Rosetta 2014.16.56682 Date: 2014-04-22 Branched off commit: 5587a8cb28a727eebd118e7e8e264171e1c5bcef Tail state commit: 5b8e80680ca9434c5d5c7d7f632c2f400a88dacf Previous version: 2014.15.56658 Previous branched off commit: 4fc8b91cf98d5947b9bb74c270f8b91658db61d4 Previous tail state commit: 52872b54c94677df268024fa550f67e7c92ae244 Release notes ============= NEWS: This push introduces lipids into Rosetta. NEWS: [DETAILED DESCRIPTION OF CHANGE] NEWS: In EnzdesBaseProtocol.cc, the default scorefxn is now talaris2013_cst. To be compatible with talaris2013, the exclude_protein_protein_fa_elec_ bool option in the constructor is now set to false by default (it used to be true, which was necessary when using the enzdes scorefxn so not to double count fa_elec of interface sidechains). Using talaris with talaris2013_cst.wts gives ~2% increase in sequence recovery on the enzdes benchmark. NEWS: As part of this week's post-minirosettacon tweak-the-release-system drive, I automated the editing of the strictly-unreleaseable mpi_msd.cc file. This requires tagging in the file for the stripped lines (the rest of the machinery is in tools/release [currently still in a branch]) NEWS: This push introduces several things: COMMIT LOG ========== commit 5587a8cb28a727eebd118e7e8e264171e1c5bcef weekly release: stripping DONOTRELEASE-wrapped code commit 37592607bf7f0d888d4a92a7a2402084cff8764d trying to remove another undefined function to get pyrosetta to compile. commit 32b4783d56374e79ee0da014a09745fcb0c76580 mininterfacesum added commit 6193d3a4f6ba0df9dc060157930e0b61427c6e1b restoring library levels. commit d182d38b333bbd75b333eec23a8d5e06b937a10e removing another undefined function to restore PyRosetta build 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 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 2f37a37976b0812a17bec2e43cdfa4646ab5a58f Carbohydrates: adding new sugars to database ---------------------------------------- Unit test status: Not Run Integration test status: Not Run carbohydrates, rings: change in number of ResidueTypes reported expected commit 56c55882f8d9b875e241c7b7ae2e34b7784c7ad2 Carbohydrates: added new sugars to database 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 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 bc9306f0b995de12813ccab3fff41653471e3423 Detect connectivity for crystal docking now works. Scores returned now correctly represent the weakest interface in the lattice. commit 0c5e45258ab998e4344c5cf0f9b78a8e5b994320 Carbohydrates & Lipids: updating centroid database files commit 623f81da6bc8ebe28563292a0f87f0649861ff36 Fixing header-only build 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 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 aa20417cc9c6d802f6893bf04054803dbc95562a DesignBySecondaryStructure now correctly eliminates ligands from the DSSP string 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 442b5deec3354bc323d0c8a7cc4b457cddde2fe8 Lipids: need to tell params file that it is a branch point or lower terminus, etc. 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 df4681f5aed429854fc536e84e83b46762530fa2 merging in master 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 327e15e8b2cdce1e2aa149779d429a50d15fc5cb PCS Scoring with multiple Tags: New scoring functions which can score PCS data with atleast 4 different tag sites are added commit bca8a65414b309835f85eb152d26b2dd522b0adb To Raijin compilation commit 6a8d317cc5e6e84d49b61766a311baea7ce19666 PCS Scoring with multiple Tags: New scoring functions which can score PCS data with atleast 4 different tag sites are added commit 2137eff80d1442ccf72d316ea2d81640a52a2123 not again... git is fast forwarding some changes. Repeating my earlier commit message: I'm removing warnings from the graphics viewer build. no changes expected. Merge branch 'master' of github.com:RosettaCommons/main commit b422bbfda98c8a6dd88fda4b20edd5c4da046ec4 the graphics build was a casualty of the just and noble war on warnings. I removed some warnings and also had to brutalize an argv in one of the main functions, because I couldn't see how to convert a const string to a char * [] as required by the argv templates. My changes allow the viewer to run now. No test changes expected. commit c8f19b3707584fe2ec91ffe21a8f681fec95e905 Better output capture on database tests. Hopefully will point to the issue with debug-mode resource_database_tables test on the server. Integration tests changes: resource_database_locator and resource_database_tables, with additional output information. commit 017f98a01650ec417eda133e44df4245b47f518c Hopefully fix gcc4.4 uninitialized variable isse in LeeRichards.cc commit b0b6ebd5542f8a37063556a6ffbd5a0457731655 Fix unused variable issue with SymmetryInfo commit 3c58bcd7f83a5d03c91f048dfa69e8af4fd29c85 Fixing a recently introduced error in LayeredDesign that broke the build. commit b8d1b11ac6c35e3894c841a7892f7fb57522fbcf merge master: Updating symmetryinfo so all information is saved/restored when reading/writing to a silent file. commit 09e541dc98c7ca2cddfcf32e70c29c0ec7e4c9b7 Updating symmetryinfo so all information is saved/restored when reading/writing to a silent file. commit d32256199abeda3e08918ccdcd37dc449e216000 Fixing clang/Xcode compiler linking error; clang/Xcode should now build fine To have things link properly in Xcode, I had to add the following include to protocols/outputter/SilentFileOutputter.cc: #include //sboyken, 03/17/14 needed for proper linking in Xcode # ---------------------------------------- No changes to integration/unit tests This commit should fix linking errors for clang/Xcode that some have mentioned recently commit 2758cee2408d7e2976cbb61675404551958f7eca Warnings Removal: 14 uninitializeds from GCC 4.4 release mode commit 6353728389e82ccb82f493081b45688c58e26e99 Updating SymmetryInfo so all members are updated in default constructor and dumping/reading from silent files exactly reconstructs SymmetryInfo. Maintaining backward compatability with older silent files. commit b6b55e0b1b2231a416783acbae0cabcd3db17776 Fix to LayerDesign parsing of CombinedTasks commit 6a0a642b7610554d891d2a4e680bbbaeb67539f8 Warnings Removal: silencing one error type specifically for GCC 4.4 commit c24aa6a8f98b5d78e0c2d48924309edd2e8154c0 Fix uninitialized variable issue reported by Tim Issues found with gcc 4.6 commit 6587c8025f524a47712d1d8f0d19d93ff738543c Refactoring SampleApplier.cc to remove construction of Pose object during static initializations commit fd8c92121e1d187f65d26ef08d0b3b6044f9b485 Better error checking re: membrane spanfiles commit 9a8d46c04d1243a68309a145741a9bf6091b1af8 Fixing an error with newly added flags for auto-detection of metals. The problem was related to invalid 'legals' options within options_rosetta.py Fixing the Xcode project to work with the recent upgrade of boost. Specifically, set BOOST_ERROR_CODE_HEADER_ONLY and BOOST_SYSTEM_NO_DEPRECATED flags, which are now part of the default build commit bb2d939ef61f6c3816271d111ca15d8c45feb548 Fix initialization issues Fix uninitialized variable issue in GasteigerAtomTyper Fix -Wmaybe-uninitialized issue with numeric/xyzVector.hh Turn off -Wno-uninitialized in cmake and scons builds. Rosetta compiles with cmake & scons, gcc & clang, at least on my machine. commit 00865d4208cbe23c84e47afbb4d01eec889969a2 attempt 6 to fix Mac PyRosetta commit b0ec822e0443dced548ffafcf0810dfcb7b7da24 attempt 5 to fix Mac PyRosetta commit 84407894bb5dacb54d1cc1ad20cb8e13ba6968e2 attempt 4 commit cfbc21c3594dd18469e38b46902310df4fe80e83 attempt 3 commit 9fffacc73e3b18bdfbaf8866dc2276363cbca813 trying to fix Mac PyRosetta commit 0328a08596b3ea44def31fe32249f107447e37ba removing warning only caught by Mac PyRosetta build commit 6dcca0ee6dc1613afefbf183c5bce2c3bb5b2673 Change to GLY.params: glycine is not an L-amino acid. Duh. This is a minor change to the database. Therefore: --Integration tests were not run. --Unit tests were not run. commit aa727100361096fe0c3d2a3e4d9ccdc1df71bf9f Updating properties and BACKBONE_AA of BPY.params. Minor change to database; unit and integration tests not re-run. commit 7ca9e371ce74598ca3f05f7e7741901d006006f9 Merging vmullig/ncaas into master to get my changes to NCAAs. --Add 4,5-dihydroxyisoleucine (a component of alpha-amanitin) to the l-ncaas part of the database. --Change is_D_aa() function in core/chemical/AA.cc to is_canonical_D_aa() --Removed some code duplication in Ramachandran.cc. --Added BACKBONE_AA lines to params files. This can be used to tell Rosetta that the rama and p_aa_pp scoring functions should treat a particular noncanonical amino acid like a designated canonical amino acid. (For example, in the 4,5-dihydroxyisoleucine params file, we have "BACKBONE_AA ILE"). --Added ALPHA_AA, BETA_AA, L_AA, and D_AA properties for alpha, beta, L-alpha, and D-alpha amino acids, respectively. --Updates D-proline with shadow atoms so that it scores and minimizes identically to (i.e. like the mirror image of) L-proline. --Fixes one more dependency problem in core/pose/util.cc, which should hopefully fix any remaining build problems not fixed by my last tweak to master. These changes have not yet been described on the Gollum Wiki, but will soon. TODO: --Update BPY.params. Unit test status: Pass Integration test status: ZERO changed tests! commit 5e8f042ad525239f040c015ad009601125896a45 Turning off things that should be off in residue_types.txt commit beffdc7c425326da9adeb49c0bb2ba2ea493a5bd Turning off newly added residue type in residue_types.txt prior to merge with master. commit 2867f0220535139dd5ad005dfd8a89bd2007c624 Merging origin/vmullig/ncaas into local vmullig/ncaas... commit 6d3b8782b181b5318073d4cf80e56fb3f18f2138 Merging master into vmullig/ncaas for integration testing prior to merging vmullig/ncaas into master. commit 16861c5610aa3a0451fda84534cfebc56cdc8ec1 Tweaking core/pose/util.cc to fix dependencies. commit 294278ead33d1893c59d4644e7a7bcb4e7047b8d Merging master into vmullig/ncaas to get my changes to metalloproteins / fix to the Mac Clang build. commit 9534b84b587d5321279432caf11ca15d840369ae Attempt at fixing Mac Clang build that I broke with my previous changes to metalloprotein handling. --I think I had bad dependencies -- something from core.3 depending on something from core.4. I've moved all the metalloproteins utilities to core/util/metalloproteins_util.cc, which is in core.4. --I have no idea why the build was working under Linux, though (with both gcc or Clang). Unit test status: Pass Integration test status: Not Run --I don't have access to a Mac with Clang right now, so I'm relying on the test server to tell me whether this works. Everything compiles fine on my Linux PC with gcc, though everything did before, too. commit 9c3da9346eb79027a833c09a26c1ed1e8a310d77 Moving metalloproteins functions to core.4 and to core/util/metalloproteins_util.cc in order to try to fix the Mac clang build. I have no way to test this, though, so we'll see... commit 02e7e94f9a47af6cdcf446e67837e59d406cfbcb Rosetta Membrane Framework Updates: - Added parse_my_tag function for RosettaScripts to CreateMembranePoseMover - Create Membrane Pose Mover will now **overwrite** the pose passed by JD2, so JD2 can handle a membrane pose - Added mover creator and full rosetta scripts hooks Unit Test Status: All Pass (linux tested, clang build broken) Integration Test Status: No Expected Changes Change Date: 3/15/14. Authors: Rebecca Alford, Julia Koehler Leman commit afd51c99d89243aecc93ba43f20b0cf8555dcd7b Merge branch 'jkleman/RosettaScripts_hook' commit 769fa3bd92bab46de8c94da18e6c9e33d75db8c0 Warnings Removal: fixing cmake to match Scons commit 5f96b2e79b648bea19a965b60bc07a44d9e5ae62 Warnings Removal: correcting basic.settings; mistake made during merge conflict resolution previously commit 2df758bc6b167c9178cf2fcf1d6374e29776af07 WARNINGS WAR Z: Turing on Werror for all builds. List of warning types removed in this round: * Wheader-guard -- This occurs when one has a typo in his or her header guards. For example: #ifndef INCLUDED_core_scoring_MyEnergy_HH #define INCLUDED_core_scoring_myEnergy_HH * Wself-assign-field -- This occurs when you write code like this: foo = foo; * Wliteral-conversion -- This occurs when you are using raw values -- which you never should be doing -- and those raw values are then cast with a loss of precision. For example: void my_function(int bar) { // do stuff } my_function(1.23456); * Wstring-plus-int -- These occur in three varieties and in EVERY case they occured within utility_exit_with_message(). (Fixing these should greatly improve the error helpfulness of Rosetta.) This occurs when you try to append an int to a string with +. utility_exit_with_message() takes a string, not a stream, so you can't do this. The three varieties are when folks try to append ints, chars, or enums, which the compiler will treat the same. To append a char to a string use: + std::string(1, my_char) To append am int or an enum, I like to use boost:: lexical_cast, but there are other methods also. (A plug for Clang -- all of these were only caught by Clang 3.4, which the test server uses.) * Wunitialized -- This occurs usually when your code makes assumptions that may well be correct, but the compiler cannot figure that out. If I could figure them out, I fixed them, but in a few cases I could not, so I have shut this warning OFF until I can find those of you who can fix this one. This also occurs if you try to instantiate an object from within its own constructor! Also, I have cleaned, sorted, and organized basic.settings. Hopefully, it will be easier to find where settings are located now. ---------------------------------------- Unit test status: Pass Integration test status: 6 tests changed, all of which are the result of my fixing what I believe to have been a bug do to a cast of raw float values to a boolean [Wliteral-conversion] antibody_designer antibody_H3 antibody_H3_legacy pepspec hotspot_graft dock_with_hotspot commit d91a1cc38b05c2db696df5c1e8306eb1b22de89b Warnings Removal: removed object initialized withing its own constructor commit 54ecd2680aa91925f55233be815da05e205f4f31 Rosetta Membrane Framework Update: - Adding parse my tag in CreateMembranePoseMover - Added mover creator header - Test inputs added to unit testing directory commit 99f292cf1f37cbd0d18fbd7c79302a29c44a5105 Warnings Removal: still another Wstring-plus-int commit 8ec91a3804a3d3f3d0217029cd892b078dfa314c Warnings Removal: Wself-assign-field and Wstring-plus-int commit a24dad2a13674ba79a431d03173e3bc6350f5f09 Warnings Removal: another 4 commit 14d21f931d69ab1eba36fe1cf6a1f1f25ed972bc Warnings Removal: missed one commit 5ab460fa078bbd314b57a6db3a89cd2a9ebf76a6 Warnings Removal: 4 more string-plus-ints commit d482e430d4df0cb1948bc6146d42484f109d9a17 Warnings Removal: fixed 4 literal-conversions commit dd56ece13f1927eff4f4a5b2966eb6209f7fbf5f Warnings Removal: temporarily turned off Wuninitialized, because I can't fix GasteigerAtomTyper commit 0f7ebab6fc2c2309958b57a8b25681051594f2c4 Warnings Removal: still another commit 21689269dc845498b471bcf77044276794a8d232 Warnings Removal: 2 more commit 013870ee61f10f5014f00d2f747716cee7d28c8a Warnings Removal: 3 more string-plus-ints commit 5db6a32137a40521fe8b1d70434fb3506f8f2257 Warnings Removal: yet another header-guard typo commit 7cbde4ad62c248a6aa0e44e0d1aca312a9cc71e9 Warnings Removal: tweaked basic.settings to avoid unusued release mode warnings commit 6238a40c1c235c9417cd528b0704b3186981296c Warnings Removal: uninitialized and string-plus-int commit ff8b5eeb4a6f90dc19a02ccaa2f19f6a1e9c0654 Warnings Removal: shut off Wstrict-aliasing for now, until we figure out what the heck it even means commit b29a77d8ae8a71274ba2e6f958f0b228e7868e1e Warnings Removal: Wliteral-conversion and static function that shouldn't have been commit 1bf13f952aaabe5301d39997569f04e2ad4ded3e Warnings Removal: yet another commit 02e9b74a698fd3e00278dab349a7b82d61b763ea Warnings Removal: and another commit ce8c59f9cb774b19dab2ddf7764ccc872e4c1950 Warnings Removal: another string-plus-int commit 921604ce9cdb883859c1d3f0bed48b9af8565e27 Warnings Removal: another header-gaurd commit dd9456499a8af0045f8eb7e2976bea4c9f971048 Warnings Removal: unused and string-plus-int commit 842d1d2b61197edf8c62174af831284e0c50990f Warnings Removal: and another commit b1b1eace16858c1cdf8632761f546d5f1b441502 Warnings Removal: another commit baeb183afd741bf904f11611abba1998e1f8540b Warnings Removal: more Wheader-gaurds and an unused commit 574fab8151e2ba2b809f215be7fc59ef19febf0d Warnings Removal: corrected bad header guard commit 7c5fd384ff6ed7ef9e122c919467fbfd8428471b Warnings Removal: didn't need boost; removed two more commit 70a99f8754ea8565df591b7f365d88d86eff2193 Warnings Removal: removed string-plus-int warnings commit c328d5ad66930572abe0f33f506f48c40b2cb198 Build Settings: removed commented out settings refering to local drive locations commit 3f232bd4dedd11ff89fc6f7aa77fd5a9647d146d Warnings Removal: Clang is clean. Prepping to clean GCC commit f1f46df798bbc1774ab31d1dd7c4d0ff3422101f Build Settings: finished cleaning/organizing basic.settings commit dc89c6974de9fd773a66b2cb6ed85fc6be374390 Merging master into vmullig/ncaas branch to get updates to metalloproteins. commit 89fc5b44a889c6400d5b81833df9fc3b044b7b82 Warnings Removal: removed eof warnings commit 479421e9fd6defdb7e8b27a267c92738b515bb7e Build Settings: basic.settings file cleaned and organized commit d4893e0c6566d6b2a513dda4a83dde1defb44f78 Fixing MySQL build. Adjusting linking path to include somewhat-standard mysql lib path. Adding mysql prefix to MySQL includes. This should allow MySQL build to work out-of-the-box for mosts Linux distributions when MySQL-devel package installed. commit 3b2066ac1a514ff5c3a3e2f5a835f732e459d8c2 Fixing MySQL build. Adjusting linking path to include somewhat-standard mysql lib path. Adding mysql prefix to MySQL includes. This should allow MySQL build to work out-of-the-box for mosts Linux distributions when MySQL-devel package installed. commit c5274e97ed07be49cae0fc75ba556403a5ed6c7e Merging vmullig/metals into master. This updates the handling of metalloproteins in a number of important ways: --Adds option of automatic detection of covalent bonds to metals on PDB load. --Adds option of automatic setup of atom_pair and angle constraints between metals and metal-binding residues on PDB load. --Adds METALBINDING property to residue types. --Adds METAL property to residue types. --Adds METAL_BINDING_ATOMS line to params files. --Adds automatic removal of protons that overlap with metal ions. --Adds flags controlling behaviour of automatic metal setup. --Adds Cu and Co (residue types and atom types). --Allows automatic identification of metals: " ZN", "ZN ", "ZN1", and "ZN2" are all interpreted as ZN. --Alters unit and integration tests that used a ZN1.params file; these now use ZNx.params. All of these changes are documented on the Gollum wiki ("Metals" section of "Rosetta Basics"). Unit test status: Pass (with some unit tests' ZN1.params files changed to ZNx.params). Integration test status: Many changed tests, but all for expected reasons: 1. Trivial output changes due to addition of Cu2p and Co2p atom types. 2. Trivial output changes due to addition of CU.params and CO.params (on by default -- adds 2 new residue types). 3. Specific integration tests now use ZNx.params instead of ZN1.params; their output now says "ZNx" wherever it used to say "ZN1". 4. The usual numerical instabilities. modified: database/chemical/atom_type_sets/fa_standard/atom_properties.txt modified: database/chemical/atom_type_sets/fa_standard/extras/NACCESS_sasa_radii.txt modified: database/chemical/atom_type_sets/fa_standard/extras/atom_orbital_hybridization.txt modified: database/chemical/atom_type_sets/fa_standard/extras/facts_born_params.epm1.txt modified: database/chemical/atom_type_sets/fa_standard/extras/gen_born_params.txt modified: database/chemical/atom_type_sets/fa_standard/extras/memb_fa_params.txt modified: database/chemical/atom_type_sets/fa_standard/extras/reduce_sasa_radii.txt modified: database/chemical/atom_type_sets/fa_standard/extras/sasa_radii_legacy.txt modified: database/chemical/atom_type_sets/fa_standard/extras/soft_rep_params.txt modified: database/chemical/atom_type_sets/fa_standard/extras/std_charges.txt modified: database/chemical/mm_atom_type_sets/fa_standard/mm_atom_properties.txt modified: database/chemical/residue_type_sets/fa_standard/residue_types.txt 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/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/GLU.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 new file: 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 new file: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/CO.params new file: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/CU.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/FE.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/FE2.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/K.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/MG.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/MN.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/NA.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/ZN.params new file: source/src/apps/pilot/vmullig/MetalNotes.txt new file: source/src/apps/pilot/vmullig/metals_notes.txt new file: source/src/apps/pilot/vmullig/test_metalloproteins.cc modified: source/src/basic/options/keys/OptionKeys.cc.gen0.hh modified: source/src/basic/options/keys/in.OptionKeys.gen.hh modified: source/src/basic/options/keys/inout.OptionKeys.gen.hh modified: source/src/basic/options/option.cc.gen.hh modified: source/src/basic/options/options_rosetta.py modified: source/src/core.3.src.settings modified: source/src/core/chemical/ResidueType.cc modified: source/src/core/chemical/ResidueType.hh modified: source/src/core/chemical/residue_io.cc modified: source/src/core/conformation/Residue.hh modified: source/src/core/import_pose/import_pose.cc modified: source/src/core/import_pose/import_pose_options.cc modified: source/src/core/import_pose/import_pose_options.hh modified: source/src/core/io/pdb/file_data.cc modified: source/src/core/io/pdb/file_data_fixup.cc modified: source/src/core/io/pdb/pose_io.cc modified: source/src/core/pose/Pose.cc new file: source/src/core/pose/metalloproteins/util.cc new file: source/src/core/pose/metalloproteins/util.hh modified: source/src/core/pose/util.cc modified: source/src/core/pose/util.hh modified: source/src/core/scoring/ScoreFunctionFactory.cc modified: source/test/apps.test.settings modified: source/test/apps/public/ligand_docking/7cpa_7cpa_input.pdb modified: source/test/apps/public/ligand_docking/7cpa_7cpa_native.pdb renamed: source/test/apps/public/ligand_docking/ZN1.params -> source/test/apps/public/ligand_docking/ZNx.params modified: source/test/apps/public/ligand_docking/ligand_dock.cxxtest.hh modified: source/test/apps/public/ligand_docking/silent.out.ref modified: source/test/protocols.test.settings modified: source/test/protocols/ligand_docking/7cpa_7cpa_native.pdb modified: source/test/protocols/ligand_docking/ResidueTorsionRestraints.cxxtest.hh renamed: source/test/protocols/ligand_docking/ZN1.params -> source/test/protocols/ligand_docking/ZNx.params renamed: tests/integration/tests/contactMap/input/ZN1.params -> tests/integration/tests/contactMap/input/ZNx.params modified: tests/integration/tests/database_jd2_compact_io/7cpa_7cpa_input.pdb.gz renamed: tests/integration/tests/database_jd2_compact_io/ZN1.params -> tests/integration/tests/database_jd2_compact_io/ZNx.params modified: tests/integration/tests/database_jd2_compact_io/test_input.flags modified: tests/integration/tests/database_jd2_compact_io/test_output.flags modified: tests/integration/tests/grid_scores_features/flags modified: tests/integration/tests/grid_scores_features/inputs/7cpa_7cpa_input.pdb.gz modified: tests/integration/tests/grid_scores_features/inputs/7cpa_7cpa_native.pdb.gz modified: tests/integration/tests/grid_scores_features/inputs/7cpa_confs.pdb.gz deleted: tests/integration/tests/grid_scores_features/inputs/ZN1.params new file: tests/integration/tests/grid_scores_features/inputs/ZNx.params modified: tests/integration/tests/kinemage_grid_output/flags modified: tests/integration/tests/kinemage_grid_output/inputs/7cpa_7cpa_input.pdb.gz modified: tests/integration/tests/kinemage_grid_output/inputs/7cpa_7cpa_native.pdb.gz modified: tests/integration/tests/kinemage_grid_output/inputs/7cpa_confs.pdb.gz deleted: tests/integration/tests/kinemage_grid_output/inputs/ZN1.params new file: tests/integration/tests/kinemage_grid_output/inputs/ZNx.params modified: tests/integration/tests/ligand_database_io/flags_param_output modified: tests/integration/tests/ligand_database_io/inputs/7cpa_confs.pdb.gz modified: tests/integration/tests/ligand_database_io/inputs/7cpa_input.pdb.gz modified: tests/integration/tests/ligand_database_io/inputs/7cpa_native.pdb.gz deleted: tests/integration/tests/ligand_database_io/inputs/ZN1.params new file: tests/integration/tests/ligand_database_io/inputs/ZNx.params modified: tests/integration/tests/ligand_dock_7cpa/flags modified: tests/integration/tests/ligand_dock_7cpa/inputs/7cpa_7cpa_input.pdb.gz modified: tests/integration/tests/ligand_dock_7cpa/inputs/7cpa_7cpa_native.pdb.gz modified: tests/integration/tests/ligand_dock_7cpa/inputs/7cpa_confs.pdb.gz deleted: tests/integration/tests/ligand_dock_7cpa/inputs/ZN1.params new file: tests/integration/tests/ligand_dock_7cpa/inputs/ZNx.params modified: tests/integration/tests/ligand_dock_grid/flags modified: tests/integration/tests/ligand_dock_grid/inputs/7cpa_7cpa_input.pdb.gz modified: tests/integration/tests/ligand_dock_grid/inputs/7cpa_7cpa_native.pdb.gz modified: tests/integration/tests/ligand_dock_grid/inputs/7cpa_confs.pdb.gz deleted: tests/integration/tests/ligand_dock_grid/inputs/ZN1.params new file: tests/integration/tests/ligand_dock_grid/inputs/ZNx.params modified: tests/integration/tests/ligand_dock_script/flags modified: tests/integration/tests/ligand_dock_script/inputs/7cpa_confs.pdb.gz modified: tests/integration/tests/ligand_dock_script/inputs/7cpa_input.pdb.gz modified: tests/integration/tests/ligand_dock_script/inputs/7cpa_native.pdb.gz deleted: tests/integration/tests/ligand_dock_script/inputs/ZN1.params new file: tests/integration/tests/ligand_dock_script/inputs/ZNx.params modified: tests/integration/tests/startfrom_file/inputs/7cpa_7cpa_input.pdb.gz modified: tests/integration/tests/startfrom_file/inputs/7cpa_7cpa_native.pdb.gz modified: tests/integration/tests/startfrom_file/inputs/7cpa_confs.pdb.gz deleted: tests/integration/tests/startfrom_file/inputs/ZN1.params new file: tests/integration/tests/startfrom_file/inputs/ZNx.params modified: tests/integration/tests/startfrom_file/mover_flags modified: tests/integration/tests/startfrom_file/startfrom_flags modified: tests/integration/tests/write_mol_file/flags modified: tests/integration/tests/write_mol_file/inputs/7cpa_confs.pdb.gz modified: tests/integration/tests/write_mol_file/inputs/7cpa_input.pdb.gz deleted: tests/integration/tests/write_mol_file/inputs/ZN1.params new file: tests/integration/tests/write_mol_file/inputs/ZNx.params commit d72f6e8307e528ec02ac6d8ae869902206ff30e6 Since ZN1 is now interpreted as ZN, I need to update integration tests that have a ZN1.params file. These are now ZNx.params (and other test files have been updated accordingly). commit 2decc1b16f33a1c437e0aa392bb09ece8642f30e Updating create mebrane pose mover to include creator with correct inteface commit d7b9883c3c1de0a27f54970af26b883847d81a61 Warnings Removal: cleared a Wreturn_type commit 77f4a3ab17531b9b0169f6ebc79d581c1194e066 merging in master commit 38e35aecdb9971022568fef3feb394ba78bc207e Adding Co and Cu to reduce_sasa_radii.txt commit 4edc655edcdcce3125035736700c05d5ff39d639 Ring Conformers: fixing major degrees-to-radians bug in my previous push 118 degrees != 118 radians Carbohydrate ring conformers now look good, even in strained cases. I also edited cyclohexylglycine params so that AtomTree does not flip out on ring conformation changes. (I was too quick to celebrate on my previous push; it is more complicated to make a ring system work with the RingConformationMover. One needs to ensure the AtomTree behaves properly by defining a CUT_BOND and at least one virtual atom. I'll document this all later once I refine things more.) Only the rings integration test changes, as expected. commit 19a8501b8d3a8387b6dc5cb85002d90751460a6f Ring Conformers: fixing major degrees-to-radians bug in my previous push commit 4a1f9f989fbeb4f39ca1193132cf76ef0be0e42b Merging master into vmullig/metals for integration testing. Resolved merge conflict with ResidueType.cc. commit fa07532a2b3f0d1b4335c6d4d2bfe281069313db Change in unit tests needed because ZN1 is now interpreted as ZN. commit 68120d96e6e0ab002cdfe3f76590db9084e0768f Fix hybridize integration test to prevent warning message commit 2eca8cb0d3cd920d90cced07b86d256509be4d5d Merge tracer changes to master. commit 0fc10d5a12e811897e63b0004913f0be1e711f49 Move some density-modelling tracer output to Debug level commit d6ec253ca60a6341faa8c1762ce199b3f28d7de7 Fixing PyRosetta build commit 70e8f828a6e2eee230a8f658df57cf1c71cbea31 Adding PyRosetta build test script commit f9a1e339f9c8331a430da15fd1b1df6fd111a696 On his behalf, revert Kala's commits. Revert test server commits 56493 and 56494 This reverts commit 12a020b263aaafa9240b00a71767d95dec49046b, reversing changes made to c4ba068409eef69b385f04b04b8b5ab322aada8c. It also reverts commit 199441208b2b2f2, which effectively duplicates 12a020b263aaafa9240b00a71 (1994412 is a merge commit of two merge commits, each of which merge the same two commits). commit 5d7c5db82e8ca846e3b64a0926b395bd4e3db743 On his behalf, revert Kala's commits. Revert test server commits 56493 and 56494 This reverts commit 12a020b263aaafa9240b00a71767d95dec49046b, reversing changes made to c4ba068409eef69b385f04b04b8b5ab322aada8c. It also reverts commit 199441208b2b2f2, which effectively duplicates 2a020b263aaafa9240b00a71 commit 3fb1ee1c8b1211f8115b730a7469ec80110ffe60 Removing dependencies on core in RingDetection so that the library build will be fixed commit 6abfcc7f3d3272f3d3f7722976d4e340e6081044 Removing dependencies of RingDetection so that the library build will be fixed. commit 98d75d6efb74cebe3783356d5ce95f92a654bc36 Reducing the scope of the metal ion parsing. Now, two-letter metal names followed by 1 or 2 are interpreted as the corresponding metal (e.g. ZN1, CU2). commit 733ac7450b665be74e108c0ef0bc31228c73accb Changes to file_data_fixup.cc that I hope will fix the unit tests. I'm also tweaking the unit tests since the failures are expected given my changes: ZN1 is now interpreted as ZN in order to facilitate PDB import, so I'm renaming the ZN1 in the test suite to ZNx. commit e6caad2401b731bb052757ca7a774a2db382eb14 Tweaking file_data_fixup.cc, since name3 requires strings of 3 characters. commit d641f4f849f27b3018ef9500957cc50c5cc8c2c1 Caught a mistake in my changes to ResidueType that was causing an assert failure in debug mode. commit 60aa8fa9e632758122aaeff8ed455afb2cf427ec Turning off BPY in preparation for merge with master. commit c524e124baaedc8b85885d8354d866ced00aa8a9 Caught a little bug in metalloproteins util.cc. commit dcd0739763f3bc651560fe09e22b7d38ab6d4e59 When the -auto_setup_metals flag is used, constraints weights are now turned on automatically. commit 2e0b631cc268815a1df17d897f1209c94ed50e15 Adding more tracer output from core/pose/metalloproteins/util.cc. commit d85f18fb6dbb5360a218bb3f7c6333c084bce7e9 Metalloprotein import options now work to control setup of covalent bonds and constraints. commit 369e77cdc12341209462b10652622f0c0ef96074 Adding option flags for auto-detection of covalent bonds to metal ions on PDB import. commit a74f8dd4cbfb3b43f163eb3865bb11cf75901632 On pose import, automatic metal setup is now carried out. TODO: FLAGS. commit 6968b25d2e60688b60e30bcb09697c37604dd563 OK -- PDB import automatically sets things up so that metal ions are connected by a jump to the nearest metal-binding residue that comes earlier in linear sequence. commit 1cfe12e2950cf374c38830b27ecd4f54266dcbf5 Trying to get metals to be connected by jumps to the nearest metal-binding residue on import. I think this attempt didn't work. commit e22b46381cca523e149ef365f41ce9fa439a8eff Adding notes in core/import_pose/import_pose.cc for what to do next. commit 9141e412047490063a82f9d2d89fc5677edd6348 Tweaked PDB import. Now, 'CU ', ' CU', 'CU1', 'CU2', etc. should all be parsed as 'CU' -- i.e. no more needing to tweak spacing in PDB files to get Rosetta to parse them. commit 152e920828b44e0826219f0b145ccd4cfa5029a7 Removing stdio.h from core/pose/util.cc -- only needed for debugging. commit 3c52e7f5369d4a4c60c6ae2c981d123c7b488062 Tweaked residue_io.cc to allow output of the METALBINDING property. commit 1bdebeefa067fe5b64abc46b07069a6d4cace332 Added angle constraints to core/pose/metalloproteins/util.cc commit aad13fd75b5908583480e0e62814468320f2a58e Updating my notes. commit 818a2f9eb2ad3ada780b7d86405f8c1acfce9616 Adding code for automatically making distance constraints to core/pose/metalloproteins/util.cc. commit c2d48a8f4688b98d635e32a820f4ad357a7c577f Caught mistake in core/pose/metalloproteins/util.cc commit 23efdeae2226b2f417f9e1e19d657d0332ee6ce4 Everything needed to set up covalent bonds to metals automatically is now in core/pose/util.cc. Also, added tests to ResidueType for metals with a non-heavyatom as the first atom and for metalbonding residue types without metal bonding atoms specfied in the params file. commit b2e0b7bcef4dfcc16ff82c9782a0d11ed78b9bb1 Working on moving metal detection code from my pilot app to core/pose/metalloproteins/util.cc commit 05c6175e3d9000a95559e8c83314c12d8b519709 Added metalloprotein utilities (namespace core::pose::metalloproteins). Added function to find metal-binding atoms. commit e4eb2dc7506df86b4f689d9acd5fc38b16f69c23 Creating util.cc and util.hh for metalloproteins. commit f649fcd4d5404b3713fc347410cdd3a55bfb66e5 Updating my notes. commit 64deceb54a69ecb4b392346432490cd210c23ded Removing some debugging output. commit 1ed3be63a9649625f3baaade6af1c1d403a0d8b8 Covalent metal geometry now works with more than four liganding atoms. commit 7846336a170eb95e914a7b87465c9d43e9d20821 Added a virtual atom counting function to ResidueType and Residue. commit f9ef50bbd54b07500b72f614affd115262413710 Caught typo in CU.params. commit c6fdd953c47621331f451cf3c8045589fd1001bd Tweaking BPY.params. commit 5624d2877a05c64d1f0b614daead36a75b6b0d82 Adding Cu and Co to the atom types. commit 1a76889358424de3d1ee2a435b6ce53a486fb137 Updating my notes. commit ba289babd30400da509081d56af3f1d6ced8d11c Adding bipyridynl-ALA to the database. commit 7cb62e03c61cc27e1ae5e81f5669cb134e6d00dc OK -- the distance constraints for metals are now working in test_metalloproteins.cc. TODO: move this to core. commit c2fa342e639652aaf194b1cad814a4161b24a362 Just adding a notes file in my pilot apps. commit fbc3b095144aedc22dd9051e6298de337c5732be Working on test_metalloproteins.cc. Moved the code to find and set up covalent linkages to metals to its own function, in anticipation of putting this into core somewhere. commit 6181921d840d420ce63bf7df94ef3a307229219a The logic to put in CONECT records in pose_io.cc was wonky, and was only putting in CONECT records between parents and their children. This meant that rings would not appear closed, and side-chain covalent connections between residues would not show up. I've fixed this, now. commit 8429847d79d976dcfc0af1dcb59235bdcc7901cb Added -inout:connect_info_cutoff flag to option system. This is used to specify the cutoff below which explicit CONECT records are written when the -inout:dump_connect_info flag is used. commit fd01588926549614cb3752a249a259dc53afd595 I think that proton deletion is working more or less properly, now. commit 762f49bc03da6eb155250646b536cab8afc272f0 Trying to find out why hydrogen removal isn't working... Don't have it yet, though the earlier crash bug is gone. commit b8ef3087c07986ddefc0a62dc67480f66df1c5b2 Okay, I think metal covalent bonds are being set up properly now, but deletion of extra protons isn't working properly yet. It's probably the residue copying that's the problem. I'll debug this next. (core/pose/util.cc) TODO: --Add constraints. --Move metal detection and constraint adding to pose utilities. --Add check for params files with METALBINDING property but no metal atoms (or the converse). commit 4211b76a9075121df5f7a46ae457b0f982089533 Still trying to get Florian's code working. commit 31573ac8b695e9b130f427b3ef8812449d72d32e Second try getting Florian's stuff to work. Still working on it. commit d40d480264f95737e47c0812420326145d95cc1f First attempt at bringing the enzdes helper functions for metal-coordinating residues into pose/util.cc. There are bugs to catch -- doesn't currently compile. commit 6a2e05374aff85f8c249a541adafc8cc7ca011a4 Working on test_metalloproteins.cc commit 5e54cbb8f3f73a7cf381ce9a99d395c27bc81892 Adding metal_binding_atoms() pass-through to Residue.hh commit 56aab7622f3d87b7793a2538874670aba90e73c9 Tweaking test_metalloproteins.cc commit 624909a46c8482530198ce86739add89959a0417 Added METAL_BINDING_ATOMS tag to params files for appropriate l-caas commit ef7fe954cefe789affcea9d59783aff64ae84109 Fixing silly mistake in changes to ResidueType.hh. commit b206e48b7ca3323d47e1fddf43861eba93e5eeaa Adding a METAL_BINDING_ATOMS tag to params files. This allows the user to list atoms in metal-binding residues that can coordinate metal ions, and is to be used in conjunction with the METALBINDING property. commit 53280dfb6b92fa803a39d71e5cea7a0afcfde529 Adding METALBINDING property to ResidueType commit 55801171e03e023584a83d2336c07c3addfa981d Trivial output change to test_metalloproteins.cc commit ecb62dd502df973a64993010c1d778bcd9b25159 Adding METALS property to residue types. commit c6da0d8bed6f229743dd25d307f79296919ff407 Initial commit of test_metalloproteins.cc commit 59ef1d98c557c9acb73ba5f42c80a9a34b57e8ad # [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. #+TEST # Uncomment the line above if you would like your commit to be tested by the testing server. # NOTE: Some commits (e.g. merges-to-master and current HEAD) will be automatically tested. commit 780c4c9be9f8ced962db68b2504cbd436c1c0920 # [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. #+TEST # Uncomment the line above if you would like your commit to be tested by the testing server. # NOTE: Some commits (e.g. merges-to-master and current HEAD) will be automatically tested. commit 159543f6988a9b575c57a5cfe470c4cb9f877054 Warning Removal: turning one error back to warning waiting on Fang to fix 3 remaining enum-compare warnings This should fix the build for those using versions of GCC more recent than the test server's. commit 58926175b7691a2498b1171e552153474a9f3b65 Adding --skip-comparison option to integration.py script. Adjusting benchmark scripts to use it. commit a20f7b2448bce7b5f8a073935e8b1883a76b8ba0 Warnings Removal: still working on the linux.clang build commit ad2f0791f0f6b8dcafba29718b8a373efebbdbdc 02/27/14 Changing Enzdes to be more campitable with talaris; default scorefxn is now talaris2013_cst, which results in ~2% increase in seq recovery for enzdes benchmarks. NEWS: In EnzdesBaseProtocol.cc, the default scorefxn is now talaris2013_cst. To be compatible with talaris2013, the exclude_protein_protein_fa_elec_ bool option in the constructor is now set to false by default (it used to be true, which was necessary when using the enzdes scorefxn so not to double count fa_elec of interface sidechains). Using talaris with talaris2013_cst.wts gives ~2% increase in sequence recovery on the enzdes benchmark. ---------------------------------------- Unit test status: Failed when I ran it by not because of my changes ("unit_tests - Broken by Kale Kundert:56400.") Integration test status: 3 changed (as expected) enzdes: outputs different results/scores due to using new scorefxn and weights (talaris2013_cst) inverse_rotamer_remodel: changed the flags file to use talaris_2013_cst.wts; outputs different results/score due to different scorefxn ligand_motif_design: I did not touch this; this test uses a custom weights file that is not in the database, so I left it as is. Let me know if this is a problem for anyone (sboyken@gmail.com). commit e4a3d0f288983f9cce8912be1a7fc0e2c5b4de2a Warnings Removal: removed many uninitialized variable warnings I am still trying to get the test server to build in linux.clang, but the version it is using is really new and higher than what most are using, I think. commit b8be9d13835e5a8bc52ab94aa86b97332ae4cc5f merging in master, now that I fixed Andy's bug commit 9afa6b8779e89ad95db6e14a06ee3bfb415f18ae Warnings Removal: fixing another linux.clang-only warning error commit 0fa1c953cd934e72e53c85bd1fc1e100bcab9a18 Warnings Removal: fixing the warning/error introduced by Andy commit f21fa98dd8f8550e4cb18b980107685d6ae774f3 Warnings Removal: several uninitialized warnings commit 86e76ba56ca080ccf9be0bb7698a8c4d2d4ec6ba Warnings Removal: bug in jd2 code fixed; hopefully, this will fix the linux.clang build commit 7e6f9015de17fa7e8e2fa851a07c5eedb8730629 Warnings Removal: several uninitialized warnings commit e23438ddf8cd5e2424a785a95dc834b8d44636b1 Fixing unused variable warnings; I'm not sure why this wouldn't have hit other people, too. commit dd31dfe0045366f09f777f0f8c41f1c5106de53d Warnings Removal: fixing gcc.clang builds; other builds may be broken still by new warnings introduced by others commit 5dd0e609109617d6001347839790ffa774dd9976 Warnings Removal: fixing bug in Nobu's code to fix gcc.clang builds commit 813508dd512ce9c877a77c56863ba0354430cca6 Merging vmullig/b3aas into master. This updates beta-3-amino acids in Rosetta in the following ways: --Beta-3-amino acids with canonical side-chains should have side-chain hydrogen bonds calculated just like their alpha-amino acid counterparts. --Beta-3-amino acids with canonical or common side-chains now have their own enum types in AA.hh. This is very useful for making sure that the score function plays nicely with them, and for writing protocols that recognize this class of amino acids. (For example, it will now be easier to get KIC to recognize beta-amino acids). --Three common cyclic beta-3-amino acids have been added to the database. These are turned OFF by default in residue_types.txt, so this should not increase the Rosetta memory footprint. Unit test status: Not Run (The debug build wouldn't compile for me!) Integration test status: 2 changed tests ligand_database_io: This is an expected change in the absolute value of certain aa enums. ligand_dock_script: This is the usual numerical instability in this integration test. Would someone PLEASE fix this? A test that fails constantly is like a fire alarm that goes off at random intervals: everyone ignores it when it actually detects a real problem. commit 5cb9ed99cab77c52fb04e31662290bff2bbdef23 Reverting changes to .gitignore in preparation for merge with master. commit a34531f8c02c6444102c1a25ed43e30211f15d85 Turning off d-amino acids in preparation for merge with master. commit 92ff07ee004057cc6fb5e8c5b155774c29dcae93 Turning off beta-amino acids in preparation for merge with master. commit a5cf4ee4f05a30d5d62379060caf31eee11ff78a Added new residue types to residue_types.txt. (Also, took out one more debugging line that I forgot to take out earlier -- loading stdio.h.) commit e93905ab14877225c736158d07475e3af8739782 Added cyclic beta-3-amino acid residue types. commit 46f31406d1a36c4f93e609d6284b5ef34a38f50e Adding enum types for beta-3-amino acids, and support for beta-3-amino acids to side-chain hydrogen bond scoring. commit a44adc8670cf50fab68adf2fed8957a2fddd528f Confirmed that backbone h-bonding is working for beta-amino acids. Debugging code will be removed later. commit 12ed9eee140268fe14558a0d7cc2604581d15ffb RosettaScripts now can use NcbbDockDesignProtocol, OopDockDesignProtocol, and OopCreatorMover as RosettaScripts movers. Now, users can proceed from (e.g.) a pose of hotspot residues to an OOP containing those hotspot residues, whatever relaxation or sampling protocols they desire, followed by a dock-design protocol, all from the comfort of a single RosettaScript. commit d04d7095cd93d902976448ad7dc3fcdf1ea330b3 Finally made it build properly; amusingly I was fixing errors in the wrong line and just needed to dereference a pointer. OopCreator is now a valid RosettaScripts mover, hooray! commit 5907d06a334bd6d16a251455eb2589c7fb5819c2 Warnings Removal: basic.settings fixes and other bug- and warning-killing Hopefully, this will fix most of the builds that have been broken today. If not, I'll push other changes tonight once the build bot catches up. Thank you, everyone, for your patience. All unit tests passed; no integration changes are expected. commit dce4bba6c4c09018d3df6180d04e73a37ad05c7b Warnings Removal: fixed bug and tweaked basic.settings commit 43db54a6f2a14c784407668392e54af1a51651ed Warnings Removal: further basic.settings tweaks commit 2cf2ff8ef2d4105855af1c762e6c345fb382e79b Merging distal b3aas branch into local. commit 360d4563635e2413b72577c39662431a633979a5 Temporary changes to residue_types.txt and .gitignore for testing. REVERT ME LATER. commit 574f5b36353f32bb1c108856707922fd1ba4d0da Merging master into vmullig/b3aas prior to tweaking scoring of cutpoint residues in cyclic peptides and beta-amino acid hydrogen bonding. commit 038e10315c7d45f0283a471c1b215925535a7a0a fix bug in kink_anion_atoms function of AntibodyInfo commit b0888691fd62ba825d6193b1d225f8b03d5cd72b changed exclude_protein_protein_fa_elec_ default to false in EnzdesBaseProtocol constructor commit 0312152466442e5ae0446e84ae5fa435bbe403d6 Warnings Removal: fixing warnings only on test server commit c4e3e886aad4e8b37b0cecc31f2204e716d53752 Warnings Removal: removing switch warning commit 9ac9d11a545e199ddc14494fa979acbd1a54d2c9 Warnings Removal: changing settings to appease the Mac version of GCC on the test server commit 5a2c933ab9b89f22ee1f7e51e3a685c086f9d844 Warnings Removal: release mode warnings killed commit 787f2ab75842df59c65861d91f2beb784d882306 fix to code only compiled for boinc commit 8db01603019a7babe87577b95f905b2ab4ae3692 WARNINGS WAR Z: a miscellany of warnings/errors fixes All unit tests pass; no integration test changes. commit 3d564bf35f9950c7bb1cd386b05a10926c2eb823 merging in new file I had forgot to add from on my laptop commit 7d3d5150327e449c3d9f77923bbc28fb2eba952b Add a 'quiet' argument to Conformation::set_torsion_angle(). If you tell Conformation::set_torsion_angle() to set an angle which can't be set (e.g. because it crosses a cutpoint in the fold tree), the angle won't be set (of course) and three separate error messages get written to the terminal. In contrast, Conformation::set_bond_angle() and Conformation::set_bond_length() will silently do nothing. The behavior of Conformation::set_torsion_angle() is usually helpful, because you would expect the torsion to be set and the warnings may reveal a bigger bug. However, in some cases it's only necessary to set whatever torsions can be set. Then the warnings should be turned off, both because IO can be extremely slow and because superfluous warnings scare users. This commit adds a quiet argument to Conformation::set_torsion_angles(), to make it possible to silence this output. Since the argument is false by default, existing behavior should be completely unchanged. No integration changes expected. commit 495f55caa241c5ffb22ef0de40d1befd6a6c9b75 Add a 'quiet' argument to Conformation::set_torsion_angle(). If you tell Conformation::set_torsion_angle() to set an angle which can't be set (e.g. because it crosses a cutpoint in the fold tree), the angle won't be set (of course) and three separate error messages get written to the terminal. In contrast, Conformation::set_bond_angle() and Conformation::set_bond_length() will silently do nothing. The behavior of Conformation::set_torsion_angle() is usually helpful, because you would expect the torsion to be set and the warnings may reveal a bigger bug. However, in some cases it's only necessary to set whatever torsions can be set. Then the warnings should be turned off, both because IO can be extremely slow and because superfluous warnings scare users. This commit adds a quiet argument to Conformation::set_torsion_angles(), to make it possible to silence this output. Since the argument is false by default, existing behavior should be completely unchanged. No integration changes expected. commit 7dd4494a23c0d06cd6f4eabb4d006c897c2b98dc Warnings Removal: forgot to add new cc file commit 7e62dc5a656931f1e0791d338e40f1751d104a5b merging in new file I had forgot to add from on my laptop commit 499ac0da36743a76733f048cf79c9dbbfc51d1be More attempts to get OopCreatorMover to build. It seems not to like my assignemnt of a vector out of a get_resnum_list... commit f3707eef806c1f549161512006c20fb52deae620 merging in master commit 3318e881c77ec37327b896e5c95f1a3091f9e208 Warnings Removal: new warnings removed found on different machine commit 3d6671e39056e3efe6be8506a0bff16eb4e09c2b Warnings Removal: removing 3 tricksy warnings commit d82f9fb6b63f044667d067e40f9a90ef9b375a52 Fix GCC warning by commenting out switch in basic SasaMethodFactory. commit fc185c6fb13329bce5d2d3896d27dde2a80e66d0 Remove a handful unused variables. This fixes the MPI and Postgres builds on my machine (GCC release and debug). commit 92a98178664923120cddef2294b7a88dff799372 Warnings Removal: 2 more warnings in public apps commit 752ad6ea061e5a59511ab3dd89518c85d05c22af merging in master commit 2f857de273572c7b5609dcab8decf63830c18e75 Warnings Removal: 2nd attempt at fixing pilot apps build commit 4f6b4796c868c7659d6f880f3bea765c353a9b8b Warnings Removal: trying something new with the PyRosetta warnings options commit f2529d730b7bf30449ca1d3f45228f079ac0b4c4 Warnings Removal: attempting to fix pilot app build commit 1abf50ddd0c1e923274b08d051e46d69598e16a5 Warnings Removal: cleared all but a handful of warnings and changed many more warnings to errors commit cae03408b5e02a7f4710e7dc0afd9ac32458683f Warnings Removal: removed warnings from unit tests commit c0afa1e23266a9bc9ab56a529e1b8a69fc01796c Warnings Removal: removing 11 of the last 20 warnings showing on linux.gcc on my machine commit a8c83234337b070783544f910ac9b3f42d3bfd19 Warnings Removal: trying to fix the linux.clang.debug build commit 1f84d085216f919d9726f24b2b4415aa09a0506b Warnings Removal: trying to fix PyRosetta build by having it ignore a parameter commit 8926b6f58536f0978d38eb4e105a7061b3fa9899 Warnings Removal: removed warnings from unit tests commit 79fe47aba04697b29d486a8881196042ac5ebc16 Tracer name fix in ConstrainIO to prevent confusing in debugging. tracer changes are likely in integration tests that use constraints. commit 1b4c3878fcfb713783549fa08baa76bfaf34c10b Warnings Removal: removing 11 of the last 20 warnings showing on linux.gcc on my machine commit 1a6644fb10d47e2ebacb3d0b47988fe314345203 Warnings Removal: trying to fix the linux.clang.debug build commit bb98da49ad7e859c4f58fac79d1dc4a34b521332 Warnings Removal: trying to fix PyRosetta build by having it ignore a parameter commit bbadbb793e15f598a37ae08c1370ea31ef10656a fixing tumble mover that broke the build, sorry commit bbd7d6be416ffdcf694c1d40b9f60359792db1a9 I needed to use a regular header, not a forward headed. Not sure why this didn't break for me locally. At any rate, this should hopefully actually fix the build commit 8a318b43b229d45bfb3cc4fdcb159a7e323e9ff8 Removing poorly resolved conflict lines in ab_h3 test flags file. No test changes. commit 8bd725ff8acd30e0f68dbb9ac351e0bbf6c9e9a6 Adding a forward header to Tumble. Without it, the build was broken commit 1406e2881645c931d1220b37f9df0937d899909e Add case-insensitivity to -out:levels "-out:levels all:Warning" is now valid. Previously, it would silently mute everything instead of setting the tracer level to "warning". Unrecognized levels ("-out:levels all:SPAM") will now result in a warning message being printed (rather voluminously in some cases) and will act like a setting of "info". (Rather than silently muting the tracer.) Additionally, "warnings" and "errors" are now equivalent to "warning" and "error", at least in the -out:levels context. commit fd7159d95dfb41b236800ead56a9c8745ae6aa6d Add case-insensitivity to -out:levels "-out:levels all:Warning" is now valid. Previously, it would silently mute everything instead of setting the tracer level to "warning". Unrecognized levels ("-out:levels all:SPAM") will now result in a warning message being printed (rather voluminously in some cases) and will act like a setting of "info". (Rather than silently muting the tracer.) Additionally, "warnings" and "errors" are now equivalent to "warning" and "error", at least in the -out:levels context. commit a108e1d4291006eea1c2693fcb0ad24b42f85d75 Added DONOTRELEASE tags to mpi_msd.cc NEWS: As part of this week's post-minirosettacon tweak-the-release-system drive, I automated the editing of the strictly-unreleaseable mpi_msd.cc file. This requires tagging in the file for the stripped lines (the rest of the machinery is in tools/release [currently still in a branch]) ---------------------------------------- Unit test status: Not Run, this is comments only Integration test status: Not Run commit 7a76ae1f342bba66b2c743a4c55c1e287f5d6a48 remove some unnecessary headers in the tumble mover commit 2a0c6afa16727d68404c80b9f35ee0a95e96fd12 Warnings Removal: still trying to fix the linux.clang.debug build commit 50e01b9697d691cc8679c74da96f6accfcf6d46d remove map::at calls from EnvClaimBroker. commit 342a8bbee78475c476e52031408dd894777cd68e Warnings Removal: removing a warning/error only found by linux.clang on test server commit e9e8d7dd4c6e6c8e1f6551ade66603562635ef99 Warnings Removal: fixing a very large number of new warnings/errors Please be sure to compile in master after a merge of your branch to avoid this sort of problem. commit 3e737cc1176606639662d21b98e5f0d14a892ca2 Warnings Removal: another Rhiju warning/error commit 476582492228377367e41ca7dbfbcb1385806a6f Warnings Removal: another Rhiju warning/error commit aab542d97ca9ea0321fe99aa0e771cccc4905ae6 Warnings Removal: another 2 Rhiju warnings/errors commit 3ef73f5d413756d2ed14bbd7452f5e0393ca8f6c Warnings Removal: another 2 Rhiju warnings/errors commit 58c80446851c5332f30afffa16fd0531ad4894e3 Warnings Removal: another 6 Rhiju warnings/errors commit cf38c175b048f1d6c9285ad2dc1f538fcde1ba5b Warnings Removal: another Rhiju warning/error commit 0d84489663ad5504e20415e50858eef0e16c086d Warnings Removal: 3 more Rhiju warnings/errors commit ffe074afbfb38b39ae316b79554c10692604fbd8 Warnings Removal: 2 more Rhiju warnings/errors commit 015c6bf5ef4f9b74581fb4dfc783277317a7e1a2 Warnings Removal: 5 more Rhiju warnings/errors commit a2369663d12e24e80baee3402c7e5954fd37a473 Warnings Removal: another Rhiju warning/error commit 976d2296de5faec995ba988c8ee70444a31b646c Warnings Removal: 5 more errors from Rhiju's code commit d29383b771e6df85ad2e78d984c65ed89cf76e61 Warnings Removal: 4 more errors from Rhiju's code commit cf8f873484dd90e48394b0d4d6a0720617e2fa18 Warnings Removal: 2 more errors from Rhiju's code commit 2554adb02f2b801c5bc3981f3dfefd96a65c851d Warnings Removal: mistake in fixing warnings commit 54735332a7975b85964adb3f3a7938aeb7bd5bc2 Warnings Removal: fixing warnings introduced by Rhiju and updating cmake settings commit 85cf28312ad023380135669eeb6da48a00613e38 Warnings Removal: fixing warnings introduced by Rhiju and updating cmake settings commit f90a77409ab8e40e718fd43e524b9d01e7e12751 Warnings Removal: fixing warnings that should have been wrapped with an ifdef commit 78c914eabed9d2ed374346ab7fbc88cee96c95ee Warnings Removal: updating cmake settings commit 7b82272d42c0e275e7b92ad7e5f02a279e90702b try to get test server to compile -- fixing int/Size comparison commit 0e9f8a712c16365a6efb69680d1ebc12d7b156b5 merge from my branch (rhiju/swm_rigid_body) which has made major progress in unifying stepwise rigid body sampling with suite sampling. some integration tests have cosmetic changes due to output of chain numbers in silent files; potential floating-point issues in density refine & ligand_dock; and changes to RNA and SWA tests due to refactoring of copy_dofs. commit 2f440416536d82cae9d5f2ad95cb035b914c013b initializing variable in count_data commit 90f7cbecb770aed2f9ad1d7bf1e6313d5c385839 fixing chain assignment to blank poses (now we no longer have '_' as possible chain) commit 5268550e2e33d5215461680966d8ea10be09fc0b was trying to disable dunbrack readin for non-protein cases, but this seems to mess up integration tests with some ligands that read in rotamers via dunbrack. commit 943474354d92bf266b0017e46938baa774d22565 getting compile on old linux gcc commit f05f89c1dea61540ff375d57f8cf91f4409245d7 restore KIC sampling in SWM resampling of big chunks. commit 7e855e6490a54c0b097026ab02ea636dc7f7cfa9 accommodating change in chr_chains to exclude '_' at beginning. commit 580637bedf0369d4033e7ff5606982c4d1b0ef31 in rna_minimize integration test, make sure that input is as 2 chains. commit afb4556c99537e75a3806222171abd616b2910ab fixing chain assignment in PDBInfo objects constructed from pose commit 559de318c9ca29e38d063156f3d6d96cdc78f787 unification of how unified ConnectionSampler is setup in StepWiseRNA_ResidueSampler. commit 7f7a5043cc296f279b3dd6a022b72376a4098fe1 useful output in legacy code commit 26083ff47aefee0c39b809578e729f0e3918ccab turning on base-level centroid screening in (unified) ConnectionSampler; caught by integration test. commit 910011da7ac22d22ae9fc5e45fef09b81616c9e0 Add "option file tab completion" Tab completion is a function of the shell, not of Rosetta, but the form "@../path/to/optionfile.flags" inhibits tab completion of the filename. Add "@ ../path/to/optionfile.flags" as a valid alternative. The space between the @ symbol and the filename allows shells (at least bash and tcsh) to use tab completion on the filename. Test score_jd2 should change in commandfile, as I've changed it to use the new system. The only changes should be the addition of a space after the @ symbol. commit f5a65c0152b170ccbdab711dcc9fd4feae1d8e93 Add a simple tumble mover. commit 7eb15f067219b24e84f0fa036f477b8823a3bcee Add a simple tumble mover. commit c8889f0ca4239ad24abb2a4f76656a8a3ea7b813 A few bug fixes for Hybrid split. commit 537be7273033f4cc15a292ec5daca165fe307120 slight behavior change in abinitio: if a trajectory is aborted early by throwing an instance of EXCN_Converged we jump now to the end of a sampling block (stageI, stageII, … ), instead of as previously to the end of the whole apply. The advantage is that now intermediate-stage output and checkpointing will be consistent with a full-run through even if early termination happened. commit e265ff882d3dd01bcbeeba2b349e20efea59bb57 Add "option file tab completion" Tab completion is a function of the shell, not of Rosetta, but the form "@../path/to/optionfile.flags" inhibits tab completion of the filename. Add "@ ../path/to/optionfile.flags" as a valid alternative. The space between the @ symbol and the filename allows shells (at least bash and tcsh) to use tab completion on the filename. Test score_jd2 should change in commandfile and log file, as I've changed it to use the new system. The only changes should be the addition of a space after the @ symbol. commit 0bb5a2597dc41812d2ac763c03a7d8acedeaf449 deleting silly ninja files that should not be in src/. commit 8caa4ce4c275ce31995aa1f9134eb46a0893bb38 Merge branch 'rhiju/swm_rigid_body' of github.com:RosettaCommons/main into rhiju/swm_rigid_body commit 81633437fdc98171c1b191adfa4a672d924752ba changes required to remove conflicts upon merge. commit 6ec273d84d25412a37cace0f48be057df5b4a567 pulling in changes from ade (linux gcc build) commit d06effe150d820be5128eb022fe8ed976df7e288 moving old and nearly deprecated stepwise sampler files to legacy/ subdirectories. commit 774994528c4ec3cddfec65046b1604b8fbb05117 fix conflict in BaseBinMapUpdater.hh commit 1c215f3faae9b50b63cdbf5e031e67f63ff6fb76 needed include for gcc build commit 944d610aa1f841831cc4c6ea667b013d947aef3a fixing kic setup in RNA stepwise sampling -- had fixed bug in StepWiseRNA_ClassicResidueSampler, but did not carry through to other samplers -- made setup_rotamer_sampler a shared funciton. commit 2e217b401009fe36bd7035ce768f0742ce1ee610 finally -- unified StepWiseRNA_ConnectionScreener, available through -unified_framework flag. Perfect match to old code and -new_framework (sample-and-screen), so those will be deprecated (or moved to legacy/ subdirs) commit a4f53257c6fc259b7a0937c85d84f0bf4033c878 some file move-around to get ready for unification of SuiteConnectionSampler and RigidBodyConnectionSampler into ConnectionSampler. commit e6f7c1cf5774d50eb31a5a644e4bdf4c38311c5d capitalizing STANDARD_CENTROID_BIN_SIZE, STANDARD_EULER_ANGLE_BIN_SIZE, STANDARD_EULER_Z_BIN_SIZE to make it clear that they are constants from #defines. commit b443c227d0c20174242ec95d0ff825ca1e922b8d factored RigidBodyRotamerValueRange out of RigidBodyRotamer, simplifying variables needed in StepWiseRNA_RigidBodyConnectionSampler. began factoring job_parameters out of StepWiseRNA_RigidBodyConnectionSampler. commit a4cc403cdd4eae45ada93ce9b8f0ef45cec1500e Rosetta Membrane Framework: Quick Fixes and Additions: - Removing old MembraneMover class - splits into MembraneUnitTestMover used in integration and unit tests and CreateMembranePoseMover which will be the actual membrane mover class - Removing some legacy code from geometric utilities - Adding correct IO_String to fullatom MEM and EMB param files Unit Test Status: gcc: All Pass clang: Same unit tests broken (symmetric rotamer trials and rotamer trials) Integration Test Status: gcc: all pass clang: all pass Library Levels Build: All pass Modifications: 2/23/14 commit da6d779407ca5ff897f61bef030223b8f8aa07e9 Removing old unneeded methods from geometry util commit 4dd7d16306a5c2398f3010cf382a328f7c350436 Adding two new movers to the membrane framework: - MembraneUnitTestMover: creates membrane and analagous non membrane poses for unit and integration testing - CreateMembranePoseMover: The actual mover to be used to initialize a membrane protein Also changed MEM.params and EMB.params to include the correct IO string for output into the PDB dumped in integration testing. MembraneMover is now deprecated. commit f39a9f205581adf1ce04c8a943dcd65b4925dae4 Hacking to update create membrane pose mover commit d18b168a026102d71eabf00cdeb9747103599b36 Pulling most recent changes from master - about to add soem additional membrane tweaks on top of this commit 29b4c262f785d72a3d6c161ac2a6939b4dc181d5 Updating IO strings in fa residue typeset to print out actual residue naming commit a53016f53a9acfd42c7c32210e3127b2be72b53f Refactoring pilot apps to call new membrane unit test mover intstead of the old membrane mover commit 2466597a4bf2c4fc142da40ab4bb59a92e37a4a8 Updated protocols b5 build settings and membrane unit test mover compiles commit 034483ad56725daaed83eedc948afe60f10d2c03 Adding the rest of membrane unit test mover (direct refactor - the copy of MembraneMover is still here commit d7f4e39c20b3ae89c2e099cc32e89f91caf51be6 Refactoring old membrane mover to the more informatively named membrane unit test mover - just moving the code right now - not switched anywhere commit f696f5f6806f5c68127987bb6bd6fc88271bd7b6 Added create membrane pose mover to build settings and build sucessfully commit 60bafeb75104ea4de704696f415ce8fb3dce2a1b Adding new Create Membrane Pose mover for regularly initializing membrane poses in protocols (no unit testing methods commit 0e94c8ac0a5463cdde514e3d2725f6e288907c62 get rid of separate screening_pose and sugar_screening_pose. These are now virt_sugar_screening_pose (which is optional and may be deprecated) and screening_pose. also checking VDW bin screener based on pose with instantiated sugar -- previously some poses were filtered out due to lack of atr. commit 85d206bb19fe87832e9cc72b424177fb818c312e get rid of SugarModeling in favor of ResidueAlternativeSet, which will allow more general exploration of ligand alternatives. commit af0da3586cab83a8ef82197850839f42525690c0 NcbbDockDesignProtocol is now a RosettaScript (by the name of NcbbDockDesign). AlaScan filter no longer gives bad residue numbers. commit af1b95f5d35b906c3c16ab97a5ad9c61028eb118 Fixed a detail in NcbbDockDesign protocol; the protocol would sometimes apply OOP movers to scaffolds without OOPs therein. commit 3fa2f0956b0dd9504116b93748031ee20f327d21 This change accomplishes two things. First, fixing a bug in AlaScan.cc. Second, making NcbbDockDesignProtocol into a RosettaScripts mover called NcbbDockDesign. commit 990df6c7a61087fe9ba7e5dffaf53f5b794f1bb2 add fix to build in EnergyPerResidueFilter.cc commit be248641bc381f6b5fb8f8a9d1721573b699f879 fixing integration tests from EnergyPerResidueFilter commit 734303cb237a5fe11fbf3f2c985cf1904ac31013 remove lines corresponding to a code not yet ready for commit commit caa1b0e06fea5cd982214d36b284b5f88092b30f manul merge EnergyPerResidueFilter.xx for large code refactoring commit 197fc05001b6d506911034b5503d6aa39c55204f Warnings Removal: trying to fix the build commit 76634d8d90d8657b61e79339160870e7b714782a Warnings Removal: ...and another commit aa822c4d598a1b862bf8a626c6a3e806e8aa1c29 Warnings Removal: still trying... commit 533dba6798edbb4a9c38ad60bf69461629665c7a Warnings Removal: still trying... commit c172fdfd5477a50c21cbcf5634b278c43277ba0d Warnings Removal: trying to fix the build commit f3df2bdaaf7d420666545acee397da69f4643562 Fixing illegal dependency. Removed devel/init.hh from protocols file. commit 73f189989ac9bb9f43f95e0afe576ecca074c681 Fixing illegal dependencies. Removed illegal header. commit f56929e8097854b98cc6c8272b7352db9d81af78 recover corrupted source/src/protocols.3.src.settings file commit a0780490ad9359cc7e91abce3ee02f310da42215 Warnings Removal: hopefully fixing Mac clang debug build commit ce0281cd9089b06960bae5e431478bc33296c61e Added scaffold_matcher app plus other changes (see long msg) Created scaffold_matcher app which takes in known hotspots as inverse rotamers and finds low energy scaffold orientations attempting to satisfy the hotspot positions with backbone stub constraints. Added integration test for scaffold matcher app Moved main design machinery out of oop_dock_design code and put into protocols directory OOP residues are automatically identified now Added functionality to ld_converter app to keep the functional group fixed when converting (default is keeping the backbone fixed) Added auto atom tree functionality to Daa's for inverse rotamer creation Created NCBB mover which can be generally applied to any backbone, the backbone type is detected and backbone specific movers are applied Generalized the implementation of BackboneStubConstraint so that it will work with non-canonical backbones such as peptoids and beta-peptids. I created two new constructors, 1) specifies atom names to use (e.g. CB, CA, N, C) and 2) auto-detects atoms to use for constraint. The 2nd constructor also takes a target pose instead of a residue so that atoms can span multiple residues such as is the case in peptoids (CA2, N, LOWER, CA1). Original constructor (that hard codes atom names for peptides) is unchanged. Fixed other bugs along the way. All unit tests pass oop_dock_design integration test has cosmetic change. New integration test for scaffold_matcher app. commit 7ca780931411f8dd463b460ef722b4d405ad6276 WARNINGS WAR Z: Removed all unused-variable warnings All unused variables have been deleted or commented out, excepting those used for asserts. Wunused-variable is now an error. Also turned off the unused family of warnings for PyRosetta builds. ~55 warnings remain in GCC on my machine. ---------------------------------------- Unit test status: Pass Integration test status: no changes commit c623044773fd22ef9ed160edf9bc7a4a4a41c796 Warnings Removal: turning off two warnings as errors for PyRosetta build commit 083fd940e7f39f63bce20c9d8f2e0347bd6669c6 1. Add flags to EnergyPerResidueFilter and FavorateSequenceProfile filter to filter around certain residues. 2. Add score_jump silent file type to allow for outputting score and jumps used for docking in boinc commit 82edc05f2879b2bc804d2e503166d7d7d68c1c4f # [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 master_scaffold_matcher_merge # Changes to be committed: # (use "git reset HEAD ..." to unstage) # # modified: source/src/core/scoring/Ramachandran.cc # modified: source/src/core/scoring/Ramachandran.hh # modified: source/src/protocols/hybridization/CartesianHybridize.cc # modified: source/src/protocols/hybridization/CartesianHybridize.hh # new file: source/src/protocols/hybridization/CartesianHybridizeCreator.hh # modified: source/src/protocols/hybridization/FoldTreeHybridize.cc # modified: source/src/protocols/hybridization/FoldTreeHybridize.hh # new file: source/src/protocols/hybridization/FoldTreeHybridizeCreator.hh # new file: source/src/protocols/hybridization/HybridizeSetup.cc # new file: source/src/protocols/hybridization/HybridizeSetup.fwd.hh # new file: source/src/protocols/hybridization/HybridizeSetup.hh # new file: source/src/protocols/hybridization/HybridizeSetupMoverCreator.hh # modified: source/src/protocols/hybridization/util.cc # modified: source/src/protocols/hybridization/util.hh # modified: source/src/protocols/init/init.MoverCreators.ihh # modified: source/src/protocols/init/init.MoverRegistrators.ihh # modified: source/src/protocols/noesy_assign/FloatingResonance.cc # modified: source/src/protocols/noesy_assign/Resonance.cc # modified: source/src/protocols/noesy_assign/ResonanceList.cc # modified: source/src/protocols_b.5.src.settings # # Untracked files: # (use "git add ..." to include in what will be committed) # # source/src/apps/pilot/kdrew/InverseRotamers_autoAtomTree.xml # source/src/apps/pilot/kdrew/disembody_residue.sh # source/src/apps/pilot/kdrew/make_stubs_from_pdb.sh # tests/integration/new_debug_pre_watkins/ # tests/integration/new_release_pre_watkins/ # tests/integration/ref # tests/integration/ref2/ # tests/integration/test_run_20131224/ commit 7ddf1d999847aa809c211dacbf38f44597a5b32a Warnings Removal: removed unused variables from unit tests commit 787be3c8ca860cf11c500e5b668b77fd951d9877 Fixed Rama goto; replaced with a function call/return Unit test status: Pass commit 3d15f7f9210404a28369ab1f029da08fad0b3595 Goto removed from Rama, replaced with a function that gets returned from. commit 6f590113c573319a4afa98d36eedb54bb47466a1 # On branch master # Changes to be committed: # (use "git reset HEAD ..." to unstage) # # modified: source/src/protocols/noesy_assign/FloatingResonance.cc # modified: source/src/protocols/noesy_assign/Resonance.cc # modified: source/src/protocols/noesy_assign/ResonanceList.cc # commit 2f8903f6376c506b38fa6a52fa55ecc632b4e956 adding a new-line at end of header-output commit dd5584df5398fb4ea8350b1e5e54bd89e64114c6 # [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 master_scaffold_matcher_merge # Changes to be committed: # (use "git reset HEAD ..." to unstage) # # modified: source/src/apps/pilot/awatkins/hbs_dock_design.cc # renamed: source/src/apps/pilot/kdrew/hotspot_placement.cc -> source/src/apps/pilot/kdrew/scaffold_matcher.cc # modified: source/src/core/pose/ncbb/util.cc # modified: source/src/pilot_apps.src.settings.all # modified: source/src/protocols/ncbb/NcbbDockDesignProtocol.cc # modified: source/src/protocols/ncbb/oop/OopDockDesignProtocol.cc # modified: tests/integration/tests/scaffold_matcher/command # # Untracked files: # (use "git add ..." to include in what will be committed) # # source/src/apps/pilot/kdrew/InverseRotamers_autoAtomTree.xml # source/src/apps/pilot/kdrew/disembody_residue.sh # source/src/apps/pilot/kdrew/make_stubs_from_pdb.sh # tests/integration/new_debug_pre_watkins/ # tests/integration/new_release_pre_watkins/ # tests/integration/ref # tests/integration/ref2/ # tests/integration/test_run_20131224/ commit 5f519955d673804cbf0da7af69b06aa523e88f5d Merge new master, fixed SasaCalculator conflicts Merged master Updated SasaCalculator to SasCalcultorLegacy Conflict in HbsPatcher.cc where two different constraint setup existed. Picked most recent circa 01/2014 commit 3d332f8b1b5bbd9a0e2479b9badcbd43f2cfb756 pull from master commit d155fad736a03dbc8c12560df4c57b641a95ee5e Split hybridization protocol commit 540c9d4645662501a63d92f3e6ba7a1bb1959abb Split hybridization protocol commit 382daa07085395e8ef4b53b207d0273e1cd0fa52 Remove Warnings: removed unused variables from 9 files commit 532849929f8ed89c4bf842b9f518653a47dde762 Remove Warnings: removed unused variables from 3 files commit 998df4a92cc9f96436654f16c51c87df93b4a84c Remove Warnings: removed unused variables from 4 files commit d3f60a88e82465499eacb8e137eda0b248665685 Remove Warnings: removed unused variables from 14 files commit 58c35b5bc844060220aad5d9d665d6eafaac3fa7 Merge scaffold matcher branches. Resolved conflicts with Andy's formatting changes and renaming hotspot_placement to scaffold_matcher. Checked scaffold_matcher integration test which has no changes. commit d4d1cd6da32e166798aef9aa0a1141a30353309c Remove Warnings: removed unused variables from 8 files commit f1dca3fd16a77aef0df9b0967216a3081f0245be Changed name of app from hotspot_placement to scaffold_matcher Changed all references of hotspot_placement to scaffold_matcher Changed name of app cc file Changed namespace and other references in app cc file Changed compiled app in pilot_apps.src.settings.all Changed integration test command to reflect new app name commit 664dd5e61ac8542e6929d7ac922065a43395459f Remove Warnings: removed unused variables from 21 files commit 3b54c4b7f4dbd5a0dc34385d9578a580e582616b Warnings Removal: turning on Wunused-variable as error commit a4d62e4ec20a570cbeba62274f87e4f55b8b81be Commented out a few TRs in scoring per Andrew's request for performance reasons commit f48250a4128f28017cb7855ae00e152014f8559e Formatting alterations, deleting code that's no longer in use commit 80eb91a1d76f58a03f941b60e5f71ef3c77c7f3d Eliminated magic number -1; now Edge::PEPTIDE as appropriate commit 273782e9808e50ce964b9a537e74be70f4429e2a improving output/input for autoNOE-ResonanceLists commit a5d311348925d0e192e8a4c79433f17e845ca7d1 Minor formatting fixes 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 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 adab7aac4111576ffc56efb82c5d95bf363e70c0 Merge with upstream. commit 145d42a97e8ad33c22665dcddb1d54ac1eadd098 Call register_options before native_ensemble. commit 11398cfd852f1711360504ecfb668b44a59dc213 Remove a redundancy from the cmake build system. commit 0845dfbebb33630ce5aa4174378a51dfa28162b0 Get the code compiling again after the refactor. commit 3d546606491b470c076c9d9f4842aff2f868a322 Merge branch 'kalekundert/devel' of github.com:RosettaCommons/main into devel Conflicts: source/src/apps/pilot/kale/native_ensemble/app_runner.py commit e064da856f33067e046db19f93cb483842c5a84f Adapt native_ensemble to canonical_sampling. commit 27af95ec638f04650f249193ff548c9e0af53c88 Refactor parts of protocols::canonial_sampling. I made two fairly small changes, focusing on the TemperatureController and TrialCounterObserver classes respectively. First, the inheritance hierarchy for the temperature controlling classes was longer than it had to be. The original hierarchy looked like this: ThermodynamicObserver -> TemperatureController -> TemperingBase The TemperatureController class didn't really do anything, and support for the ThermodynamicObserver interface seemed to have been dropped at some point in the evolution of the code. So I replaced the whole hierarchy with a single class (TemperatureController). As a bonus, this removed the need for a couple dangerous type-casts. TrialCounterObserver was a wrapper around MultiTemperatureTrialCounter. I decided that wrapper was so thin that it would make more sense to combine them into one class. This will make things easier and less verbose at the expense of some flexibility. If that flexibility turns out to be useful later on, we can always come back to the previous commit and pick out the original classes. commit 88bf7348367e88d80136c701ad3af9ee0592e9f0 Merge with origin/kalekundert/devel commit ffe8514f1702eb0a06b286a85fafa2b0fcc4519b Adapt app_runner.py for use on workstations. commit 69c9869b98afe47a11e24995e47706f4e09a9f7a Use MetropolisHatingsMover in native_ensemble. I don't actually know that this code compiles. I thought it did, but now I getting really bad linker errors. This is probably because I've been fucking around with the build system trying to get MPI going, but there could possibly be a really horrible bug in the code itself. commit 9c62b6abaf354914e65ec8b79c033dce14b22750 Add KIC to the canonical_sampling framework. The primary purpose of this commit was to make the balanced kinematic closure algorithm usable from the protocols::canonical_sampling framework. In particular this meant that BalancedKicMover had to inherit from ThermodynamicMover instead of ReferenceCount. I also added a convenience function to MetropolisHastingsMover to easily create BalancedKicMovers. At the same time, I also decided to simplify the refactored kic code by merging kinematic_closure::samplers into kinematic_closure. I decided that the samplers are the classes that most people would want to use from this namespace, so it didn't make sense to nest them so much. This commit also adds more documentation for the canonical_sampling namespace. commit 9e5fac587c24ff08d9a088ea1f7bc1d6325ff0c6 Remove my benchmark from the repository. I think this could get big, so it probably shouldn't be part of the main repository. commit 6e796872597ccdf9a3d1062e55d75cf11430fa71 Document protocols::canonical_sampling. commit 9b0424e71de9823290e8330ac9a09869ee23fdf3 Merge branch 'kalekundert/devel' of github.com:RosettaCommons/main into devel commit b1d553a3fa71167d2b1264a8acd7157258b01fd5 Add colors to the autocorrelation plots. commit cb3c37d3c583a676ee44b97b3cdfbb57209d7758 Sample all sidechains within 10A of the loop. The set of sidechains which are sampled does not update as the loop moves. This may be causing some artifacts, but I'm not sure if I can arbitrarily change the set of residues being sampled without messing up my statistics. commit bae78cf3b903f75ce6502aa7e5b858e61891c7aa Begin building a native_ensemble test bench. commit 73a35ebf0c1e0b86a0a053f10ab7bb8bad02fa5d Make small improvements to the gui. 1. Directly edit the description field. 2. Hit enter to run scripts. 3. Label plots using tooltip. commit e9d7aa1e778d8f3bd9d53d4baad6e28561970c65 Begin optimizing the native_ensemble protocol. This commit introduces a few more perturbing and pivot-picking algorithms that I thought might be slightly more efficient. It also adds the capacity for more meaningful reporting of acceptance rates. commit 512f130d82cecddeb3066686416805681c3eed30 Merge remote-tracking branch 'origin/master' into devel commit 058cab59ccf5c99efe33381643eb760dc809d216 Start adding diagnostic kic move names. commit 1d10c55048b2c69033377fc9d3aa3e422da2eadf fixing warning commit bb476f8c482f065817cf61f148e49b2f00bf9c9a Merge remote-tracking branch 'origin/master' commit 2ae0cd7ce1a1b33d394ddbceb7b70946acc93315 Merge remote-tracking branch 'origin/master' into devel commit 26a320d7adb7b49dee488eaacff3e0f1a16c2876 stupid mistake. broke the build. sorry commit 560bdf0a7e6a88a6efa93d53e4d1056f79d5ae05 Remove a C++11 feature I accidentally used. I realized that std::map::at is part of the C++11 standard, although apparently it is already supported on my compiler (and the compiler on the testing server). commit 181ed1bd01de34e073e5f1cac82b0f8009f99533 Make cosmetic changes to the job_manager gui. commit d5b6697b7cbeeb187d234e2747079a5cbf14631c fixing warnings commit 5a81b26a5eed0e06e30aa3ea930699333cf6ab8c Merge remote-tracking branch 'origin/master' Fixing warnings from src/devel/splice/Splice.cc and src/protocols/simple_moves/AddChainMover.cc commit 612a61d99413613ce698b7e5195e13f5d8bea8be Fixing warnings from src/devel/splice/Splice.cc and src/protocols/simple_moves/AddChainMover.cc commit 9517512b34ef3881e8fc0449770a749f99baf22d Fix mac build issues commit 54395851deacbc9ed89c75ee19d79c3fec418df7 Merge remote-tracking branch 'origin/master' Added ContingentAcceptMover, which moves only if a filter is true. Additionally AddChainMover now writes to the pdb which chain was added. AddChainMover now also allows swapping a certain chain from pose with a pdb from disk. Multiuse of SaveAndRetrieveSidechains enabled. commit f054241429cce957e13dabe67d9b63c0969e6547 fixing a few longstanding bugs in the mysql pose IO code commit d7901a88c720a34b8a90b28ac2982a08403fc71a Adding some debugging output commit fe4d56f9b920647a1fee11a999d0d7f9dd12ce60 missed a spot with the last commit commit a53881024eed10656b58258c80da2f530cdf5a37 make sure to delete the correct residue atom store when deleting a pose in the database commit dfe49e09a16d9dc89e9c77b314e1d7edf2dedf66 bugfixes for Transform and ShapeGrid regenerated shapegrid statistics, fixed a serious memory usage issue in the transform mover no test changes expected commit ca2ce8d3dfedc4bb657e0344c4955b3d234cebf0 Merge remote-tracking branch 'origin/master' commit 7a60b42f7628421980913dd07dd6afcb8fd17630 Add a window showing move statistics. commit 798f46bfac9f38ca558f9edc11750909b5925dfb Make cosmetic changes to the job_manager gui. commit e6b491d2be6d781080f5235e894e7117a8a2ca46 Remove a C++11 feature I accidentally used. I realized that std::map::at is part of the C++11 standard, although apparently it is already supported on my compiler (and the compiler on the testing server). commit d6fac7e82ff79886cc81b25a8a84fdc7351b397d Migrate my analysis scripts to pure sqlalchemy. commit 5839f45a0a5b0dc30f1a2e669182276ee4349471 Revamp the job_manager gui. commit b89f54109dd49c63269ca32fbf9a6d19e658b6b0 Merge 'origin/master' into devel Conflicts: source/src/apps/pilot/kale/examples/current_example.cc commit ddeb3a74e16467d405c60a061b17f3627682362b Create native_ensemble analysis scripts. commit da4c00d6f65c319a3db505d3320afcc8d81d0241 Make MonteCarlo trial counters more accessible. Specifically, there is now const access to the TrialCounter member of the MonteCarlo class and the TrialCounter class now contains some more helper methods. I also fixed a bug in one of my (unrelated) unit tests that I just now noticed. commit 07c663e88fab7a6696fc96d23a39f59300245a7e Add a method to access the tags in a TrialCounter. Also fixed a bad array-out-of-bounds bug that I accidentally put into one of the core::scoring::Ramachandran unit tests a few months ago. commit 141f2c28e248dde3a713d375ad736eba4e7c6b48 Merge branch 'master' of github.com:RosettaCommons/main commit 28c500f1c9ab91b249e484a96cb94a7c3d01433d [minor update of SandwichFeatures] - introduced primary_seq_distance_cutoff_for_electrostatic_interactions - report net_attractions - report sum_of_salt_CC_NO_bridges - report avg (min~max) of each electrostatic interactions per 1 pdb file [integration tests comment] - should not change other than features and features_database_schema (if any) commit cf5a922d83e9cc94bceeaf38df36e0e5a67e5de2 fixing mac build issues commit 3f6bf713506617f37f1ab844f3545e6ea5f86794 Give const access to the MonteCarlo trial counter. commit b5cd1b2c50dbd9deb5c8973bfdd5e058bf059390 Merge branch 'master' of github.com:RosettaCommons/main Added ContingentAcceptMover.cc, multiuse for SaveAndRetriveSidechains.cc, let addChain write which chain was added. commit 9a1a38591059d6b7520ad18c5ba1d0262896887b Undoing of rigid body orientiation comment in RBInMover.cc. Adding comment to AddChainMover.cc so it will write which pdb was added. commit 0777be7deca64d43072aea78b95b4cf8d57cd6e2 sorry, forgot to add one more file commit 3f15a96931fa8506bb67eefcf8849a6873c2860c header build error fixed. commit a98e1c66d722abdde662f3fbd56d128922a91711 Merge branch 'hahnbeom/patchs' commit 7503322b937af2501673e77941693d8411971ae4 1. gdttm added, using TMscore method instead of maxsub to get GDT scores 2. Goap debug commit 0abde7f418dc4b65ed72b6a939443cfd9fa6dbf8 ProteinResidueConformationFeaturesReporter now always outputs backbone torsions This was a little bit complicated, as the prior behavior was to output these values as 0.0 if the output structure was non-idealized. These 0.0 values were used, if the pose was later loaded from the database, to indicate that backbone torsion angles should not be loaded into the pose, as it is non-ideal and all, and the cartesian coordinated and side chain chi angles should be used instead. This behavior was less than "ideal" (ha ha) as torsion angles are useful in post-run analysis and should always be output by ProteinResidueConformation. To enable this, I added a new boolean field to represent if a saved pose is idealized into pose_conformations. This table seems appropriate as it already contains another boolean column, and comes after a struct_id has already been assigned. Now, backbone torsions are always output, but only loaded into a pose if the pose_conformations table indicates that the relevant structure is idealized. ---------------------------------------- Expected unit test status: Pass Expected integration test changes: 5 These 4 tests change either because of the new pose_conformations schema or because torsions are now output: features database_jd2_compact_io database_jd2_io features_database_schema And of course: app_exception_handling commit a7a559993f47c890aa23a34e405367a610c8c870 fixed a bug in InterfaceAnalyzerMover now it properly handles the (lack of) ss information in non-protein residues commit 7d9e18cf5d83ebe6216a7ea69cd7df56493f3ffc removing old debug output commit fffb51d9b8acec583f479d99bc08453518685b35 Add try/catch block to pH_protocol commit d7d07d75c03a42f869a227b41c86c61e8da80051 Add try/catch block to pH_protocol commit d1cd2262bbf31ead925f2e04a065fc98401ed0af cant calculated dssp of a non-protein residue commit 831354c37e3e634985456de854a0b936f1ba8836 Add try/catch block to pH_protocol commit 99c66a3e7d447cb097429d6df4992c582ea9cb6f Added new ideal column to pose_conformations table in ab_db_for_tests This is needed so that the antibody_designer integration test does not fail commit efa09232ce350a72ddbf69df15f6d460e547ca21 updating site.settings.accre and version.py bugfix the vanderbilt ACCRE cluster changed, updating the site.settings for it. version.py now works if you are compiling on a system that does not have git installed but your directory does have a .git file commit 3e02639d0539b9d3e54c49a2b5117103ad4e77ba fixing a warning commit 9f4f32eceec402c32820530f84fdbd71567e4d4f This should fix the remaining bug in interfaceanalyzer commit 53f1a2890416023a800273eed8c61184f19df79a ProteinResidueConformationFeaturesReporter now always outputs backbone torsions This was a little bit complicated, as the prior behavior was to output these values as 0.0 if the output structure was non-idealized. These 0.0 values were used, if the pose was later loaded from the database, to indicate that backbone torsion angles should not be loaded into the pose, as it is non-ideal and all, and the cartesian coordinated and side chain chi angles should be used instead. This behavior was less than "ideal" (ha ha) as torsion angles are useful in post-run analysis and should always be output by ProteinResidueConformation. To enable this, I added a new boolean field to represent if a saved pose is idealized into pose_conformations. This table seems appropriate as it already contains another boolean column, and comes after a struct_id has already been assigned. Now, backbone torsions are always output, but only loaded into a pose if the pose_conformations table indicates that the relevant structure is idealized. Cherry-picked from kylebarlow/designmixer 6dd6d9c commit 06bc1d7848cc2042152b33a73b8520b312ecdffd Some debugging output commit 3cc55b92b01d90a5d81fb2c85994ea023bd761e1 Fix architecture discovery for some machines On some machines the scons architecture discovery doesn't work right, resulting in errors. This is due to Python's platform.processor() function giving long, descriptive strings, rather than the short pithy ones that most other systems use. The platform.machine() function should get around this, so add examination of that function as a fallback. The code path for any system which didn't error out during compile should be (basically) unaffected. This should fix the issue seen with https://www.rosettacommons.org/node/3547 commit 362753bc0b6a711cf9ec525891a67996493de889 more kinemage outputter bugfixes commit 14d64af942c8979e4ee6ddb1d7f58fbf69610c78 small bugfix in kinemage outputter commit e2389efd2a53e177dbefff488f6621404c0e72ac fixed DisulfideEntropyFilter on mac compile commit e49c4f8853b437068d8bf8b4b12ff583efdc8556 Benchmark script. Altering build script so it always store command line used in the logs. commit dd9214a2c4af81fe48fde79841ff4e54b9420fe4 Benchmark scripts. Enabling comparison for integration.debug tests. commit 8826871f06c2322c5add190434a9218bd0ca736d Fixed bug when using ScoreFunctionFeatures reporter with MySQL A table name changed, and was updated in the SQLite case, but not the MySQL case. Additionally, MySQL cannot use text fields as primary keys unless a maximum length is specified, so I added some maximum lengths. ---------------------------------------- Expected unit test status: Pass Expected integration test status: No failures (except for app exception handling, which has been failing since last Friday...) commit f386d282874be68f5ead29d8f0d07515719f189e Merge remote-tracking branch 'origin/master' into kylebarlow/general_dev commit f852e8706e4635fe0e9ef0fbb058913ce3cf4e65 Benchmark scripts. Adding debug version of integration tests. commit 54f5ae1b33ea03639226c23ea693ea9cd62928c5 Added DisulfideEntropyFilter Changed defaut Remodel ordering of disulfide configurations to favor optimal DisulfideEntropy scores Added AllBB and AllChi flags for MetricRecorder commit e3b9a67267fc4939ed0d5576053b3a4e4a65d844 fixing bug in IAM and adding option to interfaceScoreCalculator InterfaceAnalyzerMover had a bug that the apply function to hang if the ligandchain option was used. InterfaceScoreCalculator can now be specified with a prefix option so that you can run it multiple times in a protocol with different score functions ligand_dock_script integration test change expected commit 74e2c9d30f11eb77c287fdf949d3ddbedce2aa70 ResidueType has two functions that check whether or not there is an atom in the residuetype. The two functions are: has() and has_atom_name(). core/conformation/Residue.hh uses the has() function and does not use the has_atom_name(). In keeping with stl, I have removed all instances of has_atom_name() and replaced them with has(). No integration or unit test changes. commit 364318169c453db53cbcc86a279bab6b24e86ccf Benchmark scripts. Adding debug version of integration tests. commit 484c1970ac632fe259e8ba415b2f14d290b67f90 Added DisulfideEntropyFilter Made DisulfideEntropy the default sorting method for Remodel creation of multiple disulfides Added min_loop parameter to Remodel for disulfide creation Added AllChi and AllBB flags for MetricRecorder commit 5ffa41344cb9d2f5260af5496c74943c22360400 Added multiuse functionality to SaveAndRetrieveSidechains, made RBInMover write the current RBO to the comment section, made addChain write comment to comment section. commit 4690550d1386c95d623d8479dc9f8374459afafd loop in IAM would never exit commit d210045967a27d8df3a604d8747006007beb9eed fixed a bug in IAM commit c241aa83e344b0d8589707e54aa211e81fbf2d6a merge of updated phosphate packing functionality for StepWise Monte Carlo of RNA, including well-tested, debugged runs for modeling floating bases (jump-connected nucleotides). commit ec880daed9bd860cab96a6a3693f529df9f61566 Fixed bug when using ScoreFunctionFeatures reporter with MySQL A table name changed, and was updated in the SQLite case, but not the MySQL case. Additionally, MySQL cannot use text fields as primary keys unless a maximum length is specified, so I added some. commit 87ab375dc9ef1eaacf2a9caff383d445c4099e12 Merge branch 'master' into rhiju/swm_phosphate commit e34dbad2ee40f593aecc7cd155b99deb5d37a076 Merge branch 'rhiju/swm_phosphate' of github.com:RosettaCommons/main into rhiju/swm_phosphate commit 617856fe906809c8e93547c9f36534e28820f153 initial merge of phosphate modeling functionality for stepwise assembly & monte carlo from branch rhiju/swm_phosphate. the only unexpected integration test change that I see is to hybridization/, which previously shows some wacky residue numbers and error messages in SymmetricConformation, which makes me suspect a problem with uninitialized variables; will be running this on valgrind. commit b081e07561416deab0f85d65191c500fb690063a stepwise monte carlo (for RNA): fixing early exits from debug builds. commit 91aafca0fb2bff1953e238ca77befb1650f2f721 adding “prefix” option to interfacescorecalculator” commit ea8018a967097b2180db71f40ed063f18b2eea07 stepwise monte carlo (for RNA): fixing early exits from debug builds. commit 972de5d836d40034106f3c5a28ae15c0c98eb477 adding include commit 882ddef3b762f435d28fbf3406464e474308a490 getting SWM to run with pack_phosphate for more than just a single nucleotide rebuild commit afad3fbbe28b9e8906d0768e5cd033f22f102b9c Small bugfix in my previous commit commit dd29b5a87214cc873ca13092e2b7f8c1c253adc9 Merge density_tool changes with master. commit 546e690d3a395f15ce3a8efb8e6d3dc1caee7358 Several bugs fixed in expected phse error calculation in density_tools. Adding code to compute erf and erfc with complex arguments. commit a3cc8f8ddaa89d7d97f112ff0e4fd49a008e3fb7 Updating crystal docking code commit 78aae1ebead4171b4718b116d94cbe78409c5b11 Fixing PyRosetta build commit 0c9dd8e30bfa311bddab3e9c7d60fa83462b93f9 Update version.py Remove superflous svn support code. Change detection system so it doesn't result in error messages for the weekly releases. commit f359f860ec1e15934beb831b70e9e83f5a364f86 Carbohydrates & Patch System: 1st sialic acid & new ResidueSelector NEWS: This push introduces several things: * The first sialic acid (neuraminic acid) and the first 9-carbon sugar has been added to the database. * A few more sugar modification patches have been added. * Several corrections have been made to sugar .params/patch files: - Bond lengths have been corrected for several O-H bonds. - Upper termini of the non-(->4) variety now patch properly. * To accomplish the latter correction, a new ResidueSelector has been added: UPPER_POSITION. UPPER_POSITION allows one to query the position of the upper connection of a polymer ResidueType from within a patch file. This is useful for residue subclasses which have varying numbers of backbone/main-chain atoms. Cur- rently, the system assumes a carbohydrate residue, but it can easily be adap- ted if anyone ever needs to add a new polymer type to Rosetta that does not have a consistent number of atoms in its backbone -- for example, terpenes. Usage Example: BEGIN_CASE # ->2)-Sugar BEGIN_SELECTOR UPPER_POSITION 2 END_SELECTOR SET_ATOM_TYPE HO2 Hpol SET_MM_ATOM_TYPE HO2 X SET_ATOMIC_CHARGE HO2 0.21 SET_POLYMER_CONNECT UPPER NONE ADD_PROPERTY UPPER_TERMINUS END_CASE BEGIN_CASE # ->3)-Sugar BEGIN_SELECTOR UPPER_POSITION 3 END_SELECTOR SET_ATOM_TYPE HO3 Hpol SET_MM_ATOM_TYPE HO3 X SET_ATOMIC_CHARGE HO3 0.21 SET_POLYMER_CONNECT UPPER NONE ADD_PROPERTY UPPER_TERMINUS END_CASE ---------------------------------------- Unit test status: Pass Integration test status: 1 change carbohydrates: expected commit 7ec59bcf6541e1432017153f5cb2a308b454747c Carbohydrates: modified upper terminus patch for sugars to correctly patch non-(->4)-sugars commit be1949bb981ae746cc775fc6c089ce942982378b Patch System: wrote code to impliment UPPER_POSITION commit cec74942c27d27b8e6699690e7b65c434ab4d772 Patch System: adding new selector for UPPER_POSITION commit 879bd938727532b604de0058367a01d63aa369d9 comment clean-up commit d1348c8d365eef0f15c1b319e4201545915600c6 Carbohydrates: correcting bond lengths for virtual atoms that become real Hs in upper terminus patches commit 671727deaaab7e1655595cf538d912600a48e6ec Patch System: commenting out new code; may not need it commit c059dd5d77fb74f76ea0c7d751e68f44500d0559 Patch System: declared ResetDistanceFromStub PatchOperation commit 676468cc1f051e2a1b3be0ef2c52c66602b7841c Patch System: adding RESET_DISTANCE_FROM_STUB to available patch commands commit 2b97546066abbfb14f27f5e385ec560905cd83bc fixed a comment commit b6fcd4a82e434187d649f7a59fbeabcbe8ec98b9 Carbohydrates: adding code for nomenclature exceptions commit 813bb9631e097a7b11ef7bae19457dcd492cb4fe bug fixes commit e0dd114bac3deafa7001dc5bc7e525ba89aa6a24 Carbohydrates: adding Neu to ResidueTypeSet commit 277d8d2031f8115bd7a024d0f59168b80fa8dbc5 Carbohydrates: adding Neu PDB file for testing purposes commit e3ca5eca663777a1122f0a4f7ab22fa417e38c7a note to self commit 731807da393fc49c753351cc6f9c67840ee29f6a Carbohydrates: adding Neu params file commit fa17a20d012d261e1755402150a9c8bb95236bd4 Carbohydrates: adding several more sugar modifications to list in database in prep for sialic acids commit ae8b10078fc3c2338209851011028570c553117d Carbohydrates: adding sialic acid 3-letter codes to database 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)