Rosetta 2014.22.56873 Date: 2014-06-07 Branched off commit: 80616601370b0cd2c5377b575b8257f3ec300995 Tail state commit: 2f18d10430598d7c734bacd5a73c74911b8314e0 Previous version: 2014.20.56838 Previous branched off commit: 8620a589f9d0d98a370ae0e82598e5ac35438320 Previous tail state commit: 63ea30abfc9a5c0990d34150a87dfc0a09a95a77 Release notes ============= COMMIT LOG ========== commit 80616601370b0cd2c5377b575b8257f3ec300995 PyRosetta. Minor fix to Windows build. commit 478018e002d3a24856ae6b292aaa8a781acd1e84 Removing src/rosetta_test dir commit b63aa35dd0d5435336a4cffe2b201cbc75ee4d3b Changing the behavior of centroid disulfide detection. Previously, disulf detection in centroid used CEN-CB distance when detecting disulfides. This leads to problems in symmetric structures where disulfides across symm interfaces are not detected symmetrically (since the distance of CEN_i to CB_j != distance of CB_i to CEN_j). According to the comments in the code, the check should be using CB-CB dist, so I am changing the behavior to that. The behavior is changed for both symmetric and asymmetric poses to be consistent. commit bf44bd828d690a877a4ededba12d7625ef56fb74 PyRosetta. Adding PyMOLPyRosettaServer.py to final binary package. commit 05d4ed0554e31f19240c498440421b418ca02467 Adding rudimentary ability to splice into chain2. It's not extensively tested but is probably close. No test changes expected. commit 7e1eaa731a484087da09dc1153bcc0e971d2c5d8 Fixing two symmetry bugs. 1: some code was inadvertently checked into CartesianMinimizerMap that led to VRTs getting moved .. this code has been removed 2: when reading symmetric silent files, update_score_multiply_factor was never updated, leading to symmetryinfo that did not match the dumped structure commit 2b45211e8ce6c8c4bc6892f6eab01f2fa3389a1e Fixing tabs, trailing whitespace in hybridize code commit 42bf3852b83c43895cee8c739b3a63b64056cb91 Fixing PyRosetta build commit f96d2c5f1aefef2c5e07125008aa8a2aae8d53e4 Add RNA suite potential score term. commit c1305ddf24cf8d2b82058e79e1bd6f94dbd44001 removed unnecessary output to log files commit 607b88d6bb1c6ea9e4167277d5520a295ed5be71 Reduce memory usage in crystal dock commit b5b0b4ecc78c229488aef150ac1974404a38f0c2 Merge branch 'master' into fcchou/turner commit a1c80b9216f5f868edc7b430894b325d4b59d95c Remove errant backslash breaking build commit 86eeaf9637e6b6b693b6570e72768c6d801daf50 Updates for crystal refinement code. Many more options for map construction when rephasing crystal data. commit c83db396342a29867da125aaf6cc5adb5759641b Disable failing make_rot_lib unit test The failing portion of the test depends on energy minimization - which (understandably) has platform sensitivity issues. Disable the test until a "better" way of testing it could be found. (note the test was recently added, so we're really back to where we were a week ago). commit 193ce68599de67cfbce7ed06b6feccace1d33081 Tweaking certain functions that sometimes break the MPI build, depending on the compiler. I think I see what Doo Nam was trying to do, now. On certain MPI compilers, MPIBPool_RSD::create_comm() is creating problems because the variable "returnval" is created and set by an MPI function call, but only used for an assert() statement. I think the compiler optimizations are completely bypassing the assert() in release mode, which means that the compiler thinks that the variable's value is set but never used -- a warning that trips us up due to the warnings-as-errors. I'm switching these assert() checks to runtime_assert_string_msg() checks. The hit in performance will be negligible, and this stops the compiler from tripping. Plus, it's an assert worth making at runtime. commit 413fde074a6befdb7e18be11909b323d5fd5a659 Trying to fix debug-mode Linux build. commit 63abdff29dae5e11c3190657eb3766e602df9d65 adding protocols_b.4 to protocols_b.5.src.settings file. This should fix the build commit af226deee07c863b06c7bc8ef08e74e2736fa2ae Uncommenting Werror flag which which got comment out in r56848. commit 08fc4100b5a15e1ea2c5e49b722cd733cee81d97 PyRosetta. Updating Monolith build namespace sorting. commit 2338d7265cf1ec7b06b685249f15c370ffea7e3c Monolith builds: Adding removing of rosetta static lib before rebuilding it. commit 526870d7232bcab83c86284d7b8e81b78d66fad9 Fix headers build. commit 52bca19717198f05900acd8673aada90d0464f7d Store filters created in Pose Selectors in a local map to support filter-filter dependencies. Unit Tests: All Pass Integration Tests: All Pass commit 8f7b631dfd5b7edd42ca037982000d88ab43d4e6 small refactor to fix the library levels problem. I don't think this will fix the clang build, still working on that mystery commit 57b4df94b444f828809b3bc7049cf5accaf0749b added site.settings.contador for compilation at Kuhlman lab commit e14055199d7c6051fe1d50dfc9d32586cb4e6280 Attempt to fix broken builds commit f6a9433a55223dc9915d4b1881471d6df3a5f924 Update sdf parser machinery This commit updates and modernizes the sdfparser facility in Rosetta. The previous sdf parser items were created by Sam Deluca in his early days in Rosetta, and never made it to usable status. At the recommendation of Sam, that attempt was gutted and replaced with a version which takes advantage of the current state of ResidueType. (The primary goal of this commit is actually to support within Rosetta all the ResidueType creation machinery which had previously been encapsulated only in molfile_to_params.py, a necessary step for the drug design efforts.) The SDF parser machinery is not quite ready for general use. Items still missing before it becomes usable: * Support for loading rotamers. * Ability to automatically match input PDB atom names with their SDF equivalents (Standard SDF does not have a concept of atom names.) On the wish list: * Input of *.mol2 files. * Support for NCAA generation. Additional unit tests added. Integration test changes observed: FAIL sdf_reader -- new integration test FAIL fold_and_dock nonempty diff ref/fold_and_dock/log new/fold_and_dock/log -- Cosmetic changes to tracer FAIL hts_io nonempty diff ref/hts_io/output_ligands/test.sdf.gz new/hts_io/output_ligands/test.sdf.gz -- Extra data added to output sdfs (Rosetta Name, Rosetta nbr_radius, etc. ) FAIL ligand_database_io nonempty diff ref/ligand_database_io/ligand_parameters.db3.dump new/ligand_database_io/ligand_parameters.db3.dump -- changes in (now) non-critical column Given that this commit touches ResidueType.hh extensively, the standard complement of sensitive integration test numerical noise is expected. commit e2b9bdfd48c55e8b85645a534ef903490e6976e7 update CrystalContactsOperation to calculate contact distance by nearest atom to nearest atom, nearest atom to CBeta (nbr_radius), or CBeta to CBeta. default is nearest atom to CBeta for symm unit to asymm unit so we can consider symm unit static while asymm unit samples rotamers during packing/rtmin. also set new default polar/apolar distances commit 3ec67f8a4ba9506cf427eb37293db1861d590bfc A few bugfixes for density code. Fixing failed assertion for annotated sequence with multichain input. commit 58a8d41ffb3af3176a3265a88583d25e8e0f920d merge with master commit 1f8afbeef2f6969519a287ae1e356a61dcb3171b Updating object sorting commit 52410f2f0b468ae66cc0808ae561d95dc44321ce Fix header file name changes commit 4757d1d5def404833dcbc352912ae79a5f15051a Merge MakeRotlib tests commit 675cc0029d17ce22ff63709d888f7f61dfb15e3f Utest for MakeRotLib::calc_centroids() commit 55236749238f50673415d1b3995c1d82f3b58ff8 Utest for MakeRotLib::calc_rotamer_clusters commit 5b9a328f5bcb097af83a34bf4728fcacc6f6de8a Utest for MakeRotLib calc_all_dist() commit b2d60a9f1103f71928ffa34b9f75b85628f24fc8 Change UTracer scheme for intermediate loading. commit cd4daa3e16b71a077f69d8421427f09757883f98 Utest for MakeRotLib::min_rotamers commit 4121314d3e86250a4bde5ae242030101e71970ee Utests for MakeRotLib::init_rotamers_centroids commit d496da5cb9a9a9c1d0aa7de5eda7d54cd2070156 Fix War of the WaRnINGs casualty Unused return value, but function modifies arguments. Integration test changes in make_rot_lib expected. commit 25447ac192815f3c2d60ed6fc1273dd31336e065 fixing library levels problem commit 21f0b9476770f55bbbaa06ff21c247faef7cd1d6 Merge branch 'master' into fcchou/turner Conflicts: source/src/core/pose/rna/util.cc commit 6a9d294783496d1bb745e2658ecf3b4da2141630 Update the rna suite potential commit 9a74b32c56c676918965119c5afde0d8644b14e3 merging RosettaTMH into master commit 1b957506adc1a6bfa8d54301ef7248abbf9f41c7 Fix recently introduced bug in ResidueCountFilter. Support for task_factory was added, but improperly initialized such that the task factory was always used, even if it wasn't specified. Also fixed a bug in ResidueCountFilter where disulfide cysteines ("CYD") would be counted twice because name3() is "CYS" and name() is "CYD" commit f9847ebc093fcbb41ad00fc4f07b374b54bff13a Fix recently introduced bug in ResidueCountFilter. Support for task_factory was added, but improperly initialized such that the task factory was always used, even if it wasn't specified. Also fixed a bug in ResidueCountFilter where disulfide cysteines ("CYD") would be counted twice because name3() is "CYS" and name() is "CYD" commit fd2f1ccd90ae5a5db5f456a9e86a81d8fb67c701 bugfix for crystal design commit 1055b8fbeb6a3939fb8efe5ac47fa7a96462b5a6 make default constructor of Batch private, as this would yield an instance with badly initialized variables commit 7c7cf177007b584fd8996f7f60ecf80e6594a537 add missing initializer to 2nd constructor of jd2::archive::Batch commit feb27bad2acc52dd21bc05348cd836b8db3822be Fixing monolith namespace sorting procedure commit 8ccbefe69f75c98d741c703f98570c2842a1608e Adding compiler switch option for Windows build commit 4d5b1eb22bd893da112a62551da59b0aa82ae34e Adding unit tests for utility::file FileName and PathName. Unit tests from Meiler Lab Powercoding. Team Amanda Duran and Alyssa Lokits. commit 7f2a127458c4f7c4cbec54a51c939fd3eaddd7bf Adding Unit Tests for FileName and Pathname from utility/file commit 67d31ca5bdd00d19901a90cdb6df18162c2cb807 Unit tests for ContactMap Meiler Lab power coding with Joerg Schaarschmidt. New unit tests for ContactMap commit a298773db96e33c2cad8f41a45b2ed956077c99d Unit tests for ContactMap Meiler Lab power coding with Joerg Schaarschmidt. New unit tests for ContactMap commit a00169b913c5f02af31a0d4ef385a98ad60c4ea5 Corrected conformer substitution in UltraLightResidue, made sure new conformer is placed in same space as old conformer. Integration test differences expected in ligand_dock_grid commit ec7454c24e75be557cc55b078649c77955012363 Corrected conformer substitution in UltraLightResidue to position new conformer in the same space as original conformer, integration test differences are expected in ligand_docking_grid commit 2dc89f96be528bb62da4ced44989c441fb63fac5 Fixing Tacc.Stampede build commit 00130f41034e11331eb3b5ad3f196edb7ab8b817 another pilot app update === END ===