Rosetta 2014.20.56838 Date: 2014-05-17 Branched off commit: 8620a589f9d0d98a370ae0e82598e5ac35438320 Tail state commit: 63ea30abfc9a5c0990d34150a87dfc0a09a95a77 Previous version: 2014.19.56789 Previous branched off commit: f1041590c913d2149ab02a57a029f6fb12ccebf6 Previous tail state commit: 00168b202aa7420a7cddfa552f7dc8403844d3f7 Release notes ============= Merged origin/master with balej/2comp_devel. Fixed conflict with ResidueCountFilter. All tests passed, except for the integration test changes explained below in the NEWS section, which are either expected or due to an unstable test. COMMIT LOG ========== commit 8620a589f9d0d98a370ae0e82598e5ac35438320 Added a bond length creator for small molecules. Bond length sizes were determined from an averaging of the CSD. Works with gasteiger atom types. Added unit test. commit ea937398d1304ef9ee34b4eedc8cd380971592d5 add file for bond lengths commit 7c77321404dcb44c7f6f8584a860b23cdef74fad adding bond lengths commit d26320a349ba229892a2f1dac3acc047aa5e4ede Switching Benchmark PyRosetta builds to monolith mode. Removing some undefined functions. commit d663c515641ca6c03c33e980419c0875784bcfcf Fixing PyRosetta build commit f67d3f66875a189b2abd733ee59665184be869d9 Updating python packaging code for monolith mode commit 678fd27b2dcabfb6bdef70437e73512dea71159b Adding Windows monolith build commit 99cbb7e8ffdea79305b1464cfd25c85c92ddf8d7 fixed: PocketGrid.cc was mangling exemplar output commit 54b5f54866f31f4581bee1be297dabc1661e3b37 Created make_exemplar as a new public app, with integration test commit 7f998eff774e63cb266938f610cc59fc9ac2f685 updates to some pilot apps commit ee46d7bdf279c5dbe39c3b194f1f6ec32bbd7877 Missing typo fix. commit c29e74bb04516973e41f1282a5f0942425700519 First commit of code to support a new symmetric minimization strategy, currently accessible via flag -new_sym_min In this approach, all dofs (including dependent ones) are added to the minimizer map, and derivatives are calculated for all dofs, but when we are actually filling out the derivatives vector to hand to the minimizer we sum the dependent dof derivatives into the derivatives of their independent "master" dofs. This approach obviates the need for the jump_clone_wts and for the derivative graph. Conceptually I think it's a bit simpler, and it doesn't actually depend on symmetry; all that it relies on is the fact that when you move the master dof the other dofs are moved in the same way. So the effective derivative for the master dof is just the directional derivative corresponding to the direction of motion in which we move all the dofs simultaneously. One problem is that it uses the function "make_assymetric_movemap" (sic) in order to make sure that dependent dofs are added to the minimizer map. I think this function may miss dofs that are set individually via MoveMap::set_dof rather than by set_bb, set_chi, set_jump, etc. So that should be probably be fixed. Use with caution, check the numerical derivs, and let me know if you see any problems. I haven't evaluated the performance costs of this approach, but I doubt that it is rate limiting in most applications. I only saw one integration test change, in ligand_dock_script. It looked like a numerical instability. Has anyone else seen unexpected changes in this test? I don't see how these symmetry-related and cmdline dependent changes could have affected it. commit 2ad40e4e46a3e7a23a294d93806c6b444569a4b0 Eliminate redundancy in HBondOptions setup. commit 22f7a3ff86b464ef57abf7215377f73d0d267f08 remove unused variable commit 866daef7c121ee22c62e9174300cfecd514028bf bug fix for the interface_allatom, changed grid to cartesian coordinates commit d8dc7ef0c5bf3dce07d1bfeaeb30d5b54e3faabf bug fix:used cartesian space for get_interfaces_allatom commit 62a404c5c38a6fa95eec2ddaad090c9b57e6c07b bug fix:used cartesian space for get_interfaces_allatom, as opposed to the grid coordinates used previously commit 58bc818a1b011732ee7b85c85a74a3ebcf381a05 Reverting the "fix" to the MPI build that broke the MPI build, step 2. commit b229aca638b3141149154913cd35d0c02a7f9a38 Reverting the "fix" to the MPI build that broke the MPI build. commit 20e5e6ac3c055dad18ef2692fce099c46b9af896 Fix segfault with ligand docking calculator commit a8801e795d028cc9584bddc3ea2a25fd784e6901 New approach to symmetric minimization, accessible with the flag -new_sym_min commit c82c108ee4615e85a0590197d6d0ef429f7b076c Reverting slide_into_contact to translate_back in DockingPrepackProtocol commit 3fcc0ed9afe78188dfec2e16a642541ae1b31ff8 Test fixes, various and sundry commit 75b4d07d5a72ad85ecf2354d51536ece659de033 Reverting slide_into_contact to translate_back in DockingPrepackProtocol commit 978f0920b30f5e52cab551593f042f9ec2af3b9c Add a -hbond_bb_per_residue_energy flag for hbond decomposition By default Rosetta includes bb hbonds in the total score, but not for per-residue scoring. There's a setting which turns this on, but it was previously accessible only computationally. This flag allows commandline manipulation of the setting, for people who look at the table at the end of their PDBs and go "Wait a momement! Why doesn't residue 23 have a non-zero hydrogen bonding energy?" No test changes expected - defaults should be the same. commit 8ff3a703895a8dfb0e1aa6f8f71f2af9aa3d87ca Allow automorphic_rmsd to do comparisons between different name3s Previously, automorphic_rmsd was written such that it assumed that the two residues were of the same type -- or at least "close enough". This meant that it checked the name3 for compatibility. This change opens things up such that you can do automorphic_rmsd between two different name3s, as long as they're equivalent in structure. A complication is that HIS has to be special cased, as the "naive" matching (atom types and bonding pattern match) means that HIS and HIS_D tautomers don't qualify for automorphisms anymore. * No test changes observed, except for things that are failing on the test server. commit f71a2f64bfb6cdeb703b16374bdd9c918af460c7 Remove unused var warning commit a3177744096914c904a942727cd0b1236b746a9b Allow automorphic_rmsd to do comparisons between different name3s Previously, automorphic_rmsd was written such that it assumed that the two residues were of the same type -- or at least "close enough". This meant that it checked the name3 for compatibility. This change opens things up such that you can do automorphic_rmsd between two different name3s, as long as they're equivalent in structure. A complication is that HIS has to be special cased, as the "naive" matching (atom types and bonding pattern match) means that HIS and HIS_D tautomers don't qualify for automorphisms anymore. * No test changes observed, except for things that are failing on the test server. commit db6ac3081bcac0d25a1c35d4e970fde9dd8901f2 Fix up tests commit b9689d95f6818e37f26621048ec78eed3a083533 finally fixed broken mpi build @gcc version 4.6.3, all warnings-as-error were unused variables. I sent email to Rhiju for possible problem, and will send email to Frank also soon commit 387bf7e392cb0540f94b5a4068b83e833c19112c hopefully fix broken mpi build @gcc (Ubuntu/Linaro 4.6.3-1ubuntu5) 4.6.3 commit 41dd14e33b370f601eab95761e10b5cc3b93e2c1 [update of SandwichFeatures] - more clear naming (primary_seq_distance_cutoff_for_electrostatic_interactions -> min_primary_seq_distance_diff_for_electrostatic_interactions) - more consistent naming (shortest_dis_between_facing_aro -> shortest_dis_between_facing_aro_in_sw) - more consistent naming (shortest_dis_between_sheets_by_aro -> shortest_dis_between_facing_aro_in_sw) - may allow to exclude sandwich that has too close distance between facing aromatic residues - like 'write_resfile_to_minimize_too_many_core_heading_FWY_on_edge_strands_' no aro for every 2nd residue for 'write_resfile_to_minimize_too_many_core_heading_FWY_on_core_strands_' - should not change any integration tests other than (expected) features and features_database_schema (if any) commit 6555ebcaf114169f549fdcda07bcd3f225b62437 Remove unused sugars/legacy file category in src.settings file to fix Xcode project. commit db3958af48d3437cd2854fa5b51ddef7c86c90ce Trying to fix debug-mode MPI build (gcc/Linux). Unit test status: Not Run Integration test status: Not Run I didn't run tests because these are trivial changes (all commenting out unused variables). commit 74015e60bddf38662ec2ce0ac9e5b6a721e9645a Trying to fix mpi build unused variables warnings-as-errors. commit acf89095b125c4e2bb11768e2300108b127ab6cf Minor change to claim strength of FragmentJumpClaimer. Nearly trivial change in untested code; no test changes expected. commit b31eced0de301dab2bfafb65b213ce5957789cf3 Modify the claim strength of FragmentJumps to allow multiple FragJumpCMs to coexist on top of one another. commit 93d7e3a64c0f7d7ecb23ff8155cf01c8dd149cb2 Trying to fix signed/unsigned comparison warnings-as-errors in the MPI build. commit 081bbace95061a79fe3cffec0f38a386ed091ffc Automatic metal setup and constraints now works within RosettaScripts. CAVEAT: Constraint weights must be turned on explicitly in scorefunctions defined within a RosettaScript. Unit test status: All pass. Integration test status: Not run. commit befc6f629cf3f851554100e341b34401feeff7a0 Tweak to PDBJobInputter.cc to allow RosettaScripts automatic metal handling with -auto_setup_metals. commit 6cf4ee3dcac4e81039ec0ca927dee013ef3d87ab ResidueType: added VIRTUAL_RESIDUE property & fixed is_virtual_residue() VRT and VRT1 now have the VIRTUAL_RESIDUE property. ResidueType now has a is_virtual_residue_ private datum. is_virtual_residue() now returns the value of the latter. All unit tests pass. No integration test changes. commit f7e2d33e74a5da7b3ed81edbbf300285c34f09cf small fix for -in::missing_density_to_jump commit 2b5b2e1099cd167ef0a040d03a1ce633fd9cd586 Merge branch 'master' into automorphism_res2 commit dbe80d9bc6c05f3b114dfe69659841b5c3d4598a restoring some units tests broken by change in patch linker from "_p:" to ":". A few more tests remain broken; will commit fixes later in the day. commit cda38d3b9ae372b08dec1a57f44919ae8532dc99 restoring some units tests broken by change in patch linker from "_p:" to ":". A few more tests remain broken; will commit fixes later in the day. commit b7f922379dd8edb00b2780df739fa2fb20ced022 Updating Windows/BOINC project files and update scripts to VisualStudio 12.0 format (VS2013). commit 8590a82430f0bfd118e4b6efe56a42fa50b755a0 Fixing Windows build (VS2013). commit 1447c83a3231ede357763063a892367cd3037cb3 updates to pilot apps. fix debug build commit f519b2e7430dcbfcac75d8ae57fa0e4e6cebd0c4 update a few pilot apps commit 93993072816c65cd7a88dd751607602a0ebeac9f the HA atoms in centroid mode did not (anymore) reflect the full-atom definitions. This causes non-ideal poses when switching to full-atom from centroid with HA. I suppose in the mean-time the full-atom definitions of ideal residues have diverged. Now the HA patch is exactly the same as fa definitions (again). commit dbd15827cec2b35fabd8f62485535f64987314ef pull from master commit d975c62297f8409432f474807ec6b3a41ba345c0 Big merge -- a few little improvements for entire code, and several important updates specifically for stepwise assembly and monte carlo code. All integration tests checked very carefully. In terms of affecting lots of apps: (1) Patch linker text is now ':', not '_p:', which was more verbose and (I found) confusing; (2) Number of default residue types has been reduced a lot, by putting patches under '-patch_selector' flags, and a warning message is triggered if a dev starts a patch explosion; (3) got rid of silly warning message from hbonds about DonorStrength.csv missing. Also, fixed an initialized variable in LigandConformation class caught by instability in cstfile_to_theozyme_pdb test (and by valgrind). In SWA/SWM, almost everything is seamlessly unified between RNA & protein modeling so that RNA/protein (and more general cases, including ligands & metal ions) can be easily set up within the stepwise framework, finally. commit a10c6afd1265cbbbb17ebb1d3c4766093e0f755a fix residues:patch_selectors to chemical:patch_selectors. Patches are part of chemical/ namespace... commit a4cb4ca2b1165319ef33f20e9b2fcf014ca6316e update of patch_linker from "_p:" to ":" -- now more concise, and (I feel) less confusing representation of annotated sequences. No integration test changes (except cosmetic ones)! commit f4d56afb9f6d0c5d5fe47e2043791fb57a74b26d note to self to unify fragment-assembly RNA_Minimizer with awesome movemap and minimizer developed for stepwise code. commit 31a1ebeabee9668854d41eced7786d8381fc9199 fixing a huge overflow error due to a int-->Size conversion in taking PDB numbering. Oops. Glad someone has an integration test with "negative" sequence positions. commit fac9ddca7aa1c755ca474acefd4789c2c4a1de42 getting rid of water adducts to RNA -- getting messed up with command_line_selector stuff, I think. commit 162c43522c4f4bb449a75bb32e0bf92d1631df3e backwards compatibility to change in patch linker for atom_tree_diff silent files (are these still in use?) commit 4bc7c080a44ce892fc5f5cbb8262b5ba22f0e0c9 reset full_model_info for pose after add_virt_res. Fang, this app should make use of encapsulated functions. commit e3711249018842b88e49bf64366db108b8d97e8b fixing rna_minimize to actually minimize when -minimize_res is not given. a difference now that AllowInsert is initialized to false for poses that are read in from files. commit befb3f0efaf483fca89962375f8c48121294a0a9 merge with master in preparation for integration tests commit 2f7831a56e0b157b28753fe775b17ae311241730 Prevent ConstraintFragmentSampler to always set cst_weight to default value if not specified by user. Cst_weight is now only set, if indicated by user (and thus not overwriting atom_pair_constraint patches). Expected Integration Test Changes (Overall Score is identical, only the atom_pair_constraints=0 entries are removed): broker ThreadingInputter broker_membrane fold_and_dock metalloprotein_broker commit f9b972ff7dbd6cb8b8c97888d65f721ef2a2a8ca fix a bug when metropolis_hastings runned with FixTemperatureController commit 2ada4bab9eda1e37f029d2bd0a55ac1de1a77961 Merge branch 'master' of github.com:RosettaCommons/main commit 645d2228caa7c582ad0c68d5207a2e0efa16a61b minirosetta_graphics fixes for newer BOINC API. Use TTF instead of TXF fonts; needs testing on Windows. commit 3add0c8926158880be831433fe25a2d3082da6cb BOINC Windows build fixes for VS2013. This likely also fixes a potential bug: misuse of return value of getline(). Unit Tests: All Pass Integration Tests: No changes commit ebb863c15711b636aae04904d1b900ea6ee05dc5 PyRosetta. Fixing namespace build. commit e177d4159e51681e6473c32863a21bfa9c745007 PyRosetta. Fixing namespace build. commit 5dd99cb8e98e3bfd11188ebbdb38930bca3e9bf8 introducing PartitionContactScreener as robust alternative to atr/rep screeners. Got rid of rama_check in protein CCD closure in stepwise modeling as it introduces unwanted randomness. commit 654b7f0a2621e67dafa89c129b943367e00c78c1 Fixing Windows build commit 7cbed239260669590a61fb18a07b9f80364dd2c3 Fixing Windows build commit 9900d16bf4d9be444827937753eda688d3523aa9 Fixing unit test build commit d9ed1a289fea928cc792e628dc002507190b983a Beautifying code commit 57a9580e83e8459abb2f414a357a2bae14cea168 Fixing unit test build commit 7796200ddd5d13ee879c709f027bebd524aae5d3 in StepWiseMinimizer, replacing old StepWiseLegacyClusterer with StepWiseCluster. commit a15375cc0cc62ad35b4587ef837961413f578183 in StepWiseMinimizer, re-closing protein CCD loops after minimizing (and then re-minimizing), just like for RNA chainbreaks. commit 2459ebebd218be857de2f80135539ad00dad7cd7 uncommneted "Werror" in source/tools/build/basic.settings commit bd11f3ec31e992501df7cb5b9f338debff5458c5 PyRosetta. Adding monolith build. Moving final binaries in to build directory. commit 4b12374e28b8ea69244fd2c2d9ebf0c15e752178 Fixing PyRosetta build commit 43b70d90d09b170297c2cc9997ee282cbdc33b56 Fixing PyRosetta build commit 6e163d197ac08a9a45d02bcd29f5300cfbd7f1ca Fixing build script on Python-2.6 commit 00bc02da6fd04faa25c82ada0528b74b05f52972 Removed unnecessary headers from core/pack/task/operation/TaskOperations.cc to fix library dependencies. commit f1a9afe86736c41ccc97ecc5c15a486385a79250 Updating MSVC build and linking options commit 7c28272301ed5939dee8306ad6ae9a24f114f8c6 Merged origin/master with balej/2comp_devel. Merged origin/master with balej/2comp_devel. Fixed conflict with ResidueCountFilter. All tests passed, except for the following integration test changes which are either expected or due to an unstable test. Integration test status: All 7 changes are due either to previous issues or expected logfile changes. See below for details. Differences in translation are observed and expected in each of the 5 following tests due to setting default for ddG filter back to 1000 for all cases except those where PB calculations are being done. No differences in the resulting ddG values are observed or expected: hotspot_hashing hotspot_graft place_simultaneously rotamer_probability dock_with_hotspot_place_simultaneously Failed to run, as with other recent commits: metropolis_hastings This test is known to be unstable and the observed very slight changes in output are similar to those observed previously: ligand_dock_script More information on previous commits since the last merge with master are provided below. source/src/core/pose/symmetry/util.cc: Commit Message: The FArray1D_bool for partitioning the pose was not actually being set in the get_symdof_subunits function and was causing a segfault when this function is used. Fixed this so that an initial array is created in which each residue number is set to false. source/src/devel/matdes/AverageInterfaceEnergyFilter.cc source/src/devel/matdes/AverageInterfaceEnergyFilter.fwd.hh Commit Message: Added functionality to permit filtering individual residues (which can be defined by task operations) for individual score terms. Removed the "return_total" option, which has been replaced with the "mode" option in which the user specifies whether they want to have the average score per residue returned, the total score, or the number of residues failing the user specified threshold; these modes are specified by the user as "average", "total", and "individual", respectively. source/src/devel/matdes/BuildingBlockInterfaceOperation.cc source/src/devel/matdes/ClashCheckFilter.cc source/src/devel/matdes/ClashCheckFilter.hh source/src/devel/matdes/MutationsFilter.cc source/src/devel/matdes/MutationsFilter.hh source/src/devel/matdes/OligomericAverageDegreeFilter.cc source/src/devel/matdes/OligomericAverageDegreeFilter.hh source/src/devel/matdes/StoreCompoundTaskMover.cc source/src/devel/matdes/StoreCompoundTaskMover.hh source/src/devel/matdes/TaskAwareAlaScan.cc source/src/devel/matdes/TaskAwareAlaScan.hh source/src/protocols/toolbox/task_operations/RestrictNativeResiduesOperation.cc source/src/protocols/toolbox/task_operations/SelectBySASAOperation.cc Commit Message: Modified the output pymol selection strings and info from the write_to_pdb functions such that if the user does not set out::file::renumber_pdb to true, then the output residue numbers are retrieved from pose.pdb_info() to ensure that they will match with the output pdb even if there are missing residues that cause the Rosetta numbering to be shifted. source/src/devel/matdes/SymUnsatHbondFilter.cc source/src/devel/matdes/SymUnsatHbondFilter.hh Commit Message: Added functionality to permit four different modes: bound_vs_unbound, unbound_design_vs_reference, unbound_mutated_sidechains, or all. The default mode is bound_vs_unbound, which yeilds the same behavior as before. 1) bound_vs_unbound: Report buriedunsatpolars that exist in bound state, but not in unbound state. Currently no repacking is done in either state. 2) unbound_design_vs_reference: For bb polars and non-mutated sidechains, compare same atoms design vs reference, identifying those that are now unsatisfied and were not before. 3) unbound_mutated_sidechains: For mutated sidechains in the unbound designed state, simply report any buried unsat polar sidechain atoms and don't compare back to the reference. source/src/protocols.3.src.settings source/src/protocols/init/init.TaskOperationCreators.ihh source/src/protocols/init/init.TaskOperationRegistrators.ihh source/src/protocols/toolbox/task_operations/SelectByDeltaScoreOperation.cc source/src/protocols/toolbox/task_operations/SelectByDeltaScoreOperation.hh source/src/protocols/toolbox/task_operations/SelectByDeltaScoreOperation.fwd.hh source/src/protocols/toolbox/task_operations/SelectByDeltaScoreOperationCreator.hh Commit Message: Added the SelectByDeltaScoreOperation in src/protocols/toolbox/task_operations/. This new task allows one to select residues to be designable or packable based on the difference in score for a user-defined score term compared to the score for that residue in a user-defined reference pose. For instance, one can use this task to prevent repacking at all residues that have a difference in fa_atr between the current pose and user-defined reference pose of greater than or equal to 4.0 REU. This could be useful for instance in restricting design to those positions that have lost a significant amount of packing compared to the native scaffold (ie, that now have "holes"). It could also be used in conjuction with the DesignableResidues filter for instance simply to output the number and position of residues that have lost a significant amount of packing compared to the native scaffold. commit 44aa6daa0477cc57da1070bf54f5f21326e53e39 Merged origin/master with balej/2comp_devel. Fixed conflict with ResidueCountFilter. All tests passed, except for the integration test changes explained below in the NEWS section, which are either expected or due to an unstable test. ntegration test status: All 7 changes are due either to previous issues or expected logfile changes. See below for details. Differences in translation are observed and expected in each of the 5 following tests due to setting default for ddG filter back to 1000 for all cases except those where PB calculations are being done. No differences in the resulting ddG values are observed or expected: hotspot_hashing hotspot_graft place_simultaneously rotamer_probability dock_with_hotspot_place_simultaneously Failed to run, as with other recent commits: metropolis_hastings This test is known to be unstable and the observed very slight changes in output are similar to those observed previously: ligand_dock_script More information on previous commits since the last merge into master are provided below. source/src/core/pose/symmetry/util.cc: Commit Message: The FArray1D_bool for partitioning the pose was not actually being set in the get_symdof_subunits function and was causing a segfault when this function is used. Fixed this so that an initial array is created in which each residue number is set to false. source/src/devel/matdes/AverageInterfaceEnergyFilter.cc source/src/devel/matdes/AverageInterfaceEnergyFilter.fwd.hh Commit Message: Added functionality to permit filtering individual residues (which can be defined by task operations) for individual score terms. Removed the "return_total" option, which has been replaced with the "mode" option in which the user specifies whether they want to have the average score per residue returned, the total score, or the number of residues failing the user specified threshold; these modes are specified by the user as "average", "total", and "individual", respectively. source/src/devel/matdes/BuildingBlockInterfaceOperation.cc source/src/devel/matdes/ClashCheckFilter.cc source/src/devel/matdes/ClashCheckFilter.hh source/src/devel/matdes/MutationsFilter.cc source/src/devel/matdes/MutationsFilter.hh source/src/devel/matdes/OligomericAverageDegreeFilter.cc source/src/devel/matdes/OligomericAverageDegreeFilter.hh source/src/devel/matdes/StoreCompoundTaskMover.cc source/src/devel/matdes/StoreCompoundTaskMover.hh source/src/devel/matdes/TaskAwareAlaScan.cc source/src/devel/matdes/TaskAwareAlaScan.hh source/src/protocols/toolbox/task_operations/RestrictNativeResiduesOperation.cc source/src/protocols/toolbox/task_operations/SelectBySASAOperation.cc Commit Message: Modified the output pymol selection strings and info from the write_to_pdb functions such that if the user does not set out::file::renumber_pdb to true, then the output residue numbers are retrieved from pose.pdb_info() to ensure that they will match with the output pdb even if there are missing residues that cause the Rosetta numbering to be shifted. source/src/devel/matdes/SymUnsatHbondFilter.cc source/src/devel/matdes/SymUnsatHbondFilter.hh Commit Message: Added functionality to permit four different modes: bound_vs_unbound, unbound_design_vs_reference, unbound_mutated_sidechains, or all. The default mode is bound_vs_unbound, which yeilds the same behavior as before. 1) bound_vs_unbound: Report buriedunsatpolars that exist in bound state, but not in unbound state. Currently no repacking is done in either state. 2) unbound_design_vs_reference: For bb polars and non-mutated sidechains, compare same atoms design vs reference, identifying those that are now unsatisfied and were not before. 3) unbound_mutated_sidechains: For mutated sidechains in the unbound designed state, simply report any buried unsat polar sidechain atoms and don't compare back to the reference. source/src/protocols.3.src.settings source/src/protocols/init/init.TaskOperationCreators.ihh source/src/protocols/init/init.TaskOperationRegistrators.ihh source/src/protocols/toolbox/task_operations/SelectByDeltaScoreOperation.cc source/src/protocols/toolbox/task_operations/SelectByDeltaScoreOperation.hh source/src/protocols/toolbox/task_operations/SelectByDeltaScoreOperation.fwd.hh source/src/protocols/toolbox/task_operations/SelectByDeltaScoreOperationCreator.hh Commit Message: Added the SelectByDeltaScoreOperation in src/protocols/toolbox/task_operations/. This new task allows one to select residues to be designable or packable based on the difference in score for a user-defined score term compared to the score for that residue in a user-defined reference pose. For instance, one can use this task to prevent repacking at all residues that have a difference in fa_atr between the current pose and user-defined reference pose of greater than or equal to 4.0 REU. This could be useful for instance in restricting design to those positions that have lost a significant amount of packing compared to the native scaffold (ie, that now have "holes"). It could also be used in conjuction with the DesignableResidues filter for instance simply to output the number and position of residues that have lost a significant amount of packing compared to the native scaffold. commit 89fd3a0fa88642caeb360e7f83fa1d73e7668d08 Finalizing monolith init commit a8828fbc417ebd0ad1720c174bd88095f3c0b2d5 Replace EnvClaim forward header with full header, hopefully fixing PyRosetta build. commit 9b05a9cfb99ca7af8876dbfd5c5ee8fa6ec4d4f2 [update of SandwichFeatures] - newly introduced write_resfile_to_minimize_too_many_core_heading_FWY_on_core_strands_ - added a new column number_of_inward_pointing_FWY_in_sw - added a new column ratio_of_core_heading_FWY_in_sw - more concise naming (inward_pointing -> core_heading) - added try-catch according to rosetta/main/source/stubs/Application.cc - should not change any integration tests other than (expected) features and features_database_schema (if any) commit d25e8d8b5f80f5bdeb5e2066c796c362ac5ab046 add AsyncMPITempering and well-tempered-ensemble (BiasEnergy, BiasedMonteCarlo) into canonical_sampling integration tests change in metropolis_hastings is expected commit 84c806d03567c4065b3ff330b2c2df6fc7cf99a7 add AsyncMPITempering and well-tempered-ensemble (BiasEnergy, BiasedMonteCarlo) into canonical_sampling integration tests change in metropolis_hastings is expected === END ===