a35833 forgot to commit options.dox. is that getting deprecated or what? commit 1413d435515a3e91f147de43b0fab2f181f2a417 in StepWise Monte Carlo now can build dinucleotides, etc., and preserve them with -allow_from_scratch. commit 1048aed0d84477f942536ac3c2f44e3c4cf1d40c setting up terminal_res functionality for stepwise monte carlo commit 6b0ecfd5fe07d4df876ac886a996a072f53f0b10 change name of VirtualSugarSamplerWrapper to clearer VirtualSugarJustInTimeInstantiator. Some code cleanup. commit fbec0bdb0dd942584ff979fbbcaa1088f24f0364 fix cycle output in SWM commit abde88853fcfa2c50afec4a0994481b1fe348719 cleanup of virtual sugar instantiation code. for floating base sampling, applying instantiated sugars at chainbreak, since they are not instantiated or checked in the sampler. commit 1bf36f6d2055fcd31ebb663972a7b0a6f4171269 updates required for building on single nucleotide, and generating movie with first frame as initial pose. commit 069d267b9f558325d8fdeee5fb686a3338e1f455 in stepwise monte carlo, setting force_centroid_interaction default to true; moving SWA apps from assembly/ to enumerate/; removing some warnings. commit d650d49aef7202c5992a2b0645fddc50846a6e4a in StepWiseRNA_MonteCarlo, get rid of native_pose_ in favor of Movers get_native_pose() commit 3bd502a9f95f4c2ef6c15c77847232a86bc05578 oops, num_random_samples was not initialized properly commit fda8802c8218569bd18077849ca5b37cd991b28d oops fix option read in for swa commit c3651c3034cdc3722b5b259989f4797c62c2ca0d movie making magic in StepWiseRNA_MonteCarlo via flag -make_movie commit b6d1b4e8cea887355e432faeddf128b9b248f5bc cleaning up options, and adding -help commit 7a8beb268b36943c53e6ef477af59dfcfde3a491 cleaning up options, and adding -help commit 56e44ecbc4a3e1ee3b3db333ecc2a3d58cd3a7ac Merge branch 'rhiju/swm_bulge' of github.com:RosettaCommons/main into rhiju/swm_bulge commit aa332f55a47fd0fa17d753a462d58014a3787c04 setting defaults for SWA/SWM to optimize o2' in minimizer and to keep base fixed in virtual sugar sampler commit 9a2269f044a4ad0f395947df82bb346975d0f9e2 in SWM, clean up setup of modeler options from monte_carlo options commit e3eb69578ff91c6459bb2fe0c471d69c5ee57ba1 further cleanup of swm_rna, including movement of options setup and util functions into StepWiseRNA_MonteCarloOptions and StepWiseRNA_MonteCarloUtil commit 977036647227214f7919ac81646ff0ae1f1b7fdf merge from ade work on swm_bulge refactoring branch. commit 98500b9b17aa0da34cb633a79313d5fb36329055 introduction of a StepWiseRNA_MonteCarloOptions object to better organize SWM code commit 010ee782d45f172a4b3667e4a8d1aa0cb26270b4 removing verbiage commit 3f1a6ebb6e5504ffbae1e04d5fbec271d6d65d1b more code cleanup, including switch of StepWiseRNA_ModelerOptionsOP to StepWiseRNA_ModelerOptionsCOP inside classes commit 6d48bb17ecb3715ce765a6f53c4165bebd1bc63e fixes to StepWiseRNA_ModelerOptions and some warning removals. commit 82bde8426138fa6b4744de2a2ab0f6cedf228bcd restoring some integration tests commit a2810de169e168e62f67dcd65c08e078e36099be minor fixes that go with StepWiseRNA_ModelerOptions refactoring commit 9e650b29a28d52843d282ad42397936c727db74e refactoring stepwise rna enumeration and monte carlo to use a StepWiseRNA_ModelerOptions object -- by popular demand! commit 40345b5a51b5f5425e85c6eb55fa2fc3d6f8fbe6 update integration tests with name of new command stepwise_monte_carlo --> swm_rna commit c3262b777bb506b68c4c9de7b3f3bb47b2945e9a Merge branch 'master' into rhiju/swm_bulge commit 5d4b129da1b4405a4b00cf80186fe09fba292b5a Fixing the two unit tests I broke by updating the way the CartBonded term behaves. Here, I'm updating the hard-coded per-residue energies for the idealized trp cage structure for the proline residues in both the CartBonded and CartBondedBBDep unit tests as well as in the tests that make sure that start-score and start-func match, and that they match a particular value. commit 52dbdca2659a65200a62e6994814614c34671530 moving RNA_HelixAssembler from farna to stepwise/enumerate/rna/helix/ commit 0d3a7f0e564cb0b990b8a43b0b4ef0375f0f8d3a move stepwise_clusterer to new stepwise/enumerate/general which might be a good place to hold stuff used for protein and rna commit d689ce1ba9db76f4b4ebd7d373fe04e1f51845b7 further renames as discussed. NO_ADD_OR_DELETE --> NO_MOVE. SKIP_BULGE --> JUMP_TO...IN_CHAIN. commit 9c626e654406713deceb1a6a8a13b10de5abdafa changing stepwise/assembly to stepwise/enumerate, as we decided as a lab. commit 91dcd970b5cd3ef8f6df2651068677032f861dab get all apps to compile after namespace renaming commit 35d414c07f0afea28920719567fc86d95daf11e5 change protocols/rna to protocols/farna. it will henceforth only hold functionality related to fragment assembly of rna commit 53e56af9a18d4df01b9a49bb0de907d19a60a9ec yes, everything compiles. drastic namespace change in protocols/swa to protocols/stepwise, and also in apps/ commit c2b4b353e968424c5050d106888cac5959502ac5 almost done with major swa rename. all code compiles except apps. commit 23d62828fceb95e46b6848edaba9c769267985ae more updates for renaming commit d1dc9b1e6912b23be3001db2c0563ddb9e474cca update to options (swa-->stepwise). protocols/stepwise/assembly/protein now compiles (xmas miracle!) commit 72ad74baae1647731d2f856a3b58528f250267c3 on the way to major renaming of stepwise filenames & namespaces. does not compile yet commit 9d073f634cbc24a16f79aeea3cedd7c2b5bf1acf on the way to major renaming of stepwise filenames & namespaces. does not compile yet commit 9732df49f6098534d243243caa1a2a9bfbd8c170 on the way to major renaming of stepwise filenames & namespaces. does not compile yet commit 40aae0245315a3def366a8b43d7a09cf64f39088 minor fix that goes with previous commit fixing sugar reference res commit 571a0b4113f34f7648b28f8bd95101a664614b80 wow another problem in virtual sugar reference residue picking. decided to just split reference res detemrination for cases in classic SWA setup vs. cases that are encountered in SWM (which are more complex but can take advantage of the fold_tree) commit e44ac83fb76223089cba6278973a6abca06b19e5 Merge branch 'master' into rhiju/swm_bulge commit fb211f6f9e292bfe34801f31d4ddc8ef50b97373 argh, fixing silly options conflicts. i thought this was ok but probably screwed up recent commits commit 4a2e94b062f5918ee3400a43d7b4e02fc0ac08c3 making rna:corrected_geo default as well as -free_sugar_bonus of -1.0 commit 44e0c8450b1c9f9d7f5b2446bb75a0018202b63a Merge branch 'master' into rhiju/swm_bulge commit 88893fe70085b29fc3ec1f44dea09e3b838bf937 making rna:corrected_geo default as well as -free_sugar_bonus of -1.0 commit 6987ad83da35e3d4d39950cf4e518ef48b2b5487 restoring coordinate constraints to rna_denovo. just that integration_test changes. commit 119668b90e5902f6241f6307df77ec0ef8b6e3cd restoring coordinate constraints to rna_denovo. just that integration_test changes. commit 1deb253671c3b8d1feb37c4c10124e246eda0181 optionskeys fix: try 2 Merge branch 'master' of github.com:RosettaCommons/main Conflicts: source/src/basic/options/keys/OptionKeys.cc.gen2.hh source/src/basic/options/keys/OptionKeys.cc.gen3.hh source/src/basic/options/option.cc.gen.hh commit 3471a6fac83c9b919ac2ec5a6a8294e92f75b052 resovling conflicts I had in a previous commit in the options system commit f6d43047bf1ef20eb6e57329ce8c7b51d91a97b5 merge from origin (was doing some fixes to branch on another server) commit ca2f0799aa0643dac43835c0df0d32606d225f11 merge from swm_bulge -- numerous updates to stepwise monte carlo -- in preparation for opening a separate branch for renaming files and namespaces. changes to rna and swm and swa integration tests. commit 415a473ad4460a54897b9f72c5ec66b06418534d merge from swm_bulge -- numerous updates to stepwise monte carlo -- in preparation for opening a separate branch for renaming files and namespaces. changes to rna and swm and swa integration tests. commit 7c5bd55b3fbeb73c0376fa0cbea37a6d498df02f returning coordinate constraints in rna_denovo minimization to be true! should not have turned off earlier this year. now can turn off with a flags to rna_denovo: -minimizer_use_coordinate_constraints false commit 76efaa359dcec5ed1b4877eefd555f4faec11667 Merge branch 'master' of github.com:RosettaCommons/main Conflicts: source/src/basic/options/keys/OptionKeys.cc.gen2.hh source/src/basic/options/keys/OptionKeys.cc.gen3.hh source/src/basic/options/option.cc.gen.hh commit 5014cd895e4c3653fe3224f09f92aa5b85d0ed69 merging from master in preparation for integration tests commit d5f722bf88f71f0c6db725b5c56d6d6ea384e3cf Adding mover AlignChain which aligns a chain from a source pose with a chain on a pose from disk. See wiki for details commit b12a57bd1d0d82923bb6fc353a93f25541e3d235 SwitchChainOrder increased verbosity commit d83af84d79c5caed7235341cd641f873afe17b3a adding option -membrane:thickness (default 15A as before) to control the membrane thickness in scoring membrane poses commit 86723fa89b3d20e3a1d65158aaa9868cbae3f41a attempt to fix PyRosetta build commit 5abc3d3a84b9f259fc9dfab6b35d7003e8f5ecf3 obey rna_phenix ideal_coord parameters when using variable bond geometry. commit 19949b29edc4a552b1a52e5e3a582e65c4c1112a Merge branch 'rhiju/swm_bulge' of github.com:RosettaCommons/main into rhiju/swm_bulge commit dc24f0bbc17cb1ec40c3c97bf3cda07a99081969 Merge branch 'rhiju/swm_bulge' of github.com:RosettaCommons/main into rhiju/swm_bulge commit a7517714e77d7e0d4978f2efcad4f917f19d0d46 Two things: Testing a flag -virtual_sugar_keep_base_fixed, which should greatly accelerate runs with skip_bulge moves. In SWM, virtual sugar sampling is guaranteed to return something with an instantiated sugar -- otherwise can get poses that have virtual sugars carried forward. Bad. commit 09820a8ffc9acef68832029aafb836de316a8b0f fixing variable_bond_geometry in RNA_Minimizer. How did this get broken? commit ca7c56ef37cb406b845c7b394b5e9e91855ccdbf remove now unused CDRClusterEnum/Real pair defined in utility_by_hand to fix PyRosetta build. commit 3fb4aa4b810ee4a1694cde3837f6f208965b9bdb remove extra print statement from AntibodyInfo. Ab integration tests will change again. commit d7ee24bf3c900851b68763256c6a124ba0afa8cb updates to AntibodyInfo and antibody CDR clusters, bugfixes to backrub NEWS: Protocols: Antibody code and applications now work with most numbering schemes and CDR definitions. These can be sepecified at the protocol level through the -numbering_scheme and -cdr_definition antibody options. Recognized numbering schemes: Chothia_Scheme, Enhanced_Chothia_Scheme, AHO_Scheme, IMGT_Scheme Recognized cdr definitions: Chothia, Aroop, North, Martin, Kabat Note that the Kabat_Scheme is recognized and works, but it is not fully supported as using Kabat with Chothia definitions can result in the wrong numbering due to the place where the Kabat scheme puts H1 insertions. http://www.bioinf.org.uk/abs/ Code: The function, get_landmark_resnum of AntibodyInfo essentially replaces PDBInfo calls when working with antibodies. This function transforms one numbering scheme to the next, so that for example an important Chothia residue can be found in an IMGT renumbered antibody. Current functions have been updated to reflect this change. Functions that return CDR start and end points or Loop objects now optionally take a CDRDefinitionEnum. This allows one to get these positions as defined by different cdr definitions. Useful for metrics that require a specific cdr definition. Numbering schemes and cdr definitions now reside in the database, with an accompanying parser object. CDR cluster code has been moved into it's own namespace and rewritten as objects. Main interface for the CDR clusters is still AntibodyInfo. CDRClusterFeatures reporter has been added. It resides in antibody/clusters since it requires classes at a different level than the rest of the features reporters. Unit tests have been updated. Features tests: cdr_cluster_recovery features R script has been added to compare the cluster and length recovery of native vs designed antibodies via CDRCLusterFeatures reporter. query_sample_sources and query_sample_sources_against ref R function now optionally takes a data frame as arg for an SQL query. query_sample_source R function has been added. save_tables R function now optionally takes quote option to remove string quotes from printout util.R file has been added with code to sort a data frame. Thanks to Matt O'Meara for all his help in this. BUGFIXES: Andrew Leavery-Fay fixed this bug in backrub.cc that was triggered in my branch somehow (bug from list): Fixed PoseOP-created-from-a-reference-to-a-stack-Pose stack corrup… …tion bug. Additional info Andrew: Creating a PoseOP from a reference is a bad idea and should not be done. In trying to fix this bug through valgrind, an unitialized variable in SideChainMover was fixed(preserve_detailed_balance_) ---------------------------------------- Unit test status: Pass Integration test status: Expected tests fail All antibody integration tests will fail for cosmetic reasons Non-empty diff in features_database_schema as expected commit 54ed3fe3d4947a915f32c3d891b1bec0fec715c5 fix bug in remove_constraints_of_type function causing infinite loop .1 percent of time it was called. commit 45abc0d1cb856c462d86344fcd0db322d402c629 merge master into schemes branch commit ea5899fc73ce940dc591692e7045e2209b71d4c7 trying to save my rna_test pilot app from code rot... commit 72ef7cb2dad23fb76f55189f409a333dd2abec2a removing assert that does not hold anymore with floating base stuff commit 7e071142766cafeae147d8f99ec0ff3d23dd61e3 do not reoutput native after readin -- causing some weirdo issues... commit 64bb9028beac395e08a287f73f638bfd39f846e2 Merge branch 'rhiju/swm_bulge' of github.com:RosettaCommons/main into rhiju/swm_bulge commit 29f985c4ea33e741590548af1edfddb53cb76d17 in virtual_sugar_sampler, removing a virtual phosphate check that I do not think is appropriate anymore thanks to improved distal partition virtualizer. commit 719b1704d8cb74f0b04e0fe0ef1507a8b6b5c9a3 fix rna_helix to handle weights files that use full_model_info commit 33c88ad0fc52be6cb7337a5609069953fe3bfc16 Merge branch 'rhiju/swm_bulge' of github.com:RosettaCommons/main into rhiju/swm_bulge commit e7b85ac8e5521c123d5ca7143c4dce76086075ab turning off an incorrect assert for virtualizing phosphate at virtual ribose sugar in VirtualSugarSampler commit 6edc8eaedef18be1ced75aacbd870799c2b29d7a Merge branch 'rhiju/swm_bulge' of github.com:RosettaCommons/main into rhiju/swm_bulge commit 0eadaa5c462883503d31fc931176228287e39798 tracked down several issues related to sampling of sugars that should not have been sampled -- now setting is_internal properly in StepWiseRNA_Modeler. Also fixing distal partition virtualization during VirtualSugarSampler (previously forgot to virtualize phosphate). commit 44454a89216d1ac0a9b1a721e2698d9034e86914 in stepwise_monte_carlo do a switch focus at the beginning to avoid bias from which pose we start with. commit 287188de7cfaff00ff2865349710b590e0aaab4b Parameters in ComputeLigandRDF no longer hardcoded. bugfix to packstat The user can now specify bin count, range and smoothing factor in ComputeLigandRDF. Also found a bug in packstat. Specifically, if an input PDB file had an insertion code and in identical residue nmber to the previous residue, it would be skipped. This was fixed by changing the SimplePDB class to read and store insertion code information hts_io test expected to change commit 43691bbb89be9b74029945796a3d785c3a39061a oops forgot to remove some debug statements commit 674261628e7054282d2e0efd34ac03fd0e0d32e8 missed a spot adding icode support to simplepdb commit be86628e11a35bf58795ecf9a094fecc0202b5fb ahah! SimplePDB doesn’t read icodes so if you have one everything breaks commit 08b35572134a34517b11d5292810a3fb65ddd060 how do i for loop commit 3fad269bbe613fef27f05d029ea201c15c771a11 adding some more debugging stuff commit 927efd4f388ed1ffc85d4a370e2c481e80c3ea68 debug line to figure out whats going wrong with packstats commit 3b6a6521ce89a635afd516dbb35566e980d9b8a0 pulling in changes from laptop for a bugfix commit 958184372b6f83c0e9931616477ef63bce650fc0 I’m an idiot, forgot to update copy constructor commit b360191de9d6083000b7325ce46ae66266266c69 updating changes from master to bring in a bugfix to interface analyzer commit 3d5f9fa0607ddc048db08908fbf9b5698ca2db5f new feature in Transform and bugfixes Transform now takes an option "rmsd" which limits space sampled to within some RMSD of start position. Transform now computes acceptance ratio and stores in job data. Fixes a bug that I introduced into interfaceanalyzermover when calculating ligand interfaces. ligand_dock_grid kineamge_grid_output hts_io expected to change: commit dd1899d051fff6612388d28edc4ea2c5b996fe20 Merging in some new domain_assembly code as well as some refinements to the ResidueSelector classes that languished in a branch for too long. The ResidueSelector classew now do what they say they do on the wiki. No integration test changes. The same unit tests I broke earlier are still broken. commit 7b6f4ecd37dbecacc8a189bb7e404fa791f8e727 Merging in some new domain_assembly code as well as some refinements to the ResidueSelector classes that languished in a branch for too long. The ResidueSelector classew now do what they say they do on the wiki. No integration test changes. The same unit tests I broke earlier are still broken. commit cb3f4772ddd8cf17f89a607db38a46a36548437b making it possible to change bin count, size and smoothing factor for ligand RDFs commit c385d52d5962a3add26ea8a3ed149c4f580f5f63 Merging in some new domain_assembly code as well as some refinements to the ResidueSelector classes that languished in a branch for too long. No integration test changes. commit 4f16503878e628804c9b608c05a296e3f2f44dbf some updates from rhiju/swm_bulge. this include proper re-rooting of fold trees for some Stepwise Monte Carlo runs; specification of -bulge res from command line; turn on/off variable bond geometry minimizations; and bug fixes to how delete/split moves work in SWM. commit 845ada68359e88ed5ef0c3d4e760ded19cd77f05 Merge branch 'rhiju/swm_bulge' of github.com:RosettaCommons/main into rhiju/swm_bulge commit e88befd6077dafcd210c1231080a7e002e958a65 allowing syn-chi to be specified from command line for stepwise monte carlo commit 1f4528fe2f17a22eee2781cb1167c52924be8550 Changing the fix for the "abandoned NV" bug. Basically, cart_bonded and pro_close both have different ways of scoring the closure of the proline ring. pro_close uses a virtual atom, NV, which it tries to keep as close to the backbone N as possible, and cart_bonded has an energy term for all bond lenghts and angles and not just the ones along the atom tree. Well, if you run a protocol that uses cartesian minimization for one part (using the cart_bonded term) and then switch off cart_bonded and turn on pro_close, you see a huge spike in the energies. Why? Because NV doesn't get assigned a derivative so during cartesian minimization, NV just stays put. This means that the rest of the structure will walk away from NV, so that the distance between N and NV might end up being several angstroms by the time cartesian minimization completes. The original solution was to have the cart_bonded term update NV's coordinate during setup_for_scoring. This has the unfortunate side effect of triggering "No structure mods during scoring" error messages (incidentally delivered quite a bit after the structure modification was made). The new solution is to put a weak force between N and NV, and now between any "virtual shadow" and the atom it's shadowing. 5 integration test trajectory changes as a result to the introduction of this new force into the cart_bonded term; ideally, only NV would be dragged around, but the force is symmetric, so NV pulls a bit on N. commit a31e9ae3b1c2ba30247b8038f5dcd0525233bb9a Merge branch 'rhiju/swm_bulge' of github.com:RosettaCommons/main into rhiju/swm_bulge commit 91c43b048bd16b499dd93bb36246952da5d956ae Adding a weak constraint into the cart_bonded term to pull the NV atom along with the N atom so that the pro_close term, when evaluated on a structure following cartesian minimization, will not be sky high. commit 89767eb85a23c901580ba48128d6ea7f1469c6c1 -bulge_res option for stepwise_monte_carlo. Specified residues are taken out of the sample_res_ pool for potential residue additions commit f478e660f31168d4057e322d1d27cf9bb3acef95 resolving conflict from merge master commit da51cb06262b79c16011ba750513e97df273d73d Fix PyAssert in ResidueType::atom_base() and abase2() Graph based natoms() and vector based ordered_atoms_.size() will differ during patch application. Change the PyAssert to use the more directly relevant ordered_atoms_.size() for check instead. commit 9187a1a49f445d1c748b1961d0b2f85bc349704f can now turn off variable_bond_geometry in 10% of stepwise monte carlo minimizations (arvind trick) with -allow_variable_bond_geometry false commit a58efc578beda2acf9f1ccdaf2ba7edf6ea4aae1 rerooting of poses that get split off -- noticed problem in building internal loop. i think this did not cause any bugs in previous code -- just inefficiency in defining moving partition -- but need to check. commit c2fdcd5af448dc1ff57de5fcf2a5f13f4e177167 fixing a delete move that can split off some free-floating RNA stuff that is not attached to a fixed domain. Might be desirable in the future actually, but not right now commit 305e3e753e1d3891ad34aa56866b28e1f5f9f7d5 Commenting out PyAssert that I accidentally left uncommented in my previous commit. commit fb0b3f4b3fa7bba09823ace3d2c88cea1e903a9f Fixing PyRosetta build on Mac commit 69a80ed67b8875c42b464c74f42e964210ed56f8 Adding a new piece of data to the residue parameter file: a virtual shadow, which declares the first atom to be a shadow of the second. This will now be interpretted by the cart-bonded term to mean that a small force should be applied to keep the shadow atom near the original atom. Hopefully, this will allow us to fix the cart_bonded / pro_closure discrepancy bug in a more graceful way than we are fixing it currently. commit b69926c12a8fb9c79cc1f490a8f229405a4fce10 PyRosetta. Fixing tests. commit 6a1f39b822aa67e62e70d95b870db128c31f8dd7 Fixing PyRosetta build. Rearranging import orders. Removing PyAssert that prevented construction of the Pose. commit b9da1ece8f1db034997d3f901232bb04a16de554 for runs specifying an RNA residue type set, go ahead and flip DNA to RNA. Ran into a case for 1LNT, where one residue does not have a 2'-oxygen but is OK to model as RNA. commit 79c7f90c01961e3e8487fcd29b6c5f1ad34bdb5f be careful when splitting pose to not split across a fixed domain! commit 9e6655eab9c0c6711928331904670d31d488ea55 fix to arvind fix -- virtual ribose check at fixed res needs to look at full model numbering commit 091501cd0c39dee7b9851966c0fb3553cbd09319 remove unnecessary file commit 43bedb83abbdcc29c2ece257e39b73ccacee5e3b Merge branch 'master' into rhiju/swm_bulge commit 2a9572cb1404ea085592a514346e944529fc9eb1 Updating options.settings, adding version 3.3 for clang. commit 91205d3ae4037e5627ab0c1625d80ede4a5d094d Updating options.settings, adding version 3.3 for clang. commit b91f3478714f0330de33a680f5882ca5b1ada3c2 oops! Fixing the logic in the app_exception_handling app after my commit earlier today added an extra line to the log file commit a4c0c9d45af4e5f0a5dff67207ac54bc68e8a8ad Adding unit tests for / fixing a few bugs in the FileContentsMap class commit 5802700516f8dd35d62f6e6c3555abb79b390491 Merging in unit tests for the utility::io::FileContentsMap class commit 7f32cd52a8ef69366bc7c805c4756d701e3ccc10 Adding forgotten file commit 6b3ecd781c845a647ddb46a93cc64832b55b5ab8 Merge branch 'master' into benchmark commit d2b53c678bc7831ff2f0d2b9b2da53f6f1b6076d trying to fix sugar reference res for SWA integration tests commit 7dd50c159f8447bf8331431540f6a06b731246e6 Adding unit tests for / fixing a handful of bugs in the FileContentsMap commit 317a45b1af298aebce0b0303e5c6d34e54f788ba trying to clean up sugar reference res logic... commit 1dc8fc72f14d30a71c88dcd9cd5df98f879f1db7 Adding unit test suite for the FileContentsMap commit e9c4edbe8500aea01034bcb8a8489e02d74882cc fix needed in determining sugar reference res... that code needs to brea really cleaned up. commit 478e65a9c15f22a71af1d9ab64d4cfb11023733e Fixing the unit test build. Adding a line to the app_exception_handling integration test so that there's always at least one line of output in the exception handling log. commit 9c31604963f4db865aadb0897b35d0ad58371105 Dummy commit to trigger test server run commit 4c1298b7cdf89dba57463f1ca6d996794ea278dd properly compute accept ratio and make best score accepted if <= commit b2c86bd4714440406df609f3b21b1b660ad1f277 Adding the very beginnings of thread-safe code to Rosetta. Starting with singleton classes, of which, only the ChemicalManager is genuinely threadsafe. Several singleton classes are safe to the extent that if two threads simultaneously try to create the singleton, then only one singleton will get created. Adding a handful of classes to utility/thread that build on the mutex classes defined as part of the C++11 standard. Multithread support can be activated with the extras=cxx11thread additon to the scons command line. Adding a prototype version of a massively-multithreaded multistate design algorithm (mmt_msd) that distributes work from a head node to a set of remote MPI processes each of which can spawn N threads that do the actual work of repacking a sequence on a state. This new code builds on the existing multistate design interface that I wrote a few years back (the one for the mpi_msd application). Currently, the prototype does not handle non-pairwise decomposable properties, but this will come online soon. Adding / extending Matt's code to debug / unit test MPI code for serial applications that relies on intercepting calls to the functions in utility/mpi_util.hh. Adding a FileContentsMap class to utility::io that holds the contents of files in memory so that they only have to be read from disk once. Fixing a bug in the code for restoring previous score12 + sp2 behavior that would have had no effect on anyone but Matt and myself, but which fortunately didn't even affect us. Thanks, Rhiju, for pointing it out. Cosmetic changes in 6 integeration tests as a result. commit c822194b13bbb8d04fbebdb23e432f4ac5c91f63 Updating the code that relies on the FileContentsMap. commit ada575912cc4823ab75b3a1b1192b723cad0dbd7 Writing documentation for FileContentsMap commit 9b14e244c7234808a9e0a10f13e844cee59eda9b Putting FileContentsMap into utility/io commit f0ca05d49423e749c7333cae00793451f0c5786f Moving the FileContentsMap to utility commit e83f9b7c8c0a7a11a017b8e0fbac5b3dcc1613fa another fix in assigning reference res. basically for standard swm just pick an upstream jump residue as the reference residue. there can be only one. do not try some kind of process of elimination... (or perhaps later do this to help disambiguate in SWA setup before fold tree is setup.) commit 514a93f126c571da8fbce46d7c917166ce5b1fa5 oops, minor mistake after refactoring virtual_sugar_util -- this should fix a crash commit 11169c269d2c5f43dcf70d0b733424606d5bc701 Hopefully this fixes a segfautl problem in interfaceanalyzermover commit 71a4a56cb0b824d738cc9f3a316505380db949bd floating base and variable geometry bug fixes Fixed a bug in SWM in which virtual riboses were placed on floating bases present in the native pose, leading to crashes in SWM benchmark runs. Code now checks to see if the residue is fixed or not in the domain map. Additionally, altered variable geometry minimization code in SWA/SWM to only operate on backbone atoms, which fixes cases with distorted base geometries. An alternative fix for the future is to put in improper angle constraints on the planar atoms. modified: source/src/protocols/simple_moves/ConstrainToIdealMover.cc modified: source/src/protocols/swa/StepWiseUtil.cc commit b8a0fcb7e30c243ceec0d8fc173ba7bb9848a210 floating base and variable geometry bug fixes Fixed a bug in SWM in which virtual riboses were placed on floating bases present in the native pose, leading to crashes in SWM benchmark runs. Code now checks to see if the residue is fixed or not in the domain map. Additionally, altered variable geometry minimization code in SWA/SWM to only operate on backbone atoms, which fixes cases with distorted base geometries. An alternative fix for the future is to put in improper angle constraints on the planar atoms. modified: source/src/protocols/simple_moves/ConstrainToIdealMover.cc modified: source/src/protocols/swa/StepWiseUtil.cc commit efa28fbc3374f252ab0d161edaebcdd12cb12de1 More updates to crystal docking: uniform sampling of rotation space, removing duplicate translational/rotational hits commit 59c6cd01668b8857aa27162491ebaff4497137a2 Appending accept ratio to job in Transform mover commit 55fb9c7bc76f9a134a26732fb0483dd64032ef5d [minor update of SandwichFeatures] report explicit electrostatic interactions among surface residues on beta-sandwiche [integration tests comment] should not change other than features (if any) commit 4296c7d52a3f0edd7105af5c495e22e50f04c729 Fixing build for min_pack.cc; replacing the default use of the MMTMinPackingJob with the new MMTOffRotamerPackingJob commit 093f2d53eab72cbfb20f85f2b22cf4ed4fa2021b adding a new feature to Transform to limit the RMSD to the starting position commit ceccae6414741e58aa6fbe8961b87d1cafe7a015 Renaming "stochastic_pack" to "off_rotamer_pack". Reducing the number of rotamer substitutions in off_rotamer_pack by a factor of 5. commit 1a3f667222b4cf0781d4a7e942eb7747b2afeb86 Adding an off-rotamer packing job class commit d550480171cee6395c1ba3ec2541a292fda322f6 Update the by-time integration test sorting. Use the locally produced ref/ timings, if availible, else use the updated test server reference timings. This should update things for new integration tests which have been added. commit acfb7e6ca0e1a2827a4576e1e10bf7a588752922 Change SaveResfileToDiskFilter to use PDB numbering SaveResfileToDiskFilter was using pose numbering with the PDBInfo chain ID when outputting the resfile. This is probably not the best behavior to have by default. Changed the filter to default to PDB numbering. If you're using an already renumbered PDB, (I believe this was the standard use case) you shouldn't see any change. If you need to use pose numbering (e.g. you're using the SaveResfileToDiskFilter in a run with -out:file:renumber_pdb), you can retreive the old behavior by using the renumber_pdb bool setting, either in the XML tag or via setter methods. (Defaults to false in both cases.) No test changes expected. commit 2bcd862ac09f60d132b3fab82671a4f42266b0fc Merge swm_bulge branch. Several bug fixes found through stepwise monte carlo runs with "floating base" and sugar instantiation moves. Refactoring of SWA_MonteCarloUtil to SWA_MoveSelector class is getting checked in now to help prevent divergence of my branch from Arvinds. commit c957862b63273da11d64bbbfe9fbad8a5ca3d997 Merge branch 'rhiju/swm_bulge' of github.com:RosettaCommons/main into rhiju/swm_bulge commit 6a0a9271e498a59706c996bbd3d76e77a75b48c2 resolving conflicts with master commit 9100456f8ec16b810ae328325164f1629817cc92 restoring automatic virtual sugar reference finder for poses without explicit jump specification. some reduction of verbosity. commit e39dd80c66c81fa0251f55d41ad8356fb2421173 Adding the option "ligandchain" to InterfaceAnalyzerMover If a chain is specified with this option, every other chain will be marked as mobile all tests pass commit 2cf8a61496f290ab00b7662629872007f798f242 Debugging "stochastic packer," which should probably be renamed as "off rotamer packer;" adding an MMTOffRotamerPackingJob class to use instead of the MMTMinPacker commit c9db31941f9394a40fd2eb73e7ba3da8d13a0984 agh if != else if grumble grumble grumble commit 707ec8cf72c0e746d77f89f02384c7c7dde6f4a8 adding option “ligandchains” to InterfaceAnalyzerMover allows for a mobile ligand chain to be specified, and for every other chain held fixed regardless of the IDs of those chains. This is useful if you are docking ligands into a heterogenous set of proteins commit c801bff3e8d1c793613458ef164531be22e302f6 Merge branch 'rhiju/swm_bulge' of github.com:RosettaCommons/main into rhiju/swm_bulge commit e656b32b883e49eecfd9586ff2fcc0dbcd80540a allowing free sugar bonus for VIRTUAL_RIBOSE variant to accept more skip_bulge moves commit d6d171f2f02f2cf85777d54dd4adc47ce48762a2 Ok, the mmt_msd application kind of sort of appears to be running correctly. commit d712146fe8f63c3b16645cf03839c61236e6144e Merge rotamer_recovery_features branch * Refactor make_pose_from_sequence to take a ResidueTypeCOPs * Add make_score_function_consistent_with_symmetric_state_of_pose (with unit tests) * Use safely_* database interfaec in DatabaseJobInputter * In the FeaturesReporter framework, change RelevantResidueMode levels from Explicit/Implicit to Exclusive/Inclusive. This better reflects their role in deciding which features to report. In Exclusive mode, a feature is reported if all residues are specified in the relevant_residues input vector; in Inclusive mode, a feature is reported if any residues are specified in the relevant_residues input vector. * In the FeaturesReporter framework, improve support for reporting and initializing poses from subsets of residues. The tricking parts are to get the residue numbering correct. In reporting features for a subset of residues: * In PoseConformationFeatures: Create a new pose of the subset of residues and renumber them sequentially and report all features * In ResidueFeatures: doesn't renumber the pose, just report the relevant residues * In ProteinResidueConformationFeatures: don't renumber the pose but also only report features for (canonical) protein residues This means that to reconstruct the pose conformation, first the conformations stored in residue_atom_coords must be aligned with residues table to get the appropriate gaps for non-canonical residues, then these need to be renumbered to align with the renumbered pose reported in PoseConformationFeatures * ReportToDB * refactor parse_my_tag to call member initialization functions, thus allowing initialization without using the RosettaScripts interface. * Add accessor to get the last struct_id * HBondFeatures reporter: * Add the hbond definition type and threshold to the default constructor list * If a score function isn't provided, use the default energy fuction (via getScoreFunction()) * Only report hbond_dehydron values for protein-protein hbonds * RotamerRecoveryFeatures reporter: * Add predicted_features_reporter option, which references a ReportToDB mover that is used to report features for the predicted conformation, rather than the native conformation. * General cleanup in the RRReporterSQLite module * Fix bug in StructureScoresFeatures where n_score_types was mistakenly used rather than total_score. Expected Integration test changes due to total_score bug fix: database_session_resource features minimize_with_elec_dens repack_with_elec_dens resource_database_locator resource_database_tables commit 1c4ceb923d0a2ddd57b2ef173f9b64094f4504fe encapsulated SWA_MonteCarloUtil into SWA_MoveSelector class commit bff2f295abdcd2c6b0140e9146e1cdebee704594 Merging 'master' into aleaverfay/mt_msd Conflicts: source/src/apps/public/design/mpi_msd.cc source/src/core/pack/min_pack.cc source/src/core/scoring/constraints/ConstraintIO.cc source/src/devel.src.settings source/src/devel/replica_docking/TempInterpolatorFactory.cc source/src/devel/replica_docking/TempInterpolatorFactory.hh source/src/protocols/flxbb/LayerDesignOperation.cc source/src/protocols/pack_daemon/MultistateFitnessFunction.cc source/test/devel.test.settings commit 2fc2d81bf47b6d9bef916a24fef6639475dad0c0 Fixing a few problems in the FileContentsMap; this class needs its own unit tests. commit 503b5fd5eab70a07c4df03313806dafe34a0ee18 minor fixes to prevent graphics crashes commit 9fd0beac8274e4d60a30024a4e598381ce66a3c0 Adding forgotten unit test suite for MMTDriver; adding mmt_msd executable (mostly a duplication of the mpi_msd application) commit ef5232a903696ed2560ae767ff2eba9ed1192d88 updating delete move in SWA monte carlo to allow "split pose" -- now the reverses of each add/merge are available moves. commit bf518013101f96e7100349a8da7364fdb5c9498d removing assert in virtual sugar sampler that does not hold for internal suites commit 7f2972246ce6c224b9820459bc6f4d30c03e7b8e numerous fixes to variant addition and jump setup -- in particular virtual riboses were being incorrectly unvirtualized by the fix_up_residue_type_variants(). Note that code to identify anchor residues for virtual riboses now requires that input poses have jumps set up properly -- will not handle classic SWA case from Parin with continuous strand and intervening bulge. commit ee0d93a96562f4631294f68efcbdb67960851e16 Moving core/scoring/func/* classes in to the proper namespace. This should fix PyRosetta build. commit d831a6613e73f6fee030e40a8f2fde0e60074d09 merging recent changes to master commit 067f65c99dd6e05654578559e10da4a32789c14b fixing merge conflicts for recent merge of variable geometry code in SWM integration test changes expected in all SWA-related code modified: source/src/protocols/swa/StepWiseUtil.cc modified: source/src/protocols/swa/monte_carlo/RNA_ResampleMover.cc modified: source/src/protocols/swa/rna/StepWiseRNA_Util.cc commit 8fa28365016f46a1e1ae3f4283ac6fde50ce2b03 implementation of variable geometry minimization in SWM calculations Integration test changes expected in all hi-res RNA code modified: source/src/apps/public/swa/rna/stepwise_monte_carlo.cc modified: source/src/core/pose/Pose.cc modified: source/src/core/pose/Pose.hh modified: source/src/core/scoring/rna/RNA_FullAtomStackingEnergy.cc modified: source/src/core/scoring/rna/RNA_FullAtomStackingEnergy.hh modified: source/src/protocols/simple_moves/ConstrainToIdealMover.cc modified: source/src/protocols/swa/StepWiseUtil.cc modified: source/src/protocols/swa/monte_carlo/RNA_AddMover.cc modified: source/src/protocols/swa/monte_carlo/RNA_DeleteMover.cc modified: source/src/protocols/swa/monte_carlo/RNA_ResampleMover.cc modified: source/src/protocols/swa/monte_carlo/RNA_StepWiseMonteCarlo.cc modified: source/src/protocols/swa/monte_carlo/RNA_StepWiseMonteCarlo.hh modified: source/src/protocols/swa/rna/StepWiseRNA_Minimizer.cc modified: source/src/protocols/swa/rna/StepWiseRNA_Minimizer.hh modified: source/src/protocols/swa/rna/StepWiseRNA_Modeler.cc modified: source/src/protocols/swa/rna/StepWiseRNA_Modeler.hh modified: source/src/protocols/swa/rna/StepWiseRNA_Util.cc modified: source/src/protocols/swa/rna/StepWiseRNA_Util.hh modified: source/src/protocols/toolbox/AllowInsert.hh modified: source/xcode/Rosetta.xcodeproj/project.pbxproj.template deleted: source/xcode/mpacella/surface_docking_jd2.cc commit d489cef4d47be721b9285d151450d8d140e1d8e3 bugfix for crystal docking commit d2215c6da4d5dd6289afb76f5b844bcd64e9714e w00t! Working version of MMTDriver commit 7c9ed2659e182e2bb1d319e9a5711142efae97bb add atom_mask_min option to ElectronDensity.cc commit 2abd1747adb3a91778a937006d87131756fdcdf1 Checking in a pilot app that does FFT-based docking of a structure into a crystal lattice. commit 3689fdf64de7244ed96c392321f057c63b670ee1 smashed many bugs... so close... I can feel it... commit 4a3c6cd8e06ff501ed624b00edfac0325fc99bbe Unit Tests: added simple testing for add_chi()s and add_nu()s to ResidueType unit test suite commit be24e5ef095fc1c1c7d01e1dcde3bab6a2c170ca debugging unit test