Rosetta 2014.19.56789 Date: 2014-05-13 Branched off commit: 0c89d62ea0b033d7f0250e864ef2470d99ca46dc Tail state commit: 00168b202aa7420a7cddfa552f7dc8403844d3f7 Previous version: 2014.18.56749 Previous branched off commit: 41a04540f1ab4cdb75b842c5ac313fdbf015001b Previous tail state commit: 2a6be8a721a64bac87b603b1d43487697b9f1775 Release notes ============= NEWS: NEWS: NEWS: This push introduces lipids into Rosetta. NEWS: [DETAILED DESCRIPTION OF CHANGE] NEWS: COMMIT LOG ========== commit 0c89d62ea0b033d7f0250e864ef2470d99ca46dc weekly release: stripping DONOTRELEASE-wrapped code commit f1041590c913d2149ab02a57a029f6fb12ccebf6 Fix app_exception_handling integration test. commit ad45276e815fa0644e60655dbde2025e7ba8715d Fix breaking app_exception_handling test. commit c8f13a1da1f6750f982ff48dce6a9b5a6e60d749 Fix unit test build. commit f478d6d0d68a769812621de26cb943560525f2c0 Modify TorsionMover and JumpMover::yield_claims to new interface. commit 8112f348dba362c4cb4356d45c827fc09cf9dace Remove unused parameter in RigidChunkCM::apply. commit 8da3ebea41dab96ff47c51dec75dd92999e136bf removing some pose.dump_pdb() in splice, which should only be used for debugging commit ae7e5a7324630b71ac91a0498223203fca0d4594 Merge branch 'master', remote branch 'origin' commit 29c5b30fbe22892857b4f07cefca7732f903f527 fixing FastRelax default options should also be used in parse_my_tags some integration changes expected commit 23007e6065bf0f704862fdb3a5a4260a42e30e43 should fix broken GenericSimulatedAnnealer UnitTest commit a5705a979dc66f6edd6812adbbda875ae4d79352 Variety of changes and bug fixes in the Enviroment/Broker2.0 framework, including new movers that provide behaviors required for RASREC sampling. Integration test status: failed tests due to trivial log file changes (fragment loading was slightly modified) or noise in ligand_dock_script. FAIL autoNOE_rosetta FAIL app_exception_handling FAIL ligand_dock_script FAIL metalloprotein_broker FAIL broker FAIL ThreadingInputter FAIL fold_and_dock FAIL broker_membrane commit ee7a051bb359223587e2c53df4e3bfbc719671ea Adding master changes that occurred while integration testing to justinrporter/env_release commit 115828dd34fdcf7fcb8903f82dfbc7ceac049d60 fixing bug in splice related to retriving segments from db commit 940df86df88eea5c6dc4886c938582587d30a33a Fix PythonBuild by removing jd2::archive::BaseArchiveManager::register_options() from header commit a6d86d6d36879df1f78908856df0ee786881b5b4 should fix an existing ResidueCountFilter unit test commit 80a988e47d1e8dc470db199f4dc654d9ca7fcdb6 Refactoring regression test comparison to make it output less cryptic commit 39ec6e58fca104c2e0009f507baddd2dfd6527c5 503 Connection timed out

Error 503 Connection timed out

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commit ff2eb406aa688e71295e51e259d8379c5cfab265 adding the talaris calibrated weights commit 90d26b3bf69da3b963a138bee6a8d8fe570f6fb8 [update of ResidueCount filter] - if a user wants, it enables count/filter by percentage, not by raw counted number - by default, it counts/fiters by raw number as before - should not change any integration tests commit 63778585b354b7d74a230f0345ecbe725c3ef4c5 Fix ambiguous references in g++-land. commit f0143c171ac1974ae2789a0b32ff542d0e67d9e8 Merging justinrporter/env_devel into env_release for integration test comparison and release. commit ae3fd6d8f84a762712a27908f135c2a12a51827e pull from master commit 205cbeb86573af6b5a05fd874621c1007d5d3c5c Added a new fold tree function to Splice.cc. Should not cause integration test changes commit 38f7e791ee1601d56e7fe71b111dbd413fa8b5d1 merge cloud_rasrec into merge_master_cloud_rasrec commit c9eca0aa61a8b12c3c94c38e89704e7b0125d401 Added a new fold tree function to Splice.cc. Should not cause integration test changes commit 6801af8871694930c895f47ce461d66e53cc7d26 merging orielg/peptiDerive to master: Added a new pilot App: PeptideDeriver Unit test status: Pass Integration test status: All Pass commit 94995b4d7df9c304e9dd56e91f15da1a5b13694b fixing exception handling commit 79d6ccbdd3f997f28d1eb6222e303c9f159fdc12 fix compilation commit 06f57794a5d9fc8995b6e027d3a1ca3d4d5f5e4d merged changes on feature branch fold_tree to master. Should cause integration test chagnes in Splice_* integration tests commit 799b2bbdfc0567072c6b4afbc4d1e5f7251baad9 Merge Master into branch cloud_rasrec commit 0e174ed9ae44aeee1056fb34f4ab428b05ffbfcf [update of SandwichFeatures] - added a new column 'shortest_dis_between_facing_aro' - sorted writing options by ABC - don't write resfile of sandwich that has non-canonical LR for subsequent design - don't write sandwich that has non-canonical LR if you want - should not change any integration tests other than (expected) features and features_database_schema (if any) commit 5a12551e50cd7db7518c77e0241a767e22aeefbb Revert "Adding two complex glycnas necessary for HIV as non-canoical amino acids" This reverts commit f2b476e2ed0f508fd2a770ec6b809c8e9d246f68. commit f2b476e2ed0f508fd2a770ec6b809c8e9d246f68 Adding two complex glycnas necessary for HIV as non-canoical amino acids commit 3d0b21081d9359ae0c5b6d382fe6a8b0cbe2bc97 fixed a bug in the base_name option in eval_natie run commit 7b0898109982aca1647f2f1d41c073de7d49869c Fixed bug to LayerDesign when parsing CombinedTasks commit 01450311136336fe4a217273b3c512136405d8c4 fixed base_name bug in eval_native run commit 4eecbf83579361850f8b45a1fe263ff0e9675fcf added the -compact flag to output only the transformation matrix commit d786ebe83aa31a66c378492902b5d0ecc308f8da updated random_rotate flag name commit 2ca47e9f5a3b56ed56c80e559e340ebf17a16dc3 updates on 050514 for cryst_design.cc. Removed some tracer outputs. commit e839e4aca3597726a7aafda1e2c7f36e4ce197fc supressed some tracer outputs commit 35c9932c092da6c5e1d8ae0c7d7f4f0ee32132ac merging orielg/fpd_multichain_receptor to master modified: source/src/protocols/flexpep_docking/FlexPepDockingFlags.cc modified: source/src/protocols/flexpep_docking/FlexPepDockingFlags.hh modified: source/src/protocols/flexpep_docking/FlexPepDockingProtocol.cc commit 632f0daf8436bc36c0ed7db9bbb2a5118e871395 Updating env_release to current master state for integration testing. commit b2b06a1047be2af3652dbaf7949bcabd487130c9 Merge remote and local env_devels. commit aaddcf468e5fd4c9e45cdf254b2986900f344e52 Move Environment creation code from ParsedProtocol to a separate Environmnent mover. commit 347fd1cef9d8de0d5148c13f5bc4637ef624f6a0 fixing build commit 14b75a73c35a57bd09047cd7b2ee2b002b8bc2c1 Movers should report statistics to Pose rather than Job. Updating ddG and MotifGraftMover. commit 236dd63ffe37fb5b5e3a3907d77cd61c7854255d Make clang PyRosetta happy. commit 6e50e6f68c945b01e87aba1d3d5ea5977cb31155 Bugfix to pilot app commit 9b35fb147ed111f18ad5c174ee12b3dca316f7e6 small bugfix to a pilot app commit ca21e6820e18c88d014613c95b839b7038d004d2 Adding uncached / lazy generation MultiplePoseMover mode. In the uncached mode (enabled by default) poses are pulled from previous mover, selected and processed on demand, without caching all input and output poses. This should allow operations on larger sets without blowing up the memory requirements. Certain selectors (TopNByProperty, Cluster) require a full set of poses to perform their selection. When these selectors are used, cached mode is automatically enabled and all input poses are cached first as before. The caching behaviour can also be controlled with the "cached" parameter in the XML script. Unit Tests: All Pass Integration Tests: No changes (vs. 85c6b69) commit dbcb6437d9fbea92703fb46b48e03d71448843e2 Small bugfix to crystal docking commit a53489922a34dc50eceb5b20364c8e3bed129556 small bugfix to cryst docking + a few new options commit 85c6b693821eb9e47a783af175c437ee778013c7 Output data added to a pose with setPoseExtraScores() to PDB and score files. Use this function if you'd like the additional scores from your movers, filters, etc. to be output by the JD2 to files. Extra scores and strings are kept in the DataCache types ARBITRARY_FLOAT_DATA and ARBITRARY_STRING_DATA. RosettaScripts filters and pose selectors now report their computed values to the pose using setPoseExtraScores() rather than to the job, since a job can operate on many poses if the used mover implements get_additional_output(). Unit Test Status: All Pass Integration Test Status: 16 test changes (vs. fe265a4df6): Additional data in output PDB/score/silent files in tests: density_refine density_refine_symm docking_ensemble Enzrevert_xml filter_termini_near_interface hotspot_graft KIC_refine KIC_vicinity kinematic_looprelax loop_modeling next_generation_KIC place_simultaneously rs_loophash score12_docking score_only_silence torsion_restricted_sampling commit fe265a4df6e8b6f639c059f759d4b26c9e2fb26a Always add a suffix tag to the decoy name when a mover generates multiple poses. The tag is used in PDB file names, and within score and silent files. As most movers currently generate only one pose, this only affects LoopHash and the MutiplePoseMover and MultipleOutputWrapper. Also change the tag for intermediate poses back to a prefix in the decoy name. Unit Test Status: All Pass Integration Test Status: Changes to file names and decoy names in score files in: AnchoredDesign antibody_designer broker_membrane dna_interface_design docking_prepack jd2test rs_loophash surface_docking commit e6dac5cee5231426b6a4bb45893e536796418830 People don't seem to mind mixed up score files, so reverting commit 63c8d3eb341e2004dd2697f0b3448a2947a23f47 by request. commit deafc186dababc636f5b43e8e29c262d0d8f19d1 temporary changes to basic.settings. DO NOT PUSHgit commit 70ae47dbd1025f76da7e1ee98b8025a4c40fd59d Added new function to Splice mover. can now splice tail segments. should not cause integration test changes commit 63c8d3eb341e2004dd2697f0b3448a2947a23f47 Don't write score file entries for unscored poses. Such entries were previously incomplete and contained only total score = 0, and potentially some data attached to the job by movers and filters. This was problematic when a score file contained a mix of entries for scored and unscored poses. The structure is still written, and as before with an empty energies table. Unit Test Status: All Pass Integration Test Status: Cosmetic file name changes to: AnchoredPDBCreator database_jd2_compact_io database_jd2_io InterfaceAnalyzer InterfaceAnalyzer_bothpack InterfaceAnalyzer_prepack InterfaceAnalyzer_resfile InterfaceAnalyzer_tracer ld_converter oop_create remodel rings scaffold_matcher unfolded_state_energy_calc commit fe5d0b70d57f7a056c211e6b6976942201479bb3 Adding build support for clang 3.5 (Ubuntu 14.04). Fixing warning: comparison of constant ... is always false [-Werror,-Wtautological-constant-out-of-range-compare]. commit ece74ce3723e26dd0cdd9dcc63f67850299de18c [update of SandwichFeatures] - write_resfile_to_minimize_too_many_core_heading_FWY_on_edge_strands - should not change any integration tests commit fdc03dcfa2202474f86078cd626b722dacc974a5 fixed broken mpi build by modifying init.cc commit 12add4504b2ad9daa1b2620b7883ee502680c3a9 Modify abscript mover not to output intermediate-staged decoys for stages that don't run. commit 77a3c63b12aced64d76837548d51dae8e59fc378 Modify some header comments for the Environment exceptions. commit 1b7378912954a1747f2a2378fe4492409c7a1414 Fix an issue where messages weren't being stored properly in environment exceptions. commit c26b18d4550d034256f50378c98349662df50960 Move the declaration of the pose inside the JD2 master loop so that it goes out of scope and is started fresh. Resolves a bug where certain portions of this loop were not exception safe (parts of the bugged state would be retained into the next structure). commit a87f907c8741f92a12f28b5d86acb68b22b43d13 JobDistributor's main loop no longer persists a pose across jobs. The "master pose" which is passed to the mover the JD runs on is no longer kept outside the main while loop's scope. This means it's reinitialized with each new pose, which makes this loop a bit more exception safe--and fixes a bug where exceptions that end with this pose in an invalid state were leading to skipped jobs. commit bf44c47f8d266cb268fe052198ce7d9789c48457 Move the declaration of the pose inside the JD2 master loop so that it goes out of scope and is started fresh. Resolves a bug where certain portions of this loop were not exception safe (parts of the bugged state would be retained into the next structure). commit a769954295a81b34b9346d0e8fea0072dd81eeb3 Fix a bug where DofPassports would render residues with nonhomogenously-accessible torsion angles as accessible. commit 0fe1efda359b135496f1456a7cbed2f127cccbd6 Remove RigidChunkCM::apply() because template-setting is done during initialization. commit b1e5cea2f5c997f2794e13baa18324c62ccd5d0e Relax template-is-fullatom requirement for centroid modelling. commit b55216d4590a69a201481160b0190bc8a63a9ee4 Move is_fullatom check in RigidChunkCM to yield claims instead of in parse_my_tag. commit 14458ed5c9f1682efd01833c1bde3c2c0b4649b6 Fixing PyRosetta build on Scientific Linux commit 75b8e6415f5a7e8e7e93839f3c179c0d53888763 [minor update of ResidueTypeConstraintMover] - requires 'AA_name3' only to run ResidueTypeConstraintMover instead of requiring both 'AA_name3' and 'favor_bonus' - should not change any integration tests [minor update of SandwichFeatures] - newly added write_resfile_to_minimize_too_much_hydrophobic_surface - should not change any integration tests other than features and features_database_schema (if any) commit 74b21eb3dadfb7e61c0f3d0c28d7c3560493a1dd Fixing some -Werror=maybe-uninitialized errors that make gcc 4.7 fail to compile in release mode commit 98f288578a05439db91bafa3b0359720d528baf4 Fixing a bug in reading foldtree chemical edge commit d2227988ffbd58529de964d192ef8ab0f52893b1 Fix two bugs with NCAAs and the PackerTask, change behavior of EMPTY Adds a new Resfile action called RESET and changes behavior of EMPTY. Previously, once a position became a NCAA, it could not be mutated back to a CAA. Also, once a NCAA was enabled at a position, it could not be disabled. The RESET action enables all CAAs at a position like the default state when a ResidueLevelTask is created. This allows the PIKAA action to behave properly. The RESET action also disables any NCAAs that have been enabled, allowing you to reenable any you want turn on using the NC action. The behavior of EMPTY has been changed to also disables any NCAAs that have been enabled, allowing you to reenable any you want turn on. To design both CAAs and NCAAs at the same position use RESET, for example... 5 A RESET NC HLU PIKAA AVL To design just NCAAs use EMPTY, for example... 5 A EMPTY NC HLU This fix has the packer tack comparing interchange ability group rather than AA type to determine if we are designing at a position. The hydroxyproline patches had to change slightly so that they did not produce a residue type with identical AA and varient types, I believe this was a bug. Additioanl syntactic changes to the packer task to get around some complicated pointer assignment when used with std::list::erase. Unit test status: [Pass] Integration test status: [1] [posttranslational_io]: decrease in the number of rotmaers during packing from the HYP bug commit d69842b8cb774aaba661a3d8b7df94ba84d77034 Update SSPredictionFilter.cc Fixed bug with mismatch probabilities commit d438de36f5b73ae1cabb58621ddc33a1dc9b4891 PyRosetta: renaming low_mem config flag to low_memory_mode commit cd924c0d35a135bf27d004a058e2c9df3f91ab36 [minor update of SandwichFeatures] - total update of resfile generation based on more accurate native data set - better namings of resfiles for easier output process [integration tests] - should not change commit 3ff97117c9f54d5adf11e90bedee06b3d22ea46b Add RigidChunkCM to the RosettaScripts system. commit 57d1121d460b08ef69fb724efd5ce086eff7b567 Add input-only option to RigidChunkCM. commit 001c6e9385aea534328b226004f24aaae9d839ca Topo driver update to full RigidChunk testing code. commit 6ad1b0d34f05e768ea517631061a9878f9f77594 Merge EnvClaimbroker fix with JumpClaim fix and RigidChunkCM test development. commit 3f8496f53012a9c9e4c33a2fcd166ef3fc2d5ac6 Removed uncontrolled DoF check, because it doesn't make sense anymore. commit 01d8cbd4785a1eb7775adaafa05a4a8a295faaf6 Fix an issue where dominant control strengths were not being correctly logged, allowing lower claim strengths to conflict. commit 5d43407e134373baea3d62c29288a9546fd754a8 PyRosetta. Fixing build and adding low memory mode. commit 5f9fb99aa267db273815e3dfcd733063180d96f8 Carbohydrates: fixing typo in a galactose topology file commit 43a2e489d37fced177a5cc53acc227791f9fa66f [minor update of SandwichFeatures] - better namings for easier output process [integration tests] - should not change commit b6f44bb4cb4b3524a457d1ad5fa576b4e5a0581f [minor update of SandwichFeatures] - make a resfile to design surface heading or loop residues - Force to write_strand_AA_distribution_files only after count_AA_with_direction - much better (easier to understand) namings (like get_vector_loop_AA_distribution and get_vector_strand_AA_distribution, write_loop_AA_distribution_files_) [integration tests] - should not change other than features and features_database_schema (if any) commit 483c51db764317794fa52ac50f094c4b127febd0 Add missing clone() function to forge::constraints::ConstraintFileRCG commit 52bc5507887a0bae82c991eaddcb08c4c1950388 Begin RigidChunkCM testing code in topo_driver. commit 7d20ac2a144ccefa4a0254b42b97317027ee7f90 Modify JumpClaim to allow non-intra-residue stubs. commit c19079d8c07dd4aef2a70ec7946df015741cf9ca Fix ParsedProtocol reliance on Environment::register_mover( MoverOP ) commit a11ac74374c5df8a53674b61f87bf2e39ff94077 Remove Environment::register_mover( MoverOP ) because it causes type conflicts. commit 90fdb79710fcb6042387501ba4afc3ba2d31984f Add extra error checking to SequenceAnnotation object for invalid LocalPosition. commit e68ff95eb28e0db35e5af07b96495f41c05b81f8 RigidChunkCM now yields it jump claim. commit d021cba483d38b3dedf37162de330b79cdc7794b Fix several unused variable errors, alter EnvClaim::wrap_dof_id to include id-setting at the EnvClaim level. commit 55e4f8327f79b7dae501f093df0d808a5f4107fc Trying to fix Mac PyRosetta build, attempt #2. (This is hard when one is neither using a Mac, nor PyRosetta.) commit 048cdec2d3a2f56760c7b580c977d158855053c0 Remove a stray line of code causing a segfault. commit 4c265fbfb7fdb8a6ab53a20bba9f8432264874e3 Refactor of DoF claiming system to be more general; finish implementation of RigidChunkCM. Compiles, runs mostly. commit 77bbdd3397a2546de13af4974ed6525ff99ab69b Now trying to fix Mac PyRosetta build. Attempt #1. commit ac5a3ee66ad6d9fa94a9c8fe1aa961afa08a7156 Attempt #4 at fixing PyRosetta Linux build. commit eb23b4729c6fbba1b22df0bce70ccd81931bd6de Trying to fix PyRosetta Linux build. Attempt #3. commit fc9b792ed5b7285b528d766937849c729bc0e965 Trying to fix Linux PyRosetta build #2. commit d492608b3f1b643ac923c668d820957aa93088f0 Trying to fix Linux PyRosetta build. commit 120e14df7161b165631ec1452830a3994529bcbf Refactoring some static variables to have proper init procedure. Updating PyRosetta Windows scripts. Adding core-only and utility-only PyRosetta build options. commit 32dc6a1085681667820262bf259a1e34394b7c9c Updating PyRosetta tests commit 93fac82026bab59d5d71912a149905713aae857d Restoring portion of __init__.py that got lost in last commit commit f0fcf8359d7fd79e4f36f7514440b165a4f83743 Updates to facilitate building cyclic peptides or other highly cross-linked geometries. Short summary: --Added PeptideStubMover and DeclareBond mover to make it easy to append, prepend, insert, or connect residues. These are fully accessible to RosettaScripts. --Added GeneralizedKIC mover. This is a generalized form of kinematic closure that can operate on an arbitary loop, including stretches of backbone, covalently-linked sidechains, ligands, noncanonical linkages, metals, etc. The only requirement is that the residues in the loop to be closed are covalently linked. This is fully accessible to RosettaScripts, and interfaces with the ContingentFilter to permit elegant failure if loop closure fails. (Note: I was going to keep this out for a while, but too many people in the Baker lab have requested to use this. Sorry, Kale.) --Added features to TorsionMover, including temporary rerooting of foldtree for a particular torsion move and full RosettaScripts support. --Updated coordinates of sidechain-conjugated residue types CYX and LYX to updated coordinates accepted for canonical L-amino acids with Talaris2013, and added ASX and ORX (sidechain-conjugated aspartic acid/asparagine and sidechain-conjugated ornithine). --Added some common chemical crosslinkers. --Updated atom types database to include sp2-hybridized Boron. --Fixed handling of noncanonical connections (e.g. UPPER->sidechain, sidechain->LOWER, etc.) in Conformation class. --AtomICoor functions have been updated to remove the assumption that polymer bonds are between the i and i+1 residue, that each LOWER is connected to the previous residue's UPPER, that each UPPER is connected to the next residue's LOWER, etc. Now, Rosetta checks for and returns the connecting residue and atom. NOTE: This is a deep core change. All unit and integration tests pass, but there could be changes needed in code not covered by integration tests. --Added an option to Conformation::update_polymeric_connection() to rebuild connection-dependent atoms. Previously, some protocols would replace a residue at a particular location in a pose with a new residue with upper and lower terminus types, remove the upper and lower terminus types (at which point connection-dependent atoms would be rebuilt, assuming connections to the i-1 and i+1 residues despite the lack of such connections), and THEN update connections to make bonds to the i-1 and i+1 residues. Now, this doesn't work, since without a connection, Rosetta can't (and shouldn't be able to) rebuild a connection-dependent atom. This is therefore done when the update function is called, though this is not the default behaviour. If other protocols fail due to improper rebuilding of backbone H and O atoms, add update_polymeric_connection( , true) to rebuild these. --Note that the above changes actually fix the zinc_heterodimer integration test, which was previously FILING to rebuild a backbone oxygen properly. Unit test status: All pass Integration test status: 23 changed tests --Most of these are cosmetic changes, since there's an additional atom type (Boron) and some additional warning messages when AtomICoor::xyz() can't find a connection atom and returns a bogus vector. --The UBQ_E2_*** and UBQ_Gp_LYX_C-term integration tests change their post-minimization output a fair bit due to the updated sidechain-conjugation residue type geometry. I erroneously thought that these were not detecting the connection properly before, but differences that I was seeing were due to an atom type that I had mistakenly switched; having corrected this, these tests seem fine -- just different. --The zinc_heterodimer and zinc_homodimer_setup tests had to be tweaked a bit to get them to work properly, since they were previously relying on quirky Rosetta behaviour that ought not to have worked the way it was working. (See above: they rebuilt connection-dependent H and O atom positions BEFORE declaring a connection, and this only worked because Rosetta assumed connections between the i and i+1 residues. Now, the rebuild is AFTER declaring a bond. This actually fixes some bad atom placement, and changes the output of these tests a bit.) Changed integration tests are: fold_and_dock assemble_domains_jd2 make_rot_lib match_1n9l match_6cpa doug_dock_design_min_mod2_cal_cal hotspot_graft ld_converter UBQ_E2_thioester features UBQ_E2_thioester_extra_bodies UBQ_E2_thioester_two_ubiquitins place_simultaneously oop_create zinc_homodimer_setup oop_dock_design ncaa_fixbb match_1c2t UBQ_Gp_LYX-Cterm zinc_heterodimer AnchorFinder scaffold_matcher swa_protein_loop_sampler 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 new file: database/chemical/residue_type_sets/fa_standard/residue_types/crosslinker/1.3_bisbromomethylbenzene.params new file: database/chemical/residue_type_sets/fa_standard/residue_types/crosslinker/BoronateLDopa.params new file: database/chemical/residue_type_sets/fa_standard/residue_types/sidechain_conjugation/ASX.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/sidechain_conjugation/CYX.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/sidechain_conjugation/LYX.params new file: database/chemical/residue_type_sets/fa_standard/residue_types/sidechain_conjugation/ORNX.params new file: source/src/apps/pilot/vmullig/design_truecycpeptide_fromstub.cc new file: source/src/apps/pilot/vmullig/sidechainKIC_notes.txt new file: source/src/apps/pilot/vmullig/test_sidechainKIC.cc modified: source/src/apps/public/design/zinc_heterodimer_design.cc modified: source/src/core/chemical/AtomICoor.cc modified: source/src/core/conformation/Conformation.cc modified: source/src/core/conformation/Conformation.hh modified: source/src/core/io/pdb/pose_io.cc modified: source/src/core/io/silent/BinarySilentStruct.cc modified: source/src/core/io/silent/BinarySilentStruct.hh modified: source/src/core/pose/util.cc modified: source/src/core/scoring/Ramachandran.cc deleted: source/src/err.log deleted: source/src/index.html deleted: source/src/out.log new file: source/src/protocols/cyclic_peptide/CreateAngleConstraint.cc new file: source/src/protocols/cyclic_peptide/CreateAngleConstraint.hh new file: source/src/protocols/cyclic_peptide/CreateAngleConstraintCreator.hh new file: source/src/protocols/cyclic_peptide/CreateDistanceConstraint.cc new file: source/src/protocols/cyclic_peptide/CreateDistanceConstraint.hh new file: source/src/protocols/cyclic_peptide/CreateDistanceConstraintCreator.hh new file: source/src/protocols/cyclic_peptide/CreateTorsionConstraint.cc new file: source/src/protocols/cyclic_peptide/CreateTorsionConstraint.hh new file: source/src/protocols/cyclic_peptide/CreateTorsionConstraintCreator.hh new file: source/src/protocols/cyclic_peptide/DeclareBond.cc new file: source/src/protocols/cyclic_peptide/DeclareBond.hh new file: source/src/protocols/cyclic_peptide/DeclareBondCreator.hh new file: source/src/protocols/cyclic_peptide/PeptideStubMover.cc new file: source/src/protocols/cyclic_peptide/PeptideStubMover.hh new file: source/src/protocols/cyclic_peptide/PeptideStubMoverCreator.hh new file: source/src/protocols/generalized_kinematic_closure/GeneralizedKIC.cc new file: source/src/protocols/generalized_kinematic_closure/GeneralizedKIC.fwd.hh new file: source/src/protocols/generalized_kinematic_closure/GeneralizedKIC.hh new file: source/src/protocols/generalized_kinematic_closure/GeneralizedKICCreator.hh new file: source/src/protocols/generalized_kinematic_closure/filter/GeneralizedKICfilter.cc new file: source/src/protocols/generalized_kinematic_closure/filter/GeneralizedKICfilter.fwd.hh new file: source/src/protocols/generalized_kinematic_closure/filter/GeneralizedKICfilter.hh new file: source/src/protocols/generalized_kinematic_closure/perturber/GeneralizedKICperturber.cc new file: source/src/protocols/generalized_kinematic_closure/perturber/GeneralizedKICperturber.fwd.hh new file: source/src/protocols/generalized_kinematic_closure/perturber/GeneralizedKICperturber.hh new file: source/src/protocols/generalized_kinematic_closure/selector/GeneralizedKICselector.cc new file: source/src/protocols/generalized_kinematic_closure/selector/GeneralizedKICselector.fwd.hh new file: source/src/protocols/generalized_kinematic_closure/selector/GeneralizedKICselector.hh new file: source/src/protocols/generalized_kinematic_closure/util.cc new file: source/src/protocols/generalized_kinematic_closure/util.hh new file: source/src/protocols/hybridization/BackboneTorsionPerturbation.cc new file: source/src/protocols/hybridization/BackboneTorsionPerturbation.hh new file: source/src/protocols/hybridization/BackboneTorsionPerturbationCreator.hh new file: source/src/protocols/hybridization/BackboneTorsionSampler.cc new file: source/src/protocols/hybridization/BackboneTorsionSampler.hh new file: source/src/protocols/hybridization/BackboneTorsionSamplerCreator.hh modified: source/src/protocols/init/init.MoverCreators.ihh modified: source/src/protocols/init/init.MoverRegistrators.ihh modified: source/src/protocols/metal_interface/MatchGrafter.cc modified: source/src/protocols/protein_interface_design/movers/PlaceSimultaneouslyMover.cc modified: source/src/protocols/protein_interface_design/movers/PlaceStubMover.cc modified: source/src/protocols/simple_moves/SetTorsion.cc modified: source/src/protocols/simple_moves/SetTorsion.hh modified: source/src/protocols_b.5.src.settings modified: source/src/protocols_c.5.src.settings modified: source/src/python/bindings/IncludeDict modified: source/tools/build/basic.settings typechange: source/xcode/Rosetta.xcodeproj/project.pbxproj.template commit 9b7d547cf3c242f95ab51d0b66783a189deb3811 Trying to fix zinc_heterodimer_design.cc. commit 5764a63c22d30877170140b787fd2d912ea6a29f Refactoring some static variables to have proper init procedure. Updating PyRosetta Windows scripts. Adding core-only and utility-only PyRosetta build options. commit bdce73de916afcf480388558d4ba0b116e2c29c0 Small tweak to GeneralizedKIC.cc to allow compilation on Linux clang. commit 87a9da56861e5d13070e5d80c3bd221e4dee52bf Correcting some of the sidechain-conjugation atom types, and reverting some changes to the mm_torsion database. commit 3d2618f2e5a33976ea220bb82348d39c6e1f64f3 minor changes to splice tracer. Will cause integration test changes to splice_* integration tests commit a55ed925f70df6e30e35f40ded3c837395ef5ee2 minor changes to splice tracer. Will cause integration test changes to splice_* integration tests commit 04b1a100791da3cd38358fc97025a7a85e815719 RelativePoseFilter can now copy specific comments (listed on the xml tag) from the reference pose to the relative pose. No test changes expected. commit f04fe568da8bf250268a4b34b051cf9fcff7db94 Fixing indentations in databasethread commit a6af2b6c2875a5a2a8d9861e130a3af19dd56fb0 Merge branch 'master' of github.com:RosettaCommons/main commit 4eda1ceca224602c16c44dbd6aa4e53636f35f9c databasethread commit e9413f3d130b55d7f9525354bf25957d3b543358 added entries to /database/protocol_data/splice/antibodies/pdb_profile_match/pdb_profile_match.H3 commit fadd717fbf189341a1becc9c7b083e5bfac922ef updating database thread commit 9c6af0a54326b4f17be2ed5055ffc2767d40c74d updating database thread commit 5920874165b546e41962abad360018b7cddb9fdd updating database thread commit 571f0646145305e7cea91da54a3dc5d108f9f915 updating database thread commit 77b4aa83390b80bdafeed18b2b0cc6695e2214e5 update to database thread commit 6799473f881c44da7aa19f3bf3c6d10bcf9bcd56 adding skip_alignment option to splice (dflt false). If set to true splice_in will copy the stretch directly without aligning to a template pose. Can only be used if the sequence numbers for the stems and the number of residues in the spliced segment are not changed between splice events. Cosmetic log changes expected in splice integration tests. commit 95799eec51f077dd9ec8cc4f9f741d26effe1614 added “sequence” definition commit ee7e2c228b1018817d9c9345e6d97df81151b7d6 added the option to enter a target sequence commit 34f3806dcc8646745949590ed95c673a4809db85 Fixed the logic for reading in database files. The previous logic used the default database directory name which may cause a runtime error if a user defined database name was provided. commit 5f5d416e8e9ec79b6ef0601c1442247d5ea8b12d Still trying to fix zinc_heterodimer_design.cc commit aedca2e9dac21730141703dffb5128d691ef0241 Fixing zinc_heterodimer_design to work properly with altered assumptions regarding connectivity (residue i is not necessarily connected to residue i+1) commit 5a0f4554eae087e85a55679569a1ef1440e353f4 Tweaking LYX.params commit 5ffe61f8bc3fccfd0eec3eb92c095f1c04a8d35c Merging from origin to local branch. commit b14d3ca3a5a05839595645635a90a35cde5ac7e3 Merging vmullig/cycpep from origin into local branch. commit c4234b3d108220f37b251421293a86b3f302783b Fixing PlaceStubMover and PlaceSimultaneouslyMover; both were relying on what was technically some bad Rosetta behaviour previously. commit 2773a6b0ae90118ebe959ca43965ccf5387e345b Added lowest_energy_selector to generalized kinematic closure. commit 6dd1c7d74499754d4af33e4d21918aa1bd069095 Updating molecular mechanics database to fix integration tests that should have been failing, but which weren't due to a bug. Rosetta previously assumed that all UPPER and LOWER connections were to the i+1 and i-1 residues, respectively. This meant that it would completely ignore a connection between the C-terminus and a cysteine sidechain, as occurs in all of the UBQ_E2_thioester integration tests. The MM torsion parameters for this connection were added previously to the database, but they erroneously referred to the sulphur as S instead of SM. This should have resulted in an error, but since Rosetta wasn't scoring this connection in the first place, it never came up. Now that it does score noncanonical connections like that, it has come up. The database has now been corrected. commit 1bfa70a9ea298f5e2a794eb5dd012b9fe1c06d78 Fixed problem with MatchGrafter. Now to see whether I've broken anything else... commit 42b3e22910baef404494ae652e25ab80693dc966 Trying to fix problem with MatchGrafter. commit 1c9e89c79dbe4d3bcc2807661803ecd21ebc259d Chainbreak Scoring: Enabled chainbreak scoring for carbohydrates NEWS: * Added cutpoint variants for sugars * Refactored ChainbreakEnergy - Made work with cutpoint variants that do not require 3 overlapping points - Removed duplicated code - Added lots of explannatory comments * Refactored add_cutpoint_variants() and add_single_cutpoint_variants() - Removed duplicated code - Enabled to work with sugars ---------------------------------------- Unit test status: Pass Integration test status: 25 rings: change in number of ResidueTypes reported inverse_rotamer_remodel, loop_creation, antibody_graft, SnugDock, hybridization, mr_protocols, antibody_legacy, antibody_H3_legacy, remodel_disulfides, remodel: cosmetic output changes swa_rna_gaga_23_append_and_kic_close, swa_rna_gaga_22_prepend_and_kic_close, swa_rna_gaga_10_append_and_ccd_close, swa_rna_gaga_18_rebuild_bulge: strange output of "10 BulgeApplier" in new (huh?) 10 other loop-related tests: trajectory changes (I don't THINK I broke anything here, as the unit tests for ChainbreakEnergy and all loop and closure unit tests passed, and I had another set of eyes double check my work; however, if you are concerned, please e-mail me. I did slightly change the logic of ChainbreakEnergy, but only in a way that should make a difference in results in a specific case I do not believe can ever happen with any ResidueTypes currently in Rosetta -- or ever likely in Rosetta. I am of course willing to revert if needed.) commit c06008143912d89f8e205293bed5ff3ae1ecdd81 Reverting previous change (debug output). commit 740ec48e83ee2bc6984824131c868c8c058a389d Finding bug introduced into MatchGrafter.cc commit 17f53c9b5a87b2d8700ebf9136f0b0be7beca9f0 Scoring: performance improvement to ChainbreakEnergy::eval_atom_derivative() commit c777c52ae6de1e93ef0d42889c7e2be97a4bb580 Scoring: refactored ChainbreakEnergy::eval_atom_derivative() to remove duplicated code and commented commit 5fe71bd3f71bf40b407e254206e5c6a302e361c3 Compile fix for gcc 4.6.3 with warnings-as-errors; there is a pseudo-uninitizalized variable in a pilot app that makes that compiler grumpy, and was holding up the release script. Also added copyright header and vi-emacs settings header to that file. No test changes expected, as pilot app has no integration test. commit 1e931356568b6e96a6db26e08c55252263956a65 Minor bug fix. Compiled on windows but not linux. commit fb854dfb8401193ebc5ffd4455c8f6584dd8fb35 Minor modification to previous bug fix suggested by Seth Cooper. commit 4e50258fe516f011c5915235fb0377c692607557 I accidentally removed the boost_1_55_0 directory when pushing fixes for the windows build. So sorry for that. I'm adding it back as a quick fix since I don't know how to properly revert a commit on the master and I want to make sure things are back to normal as soon as possible for everyone. commit 62b3a4f0f9d3af3322118f1933c9ace0cfb92d7f Updates for windows port. commit 4db4369bef421c2acd191ce2840481355d94773c Scoring: bug fix commit b0de9042dc0350b2b8db39bf21b3ae8371d95109 Scoring: getting ready to refactor ChainbreakEnergy::eval_atom_derivative() commit b54c22bc4addb42a7f6f406a6a0a305ae58f21ee Loops: refactored add_cutpoint_variants() and add_single_cutpoint_variant() to remove duplicated code commit c75bc39f1f2c500067b13f01a22a05c3c3958cc9 Scoring: fixed ChainbreakEnergy::finalize_total_energy() to work with carbohydrate chains commit b95dfab2dfe57d979234f4296c139822fd503caa Scoring: cleaned style and comments in ChainbreakEnergy files commit e822e43124d23bd0d712ee4cc7672436041ee44c Scoring: cleaning #includes in ChainbreakEnergy.cc commit 11aa5556c9d287b99e96691724ff62066b2965d3 Carbohydrates: added new patches to list commit a7e92941690a0dcfd2077e583d7f2072910dd1ad Merge branch 'master' of github.com:RosettaCommons/main commit c7d648b7b259166808e44d612a4a86171136069e Fix for access violations in the WIN32 BOINC build. No tests run; changes only affect WIN32 platform. commit bd939a8e254e759b33104db720c2b535c0994f05 add options to have PyMolObserver only update on energy on conformation changes. Options: -update_pymol_on_energy_changes_only -update_pymol_on_conformation_changes_only These should be passed along with usual show_simulation_in_pymol option. Note that by updating on energy changes only, pose length changes will not occasionally cause a segfault which sometimes happens when the observer kicks in and shouldn commit b3a6a45f885c7d0b8d82b4681d61d3c9b483e9b3 move changes from graft_optimizations branch commit 6c9e9221a1b208dab36727c9e50d91bf9df723de Fix a warning I was getting in antibody/metrics.hh due to an uninizialized templated struct. Fixed by making a default constructor that initializes templated members to 0, this should be fine as it seems usage of this struct is templating to primitives (eg. core::Real) commit 945b62ae3ae1a6e566aec9dfc8d268feee60e470 Continue to hone RigidChunkClaimer's claimed dofs... commit c0c9b4697d7b927f4177d7f0ab8ed4bbf3da1818 Turning off CYX.params in residue_types.txt in preparation for merge with master. commit 0909e1a4403f11262db6f5354038d22eec318c57 Merging master into vmullig/cycpep for integration tests prior to merging the other way. commit 78ebb927c2c3b50ccd9a0d7f4a7c0ebe2508a6af Merging cycpep/collab into vmullig/vikbranch to get Yifan's updates. commit d2ea0c784de2c7b98446c65a0ed2364dbd1d4142 Merging vmullig/cycpep into cycpep/collab prior to merging cycpep/collab into master. commit 55dfddfdad1cac55273d59936a145f1736946525 Initial commit of ORNX.params (sidechain-conjugated ornithine). commit 2c609196f859d7f400a818160f16b9f9ef792904 merge from yfsong/cycpep commit f5fb906a7c90b8f4d401c6ffd0533584b8518dec Carbohydrates: adding cutpoint variants for sugars commit 9556aabcf30cc76e8f8ac9097e699165090d0a17 Changing build settings for phenix builds. Updating option.py which fails on some python versions. commit b8dc1234f8490b9e473a5568474dce85060aa3cc Fixing gcc build which gives an error from the double-->float conversion in the center of an array initializer list in Frank's cryst_design.cc application. commit d54f05a91e473fe9265f598896a7384bd02aa355 Update CutBiasClaim, add CutBiasClaim to RigidCM commit 58cc6c39f6b969db3f1abf2aad8cd5a850cca856 Update RigidChunkCM to use full XYZClaims, begin testing. commit 882c090ad3d4c4caca0351225ae3eddb6df0a775 Add checks for jump modifications with replace_residue. commit 55fc9c7c3c0a98df3737cad22bdb4c139eab565f [minor update of SandwichFeatures] - typo corrected (@overviewprotein_tools/scripts/clean_pdb_new.py) [integration tests comment] - should not change commit 7ce53d96f15cc3041ead43190efa91e060559697 [minor update of SandwichFeatures] - added a new column 'average distance between (two) sheets via central residues in edge strands' (prints until 1 floating point like 6.4) - added a new column 'minimum distance between (two) sheets via central residues in edge strands' (prints until 1 floating point like 6.4) - debugged for a case when strands are < 3 for topology identification like in '1A21' - default of exclude_sandwich_that_has_near_backbone_atoms_between_sheets_ = 'false' - default of exclude_sandwich_that_is_linked_w_same_direction_strand_ = 'false' [integration tests comment] - should not change other than features and features_database_schema (if any) commit ecfe2bc89a81c7cd245b76fc4d9a40efcfa77c6f Fix more warnings and an inclusion typo. commit ad2cbc8d1f5a219fe109b31d59464ed3a5444424 fix warnings in EnvClaim.hh commit a0e31b53fe372971095b6b68bc1a6c45865f1b4d pull from remote commit dc450ca16f5c270a1d9b03185d6907ee8a624fb3 Modify replace_residue to do a trust-but-verify style security check. commit aec4014c485e02f0b7092a82fe87c6899e52d14f Add BondAngle and BondLength elements to the claiming system. commit 64e5271e8261ec441fead4a91293051b9dfec477 merge from master commit b2205c0961ab5cf171ae3224b54347441094d2cf Update non-canonical bond info in silent struct commit c428c138647217223d047cdd59374c6df23dc745 Add non-canonical bond info to silent struct commit 9f020707e5764ab68dfe34fbe6bacd8d7e90f9c1 Merging vmullig/cycpep into cycpep/collab. commit 0829e9a8440bcbd315b095edc4aff1178368d716 Tweaking Ramachandran.cc: random_phipsi_from_rama won't try to act on aa_unk. commit 90e112d82c92cdb1991e21b44ebc20563eabc018 Bugfix for -missing_dens_to_jump commit 1bade8a8653d8671a28dec42e6a358f3a9b2a7ca small bugfix for -missing_dens_to_jump commit 8acc4b7c4a0441b3aca90f3897a51f7da15216a9 Now fixing clang build. commit 8f120701d8dcd4ced23474ee3d10dcc0904932c1 updates to pilot apps commit 4463167e837d5db09ea8f7a996e9a55775698389 Merging vmullig/cycpep into cycpep/collab to add improvements to GeneralizedKIC and to update the database with Boron. commit b029a9d5ec674b36bc033f77d781e3b8bf87e3b5 Added sp2-hybridized boron to the atom types. I'm not 100% sure that I've picked great parameters, but I did my best. commit 617ab5278f9f47b25b5303638b3f950350453770 Fixing gcc build (wasn't an error on my machine). Also fixing NetChargeFilter to test build. commit 001941a705f8292d89ff9bb24d18795963ca8061 expansion_rounds default set to 12 commit 80dfee0f1e9bd0350a3ba4ca747621557ac0a8e6 expansion_rounds as a new option commit 8392d1b2ad95db9dc17b4592c6e34197c3f47097 MultiplePoseMover additions: task operations import support, Filter pose selector, filter status passing from sub-protocol. Merge from luki-mbi/rosetta_scripts. Unit test status: All Pass Intergration test status: All Pass commit 154b9bd7d2048e716d465523524484b1b52a0b5a Updates to pilot app. commit 208b479192a17144c3596e24f890186dfcf35a47 bugfix to pilot_app commit 4660b21d1360bd4f6e317caa83ee5c97ec93e9e8 NetCharge filter now accepts task operations. Designable residues in the task operations are used to select the residues over which to count the net charge. no test changes expected. see wiki for details. commit 89cfb3bd849a07dae62cbdcfcc93619ec71bf0fe Remove continue_selection() for now, some want to always run all filters to report values. commit 76cb9bd2408391dd6aa3a0a5343a7c239994d882 Further implementation of RigidChunkCM, realized that nonideality is required (requiring bond length/angle claiming). Compiles. commit 87bc2ee3ab4d8c9c836a8354331e87bc8b07f58e Add RigidChunkCM files. commit 77c2a8448c2a16d0a91e681772c90f83b67d63f6 Add safe deletion of OutputObserver from ParsedProtocol if ParsedProtocol::apply terminates with exception. commit 748d7657495c690ad52d0ee14678d6c00f7efc21 Reverting extra output in MPiFileBufJobDistributor.cc commit 080305ab3edaab83ef7830d136265256c4392364 remove unimplemented copy constructor to fix pyrosetta build commit cf0e440e3f0e4d90eb095592de8324435c2971f9 First compilable commit of the new CreateAngleConstraint, CreateDistanceConstraint, and CreateTorsionConstraint movers. commit efb19b0da35f5bf5abc85b521f8c98de329ce35d Remove autogenerated options files which were (re)added to the repository. commit fa2d9b6656f0967bb63afc9e17c44c24d4b4b563 Merge with head. commit 82108fc1131092332756a5d66fd0731ad3c240cb Updated the boinc build to work without the BOINC_GRAPHICS pre-compiler directive (for the android boinc build). commit 0709f610b1b18b0075f569e4db2099f4d973a97b fix more warnings that only showed up on gcc build commit a4f5a6be5c6b1ec5ae8dd5966a193d9608686539 Fixed a small bug in the boinc app. commit e5ae0051d8dca6da27763a495da58c9eeeb306a2 fix another warning, remove options files that were re-added commit 162d4f173cb1d8ccb46f453f24b8b9873d8e85f3 fix a warning that broke the build commit 3acd4509f1423da6690ac476ed7adc8a3e1aed11 Merge branch 'master' of github.com:RosettaCommons/main Conflicts: source/src/protocols/ligand_docking/MinimizeBackbone.cc commit da625a62612b32f8c2f7069fd68bae8ee882bbc8 Updates for windows port. commit e1534cc36cddcd47151c33da4d687c55714e3050 Add AntibodyFeatures reporter and R scripts, update InterfaceFeatures and R scripts, update AntibodyInfo and cdr clusters NEWS: ==Antibody== - closest North-Dunbrack CDR cluster now prints in AntibodyInfo show method - have Antibody metrics Sasa calculations use SasaCalculator2 (which means default radii is now correctly reduce like InterfaceAnalyzerMover) - add check for peptide bond C-N lengths in AntibodyInfo to check for missing cdr density or poorly closed loops. This check is default true and can be turned off using the option -antibody:check_cdr_chainbreaks false. - add optional AntibodyInfo check for wonky peptide bond geometries in cdrs. This check is default false and can be enabled using the option -antibody:check_cdr_pep_bond_geom true. The function that is called has been added to loops/util and checks the deviations from the dunbrack/karplus Conformation Dependent Library values within some user-controlled cutoff value. ==Features== - Add AntibodyFeatures reporter + many R scripts for analysis - Update InterfaceFeatures reporter (add a few more columns), reorganize R scripts and add a few more ==Bugs== -debug missing enums of some rare cdr clusters -debug some antibody metrics via testing with thousands of antibodies ---------------------------------------- Unit test status: Pass Integration test status: Antibody integration tests will change - both cosmetically and any reporting Sasa metrics *SnugDock integration test updated to not check CN peptide bond. There is a 2.56 A C-N bond at 31 H. commit 9137eb5ec484d4e18a73e2804a68776333c29bff change snugdock integration test to ignore chainbreak commit d3bd9731296033fd40b8ce0ac6f4046cc1160fb2 Initial commit for CreateDistanceConstraint mover. commit 337b8ecfd17a087d5d4deda07d2d025eaa419849 Initial commit of CreateAngleConstraint mover. commit 5277ee6b3d5223ad343d22abbc3f8831d3d0db9a Initial commit of CreateTorsionConstraint mover. commit 666f1fa33e77e36f18e8b5b982a8b7d5396544dc TaskAwareCsts is now able to constrain residues to a particular residue of choice rather than to the first residue in the constrained segment. In multi-chain poses it makes sense to put the anchor positions at the source and sink of the minimized jump degree of freedom. This way minimization along the jump dof is not affected by the chain constraints; only bb minimization is affected. See wiki for details. No test changes expected. commit 1b088af26a3a12815333bc9d70ea09e9a93fd938 Resolving ambiguous constructor for PyRosetta build. commit c261c60c9bbbfb9d68b8f007382dfe8866c116f5 Removing pilot apps from compilation. commit 724328c6a867d104d402e01df6715b9f3d0f9864 Another instance of an include file that needs to be commented out. commit 08edbd8c43f45cd59374a25780e9149ec3824e56 Commenting out include line that causes compile failure on test server. commit 950def574553a439c631406a8a6478e398ba1598 Adding svm-based helical end cap scoring. Also adds a new feature reporter, and this changes this integration test. commit 590f5d7efc106f516de1c0a62a6d8b73b505fb34 Adding svm-based helical Ncap scoring. Also adds a new features reporter. The features reporter integration test changed due to the new reporter. commit b2a4976b913adf9fe8286e61cbd5abf597f8d274 Adding a mode to AddChainBreak. Flag remove=true (dflt false) will remove the specified chainbreak rather than adding it. No test changes expected. commit 1379be0246b1e02247f23f9c3708e42729fa1ab2 SetAtomTree does some trivial testing that the foldtree is kosher right at parse time commit ea537fd339217cca3cdbc2d65078b69af7fb3e66 Trying to get GeneralizedKIC to interface with the ContingentFilter, so that a failed loop closure sets the ContingentFilter's value to false and a success sets it to true. commit 1eba62051a502a71c084668517795923054a78c4 Fixing some compilation bugs on Windows platform commit 83d50bca7e013d61138a39ce69612b354c348e2d Adding context normalization to CppType_Complex. Various build fixes. commit 240ea670c0bd712815c1ceae70262f7d6dceef2a Tweaking SG angle in CYX.params to match CYD.params commit cf500a50db83a43b8e63c9a6f63e5f9818c36713 Somehow, CYD.params was altered slightly. Reverting back to what's currently in master. commit b115b5bb59e8591171480e2d99d87113c96a724d add residue foreignkey to abfeatures residue table and struct foreignkey to interface features residue table commit 0ed4059b66d985b6499064298a1aa932c47d2ef2 SetAtomTree can now read a fold tree from an external file. Useful in cases where the fold tree is sticky and not quite general... no test changes expected commit 3e4f19220ecb8557d7a7fb02cf1cda4cc3003448 Created all the known elements as enums. Work with them in a similar way as AA enum Added unit test for the enum All other files edited were to get compile to work on my system (Werror resolutions) commit 44bbf2d59074c719cb889ca170619d2429751997 Create enums for elements commit bf4c43a2fde4e73c4b23093f86df791f8928a725 Adding helix ncap scoring with an svm. commit 999e68f039f0241941ef3cf4fa69d898cd38e5a8 Minor changes to Splice.cc. Should not casue integartion test changes commit fda95ccdf25f24152c7d5a6050d14b3f29962945 Minor changes to Splice.cc. Should not casue integartion test changes commit fbfe26748caaedddc555143ba4a9a217595f2788 Disable continue_selection() for now -- needs better implementation. commit 91329073caf35081af2e5f6b35a4e59562f9b73f Adding pose selector debugging info, stop for AND logical operator to avoid unnecessary evaluation of further statements for a given pose. commit 18c8f876b37dd36eecd27132318a8d399546a7a7 Adding Filter PoseSelector to use an exsting RosettaScripts filter as a pose selector in the MultiplePoseMover. commit 37592607bf7f0d888d4a92a7a2402084cff8764d trying to remove another undefined function to get pyrosetta to compile. commit 5d00092cc31b8c27cc557ad8ab4cc81f353591cf Fixing a mistake in DeclareBond.cc introduced in my last commit. commit e5c05a0211a801a3626fb9407261c26c06a4abb1 Tweaking DeclareBond.cc. Foldtree should rebuild properly with multi-chain poses, now. commit 32b4783d56374e79ee0da014a09745fcb0c76580 mininterfacesum added commit 15f33b6f101b471c6d4c3401fd50445c56dcf2e2 Adding unit test for taskoperations imports. commit c4f8d9c4741342ac35a4f91f4a105dd7d1b13573 Restoring legacy protocol resume support, that can be enabled with the resume_support=true option on the PROTOCOLS tag. Off by default. commit 6193d3a4f6ba0df9dc060157930e0b61427c6e1b restoring library levels. commit 28be522d4574cb48ee0f663262ac6509b7ff19cf Adding support for importing of task operations in IMPORT tag in the RosettaScriptsParser. commit d182d38b333bbd75b333eec23a8d5e06b937a10e removing another undefined function to restore PyRosetta build commit 2af025e5f3796ee315ba002c384cd2b8d46455ff MulipleOutputWrapper: Detect and pass on mover status; do several attempts to obtain a pose before failing. commit 6bdefb58d492c693636ccda68763d1b599dc1288 Update to current master. commit 2a7be35a623c4835b3b38ee292bfbe5aeb2e15c0 fix merge commit bd28178fe55e004af7fa5e3a22faae2808b0e0d7 Refactoring function UpperEdgeGraph::add_edge and making it return 'void’ instead of returning 'Edge' reference commit 8b5042480838ac667acc14b73715b26c2f349c82 PyRosetta, fixing some compilation bugs on Windows commit 86b54474e874f21db56094a7798e08ad22412c19 removing undefined functions to restore PyRosetta build commit 31b8cc5d17d95bfb63e1abe9d24592ced301079c Merging my pilot app with the trunk commit 2c0df1cc5e1518ce1c5ea78570d331815eaa9cdd my call_mover pilot app uses -nstruct option commit 00524e6767e743c66a9d25cdbc4c93d8fe7b1f3a Last attempt of the night at getting FoldTree rebuilding working right in SetTorsion.cc. commit e46012e84a5af9c25352e79da2df07297da846c2 Another attempt at rebuilding the FoldTree in SetTorsion.cc. commit bcc89b5d68972369fb1899bbfbd2698030796c0e Trying to get protocols/simple_moves/SetTorsion.cc to let me reroot the FoldTree temporarily. commit 7e961d978da499e4a222a6ab3a9b17a5f3c562b2 Reverting changes to FoldTree.cc. commit 70d28b1029b400ac84747cc4127b7a82ca8fe496 Temporarily turning on some debug output in FoldTree.cc. Revert this later. commit 032b561d5cea958af5d360923939db8a5ceb732c Adding options to SetTorsion mover for reordering the FoldTree temporarily. commit 3ee83d73f48e20ed8e24df514f5558ae9bb375c8 Fix typos in performance benchmark readme commit 56b377ae2d58cd90815c41a904a38629ed6ccf38 Fix typos in performance benchmark readme commit fecd757a7a3da102dc88b660544b68748de601b7 Trying to get the PeptideStubMover to rebuild bond-dependent atoms properly. commit 99e9cedaf680153bb77b0495b518263232e1f6ff merge cryst_design.cc changes to master commit 3d493ea79c967c6ac366f430695b5caeae629fc0 more options and cluster functionality commit 31a81b7bfe60e2c7ed5fb4d45a6e6a3e5ab30dcd Bug fixes: 1) Max pose selection count in TopNByProperty pose selector. 2) MultiplePoseMover: Drop poses for which sub-protocol failed (via mover status). Unit tests: Pass. commit ad591b9f10b2cbc8f20bd94988099a5f8806e7e2 merge master into ab features commit 2f1ff135d303d7bb32095baca35d8570daa1eca7 cryst_gen: support for O,T + small bugfix commit 901f93b2830efb39a51fc3a39be547cbb97e7b66 Fixing warning that broke the build under gcc 4.7.2 I added a cast in StructureFeatures::write_schema_to_db from uint32 to SSize to avoid 'comparison between signed and unsigned integer' warning commit c2701ceb590f54b534a9664e67690e2d2afb27c3 I think 1,3-bis(bromomethyl)benzene is working with GeneralizedKIC, now. commit ba918307a6615d8bde7c5440333e2ae53be35c43 Trying to get 1,3-bis(bromomethyl)benzene working with GeneralizedKIC. commit 3b2da506518ff15253bddc0875031a5eda2870db Turning D-amino acids off in residue_types.txt for now. commit 3a29f885c035fb29667d51bc4a087b2edc0701b7 Merging master into vmullig/cycpep to get my latest updates to automatic metal setup. 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 60600587aba933b7b0400b551c0c91d6bc7ca658 Tweaking 1,3-bis(bromomethyl)benzene params file. 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 94cc3e922813c8315cfe1b7b6ab44351ae546dd9 Fixing SetTorxion.cc so that it doesn't act on non-protein backbones. commit 893402a861a2713e33e3e4fc0f170771f6dc6918 Removing unused var in test_metalloproteins.cc commit d722e072b5b62e1a6db8ff581e4d1be0850f7e1c Removing debug output from metalloproteins_util.cc. commit 05f385b84ea325082eaa2dcfa6c54d2eef273bcf Only adding cutpoints for protein residues in PeptideStubMover.cc commit 7f996437a1b37e17f8d940015df39caac5ef506b Adding aromatic property to 1,3-bis(bromomethyl)benzene crosslinker. 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 7447d12ff55cb11e0b33dee1368dd6c19e334bab Turning on D-amino acids for now in residue_types.txt. commit 0e230aa10c0b2421e4cd97fecc948e776b74159b Updating design_truecycpeptide_fromstub.cc for rename of is_D_aa() to is_canonical_D_aa(). commit 0877f59e5bef5ad413b22a75049f62c51405961b Added design_truecycpeptide_fromstub.cc app to my pilot apps. 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 b1451a904c5e9d3f46c3d58739611f28375523d8 Tweak to metalloproteins_util.cc: added another finalize() prior to atom_is_hyrogen() check to prevent debug-mode assertion failure. commit 9249be5d1cdba45d5c17ebdd75e920f624033b53 Adding metal binding property to backbone O of Gly and His. commit 0072ed751ac3bc7d86864594d7e5adb2e3b6c4fa Stupid mistake in CYX.params -- forgot a bond declaration. commit 4623555c12c9cf6ee0ba7028ef1eb4074efa8dbd Tweaking BoronateLDopa.params commit 8c2c3cb75e304c99918a8224e381caad893496a2 Updating CYX.params. commit bdfe52512e19601d7bae2c8eeebe22ebd708028d Tweaking 1.3_bisbromomethylbenzene.params. commit 3cb8bc382a385b9393e585daab00ec9063fb93fc Initial commit of 1,3-bis(bromomethyl)benzene crosslinker. commit ff42d10b7935a5540698893d0360d0e1ed961d36 Merging cycpep/collab into vmullig/cycpep. commit b6ef9c9269b756eac4a50e1308751a28c89e12a3 Merging vmullig/cycpep into cycpep/collab to get the boronate/L-DOPA crosslinker and a small tweak to RosettaScripts GeneralizedKIC tags. commit 359f8637c89f3aef2c6c6e1a241c173061dbcafb Tweaking behaviour of SampleCisPeptideBond tag in GeneralziedKIC RosettaScripts parser. commit 6d541ff6c36bd10b17e676d028009ae3db47168b fixed some compilation warnings commit 379d56d46af15bbad754d3fa7c7b31344ff13798 Making BoronateLDopa planar to match CITZEK, DEFXUI, and PBXBOR Cambridge database structures. commit 724675bdefdbd865a2870bfe86ec4b1634dc7595 Another bugfix for cryst docking commit 73bacafd9b046650066d434bd17bc3f2d840a2e5 Looked at the CITZEK and DEFXUI structures in the Cambridge small molecule crystallographic database, and it looks like the whole ring system in the BoronateLDopa crosslinker should be planar. Tweaking the params file. commit 9aaaa641ee51fa4da439f2a3fbea44e463b2f939 updated default values for cb/n/o commit af6c84a1cee94d9827007bde1ac26b19bf28e31b Setting atom types in BoronateLDopa.params commit ebe2f08af302a639cd032093b19a88fa77a1ff21 added interface_sigwidth option commit 845b6ba45addbefdd7ed530b8ae620a55c5d16b4 Merging cycpep/collab into vmullig/cycpep to get Yifan's tweaks that allow AtomICoorID::xyz to return a null vector if a connection is incomplete. commit b340cf1b6e5d696cdd0f4a9a08d1f212a1b0fb5d Tweaking error messages in AtomICoor.cc and making sure that xyz returns null vector for POLYMER_UPPER if there's no connection there. 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 a2acfe718ecd88c8ad95d026be16b111704d8df7 Allow ICoor::xyz to be set without connections commit 128d71db62ad07cff87cf99ad3eca6f191d0d85d restoring graphics build after war(of the warnings) atrocity commited by sarel. commit d1f23964b835ef8b861605bc5ddffbd242e478a9 Tweaking BoronateLDopa.params commit 9955fde0970c6ca41f3e1350bf51f25967d87b5c Added BoronateLDopa.params to the crosslinkers. 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 f06472207d239fd0b23b4e477911d3f020d2800a commiting PeptiDerive commit feb38469e0622d748de1b91c6229f28388a7576c updated Remodel, added features to SSPredictionFilter and PsiPred, and TotalSasaFilter commit 4e4e250886ed1fde888af97db35965f999605e52 Merge branch 'master' into rhiju/swm_general commit 20566628acb4f02b3e4bb0826d96c4ecdeaab573 Merge remote-tracking branch 'origin/cycpep/collab' into yfsong/cycpep 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 b086a1adb953d452b306b68b60cd3ea159021f39 Updating AtomICoor::xyz to get the correct atom when a residue is a terminus and the atom is CONN*. commit e1851689c0036f22717d237d659bf03f70d85a12 Tweaked DeclareBond to add option to refrain from rebuilding fold tree. commit 0cae8baabd8b8077e7db856d7bb37c19f6e614d4 Tweaking ASX.params so that side-chain oxygen placement depends on connection. commit 3582f718b86a9f5dfeda01a37bd80a91acaf2448 Bugfixes to cryst_design commit 096a43791572a50957ec57d24faffae11fecb419 Changing generalized_kinematic_closure/util.cc so that fewer atoms need to be rebuilt from AtomICoor data. commit 0b020304d364f626cd6f69454212975b22eea381 This is a bit risky, but I'm updating the build / xyz function in AtomICoor.cc to remove the assumption that the residue connected at LOWER is necessarily the i-1 residue, and that the residue connected at UPPER is necessarily the i+1 residue. commit 06100c637fd8f491963667152f367ea8bed08bf2 Fix swa_rna_main for terminal residues. commit af79dcf20c901ef3bde7702eeed36af618df8f37 Fix the swa_rna_main app for terminal residue rebuilding commit a051b76056dca45dc9a95c5365df9f766b3b9cd4 fixed a typo commit 34bf23294ac05cd20cfd94bca15189879a5e884b restoring the old fold tree in the end of apply() and added a warning for long peptides commit 5beff2dd9970edffe2157a33b20828b039fe4e3f Added mroe tracer output to debug generalizedKIC util.cc commit 697393bfc4827c98eac157551c4da5526b9b7f19 Fixed a typo. commit c85ed76c0bc2b5236a8726c6590fe7aedd26c47a Trying another way to build dependent atoms in GeneralizedKIC... commit 24c3c23f70b90a016404ca84da54e64973ece889 Marked the place in the code where I need to change something. This will be a bit risky! I need to update the ICoorAtomID.xyz function so that it doesn't assume that the residues to which the upper and lower connects are connected are necessarily adjacent in linear sequence. THIS WILL BE RISKY! commit 64cada132c52ba0351889732a87381b7cb278a23 Trying another approach to rebuilding dependent geometry in GeneralizedKIC. commit 417574a8f0c02fe7248349d5d645404795f74258 Fixed typo in GeneralizedKIC util.cc commit b0a0de179333a07fcd510f372cfd2b56e9c2006c Trying to fix rebuilding of atoms dependent on inter-residue connections in GeneralizedKIC. 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 5b748ce70fc4eca74279e36fb13a6205f514c969 Whoops -- little mistake in LYX.params commit ba09f83f40e9a1745cf7ab8ccc42c543e838f3e9 Commenting out another unused variable in Yifan's code, for now. commit 187b818ace60ae3cce3c0346632cddad2b2a86e0 Yifan's changes to BackboneTorsionSampler.cc seem to have resulted in unused variables. Temporarily commenting out. commit ee467e8e569ccd8a4f238841afa2cac7e750d058 Fix swa_rna_erraser test. commit e0d3fd32f1b9c0b0b0c689f788872851a1925a7b Fix the swa_rna_erraser test. commit 6eba620acd4008c03c56622bc59e1a385c7ddfaf Pulling from master prior to push. commit dda5e3343bb809d5d0bf0d5477999423bed598cb Merging master into vmullig/cycpep. commit 590694f8ca1485f84ee6eca1660fd191b9368dd3 Added ASX.params, for aspartate/asparagine with a side-chain peptide bond. commit 5cdffca96e0fde8be0030c1f2687dbb5f88b8227 Updated LYX.params to match latest LYS.params coordinates. 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 cec64f2057ba221d9e5b0abfc93bfdc857d7fef3 Merge remote-tracking branch 'origin/cycpep/collab' into yfsong/cycpep commit 3c44db3cbb4b4930fd785cc8465273de6aa81769 Merging vmullig/sidechainKIC into vmullig/cycpep to get my GeneralizedKIC framework. Hurrah! commit 83c70bc3f54d0b10f5dae551056f0ef67d025386 merging remote master to local commit 692da2908b38c7a128bbf63b270e6c1b8c49f182 adding a simple sasa cutoff for insertion site test mover 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 bd696791460c2c9f1cfc837ade33683f99fa301b Updating my notes. NEXT STEP: GENERALIZE THE REBUILDING OF ATOMS LIKE H AND O THAT ARE DEPENDENT ON INTER-RESIDUE BONDS. commit daad5fbb021f030a2741505f2e90503a38d5fc06 GeneralizedKICperturber sample_cis_peptide_bond works now. commit 3808a677f6ba08dbcd0a09bd92256362a69e91d3 Caught a big bug in GeneralizedKIC. --Forgot degrees->radians conversion when randomizing backbone dihedrals by rama. Fixed now. commit c2d81b8ca51f3c0447403c24990cdb797fff7a4a Added a sample_cis_peptide_bond GeneralizedKICperturber (with full RosettaScripts support). commit 451ec5538243bc92d68f23949c700b823d1c7c03 Caught a couple of mistakes in GeneralizedKIC: --Bump check filter was too soft. Set multiplier to 0.6 from 0.36 (0.36 should have been the multiplier for the SQUARE of the sum of the LJ radii). --Glycine was not being handled properly in protocols/generalized_kinematic_closure/util.cc. Fixed now. commit bd2ea901db479b61abd2f9857d9ea38d1870c1d6 fix constraints in bb perturbation commit 80a99adc66e6eab2cbb1b6258a9e7f459e7731c4 Fixed problem with backbone O and H when peptide bonds are closed with GeneralizedKIC. commit 040d6a864a8fa6eccf5f0ec3c0a11648585e8753 Adding parameters to GeneralizedKICfilters. commit a70bbbf61358657130b56f63ee8dd273300925cc Softened the bump check filter in GeneralizedKIC to make it more like the old KIC bump check. 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 4c15c0bd78c29258b9f2098c99b3db4107fa513e Add prepend mode to peptide stub commit 8a4c24f1207bbb769adfda14cc005aef65a75993 Add backbone perturbation commit f7fe9d10ccbcce2ae0a092e6c1be197f2cc76c7b Merge remote-tracking branch 'origin/cycpep/collab' into yfsong/cycpep 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 903c59ddfaf554dc013a1ef298dbe502d80c2cf9 adding multichain receptor support in FlexPepDock 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 dc02c9396db47c57bc86e475105a1eb0fb49fb46 Added a randomize_dihedral GeneralizedKICperturber. commit 91b3aae81155e760d274997b73b3d9106e7661ff I think the GeneralizedKICfilter for bump checking is working, now. commit cded4032ccfdf3446ed38a154c6cabe6dff1b635 Fixing some compiling errors in GeneralizedKICfilter.cc commit 9dbd23d96e53d39b12a12a2069e179f8c563d94e Fixing some compiling errors in GeneralizedKICfilter.cc commit 42b671b3279d09d004d6e533ea99371df22d19be Fixing some compiling errors in GeneralizedKICfilter.cc commit 50953aa13c2b9ae53b5d9a818ca19d818bb7454e Tweaking GeneralizedKICfilter to make the bump check more like the bump check from the classic KinematicMover. commit 19e3e60a2b15ca68532233d44a456a143252f90e Adding output to GeneralizedKICfilter to figure out what's wrong with the bump check filter. commit c441f06eae49c4cf8ba814319e73084b03d95746 Merge remote-tracking branch 'origin/cycpep/collab' into yfsong/cycpep commit 333d6e72443128fd7917a2714a053546bb8e26ac fix compiling issues 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 7da08d0e7fb1cf0c6eb04c8c18a7ad333bc87f31 Add input tag information to MPIFileBufJobDistributor.cc debug output. commit 5e4f90a86ff13416ed3bbbc8c964b20b7517803c Add debug output for job skipping in MPIFileBufJobDistributor.cc commit 92910176e575c72e160b5fcf60d4d24320b2283e Add extra AutoCutData error check. commit 3a05e2dbd89b79993aa557ffcb6d4b8da4f2904a Updating my notes. commit 551c8689db0276c4a99c99bd81d5ea5f94e92472 Had initializations out of order. Apparently compilers don't like this. commit b4c4cd01563367abbbcf6f752d8cd36074cce45d I think I fixed a bug in GeneralizedKIC.cc. The GeneralizedKICselector wasn't being created properly. commit 2adb1886d469fef79c1c578282c7c5784b996db9 Merging cycpep/collab branch into vmullig/sidechainKIC to get Yifan's latest updates. commit 89d35386dd0ef4461a940db4d524ea6d3731e245 Fixing a typo. commit fb13205f228e71890ac088aad8243d8cd75b2fa9 Added RosettaScripts support for GeneralizedKICselectors. Also, temporarily turned down stringency of the bump check GeneralizedKICfilter. commit 535d8c3b52e6e5fa995f7b710c540337a501a210 GeneralizedKICselectors now work, though the only selector currently implemented randomly picks a solution from the set generated. TODO: --Add side-chain perturbation (random or by rotamers). --Add a rama check filter. --Add "scorers" to generate values on which a selector could base a selection --Add a rotamer check filter. --Get ideal geometry to work properly. commit 7667290478df93dd4551b9d731caae73b8f100b2 First attempt at getting GeneralizedKICselectors working. commit 5c8244e520a66f5f38f748b908404fb1c730f3e7 Working on geting GeneralizedKICselectors working. commit 6608cd291f1e58c03648e275a5f622e1aa66b02f Silly mistake in previous commit (work on generalized_kinematic_closure/util.cc). Fixed. commit 4455532ad5cf96f2852b9532b5e0381a945363dc I think I've solved the problem with GeneralizedKICperturber and randomizing alpha-amino acids by rama. Now to test. commit 7baa23db080108dafcdf7e5d0dabd5b64da8c3b2 fix early crash from erraser_minimizer in graphics viewer commit 019a766f2d35a6593240b70ab57e0033f98ea985 If given a blueprint, SecondaryStructureFilter now scans the strand pairing and determines whether it is possible for all "E" residues to be paired. For these residues, DSSP will always return "L" because there is no hydrogen bonding. The wanted ss string is modified by converting unpaired residues to "h" (which means L or E). This does not change the behavior if a ss string is specified, or if a complete blueprint with 100% paired strands is specified. This change allows checking the secondary structure of partially-built sheets, which was not previously possible. commit 253dbc8b4ec0738ec9a86d3aaa43949c8a10062e DesignBySecondaryStructure now correctly eliminates ligands from the DSSP string commit dcf00773c89fb52b2ab2235a0a01c5af767cb58f real removal of old alternative to StepWiseSampleAndScreen in protein SWA. commit de56a36952311c666135b4a4ce734f2a69773ebd conversion of StepWiseProteinResidueSampler to use SampleAndScreen. No integration test changes -- cool! commit 3e454ddecaf79d3c191302bd59844f9def243ffa Adding more debug output to GeneralizedKICperturber, as well as an update_residue_neighbors(). commit a0d4e4834e19fec5114d0f85ec305f22788d923f Trying to fix problems with getting random phi/psi values in GeneralizedKICperturber. commit 49bf50ff119963f4955a744ee8c26e75a953df6f Fixed error in GeneralizedKIC util.cc. commit 8b76ec31e92284e25a74c5ec34d435db2198e744 Still trying to track down bugs in GeneralizedKIC. commit fc398d93b97cf0927ee314392325047d0b8ea7f7 Tweaking warnings in GeneralizedKIC to track down a bug. commit cbd07211aa891e445b5ced02df63ab56fd3f36d8 deprecating old PoseFilter in favor of new StepWiseScreener class. Initial refactoring needed for converting protein modeling to StepWiseSampleAndScreen framework, though that is not default yet. commit bc9306f0b995de12813ccab3fff41653471e3423 Detect connectivity for crystal docking now works. Scores returned now correctly represent the weakest interface in the lattice. commit 8b290af2a98ff42e9e6dbe328af27e7ffd7bc00a Trying to fix bug with filters and GeneralizedKIC. commit 67288358812f2ed62e3a69ff0165e37141b8c383 Refactoring StepWiseProteinPacker into StepWiseProteinMultiPosePacker (which handles iteration through a sampler) and StepWiseProteinPacker (which retains core functionalities, incl. prepacking) commit 0c5e45258ab998e4344c5cf0f9b78a8e5b994320 Carbohydrates & Lipids: updating centroid database files commit 623f81da6bc8ebe28563292a0f87f0649861ff36 Fixing header-only build commit 2426df96c02279a4fedb62728c223f6515cd582d moving calc_rms into FullModelParameters as it does not change during the run, and simplified number of variables held in StepWiseProteinModeler. commit 53577e0db3b3f878f73ef7afffc5bc185b38ae29 In SWA/SWM for proteins, remove full_model_info setting/resetting which is now longer needed, as we no longer pass through silent structs. Found an interesting issue in which PDBInfo became obsolete for a pose (despite being accurate) during fixup_residue_type_variants, now fixed. commit d4c7fb5dc1a8f0104d403ff499ec0079b676c140 deprecate silent structs from StepWiseProteinPoseMinimizer commit 46b754f3dcc033204db1959356dfd08d1cf9de18 deprecate silent structs from StepWiseProteinPacker commit 7836228b78f619ec7e908068a30dc1cd87d34374 deprecation of stepwise_pose_setup as an alignment tool in protein SWA. I do not remember the use case for this, and in any case, we have new superposition tools to handle this now. commit 49ca9b17cf5a816e9f55a1683784b1512c8ca424 getting rid of unnecessary extra silent struct outputted in -preminimize runs from SWM commit 7454097329f3c9b2ca9b9d9471e56544594016e0 fixing StepWiseProteinPoseMinimizer to not output any poses that were not minimized. commit eed5845479a0a9ee00e06f2f60160774b6619129 factoring Protein sampling/clustering out into a ResidueSampler -- preparation for merging with RNA by creating an exactly parallel structure. Changing StepWiseClusterer to be pose-based (rather than silent-struct based) for simplicity and easier transition to sample-and-screen framework for eventual merging with RNA. commit 76d149a0f1d4f64e9dfc5bd79cc0f385061f612b Make RandomGenerator default & copy constructors private. You must provide a magic number when constructing a RandomGenerator. Also, each RandomGenerator must have a unique magic number, so copies are a no-no. Praise/blame go to Per, who got me looking at the issue. (Unfortunately, this doesn't fix his problem.) No test changes expected, as no one was really violating these rules. commit f96ec53aff2a575fbe2a4eaf1bad81d4cabee9a0 Fix GasteigerAtomTyper unit tests. The source of the problem was a *reference* to a COP that was being passed around. While the underlying object was still existing, the COP object itself was getting deleted, resulting in bad memory access. This expressed itself (intermittantly) on Mac but not Linux due to differences in how the memory was being handled, and if the referenced memory was reused or not. commit 8ea6f71f6e3f50e47da1876cad633fc33bb4f1d7 Fix magic number in StructPerturb and unusued variable errors in FragmentJumpCM and StructPerturberCM. commit 0c6b0ac365db3c9f31477fb5d32aa37739c174ca Tweaking debug output of GeneralizedKICfilter. commit 1c278077b4cb38d2191a1725e5d1eabda9e6062a Adding debug output to GeneralizedKIC to track down a bug. commit db42745b912cdbd070e9546a18bb32adcfe150f5 Small change to GeneralizedKICperturber to try to get random phi/psi working properly from replicate to replicate. commit 86d84150eed23fabea6fa164c23344891050ee61 Initial commit of GeneralizedKIC selectors. Also, fixed a mistake with RosettaScripts and GeneralizedKIC filters. commit 025517d6f4e8fd472711d1c0bd96b5487cf3585f Adding RosettaScripts support for GeneralizedKIC filters. commit 4a42c5d4c56e743dd567a89078b74f3e2471f9ab Linked the GeneralizedKIC filters to GeneralizedKIC. commit acf13de6aac8af63bc7d560de3a9ac81f67f6160 Fixing a mistake in the generalized kinematic closure util.hh header file. commit 269f281df21cfff89f6e3f9644aff1bc5d8c0e36 Working on adding a bump check filter to GeneralizedKIC. commit 4ec157d8d161707ad08480dc9c3210dfbdb5e6dc Coffee shop is closing. Committing and will continue when I get home. commit f67b8627d14ffbf0c902ff9824162e7d81d44fae Trying to fix random numbers issue with GeneralizedKIC. commit 9509cec3c7713a8068907b29b9236a84b679b110 Initial commit for generalized_kinematic_closure/util.cc and util.hh commit 7d6a8d7627090dc306cf07ce80ca755210cc75bc Trying to fix current issue with stop_when_solution_found mode in GeneralizedKIC. commit a3b14bc052035ee236c76b8aee7835b495a31285 Removing ‘using namespace std’ from some of the protocols .hh files commit 452e22d44a0bbcd93b81390bea5874ca266146a1 Make adding termini an option in DeclareBond mover commit 6797ab4d551711a5af710767b2246376c94844da For some reason, my clang version will not compile these files without the extra include(core/io/silent/ProteinSilentStruct.tmpl.hh) for files: test/core/io/silent/protein_silent.cxxtest.hh test/protocols/jumping/JumpSetup.cxxtest.hh commit 469c1cc69f279b5787607dbcc5613d260f396407 Deletion of old StepWisePoseSampleGenerator. commit 592ed5854fd000922d2386c944e4b9afa31b9e39 Add output for AutoCutData to EnvClaimBroker. commit 5b16d2f58b8d18a36e5d03af3d5639dbdd469798 Add StructPerturbCM to perturb structures by a random, small angle. Used in later RASREC stages. commit 12352bb618621d1a5780728d7718003db8689739 ParsedProtocol now uses Environment::register_mover( MoverOP ) rather than dynamic casting itself. commit ba8a56308da984ff2f1b00be4d9672b4bcff8dee Add increased debug information to ProtectedConformation failed access requests (debug mode only). commit db429e3058bcff7515bd0c2dd61d97aa16c53e9c Fix a bug in EnvClaimBroker where no jumps would cause AutoCutData system to break. commit e74f1f4044cd8b90a477af5df7454a13bf9165be Add a mover::MoverOP register_mover() method to Environment for convienience. commit 9d482c0d1a3c85eed6836e764ab3d37750bf9ca1 Fix a problem with AbscriptLoopCloserCM that requires it to have an active stage4_patch option (now can be used outside of abinitio). commit feed1c9ab6fd1b50cd407ce63aa20c6a76e0b471 Add a dof_id-based access check that doesn't require an environment to DofPassport. 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 93cd09791664449300a738f94b9946f315425ea2 Fix a bug where EnvClaimBroker wasn't recognizing AutoCutData when it was present. commit ea1ea798fe39745ed892a38ac7a1e3bb6167be90 Added inject_hash application for adding Autocut hashes to structures that don't have it already. 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 9412b2cc6e72675baa6ae396c8940d769172499c Fixed one more mistake in GeneralizedKIC. commit 329a1e9fff939e9413930956d37d07329abdb6ed Adding support for randomizing bond torsions to the close_bond function in GeneralizedKIC. (Fixed some errors.) commit 4c1d4da5a909143dfe2e680edfa2e087e86991e5 Adding support for randomizing bond torsions to the close_bond function in GeneralizedKIC. commit 66a2fe469276d353af66dbb35f4b00f7fa1656f1 PyRosetta. Adding debug environment script. Updating incremental build logic. commit 49dce46dd1449a650d7c51ee5c275b12bb854669 Finished adding perturbation of alpha backbones based on the Ramachandran map. commit 32b2571bf51f3d43ae59cef78cac182a6b15287c Found a bug in pose_io.cc: CONECT records to the first residue's nitrogen atom were not being written out. This should fix that. commit 9708da402ee4e24e6381744e33fe6c0c27aa6151 Fixing duplicate entry in compile list. commit 56e6479e15b8304f14e6299cf77f3b7b51bff986 Adding a Ramachandran-based perturber to GeneralizedKICperturber... in progress. commit 6c704ee4c0fccf0d0d328ee789a43c70c11e1f5b add ab ag contact plot and data for brians paper. fix ab-ag cdr hbond issues 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 e69be04130a8a44cff28ef7c44bd84187b01ba00 Syncing with master. commit 37fa19e40ad9515db37d91904400482647554ef8 Pulled updates from master. 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 b74d9fd74ee9fe79858568f6348f1345a35cf143 fix but where error wasn't thrown. commit 2ba2a7e8418992b5fc229d9629e8ebe446bb0858 Implement abinitio:skip_stages option in AbscriptMover. commit 7d642b5e18e37b6ae268094832bae83b174c821c resolve merge commit 20fa51fcbc7936c5e314b2478ad084f7fa7b2ac6 Fix a bug causing lost data in datacaches. commit 5835c2e5eb5dc1fc874f23471db0b43d3073fe82 Fix a bug in fragment shifting causing lost fragments. 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 ec5ccaf51948bc594b2be2be462bb3222380c708 Added multiple closure attempts to GeneralizedKIC. 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 d311216efb3381a5ae2da5c4640c763d0b264d90 Added RosettaScripts support for closure through bonds with GeneralizedKIC. 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 7e70dc0869ce80bff686a4624b8f4d1bea05314e Switched AtomID to NamedAtomID list in GeneralizedKICperturber in preperation for adding RosettaScripts link. commit 854d972712e8160cd85f2b289d4104a0079e8f11 Fix matcher error catching issue commit 467cf4a9f21031c02a9bf0304e8f02241d578aec add cdr length correlation r script 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 9665fe045651da3c9854aab2767a3cbeb4dff1a0 Fix a bug in fragment shifting causing lost fragments. 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 211aaf2c61bfac0ecd3fe1cf1fd5235c2b030d2f small fixes 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 7664a0c010dc4adbb0b4b07dba4b5d145306d8a9 I FINALLY tracked down the problem that was preventing GeneralizedKIC from working with RosettaScripts. It works 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 a99a6a669ecee18804a2253bff47714729d95b47 fix some bugs commit 54fe3658e7ae82f4f28e17e09ae3b487780d7b11 Fixing compile errors in GeneralizedKICfilter commit 8e1d8d75b101b118d2b79a911c1683c36183fd8d Added GeneralizedKICfilter to protocols_c.5.src.settings commit e93f895f68b92424ee304d3110b8e8d2ff6a3bb9 Well, I can't figure out what's wrong with GeneralizedKIC and RosettaScripts. I'm going to bed. commit 0e4b754e35aaec0c0c0c6599118d4dfed64eeba2 Changing back some of what I changed to try to get GeneralizedKIC working with RosettaScripts. commit 322bf6410c1d1515beb1f4405cb28e713ecc47bc Attempt #3 at getting RosettaScripts to work with GeneralizedKIC. commit 1a4ad17b1dfa31e49a1819bebaa919ab79b3eed1 Another attempt at getting RosettaScripts to work with GeneralizedKIC. commit 70900136db2a0553952213ff810bd8ba5de0956e Trying one more thing to get RosettaScripts working with GeneralizedKIC. commit 48921d5a4fb3e46fe1a4bddd56dde7dbdb13c3ee I think I figured out why the RosettaScripts link to GeneralizedKIC wasn't working. commit 02ad367ad0af11c37b0bf10a8a98c9189bed9b72 Trying to get GeneralizedKIC working with RosettaScripts. Something is failing right now, and I'm not quite sure what. commit 0f424085d1aca65bbd651a79bf1951f40ad496dc Another bugfix for cryst_design. All spacegroups but F4132 working. commit 6ac90f18c643ad54ea2ef81061efbb7f652e1c0e Caught a typo in GeneralizedKICfilter. commit 45380c358d11d1c72c576270070c03f485f0805b Initial commit for GeneralizedKICfilter class. commit 24343a6146603dd8664f17278f57121b13d89397 Added set_bondlength effect to the GeneralizedKICperturber. 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 4f1e83d360fe90d7dc706b0ed29a05727720133e Tweaking test_sidechainKIC.cc to test set_bondangle. 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 ad4a25149cfc140297a636bc8f7f493e484d41ed Added set_bondangle effect to GeneralizedKICperturber. 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 58beaccfba75c421b3675b36134bf76441acac8e Adding support for referring to perturber effects by name, to facilitate development of the RosettaScripts interface down the road. commit e5109eea7aff5a01aace3aa0f44947e686ed99eb Tweaked test_sidechainKIC.cc. It now rocks a backbone dihedral angle through 50 degrees, finding a closed solution at every point. commit 14d6c0a29cd519943dec66749c157f405b1376b1 Tweaked test_sidechainKIC.cc to sweep a range of angles. commit dc920e0d6e47deabd8adfe2023c42c085f7525b0 Fixed a bug in the set_dihedral_apply function in the GeneralizedKICperturber. commit 7165ea1cdaec3da4a294793ee2d89a357d2edea2 Found problem that broke compilation of GeneralizedKICperturber. commit 774ae754c75b77c56e484f1f63f294d387381ac7 Trying to debug compile errors for generalized KIC. Right now, I'm getting some 'multiple definition' errors... commit ad53a8b771c0bcfb91ba16fdd379eec6cbc2d0b6 Trying to get the generalized KIC perturber fully linked up to the mover. 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 9ca67c3fb91bca691e18b82634e80113798a1686 Adding connection between GeneralizedKIC mover and the GeneralizedKICperturber. 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 7290b087ce2022cf43bd8a0ce3121a18c42691bf Working on the GeneralizedKICperturber code. commit 4b2d7e77c3c8864143c58f78dfef52806474f373 Lipids: added new main-chain designations to lipid topology files commit 65f489dedd0132969dac91bef84686038cfa852c ResidueType: refactored to move some code into a subroutine commit 8f1f395b4c5454926c575d43ddf54b60e1dea6f7 ResidueType: improved debug output regarding main-chain designations commit dc6977a3ade710b440298528f72e16c3539e4ced Residue Type: removed default main chain definition code and restored old default commit 761ed80b6bac9f015acbb2f8b30cf057b90bf8b5 Residue Type: adding ability to set list of main-chain atoms from a topology file commit 7ddc29c2a54ccd2e8d947cdd7e70df628f6d5e70 Lipids: adding is_lipid_ datum to ResidueType with getter commit 59bc5b449485372afa0b9c70532e79210d4fac16 Lipids: corrected designation of variants commit b1a7f31930a6f679ecfafc249afee29e185aa1e1 Lipids: adding glycolipid PDB test file commit b660dbf49d4cc2f957aec2d55ff5835166ea3f54 LayerDesign fix to allow ligand-containing pdbs to run Original layerdesign didn't work on ligands. Our old fix added "L" to the ddsp secstruct string for each ligand molecule. Rocco's recent, better, fix, puts a " " for each ligand, which broke our old, hacky and un-integration-tested fix. This commit gits rid of the hacky fix and works with Rocco's fix. All Unit tests pass and integration tests pass. We should still make a LayerDesign integration test. commit dc709389aefd534a288402f73dc119946c56daa1 in StepWiseProteinModeler (and KIC_LoopBridger), complete replacement with RotamerSampler instead of old PoseSampleGenerator. commit 78025d923cf83188cddab7c48c12a7f3a1d1bf22 refactoring StepWiseProteinPacker to use new RotamerSampler instead of old PoseSampleGenerator. commit a430d85c9330f2a03c6758b2448b848ff0dda221 get rid of dumped pdbs commit f04af8c287b9052fb67d3b888206ea1cb2eeacb2 refactoring CCD closer to use new RotamerSampler instead of old PoseSampleGenerator. found a critical bug where CCD closer was not emitting all relevant moving residues (only the ones encapsulated in job_parameters, which was not updated) -- this looks like it was occuring even in master/! Not sure how long the bug has been in there. Need to be extra careful when moving ahead to CCD closing during stepwise monte carlo. commit b8cae24ee4f721cc81bcbc1bc6829663384c2083 removal of old StepWisePoseSampleGenerator stuff out of StepWiseProteinModeler commit 330fd2d67cb71df3d4192acd1c241158a377622c Adding git-branch prefix to observer emails commit ca4391aa81ea21a0bc48b077e3f0b5810c278264 complete recapitulation of old PoseSampleGenerator class into new RotamerSampler classes. commit e58f27b2f9cc30f1497f14a80d5a6d2b20b1c602 Merging my copy of the master (just one bug fix) with the trunk commit ceebb8b299013744742dbdb7ac1938b4a9464c01 Fixing a bug in SecondaryStructure class ObjexxFCL::FArray1D_float confidence_ was not initialized which resulted in segmentaiton fault commit 691c3da197c6bb9dbc898be95d353a721aff3235 Fix Performance benchmark Adjusting performance benchmark to account for metal ion changes Vikram recently checked in. Interesting note: if a non-polymeric residue exists by name in the PDB, but doesn't have any appropriately named atoms, it will be built, but fill missing coordinates will never succeed. Better error checking of this is probably necessary. commit 2f233e796e1245820c7a4176a1ae81d482cb3078 Pulling in master updates. commit 855a27020305875f9c570cf9d1a5a7ec568cdb4a Adding a set_dihedral effect to GeneralizedKICperturber. commit b1bb6544672474cc5cd8bf84fc3f69e7e2953214 Adding GeneralizedKICperturber class. commit 6d86fa04efe749fefbf6ea5b22fe7e4a2f6a6f30 Moving cyclic_peptide::SidechainKIC mover to generalized_kinematic_closure::GeneralizedKIC mover. commit 72fb8f01ed871daf117f995b148454c7ca9e6885 OK -- I think I've got SidechainKIC.cc working now (basic functionality). Now to add perturbers. commit 72509643d7696315df39f07795d757f9d9680652 Updating my notes. commit 0f026d0fc03db6bc230a90257138fa1de4b717d9 I just realized my mistake: KIC assumes 3 atoms upsteam and down to establish frame, not just one. I need to rewrite some stuff. commit 98287c08688ffb170bbc3058447fc40d2e923407 Adding notes, and fixing degrees to radians conversion in SidechainKIC.cc. commit 6914b47023a862534c64684ab800cd631fddfa04 I think I've solved the problem with SidechainKIC, now. Forgot degrees-to-radians conversion. commit 6629b88baac4c1ab0b21b03498f034b7a4c7bbca Fixing warning/errors debug problems with SidechainKIC. commit f7c754d2f835cf521420380e4bf15d1ab9f86105 Making BackboneTorsionSampler compatible with the warnings-as-errors unused variables error. commit dbca33598e1db1b9675ff05c6e4142ba1b4230bc Fixing debug build in vmullig/sidechainKIC branch. commit 442b5deec3354bc323d0c8a7cc4b457cddde2fe8 Lipids: need to tell params file that it is a branch point or lower terminus, etc. commit 792b6bd9093471ed767ad6834fc6e4b6371bfbc9 Merging master into this branch to get latest updates. commit 5f747a3c4b9ad1d336045d3cb92b9bca5b4d346f Porting integration tests observers from svn_users.py to /observers files commit 5e34c820597336ec53fcd968d71b83420a361e6f pretty up ab plots commit 331efc5d6b60abd3e93608769dbf079ed07ac3fb bug fix in sphingosine.params commit 5cc068714220c5c27d0ceb643c917401118081b9 Lipids: 2 new types added to list commit 3ce07c9f97ffa6ffa24e7679bb22005d311fb92d Lipids: adding linoleic acid to the database commit 0675475ac90656f7b02199dcc8e752b4840bcc30 Lipids: adding 1st lipid (sphingosine) to the database commit fa50b53165cdc6caff4775e9c0318e53bba84f38 Benchmark scripts. Refactoring how exclude files are handled in regression tests (i.e. store them but do not compare). Adding example observers files. commit 2aaa910afa5b3ff9da0801352521e95eb99fca21 further commit needed in converstion from StepWisePoseSampleGenerator to RotamerSampler -- need init() in RotamerSized() to set id_ = 0, corresponding to state before first get_next_sample(). commit 8b7ee80eedeabb46c73b49241424cf4fcd31bcf4 partial refactoring of PoseSampleGenerator to RotamerSampler commit 21051badf939f2cff501b7fca79a4f993d1542c2 integration tests for 'classic' stepwise assembly for proteins, in preparation for next refactoring stages, including rigid body moves. commit cadeb9f34d91223be8a779543e7265dbe30b8f0a Pulling in new changes hoping the warnings go away. commit e4d0e518c3fc4f11ad6aa9b2c739619ee1540586 OK, bridgeObjects call in SidechainKIC seems to be working, though I don't know why the pose isn't updating properly. commit be89e6e0bee0621ee1b96dd4862ec87743924e46 Fixed the bug that I was having trouble tracking down in SidechainKIC.cc. commit fbbdcb8417f873c66c61dbfef31b86222f6b195c Done debugging SidechainKIC for tonight. Will pick up tomorrow. commit dc9149b09796ff6265fcfb583f1d4f8bb73bdd13 Trying to track down why SidechainKIC isn't working... commit 6743044cc3dadf80c9f253962a9040475fbd1dfe Working on SidechainKIC -- trying to get data set up for bridgeObjects. commit b5e89a9b0e495953159d58352e7aa44bd3a4ddc8 PyRosetta. Fixing build script error when running on Python-2.6. commit 9ca94ad9c2dc346b4fbfc200ac12c970dc6925fb Removing CYZ2.params. commit 338fa4539c91f1b8d87803b95e2cb05c01c06966 refactored extra_minimize_res and sample_res to go into FullModelParameters, which is held by pose. commit 493e280ecd9de580b78345a3b726f5e7d34537be work on hbond plots commit b531a7e4899fb74905905818fc9e47581436a234 Dummy commit to trigger integration test change commit 1ccd1e0a40244600e4c91b97e58ba2cb9d733b3d Revert "Revert "Fix issues with Gasteiger atom typing"" This reverts commit b1603f390f31c154481f5b0a4fc58c208c1cc2a6, restoring cab6655af046ce82e656c1c35b9fda7c7cc9fa33 I could not get the test server changes to recapitulate locally -- more tellingly, the reversion did not see the inverse of the observed test changes. Moreover, it looks like other commits from the same time period also showed similar test changes, indicating an issue with the tests. I don't see any test changes locally with this commit, aside from the added unit tests, and the standard numeric instabilities. commit 7e16cd781ae25b1121bd2b19cbc9c8ddb7bdf71d Refactoring how exclude files are handled in regression tests (i.e. store them but do not compare) commit ac450c4b2742f710a8e028c683d1bfb7fea44148 Revert "Revert "Fix issues with Gasteiger atom typing"" This reverts commit b1603f390f31c154481f5b0a4fc58c208c1cc2a6, restoring cab6655af046ce82e656c1c35b9fda7c7cc9fa33 I could not get the test server changes to recapitulate locally -- more tellingly, the reversion did not see the inverse of the observed test changes. Moreover, it looks like other commits from the same time period also showed similar test changes, indicating an issue with the tests. I don't see any test changes locally with this commit, aside from the added unit tests, and some cosmetic tracer issues. commit af6f98f568e12b52b7be37dcc2511be558248060 Removing ‘observers’ file from ignore lists 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 a53ac3920f84a9494cf4cbbb5a61beb296aa5900 Adding example observers files for score and integration tests commit d9e72934ea7f57fa3975a51db9128023cbb1e2cc update code for cyclic peptide commit c602a297df08be034610d7c07d26aaea6e4ca6c8 fix bug in FROM_SCRATCH that did not obey -sample_res commit f1db2ea60772940edb4384c941f2624971f04679 get rid of debugging output. 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 d1239c6236f784845b47ee5403f08a5977660b60 pulling in changes from master, hoping to change some of these (now fatal) warnings in other's code. commit b486a604ec7f37df652d6cfe4406ba12ca563634 command line options for motif incorporation. commit 5cb0cdb59416e14afe9862a7956685445f4ae68d Quick fix commit 33f44cd733184465153a7b2e928ee25269c7d9d1 integration tests for stepwise monte carlo of proteins 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 41e000827794a50958b27cbc1c79c7840c61db05 completed set up of FullModelParameters, useful refactoring in preparation of storing more info in FullModelInfo. commit 46fb5bbce277882650a819cf575093d4ba99cc4d Pulled in new changes from master. commit e7ef6a7df93303fdf9d5fd716cab98f99dbd7a33 Adding rotamerization mover and application. commit e08b130d8f0c266d09446ab0749fe1280b6e41c8 A simple pilot app demonstrates how to use movers commit 3f55c95210c4e42365424beb8260104b8849bdbc fixing warning/error which should also fix the build commit eff01e50da03fadc9e4196fd777ad8ce20b36177 refactor of FullModelInfo to use FullModelParameters (const! yay!) and FullModelParameterType (an enum! yay!). Note still does not compile. But I wanted to push to save work. 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 47e0302acee35090f70456847a0a12d346663cc9 reverting runtime_assert, whichI used for debugging in release builds, to assert, for speed in release builds. 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 55df3bc632c9381c87233312890d4fd5af7976ad change name of variant tag: VIRTUAL_SIDECHAIN to VIRTUAL_SIDE_CHAIN. a source of confusion (for me at least). commit 4053c0bbfc342aa68c4ed40624706603f10618c4 changing N-acetylation and C-methylamidation variants to have virtual methyl groups -- otherwise getting lots of weird clashes -- hopefully I am the only one using these crazy variants... commit f25621131e4efcbed5279d7dd43f98e8dd53f396 adjusting -preminimize to use packer, and fix up variants... commit 9f1b7a52bb0bd0cf6ebc7884ce86d8f6a6dc4008 Reversion of peptide plane setup -- going to try an alternative... commit f3ff872ac02103cdb920640eca27945781428f7f goes with last commit -- ensure that integration test will run for old-school protein SWA commit de72716dad68be4aae6d7cf3cdadf11e86d2ec81 putting in -preminimize flags to allow testing of side chain virtualization, etc. commit 3114da1da624446b21d32b56696ec368665f3d16 for protein stepwise monte carlo, alternative setup of peptide plane variants -- must be introduced by ADD mover, not by fix_up_residue_typevariants. Not sure if this is a good solution. commit d702766839afee9182ac48e4c8f2d3ce7e8f373f some changes to torsionsampler commit 8d815fe8f2c600c5a3382a2b82e3c398057b3593 Fixing clang 5.0 build on mac commit efb59fd93b95d7a5469f221733a3df8e3ebe92c5 Fixed ideal geometry problem in SidechainKIC.cc commit a310c1772118c14687eb6726e4f1fe97596586c8 in stepwise moves, there are various places where a pose is split apart to compute atr/rep or to pre-pack -- if coordinate constraints are present, this leads to a hufge penalty and actually prevents packing due to limits in floating point computation! remove constraints for these split-up poses. might be better eventually to create two distinct poses. commit ac284c3be1c4affe534cd609214beef9a6d39eeb get rid of unnecessary PDB dump that I had for debugging. commit 5afdfeeb6c509b7a438fcc37e31fbe685c40cbbb adding -align_pdb option for initial tests of refinement protocol. set up -extra_minimize_res flag for protein modeling. commit 59e153c861247a3da20d523922f77b5e90fcca18 Merge branch 'cycpep/collab' into yfsong/cycpep commit 57b37e738cb7f75bb38d1de685f401fc69cc6653 Merging my branch for fragment picker stuff with the changes introduced to the master commit 6a82c8d2c12382482fb93564c6326451d9b8acb1 Added last atom to atomlist_ for SidechainKIC. Ready to set up the bridgeObjects data and to perform the closure. commit 27f6943dce45199c0419ac837bd84e5e5f20b5ea Tweaking test_sidechainKIC.cc. commit 5a6688280997f9db399556f734eae5ca5ffbcfa5 Merging cycpep/collab into vmullig/sidechainKIC to get Yifan's fixes to residue connectivity with nonstandard connections. commit 30a68df78c8eec5b85dfc9dda29222d558000a7a Fixing debug build commit b871b96af33fe1e3eda1d840582f9505459b0059 Working on SidechainKIC. The atom list is now auto-generated based on connectivity, but there are bugs in the setup of non-standard connectivity in Rosetta's core. These must be fixed. commit 5b68e79e91553ddcf25ec318f45cb33731514eb2 Fixing score naming bug in abinitio code commit b90f3350c18b4cd2c1909a4584302c9f3d8eccd4 Removing erroneously typed character to fix the build commit 80ee5c2e627c497b9580c726dd82db7eeafced30 Working on SidechainKIC.cc. Trying to track down current crash bug. commit e320b2651014d94c60137c338cf081f56dea3ef3 Debugging SidechainKIC... 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 b2be44472fedeb1fac959357fc7952e7127b9d6f Working on generating the atom chain for kinematic closure in SidechainKIC. 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 1cfa49b71f0a3624e37a91032970ad3ca5d96d9e make cdr hbonds faster, start by-cluster scripts 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 4d35a2573f53f6430936bbf0d4e30388c15c88c9 Working on SidechainKIC. Added upper anchor. commit d98c4f58273fba79034818b08f00f968a2922179 fix a bug on adding cutpoint variant 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 4baa339952e07d2af5284fd99b73e1aacf5278bf Fix some small bugs 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 0c1d177f35f72f904e50fe1e5b919bbf69bf25c2 Fixed bug in MPIFileBufJobDistributor where many failing inputs would cause a stall. commit 7f7b3ab10eb97620be293bb5a1a5e9a0a8826484 Fix FragmentJumpCM to behave more corretly under restart conditions and Prepare Environment to strip DataCache elements. commit 387fe2f4dc18f047f0b8d081b9b9b07c2e5e1f30 Quick cosmetic changes commit 4a925b3344b467808892ab8128d73fd3c8fc9971 add charge length histogram commit bf6fb5110cc3f96590f7cac0d800c0038246e7e2 add dsasa length histograms commit 926a6a8a6fc156bf07614d799634faaa51314304 add cdr sasa histogram and by length histogram commit b24f7c7576ff4d8e6ee006c00c82bab9a6cae29e bugfix to StepWisePoseAligner for cases with fixed domains. commit 080fee3dde3e370827bbb40bb9eeac41bbed0dd2 write cdr-cdr hbond script commit fa89ee72af6cd244e287a3af6beb0268a1664dfb Adding scripts for env, pair, pair_ang commit 07b3d751f94b74f6debc8d79b74abb7eb7c8a279 Updating scripts for calculating cenrot dunbrack lib commit 8ce4413215a690d71be56f6b01c2dedb7e59afa0 getting compile working on gcc linux commit 8abf622a4b8ace3cd8548ef9a63a81eefdc8f8a4 The problem seems to be with building ideal geometry... Hmm. commit ff0e071abb2608c3df5ed2d78d82ab874f9af251 Working on elongation in SidechainKIC... Getting problems with the Atomtree... commit 4992db4eba65740c94a1d6392cdc31a9825bdfde big update of rms calculator and constraint applier to enable native-tethered stepwise monte carlo for proteins. should be easy to unify with RNA. commit e42d979d51c64556d45f393ed1c52c3de083ec4f fixing potential bug in resampling in from_scratch case -- i was not getting all (or most?) of the resample moves in trp cage runs commit f7de30f84bdfd58c303f6dd230be1210f6b639a2 Working on SidechainKIC. Starting on apply() function. commit 04a67660261059cf565ce6ffc2031a8efc379005 Working on SidechainKIC. commit 27e5c8a45aab9bd36347ecaeda5c6921b2863d0c Working on SidechainKIC. Added ability to infer anchor connections at loop termini. commit 0ffcf0d74ef6efa1d1d3659f796640f4bbfb1e9b Working on SidechainKIC. Added functionality for adding a list of residues. commit eaa611524c3f293739d029e10a1c455a75aac14a Merge of ninja master with rosetta remote master commit bfd5ae103b00aa66b1a8073b65c8567d4ed3ba19 Clearing test_sidechainKIC.cc. commit 60b02496a2c64ef325deb3b8b85fec4f9ac416cf Initial commit of test_sidechainKIC.cc commit f1fa96684a7dc016127eda1bbc38298d54bcf93b merging with master; some files were required to remove commit 681f0405948d5bfc75ec63d6891da6bcd527739a merge master into branch. resolve interface features conflicts commit fb38bf53b5b2bac6b7bb5734d725f7dfff0c36e1 This update should fix the pyRosetta build. Library level stil broken - that fix is in progress commit 7bbcfd4cd84372745a56a54ac3bba719cea823cb work on plots 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 129a468e4a2581a0ce3c6d27b2df829c5d22cbfe Simplify jump fragment setup style in FragmentJumpCM. 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 96fa6817fd94b0fac806fc00ccd023d0e22b2c7e in stepwise monte carlo, allow initialization from silent file 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 70053c2f798958399e48cdb4bb96bf95efd5b077 Add 'restart_only' option to FragmentJumpCM. 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 8d23a52c8dc57b311587f758a7b2a2fb9f099f33 Cause SilentStruct to write 'CACHEABLE_DATA' in the REMARK lines for WritableCacheable datatypes. commit ff6ef218619544055b5f79647f82364ab0121ab1 Modify ClaimingMover interface to provide WriteableCachableMapOP instead of the whole pose (pose access is not const). Also change the way the hash for EnvClaimBroker AutoCuts is calculated (only depends on jump positions). 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 0a23665ae45ea1d904ca6b249c0030ce1bc82303 Superficial changes to ConstraintClaimer. commit 250583e2050d2b862d78e63136e8d2e5de22197b Modify ConstraintPreparer to randomize constraints only once per run by default. commit 82e6f0785ca4c518cf34712cdafda8808b2c2b50 getting NativeClient to compile commit 0e7fde1c8d68310f1deb7e15e4580e426f870aa0 getting nativeclient to compile commit 07008203773df0dea309b6b12fd2c41588a26199 Initial commit for SidechainKIC mover. Now to actually make it do something. That's the tricky part. commit f172b0ec9eb85d325c624c5bf667c03bc176770d GPSRosetta: New functions to score Pseudocontact Shift (PCS) data generated from multiple metal binding tags/centers. NEWS: [DETAILED DESCRIPTION OF CHANGE] The distance restraints are implemented in a manner analogous to finding locations uisng GPS satellites. The current implementation is directed via usage of a broker file and can be used to setup atmost 4 different tags. GPSRosetta is an extension to previously implemented PCSRosetta which uses PCS data Ref: PCSRosetta: C Schmitz et.al. J Mol Biol. Mar 9, 2012; 416(5): 668–677 GPSRosetta: Yagi H et.al Structure, 2013, 21(6):883-890 Unit test status: [Pass] commit b8f68adb4e845b007c02314a0593d313737a9795 removed option keys tracking commit 43339425ddd1204b8b992e5e0573e6b4ec49d9aa GPSRosetta: New functions to score Pseudocontact Shift (PCS) data generated from multiple metal binding tags/centers. The distance restraints are implemented in a manner analogous to finding locations uisng GPS satellites. The current implementation is directed via usage of a broker file and can be used to setup atmost 4 different tags. GPSRosetta is an extension to previously implemented PCSRosetta which uses PCS data from only a single metal center. Ref: PCSRosetta: C Schmitz et.al. J Mol Biol. Mar 9, 2012; 416(5): 668–677 GPSRosetta: Yagi H et.al Structure, 2013, 21(6):883-890 commit eb16d5c77919f6d80981e5f27df059eefcb9a979 Merge branch 'master' of github.com:RosettaCommons/main commit 327e15e8b2cdce1e2aa149779d429a50d15fc5cb PCS Scoring with multiple Tags: New scoring functions which can score PCS data with atleast 4 different tag sites are added commit c38036666087e1208b9ae79ed5221bd5a20ec1f7 Merging cycpep/collab into vmullig/cycpep to get Yifan's new movers. commit 43c8579d8ec2882989dddace5083467fcf913261 change nested mover commit b392937ff820a7caaffab0fd8f52b97cfb7d4a4a Fixing clang build (tested with 3.5-1ubuntu1). Attempt #2. commit cebb1e830c2c92736f439d06421163a962c42fbf work on cdr intra, inter, and framework hbonds commit 5a457e857002bf2b971665c7ec65528b4d3a60a0 Fixing clang build (tested with 3.5-1ubuntu1). commit 39fbf2a1bea06e634773c8eb904389c09cf9b137 Merging local and remote master branches commit b27bf47336fc4549c1c0748681fc5973a73e011e Adding MultiplePoseMover and MultipleOutputWrapper (merging branch luki-mbi/rosetta_scripts). NEWS: The MultiplePoseMover allows a multi-step "distribute and collect" protocol to be implemented in a single RosettaScript. First, it collects all poses from the previous mover in the protocol. Next, poses are selected from the complete set using Pose Selectors, some of which use Pose Property Reporters. The sub-protocol, if any, is then run on all selected poses. Poses for which the protocol succeeds are output to another mover for further processing, or to the Job Distributor for output to persistent storage. This mover can also be used to "branch out" without any selection criteria (i.e. generate many diversified poses) or purely as a selector to trim down the set of poses based on some criteria. MultipleOutputWrapper is a simple wrapper that will execute the mover or ROSETTASCRIPTS protocol it wraps to generate additional output poses from the original pose. This commit disabled RosettaScripts resume support, since it's interfering and needs a better implementation. Unit test status: Pass All test pass except SpanFileIOTests, which fails to run on my machine (Linux, gcc 4.8.2) with: core.test: src/ObjexxFCL/DynamicIndexRange.hh:103: ObjexxFCL::DynamicIndexRange::DynamicIndexRange(int): Assertion `legal_static()' failed. Integration test status: 37 test changes (all cosmetic) Cosmetic changes are expected in the following tests due to the clean-up of empty protocol reports. Additionally, there's a new message about deprecation of the tag in favor of . Enzrevert_xml add_job_pair_data dock_with_hotspot_place_simultaneously favor_native_residue grid_scores_features hotspot_graft hts_io hybridization inverse_rotamer_remodel kinemage_grid_output ligand_dock_grid ligand_dock_script ligand_motif_design ligand_water_docking loop_creation make_symmdef_file nonideal_rtmin place_simultaneously posttranslationalmod_io ppk rosetta_scripts_setup rotamer_probability rs_flexbbmoves rs_loophash score12_docking score_only_silence splice_in splice_out splice_seq_constraint startfrom_file symmetry_data_resource The JD2 now outputs additional poses generated by a mover, thus the following test now produces multiple PDBs: rs_loophash The pose tag is now at the end of the PDB file name (for clarity), hence some output file name changes in: AnchoredDesign antibody_designer broker_membrane docking_prepack jd2test surface_docking commit df74783160e50ce52b964c73496c4c628d01f1b6 Benchmark scripts. Adding ‘ignore’ file list. This should break all regression tests. commit 8e6d3410c21b5ca77ef01cc960726c5ebc6a4877 Merge branch 'centroid_rotamer' of github.com:RosettaCommons/main into centroid_rotamer commit 2e4a76a22e9e2664245e1426673e2bfd63d8bd81 Increasing VDW radii of hydrophobic side-chain (detected by fa_rep) Minor changes in cenrot-relax weights commit f3d253581039314e4721c7ba5e1ff63c2f5b758d Adding printing of tests runtime to PyRosetta tests commit b907c7afa033f4461657c32fb47e1b669dbfc0ca PyRosetta. Refactoring how debug build is done, moving it binaries in to separate dir. commit 157ca0e5ebb05e4b5143740f7ee1eaf780abd02b merge antibody_features branch into antibody_features commit 17fe662b15266a6fc464aa14d8ed4dbbfd6fc2a3 Options reorg: remove extra files confusing PyRosetta build commit 1f6a61dc5f5889f20e91146fae910bd8ffcf75a5 Changed various paths and added some ifndef statements to EllipsoidalRandomizationMover to get Rosetta to compile for NativeClient commit 7cc8381f04edecd9cc0dfdb1be94c7d31bd7a06e Better-er output capture on database tests. Also caputure stderr. Integration test changes: resource_database_locator and resource_database_tables commandfile commit 533d1ee67e16dbf47893d2d8c352f81d161f8fc8 Make update_options an always-run when compiling To avoid compilation problems when someone updated options_rosetta.py and forgets to run update_options.sh, add the running of update_options.sh to the compilation process, for both scons and cmake. It should no longer be necessary to run update_options.sh manually when you change options_rosetta.py (though it shouldn't hurt anytyhing if you still want to). The additional time added should be minimal (fraction of a second). In conjunction, remove the autogenerated files from being tracked with git, and fix a few places which depended on autogenerated files which were removed/changed. Tested compilation with both scons and cmake, and with a fresh checkout. No compilation issues seen locally. NOTE: If you have a compilation scheme that doesn't use our standard scons/cmake builds (or a non-compilation use that uses the autogenerated options files), you may need to add update_options.sh to your build scheme. (I have done this already for BuildDocs.sh and make_ctags.sh) commit 4c1229c2a9c24b15f088b1683a8f69f22bee1c8a Further messing with skip_redundant_width defaults. commit 2fa368f4de4a6b209a58a6d15dd4ca9327294b81 reverting previous push (I'll log on to the test server and try this again later, but it seems GCC 4.4 gives different uninitialized warnings even on different individual machines.) commit bca8a65414b309835f85eb152d26b2dd522b0adb To Raijin compilation commit acf4a96f45c83fed0cafbe7f0a45a82288608c27 Update ConstraintPreparer default skip_redundant_width and include options for setting this value. commit 6a8d317cc5e6e84d49b61766a311baea7ce19666 PCS Scoring with multiple Tags: New scoring functions which can score PCS data with atleast 4 different tag sites are added commit 9cb5878839144ef9640b616984c469e23042f7ee add blank cdr cluster sasa script commit ade0727e1badbae6edc6d598759c114bee62e5c6 add more sasa scripts commit 5b194bd88db0fe24bcfe288901bcb7290726633e add blank cdr cluster analysis scripts commit d0d89ff189aeedada5cf2204f4eaf0e8ca8c164b finish writing ab ag cdr hbond density and hist plots commit 5649c94a055b57f2ba9e3e422b2b6822324abb84 begin writing ab ag cdr hbond density plots commit ce1d0f723ecdc8f7b2ca0a2050cafb1b8e7a093a Warnings Removal: giving GCC 4.4 release another go with full Werror commit 79489a29e098f04da9ba3635ed22f63be2ca314a add cross interface hbond distance plots commit 02928fc98dde34004f1415e82a0ac5dfae45f176 Updating crumb master to match remote master with membrane_info changes - merge result commit e914cd6637bd801821fd9cfd006e5f32ce65d487 Final fixes on this branch - getting ready to merge into master commit f54e1e3033c74ca9e7a1eec113edeab96581370b Fixing quick bugs in unit tests - successful move to MembraneInfo object commit a3e6dee64f50c9067401ea1eb3e0a4d5ca322efb Fixing compiler errors commit 8d9cb9d77014176a35395abf7ed977342993136d Merging remote and local master on ninja commit 123c4c7a32a38c6941baeff7440b15ce278bfd17 add cdr contact and dSASA plots commit 2d3c88ff82204a62b2264e48bd9d1e4dad98c4e0 Removing old membrane conformation from the core 2 build commit 0fdfc265509484f3639b077034f69759d6f87253 Removing membrane conformation unit test from test/core/membrane commit 387ea7fd5d63ab156cf71f88dd0a869f83ed07d1 True test number 1 - removing membrane conformation from the repo commit 44c48e4cb1c684240433422153e2719cd9d1d465 Fixing new method in conformation to return the correct type commit af7cc774106dc0b536c77a9235e176979f1a4bb5 Updating unit tests to work with new membrane info interface commit a524c8c26dc91a0ff2811e5613e24c1e85ba0fd9 Merge some fixes from master commit b85dd1790d3d3c630da381bd164091ca18c0d31a updating in code calls to membrane_info" commit eb2ce36cb644037418139b3987d8dd657b64294d updating core conf interface to return a membraneINfo OP and call .membrane commit 6a39e3876186c4b4a017174bd5f4b94f96b8a51e Finishing correct implementations of setup and get membrane info object in the conformation base class. Also implemented an is_membrane boolean check - can be more sophisticated in the future commit e2826e3c1693ffedbecc3bd27f39a7e0c92e9cae General cleanup, make sure update options is called appropriately commit 970b0d2573fc18976fdb1434cc9beabe6e6d362d fixing early exit upon rerooting. commit 92f7629326e589613ced57ff09e2641c288101ae Slightly better wording commit a4e41447ef4fa257c6c86619d62c9369b3643ac3 Add files to gitignore commit dede5f56424b730dd99b98bfa65e4f10f79acbab Additional tweaks for scons commit b9de64a375f37b599745b0b4d965df0923a196db activating RMSD screener for protein stepwise monte carlo. commit 24a55ffb6b7cac11dbeeadc0a787b2b0a1ba9cf0 Run update_options for every build. commit 368fabcca1840c61153409f3b8f304bbadc4a075 Updating membrane conformation info to instantiate info object from within commit b58198765c7f6962bd8281d900af184c6af084ae use simple code for cdr-antigen contacts since the graph is not giving correct results 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 8d843094fb612c3f77beb75cf285badbdb715ba0 Add skip_redundant option to ConstraintPreparer. commit f44bb103da6e40c3329c21e9fa4cf195f928e659 Merging crumb revisions of MembraneInfo and Conformation with updated and fixed mac clang build on ninja commit 44423dd1a1e9f6d6d782d4c94f8fbe793bee795c Updating membrane info classes to take ft references 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 f0c5af24bb1107b24ae05016a76215edf62a2add 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 087034bf4b41cb3061b9b7852943b0e07c9f5c53 Adding fix for silent file linking error in clang 6.1 commit 337b31e48a19485fff6e0eb0a14fed7f0fa53fd4 Merging branch master with Rebecca's local master commit e04b0016b499e1bb3738fc02d0c8bf841a8f86b1 merge changes on cyclic peptide commit 86dac80684639499ac9fb192ad59d6a10721dce8 minor tweaks to interface plots commit ca85b6f5ad32b7e5361acec3fd6de3a9fa22420d Updating options.settings for clang version 5.1 commit b8d1b11ac6c35e3894c841a7892f7fb57522fbcf merge master: Updating symmetryinfo so all information is saved/restored when reading/writing to a silent file. commit 72bbfaa1277a9e8786231462d184a01bfb91697f Adding explicit data member for storing a membrane fold tree topology at initialization 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 e32f05188fa12b892e7905e5f463aca3355ffff4 Adjusting membrane info pilot app, fixing reference copying so the class runs cleanly and sets cleanly in both membrane info and conformation commit 4d3debaa11ffebc300d695bf474555ee73e94105 turning off an early exit from atr/rep -- can fix later by virtualizing amide hydrogen and carbonyl oxygen at takeoff atoms. 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 959b78c54be83f5b157d1988000be351b8541b30 adding options to prepack and check for contact/clash in protein packer. bug fixes to virtual_side_chain stuff, including patch application to HIS_D, which required creating a TAUTOMER property to select HIS vs. HIS_D. Commented out some patches (will hopefully catch these via integration tests before merge). commit 43af17ba774c4fa41bf499854c3892c754abaf7c more interface features plots edits commit 60420d2f7745b1bc990df4416675947acffa4e91 Merging master into cycpep/collab to get my updates to metalloproteins and noncanonical amino acids. commit 377e40b82109d47c4553d598410864817fe0f4fc updates to interface plots commit 4b371d39a72790e2ca5c0dce9510fda45c01d74b Updating pilot app commit 902c58ce4b8fa9a8683d4cae076e3378bc42d19e Removing const-ness of conformaiton in with the membrane info constructor commit 42ec40e0dceef12a8000e7e275a1d5bb17fc3101 add cdr aromatics plots, begin adding contact plots 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 88736e454bd7308480abb38a709544520fdb0d0f updating unit testing suite and adding pilot app for testing" 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 74a8ebd7183aa90d326bf835144367ecb6d0aabb resetting default bonus for free side-chain chi from -1.0 to -0.5 -- otherwise all side-chains get virtualized. commit 9217c15d814e098a10907d1956ecd8898ef53a88 adding option -allow_virtual_side_chain and score term free_side_chain so that packer can virtualize side-chains and get a bonus -- part stepwise strategy. 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 f830b801df1a4389f349c9b6354e5fafa82134fe some code cleanup, reduction in verbiage. commit fcca49aff7a6ede52c2ef7858458abe094001659 restoring -filter_native_big_bins option in SWM 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 1fcb68a87c476df967a21f9126798bc3c6bf4f1e update to integration tests to reflect new database organization of .wts files for SWA/SWM commit f46084ea18a52d125766a2363b4b33e21d74a08d update standard res_level_energy ref by +1.0 to favor flickering of protein residues in SWM, rather than irreversible instantiation commit 7eaa9eff4216f82272972149ceaec2cfa9000506 cleanup of weights names in apps; allowing input of num_pose_minimize into swm for proteins. minor bug fixes commit e0ab7602f0eb37733136c863098429b5aa034426 eliminating space in app name that was throwing off cleanup scripts 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 800c62b3714b6ca07b180bfc289ff7d092570435 cleanup of ResidueTypeSet in preparation for "just-in-time" patch initialization, which will allow RNA/protein stuff to be unified with no cost in speed to RNA applications. commit be5a06d65baec4620cdfa05d4d9eed9f04428b58 first step in removing BinaryRNASilentStruct in favor of generic BinarySilentStruct -- checked that extract_pdbs still works. commit 0f7ebab6fc2c2309958b57a8b25681051594f2c4 Warnings Removal: still another commit 21689269dc845498b471bcf77044276794a8d232 Warnings Removal: 2 more commit 013870ee61f10f5014f00d2f747716cee7d28c8a Warnings Removal: 3 more string-plus-ints commit 91a080e55198b435e1888ddd1dd0ab6844931b91 Adding const context to getter member functions 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 4233f05ec1cb974e7507305ec968fd26ff9c552f Adding tag in output info of pairwise_fa_energy commit 1bf13f952aaabe5301d39997569f04e2ad4ded3e Warnings Removal: yet another commit 02e9b74a698fd3e00278dab349a7b82d61b763ea Warnings Removal: and another commit ce8c59f9cb774b19dab2ddf7764ccc872e4c1950 Warnings Removal: another string-plus-int