commit 60692f22cd7e6e2c2e4b925bc78f09fdd08bfcff Merge: c3ea3ac 69af9e5 Date: Fri Jan 15 14:34:50 2016 -0600 Merge pull request #1026 from RosettaCommons/roccomoretti/graphviz Graphviz output for ResidueTypes Just a little utility function I had lying around which allows you to create a Graphviz DOT file from the connectivity of a ResidueType. New, unused functionality (aside from unit test) -- no test changes expected. commit c3ea3ac52ab07d0767084bd88c6626d4550a72da Merge: e3cacdb 21032de Date: Thu Jan 14 13:04:30 2016 -0700 Merge pull request #1023 from RosettaCommons/sergey/f PyRosetta: Adding extra ‘notebook’ option to rosetta.init to allow redirect of Rosetta Tracer output to Python Jupyter notebook logs commit e3cacdb086e922d724bbecc51e79f5d38ccd8045 Merge: 52d173b ff7ef19 Date: Wed Jan 13 14:19:58 2016 -0800 Merge pull request #1018 from RosettaCommons/vmullig/fix_valgrind_unit_issue Fixes source/destination overlap error with Valgrind in ParamsDataStorageTests unit tests. I was sloppy with a sprintf() statement in the unit test. commit 52d173bb0f823b30c009662efb2eb7e635176fc4 Merge: a121de3 5e499ac Date: Wed Jan 13 12:14:02 2016 -0800 Merge pull request #1021 from RosettaCommons/dimaio/hybridize_realign_fix Small bugfix for the auto-realign code in hybridize commit a121de3d7cd75a927bff74a0a91be5178f240061 Merge: 0f93ec7 4d73ec8 Date: Wed Jan 13 14:30:41 2016 -0500 Merge pull request #1019 from RosettaCommons/lqtza/pten_floppy_tail Lqtza/pten floppy tail commit 0f93ec718f7c095ab2385ecef9ed9f7cdd8535a2 Merge: 6e6b72b a2cd3fd Date: Tue Jan 12 19:02:28 2016 -0800 Merge pull request #1017 from RosettaCommons/revert-1016-revert-1015-vmullig/hbond_resselect Adding support for ResidueSelectors to the HbondsToResidueFilter (reverting the reversion) Reverts RosettaCommons/main#1016 (which reverted the premature merge) If the user provides a ResidueSelector, the filter will only count hydrogen bonds between the specified residue and residues in the selection. In the absence of a ResidueSelector, the old behaviour (counting hydrogen bonds between the specified residue and all pose residues) will be preserved. Tasks: - Add ResidueSelectorCOP to HbondsToResidueFilter class private member variables. - Parse ResidueSelector in parse_my_tag() function. - Add ResidueSelector functionality in apply() function. - Integration test. - Documentation. commit 6e6b72b1081df0a9faca04b2cdbfb6f1ce85b001 Merge: c7d7f00 8629fba Date: Tue Jan 12 18:14:09 2016 -0800 Merge pull request #1016 from RosettaCommons/revert-1015-vmullig/hbond_resselect Revert "Adding support for ResidueSelectors to the HbondsToResidueFilter." Accidentally merged prematurely, prior to testing and whatnot. Reverting. commit c7d7f003a39a290212deca22b6eb0d8f21cc6fc9 Merge: f513f38 31d91a5 Date: Tue Jan 12 18:08:43 2016 -0800 Merge pull request #1015 from RosettaCommons/vmullig/hbond_resselect Adding support for ResidueSelectors to the HbondsToResidueFilter. commit f513f38d6ab7fed769d451cbb4378a4f91730866 Merge: b553803 58c881b Date: Mon Jan 11 14:16:18 2016 -0800 Merge pull request #1013 from RosettaCommons/tlinsky/residue_count_selector Add residue_selector option to residuecountfilter commit b553803a8c759c3d4404857a40185b4e805f65c0 Date: Mon Jan 11 10:41:04 2016 -0800 make the creation of the template files sorted as to prevent stochastic diffs in the logs that can show up on the test server. commit ba90bd9bd45755e0f00a3e48c5bbfa470428eeb8 Merge: ed80362 fb834ed Date: Sat Jan 9 17:09:32 2016 -0500 Merge pull request #1011 from RosettaCommons/rfalford12/fix_cppcheck_errors Fix Cppcheck errors commit ed8036212f606d76138681a6e3a39994b219890c Merge: 16ccaf0 3d886c5 Date: Fri Jan 8 14:52:09 2016 -0800 Merge pull request #951 from RosettaCommons/vmullig/disulf_pep Add support for disulfides to the simple_cycpep_predict app This will add simple support for disulfides to the simple_cycpep_predict app. If the -require_disulfides flag is used, then the app will require that solutions have disulfide bonds between all residues of types that can form disulfide bonds. Every set of pairwise disulfide combinations will be tried. Tasks: - Add flags to the options system for requiring disulfides, and for cutoff energies. - Have these flags actually do something in the app. - Add a mover for disulfide construction and checking (trying all permutations or just a user-defined connectivity). - apply() function. - parse_my_tag() function. - Support for ResidueSelectors. - Support for odd numbers of disulfide-forming residues + integration test. - Integration test. - Documentation. - Handle the special case of an odd number of disulfide-forming residues OR throw an error (for now). - Add disulfide construction and checking to the parsed protocol called for every closure solution. - Add a post-relaxation check for disulfide energy. - The depermute() function needs to preserve disulfide linkages. - Test with Gaurav's test cases. - Update documentation. Put off to another pull request: x Add a unit test for symmetric glycine scoring when the -symmetric_gly_tables flag is used. x Debug asymmetries in gly scoring that currently persist. x Add a way for users to specify a desired disulfide connectivity. @gbhardwaj commit 16ccaf05d323b7398d8cce6330ba3c84afbd0510 Merge: 01b8426 c1b1993 Date: Fri Jan 8 14:50:02 2016 -0800 Merge pull request #1012 from RosettaCommons/kalekundert/explicit-python2 Specify ``python2.7`` instead of ``python2`` commit 01b8426868ea3787aa343316acb87a3222d91b07 Merge: ec03b3c 3aee270 Date: Fri Jan 8 00:54:10 2016 -0800 Merge pull request #1010 from RosettaCommons/vmullig/graphics_issue Fix an issue with BOINC graphics The graphics app incorrectly defaults to sphere mode if it initializes itself before the shared memory object created by the worker app has been initialized fully. This addresses that. Tasks: - Add a wait_for_shared_memory_initialization() function that halts the graphics app until the worker app has finished initializing shared memory. commit ec03b3c1ac1360e87e3e4cbd6694b5b27af9e073 Merge: a862e73 462dff7 Date: Thu Jan 7 15:22:24 2016 -0800 Merge pull request #1008 from RosettaCommons/vmullig/extrares_issue Tweaking 4-phenyl-phenylalanine.params to use tyrosine rotamer library. (Actually, added a second params file, with three-letter code BIF, that uses the Tyr rotamer library. B03 still uses the B03 rotamer library.) No test changes expected. commit a862e7328b21bf2f85c9506ea919c3f5350ff18b Date: Thu Jan 7 15:05:22 2016 -0800 Fixed a Rosetta@home specific issue where jobs with errors continue on rather than exiting and calling boinc_exit(). This should only affect the boinc build. commit c101b65d80f7cf8d773b155d5d49335cf0c0f7ee Merge: 4de00d2 862a5d4 Date: Thu Jan 7 08:40:23 2016 -0800 Merge pull request #1001 from RosettaCommons/rhiju/solve_challenges Rhiju/solve challenges + the few integration test changes are expected (from introduction of BlockStack patches or changes to behavior o PartitionContactScreener in stepwise) + srlz unit tests were broken previously. commit 4de00d2060687a7216bc62c2182b5394d0f068ea Merge: 9a1bc9d 4aeff26 Date: Thu Jan 7 10:36:17 2016 -0500 Merge pull request #1004 from RosettaCommons/aleaverfay/remove_multithread_jd2_job_dist Scrapping attempted multithreaded job distributor for JD2 JD2 cannot accommodate a multithreaded job distributor. This feature will come online with JD3. Hopefully, this fixes the multithreaded unit tests. commit 9a1bc9de83d4caa92a8419bcdeb950bdaacb88f6 Merge: 9ef22c5 003454e Date: Wed Jan 6 20:48:57 2016 -0500 Merge pull request #1006 from RosettaCommons/kalekundert/explicit-python2 Explicitly call python2 when necessary. commit 9ef22c5f0511a23e76792d9c5f965d685da27c9d Merge: 9b0242e 77ad7e4 Date: Tue Jan 5 16:52:19 2016 -0500 Merge pull request #1005 from RosettaCommons/rfalford12/revise_memb_etable Similar to the LK term for soluble proteins, the Lazaridis membrane solvation energy relies on an Etable. The membrane etable, called MembEtable, was originally implemented as a copy of Etable, creating several unused variables and redundant declarations of constants (amonst other challenges). I'm working on a new membrane solvation energy that requires modifying this class, so now is a good time for this refactoring. In this version, MembEtable is a subclass of Etable (previously, MembEtable inherited from Etable but never took advantage of this hierarchy). Below is a summary of the adjustments: No duplicate private members (constants) between Etable and MembEtable Private members of Etable are accessed in MembEtable through getters (added necessary getters) Customizable functions (e.g. solv1, dsolv1) are now virtual in Etable Removed extraneous comments, commented out blocks of code I also cleaned up the Etable - several of the private member variables were named without a trailing underscore which collides when you declare an accessor for it. Unit & Integration Test Changes: = Cpp Check errors complain 3D Farrays not initialized in the constructor, really they are just not initialized in the initialization list but in the body of the constructor = Integration & profile test failures existed before this pull request commit 9b0242e9a113382e6bb0b46260d4bad7a5840895 Merge: 89eeeb1 2d4a7f9 Date: Thu Dec 31 10:19:31 2015 -0500 Merge pull request #998 from RosettaCommons/tlinsky/tomponents Update to latest denovo classes commit 89eeeb16dc773b946102754b2475fcf0a367e3c5 Merge: 387119e 4963578 Date: Tue Dec 29 17:04:40 2015 -0800 Merge pull request #999 from RosettaCommons/rhiju/make_new_move_selector_default Rhiju/make new_move_selector default for stepwise + Includes several (but not quite all) bugfixes for -new_move_selector running with `-submotif_moves`. will put that in a separate pull request, if we think it should be default. + integration tests that change are swm (stepwise monte carlo). + saw a broken windows pyrosetta build on test server (Haraku), but then requeued and it compiled fine. commit 387119e02ffd7fa52f287fbbc49a621a10bfc7d1 Date: Mon Dec 28 11:20:29 2015 -0800 Add a new pilot app dna_motif_matcher commit 22741caa2282bbdbc87ee772a76560a53e34d87e Date: Fri Dec 25 17:05:07 2015 -0500 Updating tests states in benchmark scripts commit 2563893ddb3f658d057a30ea39659715d09c95cd Merge: cca2c09 9be0d41 Date: Fri Dec 25 09:30:50 2015 -0800 Merge pull request #980 from RosettaCommons/rhiju/unit_test_mania Rhiju/unit test mania redux Finally getting all these unit tests commited! No changes to regression tests except unstable ones; the .srlz/cxx11thread build was broken before. commit cca2c0985bc7701ae911a03f9cd7f5c1f655a87c Merge: 80a914f 5f6203b Date: Thu Dec 24 13:57:38 2015 -0800 Merge pull request #995 from RosettaCommons/vmullig/iterated_linmin Add a simple gradient-descent minimization algorithm The Hessian approximations in Rosetta really trip me up when I'm trying to use the minimizer for anything other than minimizing energy in torsion space. This pull request adds a simple Hessian-free iterative gradient descent algorithm for the minimizer (basically, iterated linmin calls with a convergence check after each iteration). Simple gradient descent (first-derivative based minimization) is generally less efficient than approaches that use the Hessian or an approximation thereof (first- and second-derivative based minimization), but there is no guarantee that the DFP or LBFGS approximations of the Hessian matrix work for all functions -- indeed they are poor approximations in some cases that mathematicians have characterized but the rest of us don't think about. Having the option of doing plain, vanilla gradient descent is therefore useful, at least for checking whether it's the Hessian approximation that's tripping up a minimization protocol. Tasks: - Add linmin_iterated and linmin_iterated_atol minimization flavours. - Add a function to do iterated gradient descent with convergence check. - Add a unit test. - Update documentation. - Add new minimization type to options_rosetta.py in branch aleaverfay/lbfgs_as_default (pull request #327). I'd suggest that we start using linmin_iterated or linmin_iterated_atol in minimizer and FastRelax benchmarks, sort of as our negative control (minimization with no Hessian approximation). It SHOULD converge more slowly (i.e. with more iterations) than dfpmin or lbfgs. If anything else converges more slowly, though, that should be a big red flag for that other algorithm. commit 80a914fd311b46d519a7985a1ffac4f783d756fe Merge: 71551be 04c4910 Date: Thu Dec 24 11:00:38 2015 -0800 Merge pull request #992 from RosettaCommons/rhiju/fix_stepwise_packer_interface_res_determination interface residues in StepWisePacker swa/swm integration tests are expected -- slightly worse energies due to residues far from interface not getting packed. commit 71551be248d12104b6d724ebcbe012b69875f659 Merge: 47a12fd 2f6ba02 Date: Wed Dec 23 15:36:32 2015 -0800 Merge pull request #975 from RosettaCommons/rhiju/check_new_move_selector Rhiju/check new move selector + integration test for swm protein loop sampler changes, apparently due to change in random number generated. other tests are 'usual' ones that change in different hardware setups. + cppcheck and linux .srlz.unit remain broken; former was just fixed by andrew i think. commit 47a12fd75243ae6bb6d4ec7784cf4617a177fab0 Merge: a82b74f 8aababe Date: Wed Dec 23 09:11:38 2015 -0500 Merge pull request #993 from RosettaCommons/aleaverfay/make_assignment_ops_return_nonconst_refs Fixing ~60 assignment operators that returned const-references Assignment operators in c++ are, by convention, supposed to return non-const references to the underlying type. All of the assignment operators I have written up until now have returned const-references, however. My bad. This is, to my surprise, a bad thing. It violates the "principle of least surprise" (not to be confused with the principle of least surprise for Andrew) in making a class behave differently from a primitive. In C++ it's legal to take two ints, x and y and do this: ( x = y )++; This commit will fix the broken cppcheck test, and removes many complaints (that don't register as failures) that cppcheck makes about our assignment operators. commit a82b74fd724be57cc91bcc8001e58d3a5b3bf01f Merge: 7b2b98c 6335713 Date: Wed Dec 23 09:06:41 2015 -0500 Merge pull request #983 from RosettaCommons/aleaverfay/document_xsd_classes Adding promised documentation to the XML-schema-generation classes. Also documenting the ResidueSelector XSD generation code. Finally, removing "return" statements from several residue-selector-creator's::provide_selector_xsd functions that were legacy from an early implementation. commit 7b2b98c2bc17fc0dc171ecb54fdd3a30a0724f33 Date: Wed Dec 23 01:28:19 2015 -0800 Added two options: 1) "rsd_wdw_to_refine" to control the size of residue-window to refine and 2) "score_threshold" to control the score cutoff of error predictors (rama and geometry) commit abf9b0ff60204c51f9ecfea774e39d9aeae3a971 Date: Tue Dec 22 12:17:15 2015 -0800 Very small parameter change in localrelax. Extremely minor change so committing directly. commit ccb835772a34c87cc2b129028d820c0e92827562 Merge: 39747f9 5120e8a Date: Tue Dec 22 08:58:45 2015 -0800 Merge pull request #994 from RosettaCommons/xtal_min_fix Updates/bugfixes to crystal refinement code commit 39747f9195012449960a6b4eb333a9de44dec465 Merge: 0867034 2c33ba0 Date: Mon Dec 21 22:37:01 2015 -0800 Merge pull request #967 from RosettaCommons/tlinsky/tomponents Updates/bugfixes to denovo design classes commit 08670349f30cc5793d892b2b34c73a24f18226bc Merge: 6abf325 492dc12 Date: Mon Dec 21 22:36:15 2015 -0800 Merge pull request #981 from RosettaCommons/tlinsky/geometryfilter_selector Add residue selector option to geometry filter, also fix uninitialized variables commit 6abf325dea10afed573ba40b7c067a2cc0822c35 Merge: be9e67f 0725096 Date: Mon Dec 21 22:35:09 2015 -0800 Merge pull request #970 from RosettaCommons/tlinsky/checkcore_filter Add option to CoreResiduesPerElement filter to specify core threshold commit be9e67f8e613d29eaedbc3b8d1f850466f69920c Merge: 9db7e6f 5f2f29a Date: Mon Dec 21 19:55:00 2015 -0800 Merge pull request #977 from RosettaCommons/rhiju/stepwise_fixes_for_kalli Rhiju/stepwise fixes for kalli + tests that change are expected... + cppcheck failure occurs in master and seems to date back to @aleaverfay commit. commit 9db7e6fe91f3977f9023f46bcf96c361baafd9c1 Date: Mon Dec 21 18:10:31 2015 -0600 Add -fno-omit-frame-pointer to release_debug build. Optimizations typically enable -fomit-frame-pointer, which makes things like tracebacks in debugging less relyable. If you have symbols enabled, you probably want that traceback information, so let's reenable it for the release_debug builds. commit 4b0926fafdf9c1b5959408706af968750510ce85 Merge: 0958823 011c5ea Date: Mon Dec 21 12:27:13 2015 -0500 Merge pull request #978 from RosettaCommons/JWLabonte/sugars/rotamers Carbohydrates: packing fixes/improvements This merge will correct a major issue with packing residues that are glycosylated -- namely, that should never have been happening to begin with. This merge will also prevent packing of virtual atoms on carbohydrate residues, something that was a huge waste of time and memory. All unit tests pass. carbohydrates and vancomycin unit test changes expected. commit 095882396a78d9042d12d9e0db73088897a3fda3 Merge: 0caa9cf e9e3a5d Date: Mon Dec 21 10:15:39 2015 -0600 Merge pull request #991 from RosettaCommons/roccomoretti/cppcheck_bugfix Fixes to the cppcheck script for race conditions and other bugs. Also, some fixes I had kicking around for some of the historical issues. commit 0caa9cf6837aa7f98d0eb4ae39a404d70e372a22 Merge: 91b6208 59b4212 Date: Mon Dec 21 10:02:10 2015 -0600 Merge pull request #835 from RosettaCommons/roccomoretti/external_build A scheme for building non-header only external libraries. Basically, you just add your external library to the main/source/external/ directory, make a conventionally formatted *.external.settings file in the same directory, and then enable the external library by adding it to the main/source/project.settings file. Scons and CMake should take care of the rest (including turning off warnings for the external library). If you have complex compilation requirements, that's also supported somewhat, but you have to muck around with custom Sconscript.external.* files, and hand convert for CMake. Currently no libraries are set up to use this scheme, but may be included later. commit 91b620841e1a396271d525e23487aec7b82eac9b Merge: 44ad285 33b5dc0 Date: Sun Dec 20 23:58:27 2015 -0800 Merge pull request #987 from RosettaCommons/vmullig/smallmover_resselector Adding a ResidueSelector input to BackboneMover. For @gbhardwaj. Tasks: - Add a ResidueSelectorCOP to the private member data. - Add setters. - Add parsing. - Add logic in apply() function. - Update documentation. - Integration test. commit 44ad2854977039c083f2955c1bd6e16c4c5d92ed Merge: 29d47c9 53a10a6 Date: Sun Dec 20 11:14:55 2015 -0800 Merge pull request #990 from RosettaCommons/rhiju/cutpoint_closed_preserve_suite_torsions preservation of suite torsions at new cutpoint closed in stepwise 'internal moves' only tests that change are the 'usual' ones susceptible to numerical instability. cppcheck test is broken, but it has been broken in master for a bit. commit 29d47c943689abb7017c87b206a2dfc00e55c13f Merge: af525b7 7004be8 Date: Sun Dec 20 12:54:35 2015 -0600 Merge pull request #985 from RosettaCommons/roccomoretti/user_database Implement Jonathan Sheehan's suggestion of caching the Dunbrack library in the user's home directory. Behavior in the standard case should be the same - the Dunbrack binary is read/written to the database directory. The big change is that when that directory is not writable, then the binary will be cached under the user's home directory. (This should be transparent for PyRosetta users.) Priority of locations for binary search (if any of these locations is not set or cannot be written to, it will move on to the next one.): * Directory specified with -in::path::database_cache_dir option * Directory specified with ROSETTA3_DBCACHE environment variable * The same database directory from which the ASCII files were/would be read * A .rosetta/database/ directory in the user's home directory, determined from the first non-empty setting of * The XDG_CONFIG_HOME environment variable * The HOME environment variable * The home directory specified in the POSIX password structure information. If none of these are writable, then it will skip database file writing. People who are working with multiple versions of the Dunbrack library may need to be slightly careful, as the location where the binary is read/written to may be different from where you expect. Use the validate_database application to check the cached binary, if you're seeing funky results. commit af525b7a94b5f13643955c6d5b360bf9d5a53b91 Merge: ea634ea fcce728 Date: Sat Dec 19 12:10:40 2015 -0500 Merge pull request #982 from RosettaCommons/rfalford12/finish_removing_conf_from_memInfo Rfalford12/finish removing conf from mem info Andrew's manual serialization pull request modifies membrane info such that Conformation& is no longer a data member. I'm just finishing this up by changing the arguments to some constructors to make this more clear (also makes my next pull request cleaner) commit ea634ea336ec98ef27af70f0b593f0cb10005e14 Date: Sat Dec 19 00:30:17 2015 -0800 Adding an "residues_to_include" option to the CartesianSampler mover eg. residues_to_include="1-1612" lets CartesianSampler know these are residues to refine. Unlike the option "residues=" which can only be used under "user"mode, "residues_to_include" can designate any residues in all the residue-selection modes (eg. auto, density, rama). This option can be useful for users to specify additional residues while using automatic error predictors to select residues to refine. commit bf37008ba55ecc97ce1ce90a892fe02495a0d43a Merge: fbf61e9 88b44c0 Date: Fri Dec 18 13:47:50 2015 -0800 merged changes commit fbf61e9c5b6fec9e27c35d39e6905ba9a541540d Date: Fri Dec 18 13:45:51 2015 -0800 changed the function call in Scotts merge from yesterday in SymmetryInfo resize_asu to num_total_residues_with_pseudo() as it should be commit 17c50ba23210417eb560d2e3a1365dfbc6d2435f Date: Thu Dec 17 20:29:53 2015 -0800 Minor updates to general_class code_templates (include refcount for general class hh template, fix class include hh for general class cc template.). Make no default type argument for generator - it was too easy to accidently create movers. integration test changes expected for code_template_tests_src. commit 6a8adb1ad10cd01bb5725707660c5d461b6cb470 Merge: 6b03955 611e29b Date: Thu Dec 17 20:19:29 2015 -0800 merge master into branch commit 6b039554c3b5a6ccfc5907d4485581366b40ba9b Merge: ec284b9 31e4cdb Date: Thu Dec 17 20:18:39 2015 -0800 pull code template branch commit ec284b9f94177b589030f96abc3b8da7d6dfd632 Date: Sat Dec 12 15:03:17 2015 -0800 fix code_templates_test_src integration test. Yay for integration tests. commit cfaf04c67218fe04c35f9da3d44a65adc5ad901f Merge: d4b043d 90c1107 Date: Sat Dec 12 12:39:23 2015 -0800 Merge pull request #971 from RosettaCommons/rhiju/stepwise_fixes_for_kalli Rhiju/stepwise fixes for kalli only tests that change are stepwise/erraser -- expected, since some post-packing 2'-OH torsions were not being copied appropriate before, but are now. commit d4b043d546c5130ad74fe2ffe5d4d769469e947c Date: Fri Dec 11 15:20:05 2015 -0800 Small bugfix to rotational search in de novo density commit 289207c4892421ef400139d50d0ef69bafba12d5 Date: Fri Dec 11 12:17:11 2015 -0800 remove my name and email from forward header stub for code templates. Thanks for finding this Doug commit b6a7fd0ce3d530fbf35a52965b15a9edff53769b Merge: fa3c14c 8a6bcba Date: Fri Dec 11 11:39:08 2015 -0800 Merge pull request #910 from RosettaCommons/jadolfbr/code_templates Jadolfbr/code templates This merge adds a directory in source and associated scripts for generating Rosetta classes and util files from stub-like templates. Two other scripts are added for unit tests and JD2 public and pilot applications. It uses a simple replacement syntax with python lambda functions that should be easy to add to. Integration tests for these scripts have been added, and each subtype is tested. See README.md in the directory for more. Implemented template types: General Rosetta Class Mover Task Operation Residue Selector abstract class util Unit Test Pilot/Public App commit fa3c14cd717bb943dd4d2f6e4daf8f7e94ea9100 Merge: 413b663 8ee59fc Date: Fri Dec 11 07:11:47 2015 -0800 Merge pull request #966 from RosettaCommons/tlinsky/tlinsky/helixkink Add secstruct option to helixkinkfilter, fix bug commit 413b66359998f504ab9d8beb1a45bd21809edb43 Merge: 776e287 db08466 Date: Fri Dec 11 05:50:56 2015 -0500 Merge pull request #969 from RosettaCommons/JWLabonte/sugars/input Bug Fix: I was stupidly accessing map data before checking if they existed. All unit tests pass. carbohydrates integration test changes expected, because I had also added output of pdbs to the tests on this branch commit 776e287b8be8d13992f612e956d76c97ae5bdd02 Merge: 09c7cdf 3ef9426 Date: Wed Dec 9 19:15:09 2015 -0800 Merge pull request #965 from RosettaCommons/vmullig/tj_bundle_issue Fixing a minor problem in MakeBundle, identified by TJ TJ discovered that reading my documentation and following the instructions produces a cryptic failure. I'm fixing this. - Adding a runtime_assert and error message if z1=0 to generate_atom_positions() in the helical bundle code. - Updating documentation to make it clear that z1 and omega1 are not options that the user should normally set manually, unless he/she really knows what he/she is doing. No unit or integration test changes expected. @tjbrunette commit 09c7cdf08d4ba8ecf486b1c52a7e58fcc06a9301 Merge: db86b0c c5eb0a7 Date: Wed Dec 9 17:10:19 2015 -0800 Merge pull request #936 from RosettaCommons/calebgeniesse/SubMotifInfo Calebgeniesse/sub motif info [only tests that fail are the ones that keep having numerical instabilities.] commit db86b0c3f9589e64ece25b5c0617c05df05c1f9a Merge: d741e95 64a9877 Date: Wed Dec 9 09:26:29 2015 -0800 Merge pull request #957 from RosettaCommons/rhiju/farna_output_resnum_chain handle output of chain along with resnum in FARFAR. commit d741e9540f12e66e04bf2fd7b238e014f3c04cbc Date: Tue Dec 8 16:33:20 2015 -0800 Bugfix in low-resolution desnity scoring. commit a73b1f4d14a9fe3b970d4e178fdf5fe962a04bdc Merge: bf6e248 217d2dd Date: Tue Dec 8 10:52:37 2015 -0800 Merge pull request #959 from RosettaCommons/rhiju/remove_time_in_stepwise_lores_test HOTFIX: remove time from stepwise_lores integration test. commit bf6e248381e50639441abc7248fbdc3c017548e0 Merge: c0acc46 b236cc59 Date: Tue Dec 8 09:36:23 2015 -0500 Merge pull request #960 from RosettaCommons/lqtza/fix_xcode_make_project fixing xcode project script which pull request #672 broke commit c0acc462593441ebfd0f66658cf279ba1f073cab Date: Mon Dec 7 18:44:25 2015 -0800 add cen_std_smooth weights that have terms replaced by Frank Dimaios smooth centroid stats. commit 2c7cf19f8d2656161935b445dc8b48a87f3e7290 Date: Sun Dec 6 16:16:20 2015 -0500 Adding generation timestamps to HTML docs commit 62e859ea30b549944fa68fb67c84ea8d6ca7c7ee Date: Sun Dec 6 00:25:49 2015 -0500 Switching from GIF to PNG format for dot files in devel documentation commit 5a674b7a01973f2f8e91186ef9f4384a13773662 Merge: f92dafe b85a1a5 Date: Sat Dec 5 17:44:58 2015 -0800 Merge pull request #950 from RosettaCommons/rhiju/farna_renovation Rhiju/farna renovation A few integration tests change -- all are traceable to small numerical instabilities in stepwise apps, which are compiled within the same library as the farna stuff (protocols.d_5). commit f92dafe39386dd20ccdea1ce2ded7dac4f6ee498 Date: Fri Dec 4 15:54:39 2015 -0500 Adding Doxyfile_release.* files and restore source in docs in devel version commit 87db6810d459cc808c6325d7f13e2b7dc324a73b Merge: 94850a7 cc2a7c0 Date: Thu Dec 3 18:09:47 2015 -0800 Merge pull request #940 from RosettaCommons/tlinsky/ss_selector_dssp Add always_use_dssp option to SecondaryStructure residue selector commit 94850a779f9fd004b966ad4f71ef03a9c549fab9 Merge: f592c7d fe79d70 Date: Thu Dec 3 18:09:24 2015 -0800 Merge pull request #941 from RosettaCommons/tlinsky/tomponents Updates to make FoldGraph and StructureData more robust and reliable commit f592c7d1adf43d15cfa33abd0c78f3650b3d69bb Merge: 60eedc5 e3b14be Date: Thu Dec 3 08:15:46 2015 -0500 Merge pull request #949 from RosettaCommons/rfalford12/fix_multi_mem_bug Rfalford12/fix multi mem bug This pull request fixes a 'once feature now bug.' Initially, I wanted to prevent the user from incorporating multiple membrane residues due to ambiguity in tracking. Now, since a single MEM can be easily tracked and changed, it makes sense to allow multiple MEM residues. This change revises IO case 2 (AddMembraneMover lines 544-605) which deals with multiple MEM residues detected in AddMembraneMover: - Old Behavior: throw an exception as a result of multiple membrane residues - New Behavior: - If the user doesn't point to a MEM, accept the first MEM in sequence by default - If the user does point to a MEM, accept that MEM I also added two new unit tests to the AddMembraneMover test suite to cover these test cases commit 60eedc55ba4632597913b05838b5fcdeb112ea51 Merge: 537490d d644eeb Date: Thu Dec 3 02:33:13 2015 -0600 Merge pull request #952 from RosettaCommons/jkleman/fixing_option fixing option to get rid of InterfaceAnalyzer and constel issues commit 537490d3693828e086dbf23c34c0b067697520df Merge: 1614ade 42c3c19 Date: Thu Dec 3 00:05:41 2015 -0600 Merge pull request #947 from RosettaCommons/jkleman/jkleman/mp_updates4 Jkleman/jkleman/mp updates4 commit 1614adef52c8bd2b4f511331629fa252e1888389 Merge: baef709 009f5db Date: Wed Dec 2 16:47:35 2015 -0500 Porting Profile tests to Benchmark-2 commit baef709fa71ce2ee7faa75e9b49daef5373f9769 Merge: 1337f65 9c5780d Date: Tue Dec 1 15:44:58 2015 -0800 Merge pull request #946 from RosettaCommons/vmullig/peppredict_boinc3 Fix remaining issues with changes to BOINC so that David Kim can deploy Tasks: -- Make background and borders more intense. -- Fix border draw issue prior to first object draw. -- Ensure that non-peptide prediction protocols do not use spacefill by default. commit 1337f657ce8386febc1afa14d453acc7917587a2 Merge: b165807 2b0e584 Date: Tue Dec 1 09:10:21 2015 -0800 Merge pull request #924 from RosettaCommons/rhiju/bps_updates Rhiju/bps updates + needed for farna renovation (which will be a separate pull request), and for use of base pair steps in various RNA modeling applications in Das lab. + changes to stepwise integration tests appear to be due to a numerical instability induced by different compiler optimization of protocols.d_5 code. Evidence for this being a negligible instability is in .swa_rna_gagu_10_prepend_and_ccd_close (where a number z = 5.89095e-14 changes to z = 5.33868e-14). + unit test for -extra_res_fa failed, but is getting fixed in Andy's pull request #943. commit b1658077a18ea220b6b9d2e0e9a0b8d56c1239e3 Date: Mon Nov 30 18:18:20 2015 -0500 Fixing PyRosetta imports in namespace build commit 1eea45875f18b3f82291b419ef4caf0d324bfde5 Merge: 70caa46 75923ea Date: Mon Nov 30 11:29:27 2015 -0800 Merge pull request #943 from RosettaCommons/everyday847/fix_vikrams_test Fix Vikram's failing unit test commit 70caa46030a742ed26438015da5a80cc88fc6801 Merge: 43bee28 d076457 Date: Sat Nov 28 22:53:05 2015 -0800 Merge pull request #942 from RosettaCommons/everyday847/fix_jordans_residues Added ALPHA_AA and L_AA properties to Jordan's residues commit 43bee283738d9f249e7e200569a3b1f95dd6b097 Merge: 51fc2f9 72bad32 Date: Sat Nov 28 19:51:57 2015 -0800 Merge pull request #939 from RosettaCommons/vmullig/fix_cassie_issue Add a unit test illustrating a current issue with params files] This merge will create a FAILING unit test, deliberately. This is to illustrate a current bug: recent changes have broken backwards-compatibility with custom params files provided by users. It seems that the L_AA property is required for the test params file to work; without it, it cannot be used. Currently, reading a PDB file with a custom residue specified in a params file passed with the -extra_res_fa flag doesn't work if the params file doesn't specify D_AA or L_AA in its PROPERTIES line. I'll let those who are more familiar with the relevant code fix this; for now, this unit test will fail since this bug is unfixed. commit 51fc2f97d2dffef372bd94ebef231b4f93e3ba17 Merge: 1d13dac 4b10db8 Date: Sat Nov 28 15:05:20 2015 -0800 Merge pull request #938 from RosettaCommons/rhiju/unify_rna_pair_classes Rhiju/unify rna pair classes only tests that change are the new one *rna_denovo_base_pair_setup* which tests cis/trans specification of RNA base pairs. The other ones are the usual ones with instabilities, and change on mac or linux but not both. commit 1d13dac524130762d3ffc6a3de2235963a8f1bc2 Merge: 389c8fe 0dad065 Date: Fri Nov 27 15:50:43 2015 -0800 Merge pull request #672 from RosettaCommons/asford/packaged_bindings Update packaged_bindings to support current master. commit 389c8fe999b1936ddb02a88a4e0714e5ccf50279 Merge: 53ffa9b 34b53d6 Date: Fri Nov 27 07:49:46 2015 -0800 Merge pull request #937 from RosettaCommons/rhiju/cleanup_core_pose_rna_base_pair_class Rhiju/cleanup core pose rna base pair class all tests pass except for the 'usual' commit 53ffa9b675358d49936e0884d9822dc63468d8d5 Merge: c76a0b6 bbb3a16 Date: Wed Nov 25 15:20:36 2015 -0600 Merge pull request #849 from RosettaCommons/roccomoretti/pymol_obs Make the PyMolObserver a CacheableObserver. On certain systems there's an issue compiling because boost::bind via the observer system is expecting a raw pointer to the PyMolObserver, and it's being given an owning pointer. This works for boost shared pointers, but isn't robust for std::shared_ptr. The naive fix of simply giving things a raw pointer to the observer doesn't work, because AddPyMolObserver et al. doesn't keep around any reference to the newly created observer object, and if the PyRosetta-level user doesn't store the return value, the observer object gets garbage collected and subsequent observer notifications mean segfaults. To solve this, I changed the PyMolObserver into a CacheableObserver, and cache it in the pose which we're observing. One complication is that pose.clear() will remove any cached observers, resulting in the PyMolObserver being disconnected from the pose. The standard use cases look to be fixed, but it may be an issue in some other protocols. (Most notably, the PyMolObserver won't persist through loading a new PDB into the pose, as that calls pose.clear()) Another consequence is that not every snapshot from the previous runs are replicated in the new runs - but this should be mostly cosmetic. commit c76a0b656a5a18447bd3f836d0c6f206da24d5a2 Merge: da92aaa 33f3f8f Date: Tue Nov 24 20:17:42 2015 -0800 Merge pull request #926 from RosettaCommons/vmullig/improve_aacomp Add user-requested improvements to aa_composition score term As listed in issue #901, users have requested a number of new features to make the aa_composition score term useful for _de novo_ protein design. This pull request begins to implement some of these. Tasks: - [x] Unify the PENALTY_DEFINITION groups. Rather than having separate code for counting amino acid types or amino acids with certain properties, let all of these be defined together. - Details: I won't implement full Boolean logic at this point, since it's hard to do. Instead, residues will be counted in a given group if: (any TYPE matches) OR (((all PROPERTIES match) OR (any OR_PROPERTIES) OR (no TYPEs defined and no PROPERTIES defined AND no OR_PROPERTIES defined)) AND (no NOT_PROPERTIES match) AND (no NOT_TYPE matches)) - [x] Move AACompositionEnergy class to a new namespace, in which helper classes can be created. - [x] Update unit tests to reflect new namespace. - [x] Modify the AACompositionPropertiesSet class to store both types and properties. - [x] Modify the AACompositionPropertiesSet class for the Boolean logic, above. - [x] Add unit tests for the more complicated Boolean logic. - [x] Update documentation for this. - [x] Add clone() functionality to ResidueSelectors. - [x] Add an AACompositionConstraint for constraining sequences, analogous to geometric constraints. - [x] Store a selector in the object. - [x] Store a AACompositionEnergySetup object in the object. - [x] Have it initialize the AACompositionEnergySetup object from an input .comp file. - [x] Functions to hand off the AACompositionEnergySetup object to the score term at scoring time. - [x] Add a SequenceConstraint base class for the AACompositionConstraint. - [x] Modify the ConstraintSet container to accept SequenceConstraints. - [x] Add a mover to add sequence constraints that takes a .comp file and an optional ResidueSelector. - [x] Strip out extraneous stuff. - [x] parse_my_tag() should let the user set an input comp file and a selector. - [x] Create an AACompositionConstraint at parse time; clone it and add it to the pose at apply time. - [x] Documentation for this. - [x] Add a mover to clear sequence constraints. - [x] apply() function - [x] Documentation for this. - [x] Set the aa_composition score method to score using one or more global .comp files (if defined -- e.g. by the user, using a flag) AND one or more scorefunction-specific .comp files (if defined -- e.g. by the user, in RosettaScripts), AND .comp files attached to constraints stored in the pose (if defined -- e.g. by the user, in RosettaScripts). These last can be filtered by ResidueSelectors to allow the user to score sub-regions of a pose. - [x] AACompositionEnergy should store a vector of AACompositionEnergySetup objects: one from global settings and many from scorefunction setup (e.g. in RosettaScripts). - [x] Add a setup_residuearrayannealableenergy_for_packing() virtual function (that does nothing by default but which can be implemented by derived classes) to the ResidueArrayAnnealableEnergy that's the parent class for the AACompositionEnergy. - [x] At score time, the score term can construct a vector of AACompositionEnergySetup objects and a vector of ResidueSubset masks that it will use for scoring. These can be taken from its internally-stored vector and from the pose. Add a version of the calculate_energy() function that takes these two vectors. - [x] Have the finalize_total_energy() function generate the vectors and call the modified calculate_energy() function directly (for scoring). - [x] Implement a setup_residuearrayannealableenergy_for_packing() function that will create the vector of AACompositionEnergySetup objects, stored temporarily in the AACompositionEnergy object, and the vector of ResidueSubset masks. - [x] Have the default calculate_energy() function call the modified calculate_energy() function, passing it the cached vectors (for packing). - [x] Integration test for this (that also tests the above two movers). - [x] Documentation for this. - [x] Fix whitespace issue identified by Zibo. - [x] Look at bug identified by Peilong. - [x] Add the following properties to the PROPERTIES table and to params files: - [x] ALIPHATIC - [x] POSITIVE_CHARGE - [x] NEGATIVE_CHARGE The following tasks were grouped into pull request #928, which was merged before this pull request: - Move residue selectors to core.4 from core.3 so that constraints can use them. - I'm moving these out of core/pack (since they don't just control the packer) and into core/select/residue_selector/. - Resolve compile issues. - Resolve library levels problems. - Resolve any unit test problems. commit da92aaaff1ffbeee37b9e433b6417d9d42483710 Merge: bffd535 971d2a4 Date: Tue Nov 24 18:29:01 2015 -0800 Merge pull request #935 from RosettaCommons/revert-934-revert-929-dimaio/rama_prepro Fix clang unit test errors and re-merge "Dimaio/beta_nov15" commit bffd535c961b72323ee1d6dfb06dd27a6d53b9ac Merge: 2ba22af bc9b1a3 Date: Tue Nov 24 01:10:26 2015 -0800 Merge pull request #934 from RosettaCommons/revert-929-dimaio/rama_prepro Revert "Dimaio/beta_nov15" Reverts RosettaCommons/main#929 @fdimaio : I'm temporarily reverting the beta_nov15 merge until we can figure out why it breaks so many of the unit tests on Mac/clang. I'll also revert the later commit to master that altered the FACTS score test as part of this pull request, so that when you later revert this pull request, you'll get all of that back. Let's fix whatever is wrong with the clang unit tests in a branch, then revert this reversion to put everything back into master. commit 2ba22afa5ea094add9fb9c59b5780d2a5cc24b3c Date: Mon Nov 23 22:02:33 2015 -0800 Update broken facts scorefunction fingerprint commit 26bcf18109a8510a55d134b5beef3855b90eaa7b Merge: 247a535 9a4c94b Date: Mon Nov 23 19:14:29 2015 -0800 Merge pull request #933 from RosettaCommons/tlinsky/geomfilter_fix GeometryFilter now skips checking omega values across chain endings commit 247a53599494c20a51ba0fc5be17e1470bdf5099 Merge: e01f4b2 c160f03 Date: Mon Nov 23 18:09:43 2015 -0800 Merge pull request #929 from RosettaCommons/dimaio/rama_prepro This checkin adds the latest version of the beta energy function. It is enabled with the flag -beta_nov15. Also adding the flag -beta which will always point to the most recent energy function version. Details of the energy function are available on the doc wiki at https://www.rosettacommons.org/docs/wiki/Overview-of-Seattle-Group-energy-function-optimization-project (overview) and https://www.rosettacommons.org/docs/wiki/Updates-beta-nov15 (this specific update). 29 integration tests fail. Most are related to: a) cart_bonded scores changing due to typo being fixed in the default set (e.g. hybridization) b) cart_bonded tracer change (e.g. antibody_designer) c) the addition of new scoreterms cause the database_* and features* tests to fail d) debug output removed from code (fuzzy) e) bugfix to symmetric disulfidize (symm_disulfidize) The following integration tests change for other reasons: ddG_of_mutation enzdes flexpepdock inv_kin_lig_loop_design membrane_relax mp_relax mp_relax_w_ligand next_generation_KIC pocket_relax splice_* On closer inspection, all of them look to have very small score changes in their logs, which then propagate (perhaps the new score terms introduced changes the order in which scores are summed?) Additionally, there are changes to sweep_respair_energies that are difficult to trace (since its just a binary diff) but I suspect they are related to the above. commit e01f4b27a69eadea38820ca55ffdd21af740a9a4 Merge: de988fb 2f583d0 Date: Mon Nov 23 14:49:06 2015 -0800 Merge pull request #927 from RosettaCommons/jadolfbr/ab_graft_mover Add AntibodyCDRGrafter mover Overview ------------ This PR adds a mover for antibody grafting with settings I've used for antibody design with a RosettaScript implementation that can graft from file or save_pose_mover reference name. It is usually quite fast, and using both graft movers (the default) results in 100% graft closure as measured by bond lengths and angles at the connection points. Unit tests and Docs added. Documentation: --------------------- https://www.rosettacommons.org/docs/wiki/scripting_documentation/RosettaScripts/Movers/movers_pages/AntibodyCDRGrafter Test Changes: ------------------- No integration test changes expected other than cosmetic changes to antibody designer due to name change of AntibodyDesignModeler. Sample Script ------------------- ``` ``` commit de988fba04b8d739ddc2d9b691eb69e0c1dc0454 Merge: 153a005 d2d3933 Date: Mon Nov 23 10:26:22 2015 -0800 Merge pull request #923 from RosettaCommons/rhiju/seg_id_update Rhiju/seg id update In tests, removes SEGMENT_ID lines from the stepwise silent files, as expected. There are still the ~10 tests that always change due to numerical instabilities commit 153a0055353ac28b0e704dd3ffe835f0e898d5b0 Merge: b097fcb bb82e41 Date: Sun Nov 22 03:18:32 2015 -0800 Merge pull request #928 from RosettaCommons/vmullig/shuffle_libraries Move ResidueSelectors to core.3 from core.4, and to a new directory This is in anticipation of development work that will allow ResidueSelectors to be used as input to Constraints (and other things). I think it makes sense for ResidueSelectors to be moved away from the PackerTask machinery: though they can be used as input into a TaskOperation, they really should become the standard way of selecting residues for anything in Rosetta that takes a residue selection. Tasks: -- Move ResidueSelectors to core/select/residue_selectors. Everything associated with just selecting residues (or atoms, or anything else that we might one day be able to select), independent of the packer, will now live in core/select (core.3); packer-associated stuff will remain in core/pack (core.4). -- Keep the ClashBasedRepackShellSelector in core/pack/task/residue_selector, since it has core.4 dependencies. Create a Creator for this, since its base class (and the Creators list associated with the base class) is now in a different namespace. -- Move interface_vector_calculate from core/pack/task/operation/util to core/select/util, and from core.4 to core.3. This resolves library dependency issues and keeps selection logic separate from packer-specific logic. -- Move SelectResiduesByLayer from core/util to core/select/util, and from core.4 to core.3. This also resolves library dependency issues and helps to group selection logic in core/select. -- Ensure that all namespaces, all tracer names, and all unit tests are updated to reflect the new directory and namespace organization. All of this should result in cosmetic integration test changes resulting from changed namespaces (which is why I want it to be a separate pull request from the other stuff that I'm doing in pull request #926), but no actual functionality changes. commit b097fcb8f3673acc3669f14b2102abe0761ea76c Merge: 8bdf585 91897fe Date: Sat Nov 21 22:56:09 2015 -0800 Merge pull request #932 from RosettaCommons/vmullig/small_aacomp_bug Fixing a minor bug in AACompositionEnergySetup Fixing a minor bug in AACompositionEnergySetup that would affect the copying of PROPERTIES and NOT_PROPERTIES definitions when using the aa_composition score term. This will likely affect the bundlegridsampler_composition_energy integration test. This is minor enough that I'm going to merge it without testing it first. commit 8bdf585ea2f8146806f14866554a8f51288cef0d Merge: f2f6851 627f89a Date: Fri Nov 20 16:10:11 2015 -0800 Merge pull request #931 from RosettaCommons/revert-930-fix-exception Revert "Fix exception" commit f2f685117ae9ccaa4162177d6922363a29c81409 Merge: 2eb0da7 efa37f4 Date: Fri Nov 20 16:07:19 2015 -0800 Merge pull request #930 from CyrusBiotechnology/fix-exception Fix exception commit 2eb0da78dbb960f203a7d6ee595870bc6fa0399b Merge: f58c8df 715e796 Date: Fri Nov 20 14:53:00 2015 -0800 Merge pull request #925 from RosettaCommons/fsee/roleMoverInt Adding features to RollMover Merged Will's RollMover with master by adding a few features. Modify the RollMover Integration test Merge latest master into branch Beautify code Update documentation commit f58c8df9d799ad80800604267d68efe70c0cc3c2 Merge: a4c7ee9 262abf0 Date: Fri Nov 20 11:39:31 2015 -0800 Merge pull request #921 from RosettaCommons/tlinsky/resie_report_energy Refactor ResidueIEFilter, add option commit a4c7ee9fed356776ee676de8ff906d1d35bbf4fb Merge: eb4d155 2c51c76 Date: Fri Nov 20 11:37:09 2015 -0800 Merge pull request #922 from RosettaCommons/tlinsky/generic_sa GenericSimulatedAnnealer now checkpoints w/ silent files instead of pdbs commit eb4d15525f656c9396cc8d422c0ec11f74167844 Merge: 057f2b5 0590b3c Date: Thu Nov 19 15:40:51 2015 -0800 Merge pull request #916 from RosettaCommons/vmullig/layerselect Create a LayerSelect ResidueSelector (like LayerDesign) ResidueSelectors were initially created because of frustrations involving LayerDesign, a TaskOperation used both to define selections of residue (core, boundary, surface, based on burial) and also to configure packer behaviour. However, LayerDesign has never properly been replaced by ResidueSelectors because there is no selector to select based on layer. This pull request is intended to rectify this. It also: Partially solves the headaches of mixed canonical/noncanonical design. (LayerDesign is a pain for that, since it can only define layers -- not regions based on linear sequence -- and can only turn canonicals off and non-canonicals on). Sets up the infrastructure for letting the aa_composition score term count residue types in different sub-regions of a pose (a common request from users being layer-based scoring). Tasks: - Move the layer selection logic from protocols to core so that it can be called by core classes. (This is useful, fundamental code that really should be in core in any case.) - Correct dependencies in LayerDesign. - Correct dependencies in RotamerBoltzmannWeight. - Correct various other dependencies. - Give the user control over sidechain neighbour parameters (cone width, cone length, sigmoid falloff, etc.) - Distance falloff. - Factor by which overall residue count is divided. - Angular factor. (Note that this is calculated poorly, currently. This needs to be refactored, albeit in a way that preserves the current functionality.) - Document these in LayerDesign. - Implement a LayerSelect ResidueSelector. - parse_my_tag() - apply() - Documentation. - Integration test. - Tweak the ReadResfile TaskOperation to accept a ResidueSelector as a mask. - Documentation. - Integration test. - While I'm at it, fix the irritating behaviour of the ReadResfile TaskOperation that has it read the resfile repeatedly, at apply time, rather than at parse time. (I'm sure the Blue Gene people are a bit sick of this.) - Track down and fix current issues: - dna_interface_design integration test failure to run. - sequence_profile_constraints integration test failure to run. commit 057f2b517c3d5328e2b1ad38056a88e3b01708a7 Merge: 61ecc85 b91c85c Date: Thu Nov 19 14:07:42 2015 -0700 Merge pull request #920 from RosettaCommons/sergey/colors - Adding channel_color and channel_name_color variables to Tracer so now it is possible to specify default colors for particular Tracer object - Adding extra constructor which allows to specify colors - Making Tracer to send color ’Reset’ before each new line - Updating ColorsDemo app commit 61ecc85e4b4fcb04d28684adb8256a1500fddc58 Merge: 16215dc b8e141d Date: Thu Nov 19 14:01:10 2015 -0700 Merge pull request #736 from RosettaCommons/antibody Adding antibody/grafting which is a C++ port of antibody.py script. Right now the following parts is ported/implemented: - regex-based CDR detection - Chothia Numberer - SCS with NCBI B+ template selection implementation - some grafting code Also: fixes to CSI code (proper detection of TTY) and various other small fixes. commit 16215dc66cbff2ca6698bbe0dba09d4bdfb18cb6 Merge: 77bd5d2 057d0d8 Date: Thu Nov 19 11:43:16 2015 -0700 Merge pull request #915 from RosettaCommons/sergey/eigen Upgrading Eigen lib so Rosetta could now be build with GCC-4.9+. Some regression tests is expected due to changes in linear algebra code. commit 77bd5d20a6276b39951a42c7c3001b9af8cc0871 Merge: 5e4789f 5ac8c72 Date: Thu Nov 19 10:19:00 2015 -0500 Merge pull request #918 from RosettaCommons/kimdn/dn - Minor updates of sewing 1) Update of ModelTrimmer * From now on, ModelTrimmer mandatorily removes any models with L terminal segment * Do 'leave_models_with_E_terminal_ss' mandatorily when 'leave_antiparallel_way_H_bonded_models_by_terminal_strands_only' turned on 2) Update of MonteCarloAssemblyMover * User can turn remove_cut_off_assembly option on/off for MonteCarloAssemblyMover 3) Update of sewing_hasher * Added comment "Only terminal Es are hash bool true to be merged with other nodes later (but as of 2015/11/14, later model assembly has 'ERROR: alignment_scores.size() == 1')" 4) Integration test continuous_sewing_hasher and discontinuous_sewing_hasher changed as expected commit 5e4789f2e22611559d8cccfddfc49c87bb570a9e Merge: 6e6aecd 3beb68d Date: Wed Nov 18 10:06:35 2015 -0800 Merge pull request #917 from RosettaCommons/dimaio/cen_symm_bugfix Bugfix for symmetric hybridization + a few other accumulated changes commit 6e6aecdca3d5395ccd1a685f6871a069a082e3f0 Merge: fdebf91 329f9a3 Date: Wed Nov 18 09:23:04 2015 -0600 Merge pull request #914 from RosettaCommons/roccomoretti/ninja_updates Change the CMake build to use absolute paths The cmake/ninja build are encountering errors on the test server because updated to the headers aren't being properly reflected in the compilation of the unit test files, leading to the test server to not update the unit test compilation when it should. This appears to be due to issues with the automatic header dependency calculation of CMake. CMake uses the -MM option of gcc and clang to get a list of headers on which the compilation of a particular file depends. This dependency calculation ignores system files, which includes any files found through -isystem paths. To avoid issues with -Werror, we have the external directory set as -isystem includes. This is an issue with the unit test builds, as when the compiler tries to find the ../../../source/test/basic/datacache/HierarchicalDataMap.cxxtest.hh include which is in the auto-generated cxxtest source file, it can also find it under ../../external/dbio/, rather than under ./ This means that any header which is included from the *.cxxtest.hh files are considered to be "system" files, and as such don't show up under the -MM output, meaning that things don't get recompiled if they change. The solution to this is to adjust the CMake build system such that it uses absolute paths for the location of the *.cxxtest.hh files, rather than relative paths. (Note that absolute paths here aren't too much of an issue for relocatability, as CMake already uses absolute paths for a bunch of stuff internally - if you move the directory you need to force a clean compilation anyway.) commit fdebf911ebb03b3da0228c58681822095acb3c37 Merge: f251110 3dfe336 Date: Tue Nov 17 14:27:02 2015 -0800 Merge pull request #909 from RosettaCommons/vmullig/energyparse Adds RosettaScripts parsing of the aa_composition setup This pull request lets the user set up the aa_composition energy from RosettaScripts on a per-scorefunction basis. (Previously, this was only possible globally, from the command line). This also cleans up some of the inner workings of aa_composition, making it easier to define new sets of things to be counted. Tasks: - Add parsing of one or more aa_composition setup file name to the "Set" subtag in scorefunction tags in RosettaScripts. - DOCUMENT the "Set" subtag somewhere -- I don't think it's in the RosettaScripts documentation. (Update: it's documented, but the list of commands is woefully out of date.) - Document the aa_composition setup stuff. - Integration test. A bunch of integration tests show cosmetic changes due to the addition of another variable to the EnergyMethodOptions, which gets reported whenever the show() function is called. commit f25111060a0957077f7d694803d6a518b117f5f3 Merge: 622db34 b13eae9 Date: Tue Nov 17 16:11:43 2015 -0500 Merge pull request #900 from RosettaCommons/aleaverfay/bugfix_symm_otf_ig_asu_starts_at_res_1 Fixing two bugs in the symmetric, on-the-fly interaction graph code 1. Fixing an iteration across the wrong number of things when initializing the SymmOnTheFlyNode::state_offset_for_restype_group_ data member (thanks Rocco for bringing this to my attention!) 2. Fixing a false assumption of the SymmOTF IG that the asymmetric unit would always start at residue 1 and run to num_independent_residues. Adding a new unit test where the asymmetric unit is subunit 4, and that checks that changes in energy computed by the on-the-fly interaction graph matches the precompute-and-store interaction graph. All unit tests pass; several symmetry-related integration tests change as a result of a bug in how the one-body energies were being computed. commit 622db3430782348c39af4446f9b038edee54fe7f Merge: 6996443 b34665c Date: Tue Nov 17 13:09:10 2015 -0500 Merge pull request #905 from RosettaCommons/JWLabonte/sugars/input Carbohydrates: Further simplifying loading-in of glycan-containing PDB files This merge makes Rosetta is somewhat more robust in handling glycan-containing PDB files. If a system of 3-letter codes is used in the PDB file that does not include main-chain connectivity, Rosetta will now rely on `LINK` records to assign the proper `ResidueType`s. All unit tests pass. fold_and_dock has tracer volume jacked way up, so it registers with integration test changes because of more tracer output I also added with this merge. commit 6996443000948ba55ef2432c4152934e4dfd5198 Date: Tue Nov 17 03:06:55 2015 -0800 Mistake in bundlegridsampler_composition_energy integration test corrected. commit 26e57d994e06c962342730f90f8e5dbef5299e70 Merge: 9c8e24b a862023 Date: Mon Nov 16 23:00:23 2015 -0800 Merge pull request #876 from RosettaCommons/vmullig/glysampling Allow Ramachandran sampling with flat and/or symmetrized Rama tables Existing Ramachandran tables are a bit too heavily biased for effective sampling, particularly if one wants to design afterwards. This pull request adds high-contrast, flattened Ramachandran tables for large-scale sampling. It also adds symmetrized tables for mixed D/L sampling. Tasks: - Add flat rama table for generic L-alpha-amino acids. - Add flat, symmetrized rama table for generic L- or D-alpha-amino acids. - Add flat, symmetrized proline rama table (for sampling D- and L- prolines). - Add flat, symmetrized glycine rama table. - Add high-stringency versions of the above tables. - Add option to use flat and/or symmetrized tables for sampling (to GenKIC). - Add storage space in Ramachandran for additional cumulative distribution functions. - Add core sampling function that can take an arbitrary rama table. - Add functionality to core for lazily loading additional rama tables. - Add options to options system for additional rama tables. - Documentation. - Add option to use flat and/or symmetrized tables for sampling to the SetTorsion mover. - Documentation. - Add support to SimpleCycpepPredictApplication for custom Rama tables for sampling. - Documentation - Integration test. - Add option (flag) to use non-flat, symmetric glycine tables for scoring and/or sampling (and to generate these on the fly, on Rama table load). - Add flag. - Make symmetrized Ramachandran gly table on the fly. - Make symmetrized P_AA_PP gly table on the fly. - Unit test for the scoring side of this. - Documentation for the flag. - Beauty While I'm at it: - Fixed D-rama sampling bug in SetTorsion mover. Put off to a future pull request: - Add AiB. - Figure out rama scoring for AiB (maybe L-alanine's probability table multiplied by D-alanine's probability table, re-normalized, and converted to an energy?). - Figure out p_aa_pp scoring for AiB (same as above?). - Add adjacent-residue clash check option to GenKIC bump checker (requested by Andy). commit 9c8e24b031dce2fcf025f72d04f3d540ae077133 Date: Mon Nov 16 21:43:41 2015 -0800 Added switch_to_residue_type_set() to fullatom at the very begining of the apply() commit f5977d5f37f900046ce22646000b06328ad492da Date: Mon Nov 16 14:25:05 2015 -0500 Saving small modifications to the refit_hbond_polynomials.py script. commit 5abe6a6f544c00e8bb3253137f359ed938fa86c5 Merge: 457404e f361216 Date: Mon Nov 16 11:20:00 2015 -0500 Merge pull request #903 from RosettaCommons/aleaverfay/fix_lcaa_nbr_radii Modifying the neighbor radii of the canonical amino acids. The neighbor radii must represent the maximum distance from a residue's neighbor atom to its furthest heavy atom under all dihedral angle assignments. Their purpose is to provide a geometry-independent bound on the reach of a residue so long as you know where the neighbor atom (e.g. CBeta) is. The radii are used by the score function and by the packer to avoid unnecessary residue-pair energy calculations where possible. I originally measured these maximum distances by building the Dunbrack rotamers for a particular phi/psi. In this new calculation, I've sweept all chi angle combinations at 5 degree increments. For a handful of residue types, this resulted in an increase for the neighbor radius. In the case of valine, it looks like the original neighbor radius was never set to the default c-beta-to- backbone-heavyatom distance (valine's c-beta-to-sc-heavyatom distance is a meager 1.5A). For HIS_D, the radius calculated by building rotamers was never applied, so that Phil's original guess at HIS and HIS_D's radius was left; but HIS's radius was updated. This meant that HIS and HIS_D ended up with different radii. This discrepancy was initialy uncovered by Andrew Ban in 2009 and has reared its head intermitently in the past six years, but was never fixed. HIS and HIS_D now have the same radii. This pull request cause widespread integration test trajectory changes. All unit tests pass. commit 457404e5e039dab46dbddb44aa2ed6c7d3ab3d76 Merge: 85008d8 874b99b Date: Fri Nov 13 15:46:12 2015 -0800 Merge pull request #904 from RosettaCommons/rhiju/rna_helix_force_enlarge_h_lj making sure that rna_helix always uses enlarged hydrogens by adding t… changes rna_helix, as expected -- and the other tests that are now failing regularly. commit 85008d8d05a9e2e36a0fd5d41ca9489fed12aa7b Merge: 9d6d96d ebd6de0 Date: Fri Nov 13 13:27:45 2015 -0800 Merge pull request #906 from RosettaCommons/dimaio/lattice_symmetries Several modifications for modelling structures with 2D and 3D lattice symmetries. Checkin implements a new rosettascripts movers for creating systems with 3D lattice symmetries: * MakeLatticeMover name=make_lattice contact_dist=24 Make a lattice from the input PDB and CRYST1 line. Include all subunits within 'contact_dist' There is also a mover aimed at handling 2D lattice symmetries: * MakeLayerMover name=make_layer contact_dist=24 Make a 2D lattice from the input PDB and CRYST1 line. The CRYST1 line must correspond to one of the 17 layer groups. There are two movers aimed at manipulating these lattice symmetries (both work with 2D & 3D): * DockLatticeMover name=crystdock fullatom=1 trans_step=1 rot_step=2 ncycles=100 scorefxn=talaris2013 Docking within the lattice. If fullatom=1 it does fullatom docking with repacks and min steps; if fullatom=0 you need to provide a centroid energy function (e.g. score4_smooth) and it will also add lattice slide moves. trans_step and rot_step gives magnitude of perturbation; ncycles is # of steps to run. * UpdateCrystInfo name=updatecrystinfo Convert back to an asymm pose with a valid CRYST1 line Finally, there are a bunch of useful helper functions in src/protocols/cryst/. NOTE: In all cases, these movers _MUST_ be run with the flags: -in::preserve_crystinfo -optimization::new_sym_min -symmetry::symmetry_definition dummy (and probably -symmetry::detect_bonds false as well) commit 9d6d96dd6b972ce3290d1b1c41670895e0961e31 Merge: 52e3855 471d565 Date: Thu Nov 12 12:28:11 2015 -0500 Merge pull request #864 from RosettaCommons/JWLabonte/sugars/input Carbohydrates: improving creation of glycans from sequences This set of changes introduces the following: * Glycans with modified sugars can be created from IUPAC sequences. * Branched glycans can be created from IUPAC sequences. * Protein poses can be "glycosylated" at requested positions. * ResidueType::show() now gives information about branch point atoms. All unit tests pass. carbohydrates test changes expected CCD_loop_closure test changes expected (output modifications from assigning a name to PDB_Info for sugars made from sequences) ThreadingInputter test changes in output from change in namespace of a FoldTree function All other integration test changes are from the usual (15) suspects, which are all (still) unstable. commit 52e3855cf6af05a9054c3953b14818655e672f93 Merge: 0909693 6022db2 Date: Wed Nov 11 08:13:50 2015 -0800 Merge pull request #902 from RosettaCommons/everyday847/revisit_mm Fix bug in MMLJEnergyIntra commit 0909693dc63d017539f2b6c30f507ed5b3144985 Merge: 776f82b 02bad67 Date: Tue Nov 10 23:09:04 2015 -0800 Merge pull request #895 from RosettaCommons/vmullig/removeSPs Removing all Lua scripting support from the codebase Certain key classes seem to have a second type of owning pointer defined, apparently for use with the Lua scripting hooks. This creates confusion, particularly for new developers, who might think that they should be using, for example, PoseSPs instead of PoseOPs. These owning pointers are hard-coded to be boost::shared_ptrs (unlike our owning pointers, which could be std::shared_ptrs, boost::shared_ptrs, or something else, depending on compilation settings). This pull request tears 'em all out so that they're not cluttering up our codebase and confusing new developers. UPDATE: This pull request now has the goal of ripping out all of the Lua hooks. Lua scripting was never implemented well, and has not been maintained since the original author left the Baker lab; it is almost certainly no longer a functional feature of Rosetta, and it is certainly one that no one uses. If I'm going to reduce useless codebase cluster, I might as well not bother with half-measures. (Plus, it actually turned out to be easier to solve the SP issue by tearing out all of the Lua stuff, since the SPs were mainly only used in the Lua code and this way I don't have to convert them all to OPs.) commit 776f82ba69b17a6e3fcb1adda9f150e5cf70a77c Merge: ce45cbf 3f30c40 Date: Tue Nov 10 14:48:06 2015 -0800 Merge pull request #897 from RosettaCommons/vmullig/cycpep_checkpoint Add flag for the cyclic peptide prediction app's checkpoint file This adds the -cyclic_peptide:checkpoint_file flag, which allows the user to specify the filename of the checkpoint file. commit ce45cbf05e640fe6e02460785765d7ce07a00229 Date: Tue Nov 10 12:35:42 2015 -0800 Accepting utracers commit 74aff951a185e2c1ef8d6d1b9a512b78c6d636b8 Merge: 2e83abf a908b34 Date: Tue Nov 10 09:57:11 2015 -0800 Merge pull request #892 from RosettaCommons/everyday847/modified_rna_readin 1. cppcheck test failure has been fixed by my most recent commit 2. integration test changes stem from three sources: PDB or silent i/o now retaining segment IDs, the addition of the 0TD NCAA, and the 15 that inconsistently break these days. commit 2e83abfea4fef475297e7730b8f4cf7bf4400e2a Merge: 9a11253 1097c81 Date: Tue Nov 10 07:33:38 2015 -0800 Merge pull request #898 from RosettaCommons/everyday847/elcapitan Account for boost issue on El Capitan commit 9a11253d88396938becca72d769e74d842cad907 Date: Mon Nov 9 18:47:17 2015 -0800 Removing generated optionkeys from git control. commit 1402a8136e703234f642d5596e718d27292f87c4 Merge: 05ab30d 8f515df Date: Mon Nov 9 15:53:53 2015 -0500 Merge pull request #896 from RosettaCommons/dougrenfrew/remove_generated_sewing_options Remove sewing options file. This and all other generated files, should be automatically generated by a script and not under version control. I suspect it was checked in by accident, possibly before the git transition. commit 05ab30d826fd2937916dac650e9d4728516ae027 Merge: aaf2741 916a083 Date: Sat Nov 7 16:45:13 2015 -0800 Merge pull request #894 from RosettaCommons/tlinsky/cmake_fix Remove defunct library references from all cmake builds and devel.src… commit aaf27411ff203ac5bcb2f7bfbf20aa5b0e139e07 Merge: 45988bf c6a1679 Date: Sat Nov 7 16:21:06 2015 -0500 Merge pull request #890 from RosettaCommons/kimdn/dn [SEWING update] * Integration test Change of results of 'continuous_sewing_hasher' and 'discontinuous_sewing_hasher' during pull request are expected ones. * sewing_hasher update - Even three_secondary_structure_based models have better defined model_file_name - Even three_secondary_structure_based models can specify between 'hash_tag_only_terminal_Es' and 'hash_between_any_HEs' - Unit test input file name updated * ModelTrimmer update - user can give 'leave_models_by_ss_num' and 'model_should_have_this_num_of_ss' option * EnumerateAssemblyMover update - name change (ExhaustiveAssemblyMover -> EnumerateAssemblyMover) - now EnumerateAssemblyMover spits 'path info' like MonteCarloAssemblyMover does - now EnumerateAssemblyMover can use min_assembly_score cutoff like MonteCarloAssemblyMover can * AssemblyConstraintsMover update - newly added 'native_pro_bonus' commit 45988bf95c76d36e368e83e7aa69a8714d73f5c3 Merge: 74c7dc3 00a37eb Date: Fri Nov 6 11:24:12 2015 -0500 Merge pull request #873 from RosettaCommons/bioragul/plab Bioragul/plab commit 74c7dc38aa853030dfe7793f01e928befc88eee2 Merge: 0d3b031 5dd397d Date: Fri Nov 6 09:42:19 2015 -0500 Merge pull request #887 from RosettaCommons/aleaverfay/more_rlts Added four new ResidueLevelTaskOperations to expand the utility of the ResidueSelectors. commit 0d3b0319dedc69ecd7e2d774c78c65ea21076af2 Merge: 1b2f0fe 2741f64 Date: Fri Nov 6 01:11:53 2015 -0800 Merge pull request #893 from RosettaCommons/vmullig/fix_sewing_hasher_tests Fixing app_exception_handling AGAIN. This is the danger of letting an integration test sit around in a broken state: when people check in additional code that ALSO breaks what the integration test is meant to test, they don't know that they've done something wrong. Because Rhiju's gaussian_chain_func_test was causing app_exception_handling to fail, two more apps slipped in under the radar without try/catch blocks. The struc_set_fragment_picker app, which was newly-added, had no try/catch block. Fixed now in this pull request. commit 1b2f0fea47bd1763adf859a08b0d4678f3f724e6 Merge: f6d87c3 e1f603e Date: Thu Nov 5 18:35:07 2015 -0800 Merge pull request #891 from RosettaCommons/vmullig/fix_sewing_hasher_tests Still trying to fix app_exception_handling test. Problems remain in Rhiju's gaussian_chain_func_test pilot app. Fixed now, I think. commit f6d87c30f5552a667834ef54571aaa8575b05a97 Merge: 9504df4 0f7d31d Date: Thu Nov 5 17:27:55 2015 -0800 Merge pull request #884 from RosettaCommons/raemisch/cc_frag_picker Raemisch/cc frag picker commit 9504df4defa95b289af66764f67417ebfdfa604b Merge: 8a9352e 1a73a5f Date: Thu Nov 5 03:52:07 2015 -0800 Merge pull request #888 from RosettaCommons/vmullig/fix_sewing_hasher_tests Fix failing integration tests This fixes the app_exception_handling, continuous_sewing_hasher, and discontinuous_sewing_hasher integration tests: - app_exception_handling is fixed by adding try/catch blocks in the gaussian_chain_test and ModelTrimmer pilot apps. Please don't add a pilot app to pilot_apps.src.settings.all unless you have its functionality enclosed in a try/catch block. - The sewing_hasher integration tests are fixed by removing datestamps from sewing_hasher.cc. If you write an integration test, don't have it write out the date on which it was run. This WILL cause a daily failure. commit 8a9352e6ca637260866592bd25c8e5eabdc9610a Merge: 74ef325 7461c4a Date: Thu Nov 5 00:15:03 2015 -0800 Merge pull request #886 from RosettaCommons/vmullig/fix_setup_for_symmetry Minor tweak to MakeBundle mover Tweaking MakeBundle to clear the PDBInfo of the input pose if it exists (since it won't be accurate any more once the new geometry is added). commit 74ef3254c1380b93cd937c759af78224aee4eb86 Merge: dcc326f1 f98ed15 Date: Wed Nov 4 17:44:59 2015 -0800 Merge pull request #881 from RosettaCommons/rhiju/general_bps Rhiju/general bps Adding 'base pair step' moves that allow efficient sampling of RNA structures in FARNA if you know which residues for noncanonical pairs. Includes database file additions (not too big after gzipping!). some integration.release_debug tests on linux change -- this appears to be due to testing on the different linux servers, as the integration tests (on mac clangrelease) look OK. commit dcc326f10f0479907d1aa1413eb046ccdaea6900 Merge: f0f8981 a968fe7 Date: Wed Nov 4 11:48:41 2015 -0500 Merge pull request #885 from RosettaCommons/everyday847/extra_rotlibs Extra rotlib paths don't have to have a hierarchy. commit f0f89815df465c9a7b558144adedf6d56212dca3 Merge: 59462cf 1f221bf Date: Wed Nov 4 09:54:29 2015 -0500 PyRosetta. Refactoring how C++ ‘struct’ handled (now binding access to data-members by default). commit 59462cfcdc6853cfae6d8e3f747682327083a7cd Date: Tue Nov 3 15:29:17 2015 -0500 Commit without Rosetta Benchmark test (this commit will be safe though). Now I add a missed "generate_five_ss_model" option for sewing_hasher. commit 18440f18949698a7cd0342901e57846481a6b70d Date: Tue Nov 3 11:55:42 2015 -0500 More work on the hbond distance-polynomial refitting script commit 81fb75ba6ce92f27e014c139bbb0aa78f2e4048a Merge: 54dc880 2c46c0c Date: Tue Nov 3 11:52:19 2015 -0500 Merge pull request #882 from RosettaCommons/everyday847/loop_simplify Loop structure simplification and miscellany commit 54dc8800d3e6dae70f57b021c224e8f7ebceea59 Merge: 5b556a5 2ec3aee Date: Tue Nov 3 10:44:29 2015 -0500 Merge pull request #883 from RosettaCommons/kimdn/master_sew [what has been updated for beta-sandwich_analysis] * Add a more rule so that two parallel short strands can be "sheet" for Tim-barrel [what has been updated for SEWING] * [model generation update] - sewing::hash_tag_only_terminal_Es is possible - User can provide an option (generate_five_ss_model) so that 'db -> node (model)' can generate '3_or_5_secondary_structure_based models' - added unit test (SewingHasherTests.cxxtest) for "db -> node (model/substructure) can generate 5_secondary_structure_based models" * [Model_trimmer update] - becomes little faster (don't care rest trimming steps if any preceding trimming decides to erase the model) - can do 'leave_models_with_E_terminal_ss' - can do 'leave_parallel_way_H_bonded_models_by_terminal_strands_only' - can do 'leave_antiparallel_way_H_bonded_models_by_terminal_strands_only' - can do 'model_should_have_at_least_one_E' - can do 'model_should_have_at_least_one_E_at_terminal_segment' * [hashing update] node (model) -> edge (score) can handle 'any number of secondary_structure' based models * [model assembly update] - User can choose between 27 and 125 boxes for neighborhood_lookup (-sewing:box_length), both scoring and assembly should use same box numbers * [ExhaustiveAssemblyMover newly added] - Enumerate every possible assembly exhaustively - User can choose 'dump_every_model_for_devel_purpose' option * [MonteCarloAssemblyMover update] - User can choose not to stick to best_score if specified 'min_assembly_score' as an option in parser - User can choose 'offset_bump_dsq' as an option [beautified some other's files] beautified except File utility/json_spirit/json_spirit_writer_template.h could not be beautified File utility/json_spirit/json_spirit_error_position.h could not be beautified File utility/json_spirit/json_spirit_writer_options.h could not be beautified commit 5b556a55a3551d6c772a17aae6a38e15e7a9e64e Merge: 75b7c94 b8b3bfe Date: Sun Nov 1 16:08:40 2015 -0800 Merge pull request #878 from RosettaCommons/tlinsky/hotfix Fix gcc 5.x.y cmake build commit 75b7c9466e48a2b13516989b00f17bc8a5191e45 Merge: b167ac6 89aa1d4 Date: Sat Oct 31 00:32:49 2015 -0700 Merge pull request #880 from RosettaCommons/vmullig/reset_issue Fix the functionality of RESET The commutativity-breaking resfile command RESET, which is necessary for noncanonical design (since noncanonicals can only be turned ON while canonicals can only be turned off) wasn't resetting canonicals properly. This command now: - Disables all noncanonicals (as it did before). - Enables all canonicals (which it was not doing properly before). - Enables design and repacking. Which is what the documentation claimed that it was doing. I've also moved the RESET functionality to a single function in the ResidueLevelTask class, so that we don't have a lot of ways for external things to break commutativity. (Anything can call the reset() function, but it will always break commutativity in exactly this way.) commit b167ac6b7fa079c9eae3438c683bfb17b583ca6c Merge: d8d67dd 89bc48a Date: Sat Oct 31 00:30:04 2015 -0700 Merge pull request #879 from RosettaCommons/vmullig/bintransition_bug Caught a mistake in BinTransitionCalculator.cc. This was affecting the setup of sub-bin cumulative probability distributions for the i+1 residue. commit d8d67dd2ae1ff7d7f1e6d2ca1abb035459d31b38 Date: Fri Oct 30 17:08:27 2015 -0400 Updating the refit_hbond_polynomials.py script to more robustly handle cases where the new polynomial does not reach it's requisite height (+1.1). commit 768492fdfa0c992155c55a31968e2409497223d9 Merge: 5c82e1c 359aeaa Date: Fri Oct 30 09:04:59 2015 -0700 Merge pull request #877 from RosettaCommons/rhiju/fix_up_to_virtual_phosphate Rhiju/fix up to virtual phosphate changes to integration tests are expected – due to virtualization of 5' phosphates of RNA that should have been happening anyway. commit 5c82e1cc2c9132ff80e361e4ab8056b235117043 Merge: 5acb7f6 1770fec Date: Thu Oct 29 16:59:45 2015 -0700 Merge pull request #870 from RosettaCommons/vmullig/peppredict_boinc Add checkpointing to simple_peptide_predict app David Kim rightly pointed out that my peptide structure prediction app isn't checkpointing itself properly. While results would still be returned on BOINC, trajectories would likely be repeated if users stopped a work unit and re-started it. This will address that. Tasks: - Figure out how the BOINC stuff currently talks to the classic ab initio JobDistributor and to JD2. (I'll probably want to use the nstruct-level checkpointing of JD2, but first I want to understand how everything currently works.) - Figure out whether JD2's nstruct-level checkpointing somehow knows to skip jobs that failed. (I'll definitely need this, since my app heavily filters, so that many trajectories return no result.) - Get simple_cycpep_predict to checkpoint. (It was simpler to add checkpointing than to get it to use an existing JobDistributor, and I was able to time the checkpointing to my short jobs rather than the over-frequent checkpointing that I'd have if I relied on the BOINCJobDistributor). - Get the minirosetta with the simple_cycpep_predict protocol to talk properly to the text overlays in the BOINC graphics. - Test with the text overlay on the graphics (not tested yet). - While I'm at it, tweak the energy and RMSD updating in the graphics display. - Beauty - Documentation Cosmetic change to simple_cycpep_predict integration test expected (one extra line of output). commit 5acb7f6f6879b41e89bd99076e58be728c88e060 Merge: 24eb779 44c2fb1 Date: Thu Oct 29 00:22:56 2015 -0700 Merge pull request #875 from RosettaCommons/indigogo/hbscan Indigogo/hbscan commit 24eb77939276570292c507350592d820ec028d7d Date: Tue Oct 27 22:43:40 2015 -0400 The big green button somehow did me wrong. This should fix the build. commit 4a946503caccfc1bceb59192631e71782f2be9b9 Merge: 48f5f75 0ee1b99 Date: Tue Oct 27 22:09:53 2015 -0400 Merge pull request #872 from RosettaCommons/everyday847/remove_ncaa_rotlibs Remove most NCAA rotlibs from RosettaCommons/main commit 48f5f7558bb6188d8f1b08cbdc5cb5c4037de825 Merge: cb11c3c 10dbbe7 Date: Tue Oct 27 20:14:03 2015 -0400 Merge pull request #862 from RosettaCommons/revert-860-revert-676-tjacobs2/sewing_motifs Merge of the SEWING framework for de novo protein design. Thanks to Sergey for fixing an issue with the Windows PyRosetta build. All tests pass. Expected changes to features and features_database_schema integrations tests. Also, two new tests for the continuous and discontinuous sewing hasher. commit cb11c3c576be8cbe9f2eb001249da19056f6b115 Merge: 89c9cdb 89b0ad9 Date: Tue Oct 27 18:19:33 2015 -0500 Merge pull request #871 from RosettaCommons/roccomoretti/valgrind_mpi Fix integration.py w/r/t valgrind and MPI Not all test directories have non-MPI command files - don't fail if one isn't present commit 89c9cdbb90cb74773bd482941b6109a0069c874f Merge: 7523896 5a6523f Date: Sat Oct 24 00:25:36 2015 -0700 Merge pull request #869 from RosettaCommons/vmullig/peppredict_boinc Make the simple_cycpep_predict app into something that runs on BOINC Tasks completed: Promote simple_cycpep_predict to a public app. Move much of its core functionality to protocols. Move options to options_rosetta.py. Load options from the options system on initialization, and store values in private member variables. Modify the minirosetta app to allow the SimpleCycpepPredictApplication class to be called. Add support for BOINC graphics. Figure out inputs and outputs. Figure out a reasonable definition of a work unit. Add RMSD output to the score in the output silent file. Test. Gave the BOINC graphics a little bit of a facelift while I was at it. (Rosetta@Home did celebrate its tenth birthday earlier this month, so it was about time.) Beauty. Documentation. commit 752389624ee1e760710a165bbb213e003d28a78f Date: Fri Oct 23 15:46:26 2015 -0400 Adding a talaris2014_cart weight set, with reference energies fit with optE. commit 488b457ca0ed3182645ce1ad17e8159b7cd105ad Merge: 05592f6 ee210cd Date: Thu Oct 22 23:36:01 2015 -0700 Merge pull request #866 from RosettaCommons/tlinsky/rotamer_boltz_max Add compute_max option to RotamerBoltzmannWeight commit 05592f6be1c58e2056bc9d6d45b845ef8c858615 Merge: 3171c80 0ef6a32 Date: Thu Oct 22 20:39:40 2015 -0700 Merge pull request #868 from RosettaCommons/tlinsky/tomponents Improved support for non-polymeric bonds in denovo_design classes - the usual 15 unstable integration tests fail commit 3171c80e5cfb93bef87e71728d6200f949abae06 Merge: 034260e 12293d6 Date: Thu Oct 22 13:44:37 2015 -0700 Merge pull request #867 from RosettaCommons/tlinsky/matchermover_residue_selector Instead of a positions file, the MatcherMover can use ResidueSelector commit 034260ee58cd64cfa5de22cfb77526af259859ad Merge: 9ab0001 668f3ad Date: Thu Oct 22 08:54:12 2015 -0400 Merge pull request #854 from RosettaCommons/everyday847/include-what-you-use Now that we build under Windows/PyRosetta, we are ready to merge. There is a lot of work left to be done in this domain, but it will be done under separate pull requests--this one is already substantial in size. Basic/numeric/utility/core1/core2 are done (but could always use separate passes), as well as a couple public apps. It is not fun to attempt this from a Mac, as the Linux builds are more persnickety. And I really wish I had the opportunity to locally test the Windows build--maybe, just maybe, I'll set that up before I try again. commit 9ab00014477db75a3cd56759a7f70f5502f30f4d Merge: c6e0a23 0dfba5f Date: Wed Oct 21 17:19:49 2015 -0400 Fixing PyRosetta on Mac OS El Capitan commit c6e0a2317b4217dbb1087ad019cbe14ef31cf23a Merge: 9b577fb 91ad026 Date: Wed Oct 21 12:07:59 2015 -0700 Merge pull request #865 from RosettaCommons/tlinsky/consensusdesign_option Add include_adjacent_residues option to ConsensusLoopDesign. In the pull request, 16 integration tests failed, but I believe these are the ones that have been showing instability. commit 9b577fbee0edc4340dab17e664ae94c4039d59ce Merge: c0dbe17 a9c2d6d Date: Tue Oct 20 18:55:29 2015 -0700 Merge pull request #863 from RosettaCommons/tlinsky/ss_selector_fix Register secondarystructure selector commit c0dbe17f6ede370e493868066a034a835a6935e4 Merge: f654950 8889ff5 Date: Tue Oct 20 10:53:50 2015 -0700 Merge pull request #498 from RosettaCommons/tlinsky/coreresperelement Add CoreResiduesPerElement filter -- Integration test changes expected for sweep_respair_energies, database_jd2_compact_io, database_jd2_io, and features commit f6549502cff83eb166d2ecce63983454948fab53 Merge: 6ecc3ad e8b4edc Date: Mon Oct 19 12:11:32 2015 -0600 Merge pull request #859 from RosettaCommons/PyRosetta Adding bindings for std::list<> for basic types, fixing namespace build import orders commit 6ecc3ada0343026fffaa50b74e809e09b5022589 Merge: 0ad3873 5edaec6 Date: Sun Oct 18 18:55:13 2015 -0600 Merge pull request #860 from RosettaCommons/revert-676-tjacobs2/sewing_motifs Revert #676 "Tjacobs2/sewing motifs" commit 0ad3873ab091d136b2dbe9719eb34d90f365b410 Merge: c9c15ce c01da1e Date: Fri Oct 16 11:58:17 2015 -0700 Merge pull request #726 from RosettaCommons/jadolfbr/antibody_design Updates to RAbD and IAM Rosetta Antibody Design Changes ---------------------------------------------- Add two new antibody design protocols to more evenly sample lengths and clusters from the ab db for design. (even_cluster_mc and even_length_and_cluster_mc). Seem to work very well for analyzing potential binding surface during preliminary design runs. Make RAbD program fail more gracefully when -s or -l is forgotten. Change a few names of options to make them more consistent with the rest of the protocol. -instructions -> -cdr_instructions -base_instructions -> -base_cdr_instructions -benchmark_graft_design -> -random_start Run IAM (InterfaceAnalyzerMover) at end of run on each ensemble by default. Add score information to output score file for each PDB (See below). Run a dualspace relax on each output PDB and ensemble by default. Run IAM on these as well. Name them special for post-design analysis. Antibody design enums now have their own manager class. Bugfixes ------------ Fix a major bug where sequence design fallback strategy was overriding the primary strategy. Add function to test this in unit test. Fix 'hopping' which can occur for conservative sequence design (design a residue, then use that residue for a possible new set of conservative restypes). Here, we keep track of the native positions and the sequence of the grafted CDR structures/sequences by a separate class (antibody/design/NativeAntibodySeq) that is set in the pose DataCache, which accounts for possible pose-length changes and works with our monte carlo algorithm. Add util functions to help with this. Add unit test for this. Now, we always run conservative design as one would think. No val to arg mutations in L1 stability position ever again. That hydrogen bond you created was just too tempting, wasn't it Rosetta! Fix deterministic graft-permutations. This is not enabled yet, but will allow you to try all possible CDR combinations. The next step is to integrate this into JD3, where it could be actually useful on a cluster for center member trials... IAM ----- Fix up InterfaceAnalyzer to not rely on the main global calculator. Separate logic of IntergroupNeighborsCalculator into its own class, which is called by IAM. This allows IAM to be integrated into any protocol with any number of PDBs. Add a function to IAM to add score information for the pose instead of the Job to be called after analysis. This enables any protocol to use IAM and output score information. Add output of number of hydrogen bonds to IAM. Test Changes ------------------ Antibody Designer integration test changes expected. All integration tests which test or use IAM will change with the addition of an additional score in the output score file. commit c9c15cef84ffcc17fee861b45cd7278669091e30 Merge: 6734c20 1e76c78 Date: Fri Oct 16 13:02:50 2015 -0400 Merge pull request #676 from RosettaCommons/tjacobs2/sewing_motifs Committing the SEWING framework for de novo backbone generation into master. Integration tests expected for features and features_database_schema. Also, two new integration tests have been added: continuous_sewing_hasher and discontinuous_sewing_hasher. commit 6734c20df1c2e232d981e10f6932c41baf3d400c Date: Fri Oct 16 00:43:26 2015 -0700 fix features mpi test. commit 43e7f57339dce22e0b115422e0dcae02e8d2ca65 Date: Fri Oct 16 00:22:38 2015 -0700 fix features.mpi integration test. commit 6434c46dab068b78ed45b0a615be60faf6e63bba Date: Thu Oct 15 22:44:41 2015 -0700 fix features mpi db test. set some output to ignore so that it is on test server if needed, but stochastic changes with ordering are not present. grep out sqlite_sequence which seems to be not needed too. commit 0f9eab7f4057914a1a2a5580c664c13e835b4776 Date: Thu Oct 15 17:23:08 2015 -0700 fix neighbor residue repacking through the FullControlWindow in the pyrosetta toolkit GUI. commit 262dc0cb140b2dc759e8aab31ea6a7cacc699d99 Merge: e9b072f f0505e2 Date: Thu Oct 15 16:45:43 2015 -0700 Merge pull request #858 from RosettaCommons/vmullig/tweak_helixfit Adding an error message in a case of a cryptic failure. Adding a proper error message when the ResidueTypeSet tries to create a residue type for which no params file exists. commit e9b072fddfac04ef57bbdaa925009b224639fd82 Merge: c50cd71 2780127 Date: Thu Oct 15 14:12:33 2015 -0700 Merge pull request #795 from RosettaCommons/jadolfbr/mpi_dbout This merge fixes 2 FeaturesReporter MPI Issues: Bugs Fixed --------------- 1) Allows the use of the command-line flag for separate_db_per_mpi_process to work in with the XML. 2) Fixes a nasty bug that was sending the MPI JOB_FAILURE_TAG instead of the REQUEST_MESSAGE_TAG when requesting batch and protocol ids for MPI. This fixes sqlite3 MPI and may fix MySQL MPI if it was broken as well. Code and Test ------------------- Reorganized basic/message_passing into basic/mpi and moved enums out of MPIJD and into this namespace. This allows use of the enums instead of ints, which should help prevent something like this in the future (Thanks Vikram!) Add MPI integration test for this (Again, thanks Vikram!). Expected Test Failures ------- Some cosmetic changes in integration tests that used the message_passing namespace. MPI integration test will fail for being new. commit c50cd7197f2e3911a7ac68eab2d9983aa3caac04 Merge: 5ef2748 30a8135 Date: Thu Oct 15 00:44:27 2015 -0400 Merge pull request #832 from RosettaCommons/JWLabonte/sugars/scoring Carbohydrates: sugar_bb scoring term completion All unit tests pass. carbohydrate and vancomycin test changes expected, because of improvements to sugar_bb score term> c-terminal_conjugation test changes expected, because I corrected a wonky pdb input file. commit 5ef2748a353516351fe43e08984cd7f842362077 Merge: 12486c8 71914f6 Date: Wed Oct 14 14:59:57 2015 -0700 Merge pull request #855 from RosettaCommons/tlinsky/consensusloop_bp Add "blueprint" option to ConsensusLoopDesign commit 12486c8ec7e8c6be2dcd06abf4f010608ae9737c Merge: a6f48f9 5484573 Date: Wed Oct 14 13:12:46 2015 -0700 Merge pull request #788 from RosettaCommons/tlinsky/tomponents Updates/cleanups/bugfixes to denovo_design classes commit a6f48f94d5927490ce8cc01571b4a3fb5564044e Date: Wed Oct 14 03:10:20 2015 -0400 Oops. Was in wrong branch. Restoring. Sorry! commit 5f62ee5881998f638ad946400b78c716a96dbc11 Date: Wed Oct 14 03:02:26 2015 -0400 fixing unit tests commit ef50d9007837ef35e9afe7f31750701ac1f28397 Date: Tue Oct 13 13:25:38 2015 -0700 15/10/13 updated the Xcode template project.pbxproj.template file to remove links to protocols_f.5 and add libz to protocols_a.5; current master now builds correctly in Xcode using this new template file. Because the only change is this template file, I am pushing this file to master without a pull request commit 797b30f05d1a9997b4815fd8425b343833984c3a Merge: f3b75b1 8961dc8 Date: Tue Oct 13 07:07:38 2015 -0400 Merge pull request #801 from RosettaCommons/JWLabonte/AtomTypes Turning on GasteigerAtomTypes by default carbohydrate test changes expected. commit f3b75b1585d1b0b3d6abd904f7ed04945d20a357 Merge: f072872 2309119 Date: Mon Oct 12 23:39:09 2015 -0400 Merge pull request #846 from RosettaCommons/kmb413/LooDo Kmb413/loo do commit f072872d5414a901b2ffb351b3e74805c5c75450 Date: Mon Oct 12 17:30:42 2015 -0700 Updating thread_local to THREAD_LOCAL in apps/pilot/chrisk/hbscan.cc. commit d3b65575b73498df677aa8d0536af63cc59ef74e Merge: 688e820 dc68abc Date: Mon Oct 12 15:12:38 2015 -0700 Merge pull request #853 from RosettaCommons/indigogo/hbscan Indigogo/hbscan commit 688e820296fec708d07e61469d6631c6c0520987 Merge: 1f7155c 22929d1 Date: Sat Oct 10 20:43:39 2015 -0400 Merge pull request #852 from RosettaCommons/everyday847/fix-valgrind-errors Fix two valgrind errors commit 1f7155ca99dddb038ca5cfecb6b0ec5c66da3547 Merge: 827a2f3 858607b Date: Sat Oct 10 03:10:02 2015 -0400 Merge pull request #844 from RosettaCommons/everyday847/real_metapatches "Metapatches": a framework for atomwise manipulations commit 827a2f3e6378d230310e6b223be499d78d8dc02d Merge: b7c7d78 88244c3 Date: Fri Oct 9 03:05:14 2015 -0700 Merge pull request #840 from RosettaCommons/vmullig/asford_multibody_copy3 Add support for non-pairwise decomposible score terms to the packer This merges Alex Ford's recent changes to the packer into master, adding support for score terms that are not pairwise decomposible but which can be made fast to compute or update by other means. (An example is the aa_composition score term, which imposes a nonlinear penalty for deviation from a desired amino acid composition. It's very fast to count amino acids of a given type.) Tasks: - Fix issues introduced by recent changes to disulfide code. - Add full Doxygen documentation for new classes. - Re-beautify. - Check the (many) integration test changes. - Fix PyRosetta issues. - Re-beautify. - Fix failing unit test. - Rename variables with leading underscore to have trailing underscore instead. - Figure out PyRosetta unit test issues. - Re-beautify. For a future pull request: - Add RosettaScripts-accessible means of setting up the new score terms. - Add a better base class for packer-compatible non-pairwise-decomposible score terms. - Revise the aa_composition energy, adding more user controls (e.g. layers, regions of the protein, etc.) Integration test changes expected: - Many tests have small cosmetic changes (because some packer-related namespaces and corresponding tracer names change). - bundlegridsampler_composition_energy actually changes (because the aa_composition energy now works with the packer, so the output from this test is much better) commit b7c7d78cb1b7cc69dcce5c088c528dc826a91fcd Date: Mon Oct 5 19:05:18 2015 -0700 Remove protocols_f.5 library from devel unit test src.settings (we still have that?) and core. This actually does what my previous commit should have done. commit d0a0df5b9c58bf06e2a8ad5e5dd46a4ec90ee8cd Date: Mon Oct 5 17:23:03 2015 -0700 Remove protocols_f.5 from apps.test.settings. This will restore the mac unit tests to go with the removal of the library in Pull request #810. commit e31164f231ca23bbdc8d211b53d21b9a5804974c Date: Mon Oct 5 17:27:51 2015 -0400 modifying the xcode project build_util.py to work with the latest master. Pull request #810 removed protocols_f.5 from all src.setting files (it appears to have been an empty library anyway), in order for the xcode make_project tool to work protocols_f.5 must be removed from the KNOWN_PROJECTS dictionary commit 608068d0537e7a63960ab4c649edb48a3cf145d5 Merge: af43864 30223fb Date: Mon Oct 5 10:51:41 2015 -0700 Merge pull request #845 from RosettaCommons/davidekim/minimal_fragments Added support for multiple Vall database files when generating commit af43864e0fc28c0877dc3596bdfc376e9cae297d Merge: 47d25c40 2b9a8f8 Date: Mon Oct 5 20:05:08 2015 +0300 Merge pull request #839 from RosettaCommons/kwikwag/peptiderive-talaris Kwikwag/peptiderive talaris commit 47d25c40cab5d2c6c4ca93603e2e4212a3946997 Date: Mon Oct 5 11:26:40 2015 -0500 Fix inverse_rotamer_remodel integration test. If you put a tracer output statement that prints object addresses in the code, yeah, that's going to cause integration tests to fail. commit 501b202404d177da5dfc4fa2416be0ef1e362102 Merge: 0f58a6a e2492d7 Date: Mon Oct 5 08:53:20 2015 -0700 Merge pull request #756 from RosettaCommons/rhiju/remove_patch_selectors_from_daslab_code + Remove patch selectors from daslab code + For residue_type_set, name3_map_DO_NOT_USE and aa_map_DO_NOT_USE calls are still not suggested as best practices, but now run over a set of about 30 patches that were on by default in 2015 rosetta -- this allows unit tests and a few integration tests to not time out. Any new patches (e.g., upcoming metapatches) are not covered. + got rid of some legacy code (e.g., for setting up packer jobs for residue types with custom_variants in ResidueLevelTask_) since I could expand ResidueTypeSet to handle them. Only tests that change are integration -- inverse_rotamer_remodel remains broken; and ligand_motif_design generates fewer FullatomCustomPairDistanceEnergy AtomPairFunc lists, but that does not affect test results. The linux integration_release_debug_no_symbols show some change, but I think that's due to clang versions -- will monitor carefully. commit 0f58a6a16e769f6da97f65acfa43df0bd4c7d352 Date: Mon Oct 5 16:10:01 2015 +0300 Update Doxyfile.01 commit 19257b04c137a658393260732f56047cd914092e Merge: ddbdc3c c176700 Date: Sun Oct 4 15:01:43 2015 -0500 Merge pull request #842 from RosettaCommons/roccomoretti/inv_rot_remod Attempt to fix the inverse_rotamer_remodel integration test Recent changes mean that the inverse_rotamer_remodel integration test has gone from crashing silently to failing with a recognizable error. This provided an opportunity to start picking things apart. The current cause of failure looks to be an issue with the ReadResfileAndObeyLengthEvents taskoperation. The ReadResfileAndObeyLengthEvents taskop collects a number of Conformation LengthEvents and combines them to get a mapping of before to after residue numbers. The issue here is that the mapping code was pulling the total size from the stored Conformation (raw) pointer in the LengthEvents. This has two problems. The first is that it gets the length from the final conformation, rather than the length at the time the LengthEvent occured. The second is that the raw conformation pointer might have been invalidated, due to copying, etc. resulting in an invalid read. This pull request fixes that by storing the current value of the Conformation length when the LengthEvent is created, and then using that value (rather than the value from the Conformation pointer) when making the mapping. It does not address the more general issue of long-term storage of a raw Conformation pointer in Event objects, where the underlying Conformation might be invalidated in the meantime. commit ddbdc3c921c8f15ab7386db039756bff862b935a Merge: 50a4078 a9841dc Date: Fri Oct 2 21:35:49 2015 -0700 Merge pull request #803 from RosettaCommons/rhiju/remove_placeholder_residue_types *Removing last exponential blow up in ResidueTypeSet* Reduces setup time for FA_STANDARD residue type set from 1.1 seconds to 0.40 seconds on my machine. Allows activation of all available patches (e.g., ones currently under command-line control; see https://github.com/RosettaCommons/main/pull/756) and new 'metapatches' (see https://github.com/RosettaCommons/main/pull/844) without blowup of setup time & memory. All Rosetta modes now compatible with refactored ResidueTypeSet and accessor function, including adducts; and lots of code cleanup. Only tests that change are integration tests: + _fiber_diffraction_fad_, _fold_and_dock_ (cosmetic, tracer debug now registers instantiation of D-AA residue types) + _inverse_rotamer_remodel_ (broken before at SequenceMapping) + _mm_params_ now loops through D-AA residue types, though does not actually check mm parameters for those-- could do so. + _dna_interface_design_ changes at late stage; tracked down to a difference in a random number in a SmallMin move -- all the 'physics' of the simulation, including number of adduct rotamers used in design, appears preserved up to that point and later -- may be a sign of a memory leak. + _number_of_residuetypes_ now does not report on total number of residue types, which is no longer computed, but on the components of ResidueTypeSet, e.g.: ``` apps.pilot.doug.number_of_residuetypes: The FA_STANDARD ResidueTypeSet contains 364 base ResidueTypes, 71 Patches, and 0 custom ResidueTypes ``` instead of ``` apps.pilot.doug.number_of_residuetypes: The FA_STANDARD ResidueTypeSet contains 42632 ResidueTypes ``` commit 50a40789725c36ea42bfd1b4f602f431e6746a68 Merge: c09d7d9 4013ecf Date: Wed Sep 30 17:43:02 2015 -0500 Merge pull request #843 from RosettaCommons/roccomoretti/mm_params_fix Attempt to fix issues with the mm_params integration test. Use Rhiju's ResidueType sorter to fix the order of iteration in mm_params.cc commit c09d7d950c718e8c90b7bc7ec6b8227d88a3eaac Merge: b1eb140 aede2bb Date: Wed Sep 30 13:00:46 2015 -0700 Merge pull request #810 from RosettaCommons/tlinsky/sheettopo Update SheetConstraintsRCG and SecondaryStructureFilter to work with … commit b1eb14003265987a7f869d5211a39043f8d4d37c Merge: 876fac6 eb3f582 Date: Wed Sep 30 08:24:36 2015 -0700 Merge pull request #841 from RosettaCommons/tlinsky/matcher_multiplepose Matcher now appends existing remarks to new matcher remarks commit 876fac6a3fa16f99b3bf41f42f895c33927eb0cb Merge: 50f2cf3 71e7b57 Date: Tue Sep 29 14:40:52 2015 -0700 Merge pull request #834 from RosettaCommons/vmullig/disulfidize_symmetry Allow the Disulfidize movers to add disulfides across a symmetric interface. Tasks: - Add declare_chemical_bond() function to SymmetricConformation class. - Add ScoreFunctionOP to DisulfidizeMover class. - Edit DisulfidizeMover's parse_my_tag to let user set scorefunction. - Get global scorefunction if user specifies no scorefunction. - Check symmetric iff symmetric pose. - Get core::utility::rebuild_disulfide() to work with symmetric poses. - Use symmetric packer. - Use symmetric minimizer. - Fix issue in case where the symmetric copy is the same residue as the original. - Fix additional strange issue causing rare failure. - Seems to be caused by independently finding multiple disulfides at equivalent positions. - Beauty. - Add integration test. - Update documentation. - Set scorefunction. - Use with symmetric pose. commit 50f2cf33691711f97c7303924af1bb8fb6673520 Date: Tue Sep 29 14:13:29 2015 -0700 Fix option naming in parse_my_tag commit 9d3b69a7a8ab0e9791a31b0e8820e2edee7093a7 Merge: 7df645a e665eaf Date: Tue Sep 29 14:02:20 2015 -0700 Merge pull request #825 from RosettaCommons/tlinsky/pdbinfo_selector Create ResiduePDBInfoHasLabel residue selector commit 7df645a61ee84e4afa80746d5caf30351dae2eed Merge: ac1e7bb 7f73987 Date: Tue Sep 29 13:55:23 2015 -0700 Merge pull request #812 from RosettaCommons/tlinsky/sequence_selector Initial commit of PrimarySequenceNeighborhoodSelector commit ac1e7bb408fd067c65db31fa69b7a35536a65b1c Date: Tue Sep 29 20:31:11 2015 +0300 hiding source code commit 5618f4f7fd7979ca6ec8e02f728019c18728c34d Date: Tue Sep 29 20:29:03 2015 +0300 hiding source code commit ac1ba5c978fa275a54043ace3c946742bb9a3bd2 Merge: ed67285 17fd56a Date: Tue Sep 29 10:17:38 2015 -0400 Merge pull request #833 from RosettaCommons/dougrenfrew/gfp_chromophore_params Adding params for the chromophore in GFP (eg. 4EUL) commit ed67285c387dd0f3b1e05cec5cc3dc8cf463df96 Merge: f9d95e2 3d661de Date: Tue Sep 29 02:50:44 2015 -0700 Merge pull request #824 from RosettaCommons/tlinsky/matcher_multiplepose Add option to restore the previous behavior to MatcherMover commit f9d95e2ca04fd6a56a1a7c139434a9ea924e8670 Merge: 3b94d13 236df7a Date: Mon Sep 28 16:34:24 2015 -0700 Merge pull request #838 from RosettaCommons/vmullig/fix_integration_tests Fixing mistake in HbondsToResidueFilter that was causing two integration tests to fail. I was cloning the scorefunction even if the owning pointer were NULL. Fixed now. commit 3b94d13f5707a1c56c70022772549c1849b59ed4 Merge: 930861e c6d62e0 Date: Sun Sep 27 19:32:36 2015 -0400 Merge pull request #454 from RosettaCommons/smoe/gcc-5_compatibility_PeakFileFormat_arraySize g++-5 found fixed array with variable limit commit 930861e92d428daf723db85cf7cddd863c0d5fde Merge: 2cbe954 6d3ef33 Date: Sun Sep 27 11:18:34 2015 -0400 Merge pull request #784 from RosettaCommons/everyday847/analytical_mm_etables Analytical etables for MM LJ potentials commit 2cbe95487f058c17e9e923ee9a14b368dac152c9 Merge: 99dbfb9 893ea2d Date: Sun Sep 27 09:41:07 2015 -0500 Merge pull request #827 from RosettaCommons/havranek/new_multipole_derivs Havranek/new multipole derivs commit 99dbfb911bc8cc5e81a326bfd3b935a5a9b88113 Merge: d4db59e 2e805f4 Date: Fri Sep 25 20:17:05 2015 -0400 Merge pull request #791 from RosettaCommons/everyday847/residue_pair_deriv Integration test changes are only present in circumstances where minimization uses the new method, as might be anticipated. In general, minimization seems more effective, if anything. commit d4db59e2a0a8414623013a74e28463894471a83a Merge: 9184a65 09aedfc Date: Fri Sep 25 11:55:56 2015 -0600 Merge pull request #826 from RosettaCommons/PyRosetta Updating PyRosetta dependency calculation algorithm. Adding detection and deletion of stray dir in build directory's. commit 9184a652bc35c3c1cd2a77d1f9c77d580d0c209b Merge: ecf9ce8 dba492c Date: Fri Sep 25 03:42:27 2015 -0700 Merge pull request #831 from RosettaCommons/revert-830-revert-829-vmullig/clang_fix_master Re-merge "Fix library levels and Mac clang builds" Reverts RosettaCommons/main#830 commit ecf9ce868e516c82c7618a1c8b6c75dffbfc5c9f Merge: 21af408 c6d19d2 Date: Fri Sep 25 03:25:14 2015 -0700 Merge pull request #830 from RosettaCommons/revert-829-vmullig/clang_fix_master Revert "Fix library levels and Mac clang builds" Reverts RosettaCommons/main#829 Blargh -- I was too quick on the merge. commit 21af408d3374a577d84871e2a2439bd6b59182a2 Merge: 6842695 96a3344 Date: Fri Sep 25 03:18:01 2015 -0700 Merge pull request #829 from RosettaCommons/vmullig/clang_fix_master Fix library levels and Mac clang builds @davidekim: Please use the test server next time. Your merge messed up the library dependencies. Restoring by moving cyclize_peptide() and fixH() functions from protocols/forge/methods/util.cc to protocols/relax/util.cc. In the process, I'm rewriting fixH() to use the proper functions in core for rebuilding polymer bond-dependent atoms (rather than manually placing the atom named "H" at a hardcoded position). commit 684269596b1a88146e87337f659832c326457e1d Merge: fd66021 ea2bdc4 Date: Fri Sep 25 01:31:40 2015 -0400 Merge pull request #808 from RosettaCommons/everyday847/more_ring_work Pack with ring conformers commit fd66021f71d2e80c60c7ea4ee4896cc00cd11c46 Merge: 8070d21 84a79d1 Date: Thu Sep 24 12:43:57 2015 -0700 Merge pull request #828 from RosettaCommons/davidekim/gaurav_cyclic_peptide_stuff Adding in Gaurav's cyclic peptide code for ab initio. commit 8070d21e80be50aed58d4daf8f1aa658105e78d7 Date: Thu Sep 24 10:28:50 2015 -0700 Added a torsions only vall for the older vall 2001 version. commit c9daadbe3fa6919b7b91a9118aaf3d7d79d28704 Merge: 60a7a14 6d13d56 Date: Wed Sep 23 14:25:29 2015 -0700 Merge pull request #771 from RosettaCommons/kylebarlow/general_dev Fixing cmake cppdb linking errors in 2013-onward linux g++ versions Committing fix suggested by Tom Linsky on rosetta-devel@googlegroups.com on Fri, May 8, 2015. Solution also referenced at: http://stackoverflow.com/questions/20369672/undefined-reference-to-dlsym This doesn't break the Clang builds on my machine, but I'll be testing that, and the behavior of other g++ versions, on the test server shortly. Linking error fixed by this: libcppdb.so: undefined reference to dlsym' libcppdb.so: undefined reference todlclose' libcppdb.so: undefined reference to `dlopen' collect2: error: ld returned 1 exit status commit 60a7a14b4718b00f4f4875752d0201397384bc2d Merge: 1a50248 e66ef97 Date: Wed Sep 23 13:33:43 2015 -0700 Merge pull request #804 from RosettaCommons/vmullig/peptide_predict Adds a pilot app to predict structures of backbone-cyclized peptides This is basically one of my RosettaScripts converted to C++ and enhanced with tunable parameters that can't be adjusted easily in RosettaScripts without rewriting the script. Tasks completed: -- Add simple_cycpep_predict.cc in apps/pilot/vmullig. -- Read in sequence and build peptide. -- Cyclize. -- Circular permutation. -- Add constraints. -- Read native. -- Set omega and randomize mainchain torsions. -- GenKIC closure -- GenKIC filtering by rama and total hbonds. -- Added rama filter to GenKIC. -- Documentation for new rama filter. -- Integration test for new rama filter. -- Added scorefxn option to HbondsToResidue filter. -- Documentation for this option. -- FastRelax with high hbond strength of each GenKIC solution. -- FastRelax top GenKIC solution, updating cyclic O and H. -- Re-filter by total hbonds. -- De-permute (undo the cyclic permutation). -- Calculate RMSD to native. -- Dump pose and filter results. -- Repeat nstruct times. -- Add integration test. -- Add internal documentation. commit 1a502488edd6566290db2fa7b5f04191a86f7c1d Merge: 551a664 84ac553 Date: Wed Sep 23 13:29:10 2015 -0700 Merge pull request #820 from RosettaCommons/vmullig/mac_clang_issue Trying to fix Mac clang unit test build Removing the "#define private public" and "#define protected public" lines from unit tests. Updating LoopModelerTests and DsspDesignOperationTests to be friend classes to the classes that they're testing. commit 551a6648e43bcdb0bf6bbca430333c5b26713e24 Merge: 0209414 6e2fd85 Date: Wed Sep 23 14:37:09 2015 -0500 Merge pull request #823 from RosettaCommons/roccomoretti/fix_dna Fix for dna_interface_design test Convert the debug_assert() which is failing to an if(){ utility_exit_with_message() }, with extra debugging output to (possibly) assist users, and increased output levels on dna_interface_design integration test. Also, fix the underlying issue with the triazolamerN patch, which is related to deleting the H atom when it's used for the internal coordinates of the base residues types. Instead, just make the H virtual, like N. This may or may not be the long-term fix for this patch. commit 0209414da0bc1eedff43ede717fae47258a5e205 Merge: ecc3369 928c7ee Date: Tue Sep 22 20:38:07 2015 -0700 Merge pull request #822 from RosettaCommons/davidekim/indexed_fragment_dev Davidekim/indexed fragment dev commit ecc3369e2f7c3596dc4611d0e74a7c90885003bb Merge: ef0ed1c c2df409 Date: Tue Sep 22 18:23:51 2015 -0500 Merge pull request #821 from RosettaCommons/bazzoli/ppi-weights Updated PPI_discrimination.wts commit ef0ed1cdfdbd5ccd64b8a43b44802ac72f2ee7fe Date: Tue Sep 22 16:12:10 2015 -0700 add crued residue-pair-motif scoring pilot app commit 562bba3f5b43e9a366c69d69475e182f4b599c86 Merge: 37fcd29 ec92a57 Date: Tue Sep 22 15:49:53 2015 -0700 Merge pull request #819 from RosettaCommons/vmullig/tweak_bettercluster Small tweaks to bettercluster pilot app Small tweaks to bettercluster pilot app. No test changes expected. commit 37fcd291840346f4a86a780e4ebbe9301cd00e7f Merge: 45d2d62 a6ff0f9 Date: Tue Sep 22 14:46:11 2015 -0700 Merge pull request #814 from RosettaCommons/revert-813-vmullig/unfustercluck Revert "Vmullig/unfustercluck" Reverts pull request #813. This restores: -- Merge of pull request #798 ("Use SSBOND records, if available...") -- Merge of pull request #793 ("Remove exception from annotated sequence") -- Commit 68a6a18 ("Fixing library levels build") -- Commit 36de51b ("Fixed unused variable") -- Merge of pull request #807 ("Exclude PNA from chirality checks...") -- Commit d475d31 ("Using two vectors... ugh.") commit 45d2d6299afa7e97169b7136edf3f55deab97387 Merge: 4c3e326 03adf56 Date: Tue Sep 22 09:59:56 2015 -0600 Merge pull request #818 from RosettaCommons/PyRosetta Adding PyRosetta binding for RotamerVector commit 4c3e326484b53e1061a1d77427e00ef88c9afc6a Merge: ab66592 e94a399 Date: Mon Sep 21 23:45:51 2015 -0700 Merge pull request #817 from RosettaCommons/vmullig/mac_clang_issue Fix the Mac clang 3.7.0 issue Mac clang 3.7.0 has thread_local as a C++ language keyword, albeit one that throws an error if used in the absence of c++11. This means that our attempts to define thread_local when not using c++11 throw an error. This is an attempt to remedy this. Instead of defining thread_local, we define THREAD_LOCAL as: -- nothing if we're not using c++11 -- thread_local if we are Then we replace all instances of thread_local in the code with THREAD_LOCAL. Note that there's still an issue to resolve in one unit test (ResidueGraphTypesTests), which has the following lines in it: // Unit Headers #define private public #include #undef private This is still preventing the Mac clang unit tests from compiling. I can see why someone would do this to expose the private functions in the class that they're trying to test, but I also think it's important that the compiler flag attempts to redefine language keywords. commit ab665922d6a1494d0443a7e1b4dbd0c7f435a3f2 Merge: 17f845e a62fd7f Date: Mon Sep 21 11:17:27 2015 -0700 Merge pull request #816 from RosettaCommons/hpark/beta adding beta_july15_cst.wts for cst usage with the energy function commit 17f845ee9e12ca5b286594aafa51e8e3c1ef6296 Merge: d475d31 263deb1 Date: Sun Sep 20 22:07:16 2015 -0700 Merge pull request #813 from RosettaCommons/vmullig/unfustercluck Vmullig/unfustercluck Rolls master back to Sergey Lyskov's commit 1da8a4c, before a whole lot of stuff was broken. @everyday847, @rhiju, I'm going to create a branch and a pull request for reverting this pull request (i.e. restoring all of the broken stuff). IN THAT BRANCH please fix all the broken stuff, test the branch, then re-merge with master. commit d475d31a34bcce75565e04ec7665a91adbb4e6dd Date: Sun Sep 20 17:53:28 2015 -0400 Using two vectors... ugh. commit aafd27f0b141606896785df14148c5a8cd1beefd Merge: 36de51b be07da8 Date: Sat Sep 19 19:27:36 2015 -0700 Merge pull request #807 from RosettaCommons/rhiju/fix_pna_integration_test exclude PNA from chirality checks to determine D- or L- amino acids, … Fixes PNA integration test. commit 36de51b986fd4efb3a21054529f719db3766368b Date: Sat Sep 19 17:51:00 2015 -0400 Fixed unused variable I had intended to cut down on having too much warning output per annotated sequence read-in that I left half-implemented. So sorry! This should be it for now... :-( commit 68a6a189e8cbe3dd267cd65d0b3004ea7eb37697 Date: Sat Sep 19 14:54:57 2015 -0400 Fixing library levels build; sorry! commit 791ade228547653e8dc189c8eb851113b4381ead Merge: 450d750 dc32015 Date: Sat Sep 19 14:47:43 2015 -0400 Merge pull request #793 from RosettaCommons/everyday847/deprecate_disulfide_exception Remove exception from annotated sequence commit 450d75095dfa6bb8ebca173cd77ef5190b5423e5 Merge: 1da8a4c dac22cf Date: Sat Sep 19 09:32:01 2015 -0400 Merge pull request #798 from RosettaCommons/everyday847/ssbond_input Use SSBOND records, if available, to prompt conformation::detect_disulfides. Integration test changes are all cosmetic/reflect that NtermConnect and CtermConnect are no longer silenced by CMDLINE_SELECTORs. commit 1da8a4c0bcd967364f2acc107fa553b147a4a786 Date: Fri Sep 18 18:58:17 2015 -0400 Updating HPC ‘execute’ so it uses test working dir for logs by default commit 0184b0529438399008749f63994991f4cc59bfa6 Merge: dbcf6ff 01efea3 Date: Fri Sep 18 14:54:21 2015 -0400 Merge pull request #799 from RosettaCommons/everyday847/branching_in_centroid Rudimentary centroid mode for branching commit dbcf6ff6e9024aa6ed2e280ff5ed6eac7f3b655f Merge: c0e92cf 08414b5 Date: Fri Sep 18 09:26:02 2015 -0700 Merge pull request #806 from RosettaCommons/rhiju/fa_stack_updates Rhiju/fa stack updates all changes are OK: +broken tests are the 'usual' ones in integration (pna, inverse_rotamer_remodel), which I'm fixing in a separate branch. + also saw a 'cosmetic' line ordering change in integration.release_debug for mm_params. + last, dna_interface_design is also broken, but only in integration.release_debug (not integration). seems to be affecting everyone.