commit 944115c091102e1bcc3ffa5875f11e0edf5debb9 Merge: 29ced55 e4effc5 Date: Tue Aug 19 18:36:09 2014 +0300 deleted a tracer in SSMotifFinderFilter commit e4effc5cecfb1620a13d09de4db8383908c27be2 Date: Wed Aug 20 13:56:40 2014 +0300 some documentation in Splice, lest we forget... no test changes expected. commit 240c100420d85de87ae0a28e8494de8fedc0a2cb Date: Wed Aug 20 00:57:02 2014 -0400 Dummy commit to trigger tests run commit a53bc9e9b6c9ecc45965d148887d8df7df4f6d08 Date: Wed Aug 20 00:03:57 2014 -0400 Updating benchmark integration scrip to use _S_script_failed_ state on tests that did not run. Temporary breaking HOW_TO_MAKE_TESTS test so it fail each time. commit 129219784e299269086e44122c0fdfdfba74b0eb Merge: 40d212b dca1ba8 Date: Tue Aug 19 18:53:23 2014 +0300 Updated the follwoing integration tests: 1. splice_out_generic 2. splice_out 3. splice_in_genric 4. splice_in 5. splice_seq_const These ofcourse will fail compared to previous commits In Splice.cc: 1.Add Carbonyl coordiante constraints 2. Changed the current segment behvaiour so it reads the current segment from the XML rather than the pdb 3. In SpliceSegments the occurrence data for H3 loops with no occurrence data is filled in by Rosetta (previously this caused a segmentation fault) 4. In SequenceProfile I added getter and setter functions for accessing the occurrence_data array 5. In SeqprofCons I added tracer lines to check correctness of occurrence_data array commit 40d212b823091026ccfbe147c905a3ed451edf59 Merge: c833d13 4dddd40 Date: Tue Aug 19 18:52:15 2014 +0300 esolved conflicts between Splice.cc on local branch and remote branch Conflicts: source/src/devel/splice/Splice.cc commit 29ced5551f91bb8104618e164337b67f39a71374 Date: Tue Aug 19 18:36:09 2014 +0300 deleted a tracer in SSMotifFinderFilter commit 4aeae49e3f57922329eadcb7284528833ad6cb76 Date: Tue Aug 19 10:25:03 2014 -0500 Remove unused flags from integration tests. commit dca1ba8a5cf102a30f3ec361438ddd2f2f4fa878 Date: Mon Aug 18 21:06:41 2014 -0400 Making inv_kin_lig_loop_design add the appropriate cutpoint variants for compatibility with the CCD mover. This was causing an exception to be thrown, which in turn caused the inv_kin_lig_loop_design integration test to fail. This fixes the inv_kin_lig_loop_design integration test. commit c833d13902eb2eac395c50c9c384a9a4cd99c0a1 Date: Tue Aug 19 15:35:52 2014 +0300 Updated the follwoing integration tests: 1. splice_out_generic 2. splice_out 3. splice_in_genric 4. splice_in 5. splice_seq_const In Splice.cc: 1.Add Carbonyl coordiante constraints 2. Changed the current segment behvaiour so it reads the current segment from the XML rather than the pdb 3. In SpliceSegments the occurrence data for H3 loops with no occurrence data is filled in by Rosetta (previously this caused a segmentation fault) commit 4dddd4039d9f5e131bff5cb21121e334146a85da Merge: 9d5e18a 87c1998 Date: Tue Aug 19 13:19:25 2014 +0300 Merge branch 'master' of github.com:RosettaCommons/main commit 9d5e18a7c060061a418e9e16a4678851dbb68f5a Date: Tue Aug 19 11:56:45 2014 +0300 In Splice.cc I added the option to use pdb numbering in the flags: source_pdb_from_res, source_pdb_to_res. In superimpose_source_on_pose function I changed the superposition to be not only in the stem sites but also in the neighboring residues. In splice.hh I added source_pose_ as private PoseOP. I created a new filter called SSMotifFinderFilter which allows searching for secondary structural motifs that resemble a given template motif. The filter does the following: it searches for pairs of residues in the pose (with some predefined distance from each other) that have the same secondary structure as the template motif's stems. Then it superimposes each matching pair and its neighboring residues onto the template stems and calculates the rmsd from the template stems. Pairs with rmsd lower than a predefined rmsd cutoff are written to a file. ---------------------------------------- Unit test status: Pass Integration test status: 0 commit b6138e8e893eeaea62400e8743cb2a20204a8ca0 Date: Mon Aug 18 23:31:44 2014 -0400 Adding _api_version_ to benchmark build script. Adding awareness of memory limit to PyRosetta build test. commit 87c1998e332f3d3ddd124990cff22761b8cb6ea0 Date: Mon Aug 18 18:35:08 2014 -0400 Patch System: added 3 new PatchOperations NEWS: This push introduces three new PatchOperations to the patch system: - ADD_ATOM_ALIAS -- allows one to specify alternative atom names that Rosetta will understand when reading in a PDB file - ADD_BOND_TYPE -- an alternative to ADD_BOND that allows specification of bond type - SET_FORMAL_CHARGE -- sets the formal charge of a specified atom All of the above new operations rely on code written by R. Moretti and co.; I simply added the functionality to the patch system as well. (Previously, atom aliases, bond types, and formal charges could only be added/set from .params files.) The above operations were added to carbohydrate patch files were applicable. The carbohydrates integration test was expanded to specifically test that the atom aliases work: a pdb with non-Rosetta atom names correctly loads in. In addition, centroid-mode sugars were updated, (which at this point are simply copies of the fa_standard ones). ---------------------------------------- Unit test status: Pass Integration test status: Not Run (Only sugar code makes use of the additions.) carbohydrates: test expanded commit 72dafb235eabd471c101d81261136fa99579afd4 Date: Mon Aug 18 18:31:47 2014 -0400 Carbohydrates: added ADD_BOND_TYPE and SET_FORMAL_CHARGE lines to sugar patch files where needed commit a1bacc76c3c140aeeeb65db5878ee330f4de6601 Date: Mon Aug 18 18:15:02 2014 -0400 Patch System: implemented the two new PatchOperations commit f0f1286d1c50e0bc50acab8b4899ea5df4107fc1 Date: Mon Aug 18 17:48:21 2014 -0400 Patch System: adding AddBondType and SetFormalCharge PatchOperations commit b24d2c84ec79c0c6f1c2a691f0e57e8686128369 Date: Mon Aug 18 17:23:40 2014 -0400 Carbohydrates: the changes I meant to make a few commits ago commit fff0bce9c22e0fd82c456b54d9930461aef6cd19 Date: Mon Aug 18 17:16:20 2014 -0400 adding forgotten file commit 3da344846bdff26dfa69d7e648f5d61a00c20e3c Date: Mon Aug 18 17:08:18 2014 -0400 Carbohydrates: moved integration test app commit 115a7696a00512d0eb44830bcf016928062b6b5d Date: Mon Aug 18 15:56:46 2014 -0500 Reorganize options - subgroups should come after regular options. commit f64a0efc6ea780748426e0b7f4c877b8b06eaccc Date: Mon Aug 18 16:56:06 2014 -0400 Carbohydrates: adding ADD_ATOM_ALIAS lines to N-acetylation patches commit 4ddb798b61550ebbf7804dba567549084f866ac4 Date: Mon Aug 18 16:40:46 2014 -0400 Patch System: new PatchOperation now set from reading patch files commit 79eebae7d64189d0373c5da64eb53679f46a1ab2 Merge: 4716d05 0eb0f73 Date: Mon Aug 18 15:39:05 2014 -0500 Merge remote-tracking branch 'origin/master' into roccomoretti/option_cleanup commit fb64e8ae1f94056c4e5ff497cce7df837550d76c Date: Mon Aug 18 16:13:51 2014 -0400 Patch System: implemented new class methods commit 48789790a5e5977977811a498f5a8cb498621cad Date: Mon Aug 18 16:00:26 2014 -0400 Patch System: adding new PatchOperation for atom aliases commit ab97f394660a41687cba8e92c02fdff28f833a13 Merge: ed2b6dd 0eb0f73 Date: Mon Aug 18 15:40:15 2014 -0400 merging in master commit 0eb0f73291058a58b54e710b406af483629eba35 Date: Mon Aug 18 15:08:26 2014 -0400 Loops: bug fix for when overlapping loop is found In the case when one adds an overlapping Loop to a Loops object, there was a dormant bug that our recent CCD refactor uncovered where the Loops object would attempt to output the Loop information after deleting the no-longer needed loop. I just fixed that. This push also includes the removal of two deprecated/legacy antibody integration tests. commit 263751120904a222dfaf7b5a04d1c20e07f75899 Date: Mon Aug 18 13:35:12 2014 -0400 removing deprecated/legacy antibody integration testing commit 4716d052cf0088611a0b5cf0af36002c53945b0c Date: Mon Aug 18 11:10:32 2014 -0500 Option cleanup - mh is an application level group commit e308006fffa5e3c6e12c59f49a8b4764d0cd8f6d Date: Mon Aug 18 10:51:36 2014 -0500 Option cleanup - personal options. commit c8392553e05f31ab18cf14d0945098fe97542c0f Date: Mon Aug 18 08:08:05 2014 -0500 Option cleanup - application specific options. commit 55c70075d8344c6f9f490469211f29849bca6771 Date: Sun Aug 17 21:21:08 2014 -0500 Option cleanup - remove unused general options. commit 89b4a3f506e92405a99710b4a5492f609a74f53c Date: Sun Aug 17 19:40:09 2014 -0500 Option cleanup - remove unused from in,out,etc. groups. commit d53b7d961101b866f71272c1bc4b9914afc83402 Date: Sun Aug 17 17:23:11 2014 -0500 Remove option.cc.gen.hh use This is an internal option system file, and shouldn't be used by applications. commit a9f80cba802098898b1d864c548760d868cdd709 Date: Sun Aug 17 16:47:46 2014 -0500 Option system cleanup. Reorganize options_rosetta.py. commit 7cbfafc5a18115c9a2eac06d3a2146033d35e50a Date: Sat Aug 16 17:14:42 2014 -0400 Fixing header build commit a8217adf68b70bfbeedff32c19f8d5165f5f4b22 Date: Sat Aug 16 16:01:03 2014 -0400 lowering tracer volume on test to avoid 30-GB log files commit 7174e8b54b08731ef43197adfe756533b4586e5e Date: Sat Aug 16 12:55:08 2014 -0400 Fixing PyRosetta Mac build. Adding settings for Clang 5.1. Minor improvements to dependency calculation. commit 0c2306353b86c6f647daf6f70f7036af1e55b80b Date: Sat Aug 16 10:56:00 2014 -0500 Fix "Possibily uninitialized variable warning" on my machine. commit 600faad98dde20f26a93e7df6f7c3a0fe03ae84d Date: Sat Aug 16 01:34:39 2014 -0400 fixing build broken by sarel commit 4309f54708e52331794ea3c5565efce1b27da6a1 Date: Fri Aug 15 18:07:52 2014 -0700 Bugfix for helical symmetries in setup script commit 4345a86a797c07f4e8581181a4c436a73dbf60db Merge: df5c39b 844bdae Date: Fri Aug 15 18:28:01 2014 -0400 Merge pull request #51 from RosettaCommons/weitzner/make-ccd-a-class Weitzner/make ccd a class HUZZAH! :camel: The integration test changes are plentiful and totally expected. If your code is affected and you are concerned, shoot me an email. commit df5c39b8ba32fab0ae75b2910b4c513d5915ba1b Date: Fri Aug 15 15:23:53 2014 -0400 Turning off the membrane relax 2 test until we can figure out what is going on. Jason labonte fully endorses not pre-testing this commit before pushing to master ;) commit 266fd4cf73c331dbb0b66a508ef47aea9b87e572 Merge: 2a22d88 d4e7d5e Date: Fri Aug 15 15:10:34 2014 -0400 Carbohydrates: adding CHARGE and BOND_TYPE records to sialic acid topology files commit 2a22d888831d3704d6ee37782cc7335b99b41212 Date: Fri Aug 15 15:10:16 2014 -0400 Carbohydrates: adding CHARGE and BOND_TYPE records to sialic acid topology files commit d4e7d5ec5872c6be64a5a1326a32a5b2e5440cfa Merge: 3383c70 de3b815 Date: Fri Aug 15 15:09:07 2014 -0400 PyRosetta. Adding type alias for gnu vector implementation. commit de3b815d26f626b2896a23180437bfae35efd5f5 Merge: c9d6f7b 989d118 Date: Fri Aug 15 13:53:19 2014 -0400 Carbohydrates: adding VIRTUAL_SHADOW lines to sugar topology files commit c9d6f7b05022c97eccf37d807e148bf05b3bcbfd Merge: 988e8c3 8c96e40 Date: Fri Aug 15 13:52:10 2014 -0400 Carbohydrates: adding VIRTUAL_SHADOW lines to sugar topology files commit 8c96e401e0fc23a4e5766a55393e7b0bf2a7ca78 Date: Fri Aug 15 13:51:15 2014 -0400 Carbohydrates: adding VIRTUAL_SHADOW lines to sugar topology files commit 989d1189896b66e33d1a1f5bc19d0298a9464d14 Merge: 93ede97 3ca47d2 Date: Fri Aug 15 08:24:50 2014 -0700 Merge pull request #61 from RosettaCommons/luki-mbi/rosetta_scripts_include Adding file includes to RosettaScripts. This addition is intended to help break up long RosettaScripts protocols into reusable code blocks or modules, which live in separate XML files. Multi-level includes and variable substitution are supported. commit 93ede97231efe9da629b5d527757beacb22e502b Date: Fri Aug 15 11:16:57 2014 +0300 removing CircularPermutationFinder dependency on TMalign. The filter is currently not working as intended. Fix will be committed later commit 3383c70bd041477a87a319c116d814317e712ad5 Date: Thu Aug 14 23:34:06 2014 -0400 PyRosetta. Adding type alias for gnu vector implementation. commit 844bdaedc920b7ffc65cf327453444a7d055ef26 Merge: 07800d6 adfd359 Date: Thu Aug 14 20:12:18 2014 -0400 merging in last good master state before pushing the BGB commit 07800d666798667a5b7dbdda1f11c1dfdb0c2333 Date: Thu Aug 14 20:07:12 2014 -0400 typo fix commit e3ae979439963c9260f28d4c42f67f604c0c5f8c Date: Thu Aug 14 19:58:57 2014 -0400 CCD Refactor: few more unit tests -- (as an aside: what the heck is catching these exceptions and changing their messages?) commit 2d35d30a5af3cf0b3cb1597e4df1e17eb11000d1 Merge: 1f39947 f5df8d9 Date: Thu Aug 14 18:17:41 2014 -0400 merging with Brian's work commit 1f3994773b6220a858346ce77ee2875e34620c5f Date: Thu Aug 14 18:16:28 2014 -0400 CCD Refactor: added integration test commit f5df8d983b254cdbf8d9bdfc1a5f08ebfcffb454 Date: Thu Aug 14 17:53:12 2014 -0400 Removing string-based variant types in unit test in anticipation of a change Jason is about to make in another branch commit fb0cab5ddddcc03effa08c189802bc8948ea8d03 Date: Thu Aug 14 17:51:58 2014 -0400 Testing CCDLoopClosureMover's parse_my_tag via the MoverFactory. Fixing bugs in parse_my_tag -- thanks unit tests! commit d52201b979c304caa11efba4baf7e1a30c87d0d9 Date: Thu Aug 14 17:02:14 2014 -0400 Adding unit tests for CCDLoopClosureMover -- specifically for the MoverFactory and copy ctor commit f47c299a626b0c1d3639c3b46ad2857e4f1f16a2 Date: Thu Aug 14 16:19:59 2014 -0400 Enabling AtomID_Map_bool. Adding extra includes for Windows build. commit 988e8c339210c5329551e7e912884c8e067b55aa Date: Thu Aug 14 16:10:44 2014 -0400 Commenting out AtomID_Map_bool for now until i figure out whats going with Windows build commit 2601c1286c169ec2c26f41755ae1287c4a5f6745 Date: Thu Aug 14 14:50:34 2014 -0400 Adding a test case for closing a loop C->N. commit 56393b4f6ce8c3eaa8a232ed789d5e0f91933e3b Date: Thu Aug 14 15:26:57 2014 -0400 fixing namespacing error commit a46982d837a5a330596aafc2a2cd60f44e3e2397 Date: Thu Aug 14 15:07:59 2014 -0400 CCD Refactor: completed renaming commit aae2d4be7fab58891a119093ac67e0770c634469 Date: Thu Aug 14 15:03:04 2014 -0400 CCD Refactor: renamed the class commit ca633b0573df73f2002b285574e29e47929a59b2 Date: Thu Aug 14 13:49:56 2014 -0400 PyRosetta. Adding bindings for AtomID_Map_bool and AtomID_Map_Real classes. commit 3d111b7d6dfd80e714a03093ba4ea563f96939c2 Date: Thu Aug 14 13:14:56 2014 -0400 Benchmark scripts. Reversing order of diff arguments in regression tests comparison functions to make logs less confusing. commit bdef871ea0f9cfd3bd76188d3ba0724dd72cee5b Date: Thu Aug 14 00:30:00 2014 -0400 Reverting disulfide changes until they can be done with better understood side effects commit f2d8102e834f07d84c8acc206e94d6c91dd29ec8 Date: Thu Aug 14 00:21:58 2014 -0400 reverting disulfide commit f5bf83eae6d60246ebde02f8a0f4efca6744255c commit e2ca0ccba5ebd3d958ddea9b537292a4c8786eff Date: Thu Aug 14 00:21:11 2014 -0400 reverting disulfide commit 583edd552b0bc7af9ef1456a1fc342c17c03856d commit 8502f321efaacd0f14c48a4f3ebf992d427b3764 Merge: 78c7260 5059e1d Date: Wed Aug 13 20:13:33 2014 -0700 Merge pull request #63 from RosettaCommons/daslab Daslab -- restoration of efficient protein stepwise monte carlo commit 3e30413db160bf24acb69bd0b208fd01295a5d71 Date: Wed Aug 13 21:25:17 2014 -0400 Adding a second test case to the ccd_angle unit test. commit 86bd4b3ea118c0449b1a8b46cd465e169dd2f89d Date: Wed Aug 13 20:51:09 2014 -0400 Adding a unit test for the CCD math that lives down in numeric. This is a simple test -- if you start with a closed loop, and change just one angle, make sure that CCD can recover the initial angle. commit 78c7260ebb94d5a25c99c4d9f4a5b80b8b78a87e Date: Wed Aug 13 13:57:50 2014 -0400 Fixing bug #0000349. Fixing PyRosetta Linux version detection for cases when version is two digits. commit 7c95aa7b2ee720baec076623fd596330ef5030c1 Merge: 2899a83 e84f365 Date: Wed Aug 13 11:41:16 2014 -0500 Merge pull request #55 from RosettaCommons/roccomoretti/scoredir Don't treat directories like empty score files. Fixes issue Amelie (via Andrew) wrote the devel list about - that local directories (e.g. ./talaris2014/) are treated like empty scorefiles. Alter izstream to error-out when opening a directory on all platforms. Unit tests for new izstream behavior added. commit 2899a83daaed69a1023462945492509f8fe3731e Date: Wed Aug 13 11:36:22 2014 -0400 Fixing debug build. Unit test status: [Pass] commit 094bccbd94a357e3d73224ac652c7b803bfeee47 Date: Wed Aug 13 13:25:28 2014 +0300 fixed a bug in foldtree creation commit d936ff5dca475b72f744298419663af7e9e42527 Merge: 5a099d9 adfd359 Date: Wed Aug 13 10:25:10 2014 +0300 Merge branch 'master' of github.com:RosettaCommons/main commit 5a099d9c74770d2b576a53a6bb135c7dd780451a Date: Wed Aug 13 10:21:29 2014 +0300 DesignableResidues will now print results only once commit adfd359011376ecb08ea437991caf24f5f0804ea Date: Wed Aug 13 09:08:30 2014 +0300 ppk integration test only showed a failure now, even though the error is due to an energy function evaluation that was likely introduced in the far past. Not sure why this is the case. This commit will restore the test commit e84f365f5c28eb2cb72be07abad68c8f771efac1 Date: Tue Aug 12 18:20:29 2014 -0500 Add unit test for izstream directory behavior commit 8c6aa4995789386fa9a61ccaf67fc7f2482af4f3 Merge: 2eaeee9 d2f17aa Date: Tue Aug 12 17:59:20 2014 -0500 Merge with recent master commit 97075e151a0aa3edd3d584750316c1277a533269 Date: Tue Aug 12 16:52:12 2014 -0400 [update of SandwichFeatures] - table name change ( sw_by_components -> sandwich) - generate resfile for more general case also (before this, it supports for poor seq_rec case for RelaxDesign only) - finished refactoring in accordance of better naming convention (use 'using namespace' inside of specific strand_assembly namespace) - should not change any integration tests other than (expected) features and features_database_schema - I think that there is no need to ask 'pull request' since I think that I am the only one who uses SandwichFeatures as of now commit bd2c8002ccb5b1ede60aa3fbdaed0a9aa6c61809 Date: Tue Aug 12 16:29:34 2014 -0400 Updating release_debug settings for all compilers. Making release_debug exactly like 'release' settings but without 'NDEBUG'. Thanks to William Sheffler for pointing this out! commit 61c4bcdf67484ef059162899b06b4a13b7472cb8 Date: Tue Aug 12 16:03:27 2014 -0400 CCD Refactor: response to response to TODO comment: commit dafc665b4af368db5f00b5681660c6b7d46be671 Date: Tue Aug 12 16:02:51 2014 -0400 CCD Refactor: removed 3 anchor points assumption commit e8b333e516f839de279324c1e4e7c20a52479df3 Date: Tue Aug 12 15:10:36 2014 -0400 CCD Refactor: completing renaming commit 3ca47d2007757ad249b10471b1a835852e2be48c Date: Tue Aug 12 10:45:13 2014 -0700 Adding support for variable substitution in included scripts from variables specified in the include tag (see below). Tags inside the INCLUDES tag now specify the include type; currently only XML is supported. Examples: Where module.xml: commit d35572569672962c1e78df8e25a62472542afdf9 Date: Tue Aug 12 13:25:45 2014 -0400 CCD Refactor: renamed a method commit 6b0327c667910df4ccce9aac81480fc617491098 Date: Tue Aug 12 09:56:53 2014 -0700 Adding variable substitution support for included scripts. commit 0dac84d31b34210deb47522125fe07c949cbe1e3 Merge: d2f17aa 38f49ac Date: Tue Aug 12 07:16:57 2014 -0700 Merge pull request #54 from RosettaCommons/dougrenfrew/tempnam_mpi Remove use of tempnam for MPI builds. commit 38f49acbf408207ddd1c9a0cadf4d6d9722c1d4d Merge: e448ffb d2f17aa Date: Tue Aug 12 09:53:55 2014 -0400 Merge master commit d2f17aaaf57dc0f7ae97fdfc3fbef3c40af93870 Date: Tue Aug 12 09:24:41 2014 -0400 Fix an extraneous cout message that got pushed to master. commit 073495bbc44a7df30976523633890c7471c16825 Date: Tue Aug 12 09:10:31 2014 -0400 Hooking CcdLoopClosureMoverCreator into the MoverFactory. commit edf793333b79468816a389af9ca59786ea4d749f Date: Tue Aug 12 09:09:45 2014 -0400 Implementing CCdLoopClosureMoverCreator. commit ae67f5baecec725ee7930fcba4fba56d15107695 Merge: 04b2161 a744258 Date: Tue Aug 12 14:58:56 2014 +0300 Merge branch 'master' of github.com:RosettaCommons/main commit a744258ee38478c844d507f77540e6ee966ad94b Date: Tue Aug 12 14:58:29 2014 +0300 Splice fixes for cases where the template and source pdbs are not aligned commit 04b21617926a9383e7e6faec9d484854a8a21e9a Merge: cc029eb 5268380 Date: Tue Aug 12 14:58:14 2014 +0300 Merge branch 'master' of github.com:RosettaCommons/main commit 52683809448142fa76459c588eea67858e827059 Date: Tue Aug 12 14:56:51 2014 +0300 DesignableResidues tracer fix commit f4f8a60ef2d04323ffe19bb19b317a634c0ae445 Date: Tue Aug 12 14:56:20 2014 +0300 SetAtomTree can now generate a fold tree starting from a specified chain in PDB format (e.g., chain=L) commit 6988348c51b57284b5ab0cb4c85b9f74fb25039c Merge: 5aa052b 3af0b5b Date: Mon Aug 11 19:12:17 2014 -0400 Merge pull request #60 from RosettaCommons/Smotiff_fix Smotiff fix commit e65bb4bda99606751517accf1c739591027f6863 Date: Mon Aug 11 15:15:20 2014 -0700 Tracer cleanup. commit 5c628597c76961273c30cfcb1809409d3a1f720d Date: Mon Aug 11 15:06:05 2014 -0700 Fix accidentally dropped const. commit 8562d33168d3b15888477087a1a0a6a3b9d1a043 Date: Mon Aug 11 14:50:20 2014 -0700 Adding INCLUDES tag to RosettaScripts. This addition is intended to help break up long RosettaScripts protocols into reusable code blocks or modules, which live in sepatate XML files. Example: Included files may contain additional INCLUDES blocks. commit 3af0b5be002b7c0a5d585558e984b7e1fbaed2d5 Merge: 92c1442 5aa052b Date: Mon Aug 11 17:00:39 2014 -0400 Merge branch 'master' into Smotiff_fix commit 92c1442f234228e19c2f5773c80eb48c1d2174b6 Date: Mon Aug 11 16:58:02 2014 -0400 Fixing some logic bugs in secondary structure segment features reporter commit 5059e1d159a51eb5d80d7aa7e9f3d0646e0f625c Date: Mon Aug 11 13:02:30 2014 -0700 updates to rna_graft to close chains if needed and also to allow input of more than one PDB commit c3de69b8654a22818e8dcef93f5ce522cebb4e2f Date: Mon Aug 11 13:11:30 2014 -0400 Attempting to fix windows PyRosetta build commit e448ffb1f1b2b359b8b12c8a02cd99238d6f2149 Merge: 3f31994 5aa052b Date: Mon Aug 11 09:34:39 2014 -0400 Merge master commit 5aa052be34a075adcac832ecea1e5dd915be9771 Merge: 9bdec3e 6dfd6b7 Date: Mon Aug 11 07:36:00 2014 -0500 Merge pull request #59 from RosettaCommons/dougrenfrew/fix_aeh Fixing the application exception handling integration test. Passed tests and got the thumbs up from Julia, whose code it mostly changes. commit 5c2cadefc6c98475cc7ec957221b5444907fb740 Date: Sun Aug 10 16:53:05 2014 -0700 in silent file readin, detect patches that only show up in fa_standard fullatom, and make sure to set fullatom to true for those. commit 326ac7f9ab837ada36a9504b9149ce339ecf1d0f Merge: 34a71c6 9bdec3e Date: Sun Aug 10 16:04:53 2014 -0700 merge from master into daslab commit 9bdec3ef29174144976af06b44dec750e6455708 Merge: c2855c4 b618cfd Date: Sun Aug 10 17:38:10 2014 -0400 Merge pull request #58 from RosettaCommons/tjacobs2/fix_link_residues This commit fixes a few issues I ran into while using LinkResidues task operations. In particular, it seems residues were being linked to themselves (which will always cause an assert failure when run in debug mode). Also, added some robustness to the addition of residues after creating links. Previously, this would cause an index-out-of-bounds error. My fix might cause undesirable behavior if residues are added that change residue-numbering (e.g. add rotamer links, create a new residue with resid = 1, repack). Is there a better way to implement this change? commit 34a71c6c1b8e8b66259ec0b1c4878291e8d12543 Date: Sun Aug 10 12:35:33 2014 -0700 setting number of pose samples to minimize in stepwise monte carlo to be 5 for protein-containing poses. Still 1 for RNA-only problems. commit 745c2d84cf2847966e8c698104f752f36893e333 Date: Sun Aug 10 12:34:56 2014 -0700 remove irrelevant options from help output for stepwise. found during documentation. commit cc029eb6235d92b2a650f6e2798df1ecac1ae89e Merge: 93d55a0 c2855c4 Date: Sun Aug 10 17:38:07 2014 +0300 Merge remote branch 'origin/master' commit 93d55a0a2b522a17a0f884713f4e28327abbdd63 Date: Sun Aug 10 17:37:27 2014 +0300 CircPerm commit c2855c4bdf264b2f5791bd4537be4e45a4376808 Date: Sun Aug 10 17:28:45 2014 +0300 CircularPermutation bugfixes commit 30d57fd550ef946a58fb02dcdef4d4dd6a8dba94 Merge: 454a48e 3c44542 Date: Sun Aug 10 15:27:15 2014 +0300 Merge branch 'master' of github.com:RosettaCommons/main commit 454a48efbd3c0165d67679a51f2a6725129f4906 Date: Sun Aug 10 15:20:33 2014 +0300 Added missing PSSMs to the database needed for Splice mover commit 36f8298239e39e3e93e2255f878945548f29179a Date: Sat Aug 9 19:21:10 2014 -0400 Updating WobbleMover to be compatible with the new CCD closure mover. The mover requires cutpoint variants to be added before it is applied. commit 4414e687c065c91026966edda522c4468b494c77 Date: Sat Aug 9 15:26:22 2014 -0400 Bug fix: We were creating a message exception, but we neglected to throw it. No more! commit 3c44542a2d9700eabd7e987bfcc79fcba27d886b Date: Fri Aug 8 16:42:22 2014 -0400 Rings: fixing broken integration test The rings integration test had been silently broken since @rhiju set the max `ResidueType` limit. commit 600b28713b5f8fb86db3ee56f1d1c390f571d288 Date: Fri Aug 8 14:20:13 2014 -0400 Benchmark scripts, adding integration.release_debug test. commit 6dfd6b7ba557b56839983b9f6cbce2012334bff5 Date: Fri Aug 8 14:15:55 2014 -0400 Fixing the application exception handling integration test. This time, with feeling. commit 47cda5d6fe14a071328abe39dc0ceb8fe5d36197 Date: Fri Aug 8 13:44:50 2014 -0400 Fixing some issues that prevented compilation post-merge commit b618cfd39bd19bf9c0af325b40a4691cd8e5a2c4 Date: Fri Aug 8 11:56:13 2014 -0400 This commit fixes a few issues I ran into while using LinkResidues task operations. In particular, it seems residues were being linked to themselves (which will *always* cause an assert failure when run in debug mode). Also, added some robustness to the addition of residues after creating links. The latter seems like something that should be avoided if possible. There may be a more elegment solution than what I've implemented. commit 9253294ed908bb8cd5641f467e12b0638ecbc077 Merge: e6b365c 12b9917 Date: Fri Aug 8 11:16:42 2014 -0400 Merging the current version of master (8/8/2014 @ 11 AM EDT) into branch so we can show some test results. commit 12b991798eecc4b9e508ce17bef3bd4851d965c9 Date: Fri Aug 8 13:43:38 2014 +0300 Skipping non-protein residues in CircularPermutation and SSMotif Finders commit 2b2f1d0b8356c79c74d51cf17b35eff7c2ef55a5 Date: Fri Aug 8 11:11:09 2014 +0300 CircularPermutation can now align only binding surface residues commit 506c2c50eb47a2a2ac7a383a02515573b444e588 Date: Fri Aug 8 11:00:56 2014 +0300 CircularPermutation code cleanup commit 1dddcbabc6c77bddbb6e715653e32ace87f573a2 Date: Fri Aug 8 10:38:30 2014 +0300 CircularPermutationFinder is a new filter that looks for evidence of circularly permuted proteins commit 32d4feee30a9a9b0bf0c886f641ef2c6f94e92f6 Date: Thu Aug 7 14:28:59 2014 -0700 Adding a unit test for the -in:auto_setup_metals flag. commit 1661068b3203fb5b3e6d7a1376513c24d353d8ea Date: Thu Aug 7 14:12:39 2014 -0700 Switching metalloprotein unit test to structure 2c9v. This is the better test case, since it involves a hiistidine bonded to TWO metals. commit c575810ee2cc3cdc5f223a4635f85080b4319167 Date: Thu Aug 7 13:51:27 2014 -0700 Working on unit tests for metalloproteins. commit 296439b0b84fa2369307155d83d41738484c1d6e Date: Thu Aug 7 13:49:16 2014 -0700 Removed a file. commit cedcc2f603ac8c13fe95a6cca75fea8b76a810a4 Date: Thu Aug 7 13:43:20 2014 -0700 Working on unit tests for metalloprotein import. commit 14582cb24f8dd4d25e61e68574659430a24d216a Date: Thu Aug 7 13:27:34 2014 -0700 Created a unit metalloprotein unit test (testing import with the -in:auto_setup_metals flag). commit 211b3d3e6dcdd50a17b844eb585ef3d367d2658c Date: Thu Aug 7 13:26:17 2014 -0700 Adding 1PU0 structure to unit test suite for unit testing. commit 399f9c1cf23d1dcae9681b4742ce080979583355 Merge: 3cf9e3a 3be9aa6 Date: Thu Aug 7 10:38:32 2014 -0700 Merge pull request #57 from RosettaCommons/dougrenfrew/fix_aeh Dougrenfrew/fix aeh commit 3be9aa6172b460c500e9cb1d599a21ff299b5e4d Date: Thu Aug 7 11:48:30 2014 -0400 Fixing apps currently causing the app_exception_handeling intregration test to fail commit 15bc30fa013735d31f4d6044a681e55b18d41ce6 Date: Thu Aug 7 11:46:24 2014 -0400 Updating Application stub with proper return values. commit 3cf9e3a199bfd68a9422eee8b907472da4ec6530 Date: Thu Aug 7 10:17:20 2014 -0500 fix tookit main GUI tracer function name commit fa618d234fc95f1d51ee408d4da8d84c95426ec7 Date: Thu Aug 7 10:03:38 2014 -0500 update toolkit doxygen file to reflect any directory running of SetPyRosettaEnvironment script commit 9c0293a10006ec1080562b0b3fa2428a660cc43f Date: Thu Aug 7 09:55:07 2014 -0500 fix tracer function name change in toolkit to reflect C++ commit 736cbbfce72401371a205178a251c251610e75c0 Merge: f522b38b ebe8ff7 Date: Thu Aug 7 09:52:21 2014 -0500 fix PYROSETTA_DATABASE environment variable not being set properly in SetPyRosettaEnvironment commit f522b38b37902f85778370f0b6393b6a0e208398 Date: Thu Aug 7 09:48:52 2014 -0500 fix PYROSETTA_DATABASE environment variable not being set properly in SetPyRosettaEnvironment commit 889ba9b88d2ea64ce3cea6ea174cd5a05b6cb662 Merge: 0138355 12ae976 Date: Thu Aug 7 09:47:35 2014 -0500 merge master into branch commit ebe8ff77ee79d4a476c3681214098dc732ce659c Date: Thu Aug 7 14:54:37 2014 +0300 SSMotifFinder more useful output commit f69df792e603d4a21c2536d405e0f1cb958282b2 Merge: 27980d8 f9d5d1e Date: Thu Aug 7 09:54:43 2014 +0300 Merge remote branch 'origin/master' commit f9d5d1e56aecebc12cdb9dba4ef7adaebbb9ea88 Merge: e898ff8 12ae976 Date: Wed Aug 6 17:23:12 2014 -0400 Removing some debugging output from surface docking that I foolishly left in after it was pointed out to me at Rosettacon. commit 12ae97634dcff17212bea6eebcb34e5523528965 Date: Wed Aug 6 15:23:04 2014 -0500 Change PDB_Info to PDBInfo in unit test include - which was part of the branch changes and the master merge did not change it back commit e898ff8eb0082767ae099afef5e3f73feb6590c1 Date: Wed Aug 6 16:14:14 2014 -0400 removing debugging output that was mistakenly left in commit 2eaeee9af52e4c5f862b24bb22f775b302be9cd0 Merge: 0188cc9 ae4e048 Date: Tue Aug 5 13:39:09 2014 -0500 Fix scorefunction/directory opening problem Fix issue Andrew/Amelie pointed out on the devel list, where having a "talaris2014" directory in your local path, you'll get an empty scorefunction. The reason for the problem is that on some platforms you can "open" a directory without errors to get the equivalent of an empty file, which means the scorefunction name resolution prefers the empty local directory rather than the database file. This commit adjusts the izstream code logic such that attempting to open a directory for read access results in a bad stream. (Similar to if the file didn't exist at all.) This fixes the scorefunction name resolution in the case of local directories. commit e6b365c2b93b747d8a74b6b302076bb30bd2537b Date: Wed Aug 6 09:45:37 2014 -0500 add params dox tag to ccd_angle function commit e308cb4d50595575777e23bcd7bfd3d8e5a7ba2b Date: Wed Aug 6 09:31:17 2014 -0500 add some additional details to CcdLoopClosureMover doxygen tags commit ae4e04837766930c5196b132ca6f39e16b6c1ae7 Date: Wed Aug 6 08:25:35 2014 -0500 add pdb file missing from previous commit. commit a826e182fc4adf71cfa0e06eb07bef737b470e26 Merge: 4678e1f d7d5048 Date: Tue Aug 5 22:58:56 2014 -0500 fix bug in CCDEndsGraftMover and remove all.hh files Fix a bug in CCDEndsGraftMover where the wrong loop was being used for modeling through incorrect setting of insert_length with the refactoring. Add more testing within the grafting unit tests so this never happens again. Replace 2j88 unit test PDB with pre-loaded one from Rosetta to increase load speed. Add option in AnchoredGraftMovers to idealize the insert which defaults false - keep idealization on for AnchoredPDBCreator. Remove most all.hh files. Integration test changes expected in antibody_designer app. commit 01383551b8b3167f43d821bc2ca428f26ea31805 Merge: 4678e1f d7d5048 Date: Tue Aug 5 22:58:56 2014 -0500 merge master into branch commit 4678e1ff2c1550c336a93ba768eb02150525ca91 Date: Tue Aug 5 22:55:38 2014 -0500 fix bug in CCDEnds loop being slightly off. Add additional tests in grafting unit tests so this never happens again. Give the grafting unit test a different cdr to graft in, fully test combine_movemaps function. We should move this function to core::kinematics. Add idealize_insert options to AnchoredGraftMover, default being to not idealize the insert - keep AnchoredPDBCreator as it has been. commit d7d50481784d83ae786c671114dd0dfd0e319757 Merge: 8d33903 09255ab Date: Tue Aug 5 20:16:49 2014 -0700 Merge pull request #47 from RosettaCommons/PDBInfo_revert Revert PDBInfo to PDB_Info and PDBPoseMap to PDB_PoseMap rename. commit 09255ab495b73c9e754646344388b450e3f6473d Date: Tue Aug 5 16:12:49 2014 -0700 Update PDB_Info to PDBInfo rename. commit 5bde130bdb037da45aa6b15c3d03087288ab623a Merge: 90c4f29 8d33903 Date: Tue Aug 5 16:10:04 2014 -0700 Merge branch 'master' into PDBInfo_revert Conflicts: source/src/apps/pilot/rhiju/mg_test.cc source/src/apps/public/stepwise/legacy/swa_rna_util.cc source/src/core/io/pdb/file_data.cc source/src/protocols/features/strand_assembly/SandwichFeatures.cc source/src/protocols/features/strand_assembly/WriteToDBFromSandwichFeatures.cc source/src/protocols/stepwise/legacy/modeler/protein/StepWiseProteinModeler.cc commit 631eaddf834b1dd76f912a9810cdbc74c978b38c Merge: 1749f18 8d33903 Date: Tue Aug 5 17:14:14 2014 -0500 merge master into branch commit 8d339032d5cb406ed07360e6bc6a6866e48f4c42 Date: Tue Aug 5 17:34:58 2014 -0400 PyRosetta, updating dependency calculation for Windows build commit 0188cc98e752c3c44c7d6eb39682cc4cfd2c65c0 Date: Tue Aug 5 15:16:45 2014 -0500 Add missing define for Windows builds commit 3f319949c7592028e024483f5f05dd839dea907f Date: Tue Aug 5 15:54:08 2014 -0400 Remove use of temp_nam for MPI builds. This fixes issues with MPI on newer version of clang on macs that fail with the Wno-deprecated-declarations warning. I do not think it is any less safe against race conditions than the non-MPI version. commit 3bff3789206b2134a8449fb3693104c406c87610 Merge: da94617 c7136d0 Date: Tue Aug 5 13:39:09 2014 -0500 Fix scorefunction/directory opening problem Fix issue Andrew/Amelie pointed out on the devel list, where having a "talaris2014" directory in your local path, you'll get an empty scorefunction. The reason for the problem is that on some platforms you can "open" a directory without errors to get the equivalent of an empty file, which means the scorefunction name resolution prefers the empty local directory rather than the database file. This commit adjusts the izstream code logic such that attempting to open a directory for read access results in a bad stream. (Similar to if the file didn't exist at all.) This fixes the scorefunction name resolution in the case of local directories. commit da94617a26d70917b15d86990fc0a9f183c558bc Date: Tue Aug 5 13:39:09 2014 -0500 Fix scorefunction/directory opening problem Fix issue Andrew/Amelie pointed out on the devel list, where having a "talaris2014" directory in your local path, you'll get an empty scorefunction. The reason for the problem is that on some platforms you can "open" a directory without errors to get the equivalent of an empty file, which means the scorefunction name resolution prefers the empty local directory rather than the database file. This commit adjusts the izstream code logic such that attempting to open a directory for read access results in a bad stream. (Similar to if the file didn't exist at all.) This fixes the scorefunction name resolution in the case of local directories. commit 27980d86446863c89e857726e19764761d362dd1 Date: Tue Aug 5 15:41:36 2014 +0300 SSMotifFinder to work on multiple chains and report PDB numbers and chain IDs commit c7136d0f3c08a266870ac73762787b9bc8f2bbc3 Date: Mon Aug 4 23:55:17 2014 -0400 Fixing Windows build commit 81b0c87e87f1bf5f3ffaa19df45d967c71347792 Date: Mon Aug 4 18:52:43 2014 -0700 added n-start helices functionality commit 1b7c2a4eefdfd08dc053b19169da8911c5bffbc4 Date: Mon Aug 4 19:50:29 2014 -0700 Reverting Zibo's merge, which brought in a lot of unanticipated changes. commit ecc7fc85b7ad44d34ddcf3710a1a8c10658285eb Merge: 9847c75 bf345f0 Date: Mon Aug 4 18:55:14 2014 -0700 added n-start helices functionality commit 9847c755f45970361d9b929a42faeb01853b8377 Date: Mon Aug 4 18:52:43 2014 -0700 added n-start helices functionality commit bf345f0e1d8d6822146a769f37274570d4583d1d Date: Mon Aug 4 15:40:00 2014 -0500 Fix performance test build. We're still apparently supporting Python2.5 for the build system. (e.g. the performance test machine.) Fix add_residue_properties.py accordingly. Also, update the scons build system such that errors in subsidiary scripts bubble up to the top level, to better catch such issues in the future. commit 0747a2f00d2d7fc7b70ea43e7adba4b2e4730665 Date: Mon Aug 4 16:14:24 2014 -0400 Dummy commit commit ffbb81ff07399bb9b4d34255c1b601e6bdd0a847 Date: Mon Aug 4 16:09:30 2014 -0400 Fixing PyRosetta build commit 599e2d08342ff87fc9fc86a95ec8089b7f01575b Date: Mon Aug 4 17:37:06 2014 +0300 removing boost/regex includes from SSMotifFinder commit 6db13faa7273491b5be33d14ebe7e9e4cff80173 Date: Mon Aug 4 16:55:02 2014 +0300 removing debugging dump_pdb statement commit c0b34e9d1681755466d9b06232af025faf7f29e2 Date: Mon Aug 4 16:51:13 2014 +0300 removing unused parameters commit 9abc742adfc86b2c116c562ab6795d1a26c4f6e6 Date: Mon Aug 4 16:48:11 2014 +0300 SSMotifFinderFilter bug fixes commit ad793f1feb994d54fb5a69c4558b8f78dc0c75f0 Date: Mon Aug 4 09:25:42 2014 +0300 SSMotifFinderFilter finds structural motifs in nonhomologous proteins. commit cff9b7ecd7fb54dfdcc341ce97d6db7e5e35501a Date: Mon Aug 4 09:22:00 2014 +0300 adding previously unimplemented function in StemFinderFilter commit 32f40584285aee8d503aabc57d08a4f6d9ae3e47 Date: Sun Aug 3 13:04:13 2014 -0700 another keyword replace (in perturbers/LogFilePerturber.cc) to try to fix Windows PyRosetta build commit f3ec91e4c2ebeee36d885670cc72f594c0ed250a Date: Sun Aug 3 12:45:56 2014 -0700 replacing non-standard keywords to fix the Windows PyRosetta build commit 6ff8b7b6c1283146b009655cc31291fd04cf70c7 Date: Sun Aug 3 11:46:46 2014 +0300 exposing some utility functions in StemFinder from its header file commit a33291987e4448e08d75522092977fc4b29652f2 Merge: a2c9a2f a1df646 Date: Fri Aug 1 20:06:30 2014 -0400 resolving merge conflicts with master commit a1df646c0052d6f3f05188bf41691cb89c50af9f Date: Fri Aug 1 16:39:57 2014 +0300 StemFinder improvements commit 9132236263a83fd1d742cb26680240fa91727e4c Date: Fri Aug 1 11:43:10 2014 +0300 StemFinder documentation. See wiki for details commit e24cf55ae3305ae4494ee7578605a128adc78a57 Merge: 5662e8b a77c424 Date: Fri Aug 1 11:20:06 2014 +0300 Merge remote branch 'origin/master' commit 5662e8b2f9302e164c3a90b142094ac230b5381b Date: Fri Aug 1 11:19:28 2014 +0300 StemFinder cleanup commit 0cfea2cf58fffe090f508ff90e2c8ae95c2fd4fe Date: Fri Aug 1 11:07:54 2014 +0300 StemFinder defaults, activating from_res to_res commit 9dd9cec6b89a5e1c90b20ddbb8773c4a7779471a Date: Fri Aug 1 10:56:59 2014 +0300 StemFinder now finds two contiguous segments commit ba0f5fad59ccc09d14ad073e6867fd752fcd4c32 Date: Fri Aug 1 10:26:21 2014 +0300 StemFinder now measures distances between stem sites commit 10fe2e7e8664e125b3653d16b4e742d750e95a7f Date: Thu Jul 31 18:27:57 2014 -0700 fixing flag to allow turning off/on phosphate packing. commit a77c424fe883481fde9c12b62241c7a379f9726b Merge: 38e42df 5fbc19a Date: Thu Jul 31 16:53:34 2014 -0700 Fixing a typo in the cis/trans torsion bin mapping that made torsion-restricted sampling crash. Also re-enabling the rama2b flag in the NGK integration test - now with the reduced memory usage (thanks Andrew!) this can be tested on the server. Torsion-restricted sampling and next-generation KIC integration tests will change. No other changes expected, other than already-failing candidates. commit 38e42dfa81cdbf31bc7700005239fe580834e397 Date: Thu Jul 31 16:47:13 2014 -0700 re-activating the rama2b flag for the NGK integration test - now that the memory usage is so much lower this can be tested on the server commit a2c9a2f6eb7d1ee7f76d5e6589231488acf36c70 Date: Thu Jul 31 16:18:43 2014 -0700 Adding a note about how the current RamaCheck2B doesn't really work just yet. Commenting out unused parameters because it's the right thing to do. commit 6708919891af1908aaecfb5234b3d9b74318a5c9 Date: Thu Jul 31 16:17:38 2014 -0700 Hmm... I think this might should fix the PyRosetta build commit 09c635adb2c7a98e132c9a60a91fbd77acb2ae66 Date: Thu Jul 31 16:16:34 2014 -0700 Oh right. Need headers for classes that are being used. commit 837a8c87aff829306c8766a661c1c729b6a706ef Date: Thu Jul 31 15:55:51 2014 -0700 Fixing phil's test1. Well, I think I'm fixing it. I'm not going to build on my laptop at RCon. commit fc2ff785a0a9ec4121fdbf4102d0459d1845a497 Date: Thu Jul 31 23:07:41 2014 +0300 StemFinder changes commit b89c32aa57b0d0000749f5ddded8274b65ab4cd2 Date: Thu Jul 31 22:19:34 2014 +0300 StemFinder change commit 2171fab478ca0276bfd1115028fc29d136a1b323 Date: Thu Jul 31 22:04:49 2014 +0300 StemFinder fixes commit 401731158739eb5629b3b2bcd9e1339310faf7c3 Date: Thu Jul 31 17:18:01 2014 +0300 adding StemFinderFilter to report well-aligned positions commit 0ec552d1ad4bb5f6828763ef7036aa2533787654 Date: Thu Jul 31 17:17:01 2014 +0300 adding find_nearest_res utility function to report also the distance commit 5fbc19a7c1f37e2ee8d994bfd569bc55b5a3d4b8 Date: Thu Jul 31 09:41:11 2014 +0300 Adding option superimposed to splice. Normally it is set to true. If false, the XML is expected to provide source_pdb_from_res and source_pdb_to_res during splice_out and splicing will be done between these and the template's from_res to_res. Coordinate restraints and rmsd calculations will be shut off in this case and only dihedral restraints and chainbreak will be evaluated. commit 079f8b88e133933873e47a0a0d391ebef783ff69 Date: Wed Jul 30 23:39:29 2014 -0700 Fixing a typo in the cis/trans torsion bin mapping that made the torsion-restricted sampling integration test crash. No other test changes expected, apart from already-broke ones. commit 47e5b85e661abf3eac15cfdcb353ad052f2c25c6 Date: Wed Jul 30 11:31:50 2014 -0700 have RMSD to native in rna_score and other applications give back rmsd over whole when superposition is over whole. commit 42837ac6a7cf6c6481447b67378d26cae8e6b62a Date: Wed Jul 30 07:03:16 2014 -0700 continuing fixes to compile_all_headers, gccdebug build, unit tests, etc. Helped a lot to have new commit-testing server from Sergey! In the future, that server will allow all tests to be run on branches, and should prevent these kinds of iterative fixes (which are not reproducible locally for me). There may still be an issue in pyrosetta build -- working on it. commit 83283a8bc505e27e42684cf0d4b5dc47e0fb3e4e Date: Wed Jul 30 07:02:52 2014 -0700 continuing fixes to compile_all_headers, gccdebug build, unit tests, etc. Helped a lot to have new commit-testing server from Sergey! In the future, that server will allow all tests to be run on branches, and should prevent these kinds of iterative fixes (which are not reproducible locally for me). There may still be an issue in pyrosetta build -- working on it. commit 65038da82060fc62bb44754e241442c345f3ff08 Date: Tue Jul 29 22:02:55 2014 -0700 trying to revive pyrosetta build commit a7aa8274651d388ccce56b9935ec7df81107e0e9 Date: Tue Jul 29 21:48:11 2014 -0700 merging fix to linux gccdebug build commit c61fc0311009b47d7615ced796dd27dd7347b3fb Date: Tue Jul 29 21:07:30 2014 -0700 trying to fix compile_all_headers test commit e8c4338636932c4581edf927e4caf2a1ed142aa3 Date: Wed Jul 30 14:17:40 2014 +0300 Unused parameters in Rhiju's code commit 11a5da6387e240bdc8d93b42b89da7e013c0923f Date: Wed Jul 30 13:48:30 2014 +0300 In some cases DeltaFilter doesn't need to relax the pose and record the baseline since FilterScan can do that instead. Fixing a bug that didn't allow this to happen properly in some cases. No test changes expected commit 1109141f5c9e3b941bc121d9ca04a02353091d90 Date: Tue Jul 29 22:55:17 2014 -0700 Commenting out call of ramp_score_function in the refactored loops code, since it breaks the KIC_with_fragments integration test. The following list of integration tests were failing before and are not affected by this commit: centroid_disulfide_scores membrane_relax2 torsion_restricted_sampling app_exception_handling No other test changes expected. commit 8ed50d751b16f32badb0c55a9888d49d18245965 Date: Tue Jul 29 22:02:55 2014 -0700 trying to revive pyrosetta build commit 4103e91df2951f0d9515533c9633f1742b9174cd Merge: cd1492d ad052e1 Date: Tue Jul 29 21:54:53 2014 -0700 Merge branch 'master' into rpache/KIC_with_fragments commit cd1492da1e591ee7c0e0016436d51a3829d1e042 Date: Tue Jul 29 21:51:34 2014 -0700 reverting hack due to integration test changes commit a0a9c642c76eca248c71e77c0652a449e22ab78b Date: Tue Jul 29 21:48:11 2014 -0700 trying to fix unused variables for linux gccdebug build and test on commit-testing server commit 6d31e10b7b9d663995ff97698e300e17a8013aa2 Date: Tue Jul 29 21:07:30 2014 -0700 trying to fix compile_all_headers test commit 9c5eee9e5a5f71d44bc02902a2b08ab41fb77a93 Date: Tue Jul 29 20:42:13 2014 -0700 hack to fix KIC_with_fragments integration test commit ad052e1865179f95ac1874ead1ae99c4d33b7417 Date: Tue Jul 29 18:46:44 2014 -0700 trying to fix build, and also I want to test new SHA-based test server commit 3d4c5d0c14c966f15ccbd380bfd37a9564d25dca Date: Tue Jul 29 18:46:44 2014 -0700 trying to fix build, and also I want to test new SHA-based test server commit 377db895b96f6badb970809f4759535d0dbee488 Merge: be03ef9 340a193 Date: Tue Jul 29 17:26:47 2014 -0700 a testing server for branches and pull requests would prevent this -- checking in fixes for unit tests and linux debug build commit be03ef983db291702d51bf5f8d340e28cd6c63fc Date: Tue Jul 29 17:26:27 2014 -0700 a testing server for branches and pull requests would prevent this -- checking in fixes for unit tests and linux debug build commit 340a1937f55e9def0253f4d3db868d5033336a01 Date: Tue Jul 29 17:24:27 2014 -0400 CCD: fixing severe rama check bug commit 5df353417237bb33a2d161a2cc9dcb1a6289105a Merge: 56522ef 2d9f308 Date: Tue Jul 29 14:19:46 2014 -0700 trying to remove unused parameter warning/error from debug build. commit 56522ef9bf2c43372547e6e50c80575ad1b68287 Date: Tue Jul 29 14:18:50 2014 -0700 trying to remove unused parameter warning/error from debug build. commit 2d9f308ce89a9ed5dcc5b50dd312a1f3f339b6ff Merge: 5b801c5 0917614 Date: Tue Jul 29 10:57:12 2014 -0700 Pushing Kale's attempt to fix the header-only build. commit 157d27c181ed41228e5c29830794fd8313424fd3 Merge: 5b801c5 0917614 Date: Tue Jul 29 10:57:12 2014 -0700 Merge branch 'master' into rpache/KIC_with_fragments commit 5b801c5d54b50006ed4f24cb50373139f95b2425 Date: Tue Jul 29 10:47:04 2014 -0700 Fix header only build. commit 0917614b4093af986c7653f6b654748f46122ecc Merge: 7aa7ef7 ea37808 Date: Tue Jul 29 09:53:45 2014 -0700 cleanup/reorganization of stepwise code to prepare for rosetta dev meeting. merge from branch rhiju/swm_cleanup. integration tests checked -- all changes cosmetic or recurrent floating point deviations on my mac (e.g. in match). commit 7aa7ef78510ec86a29ef7ebc3091e8996a584dd1 Date: Tue Jul 29 09:03:05 2014 -0700 cleanup/reorganization of stepwise code to prepare for rosetta dev meeting. merge from branch rhiju/swm_cleanup. integration tests checked -- all changes cosmetic or recurrent floating point deviations on my mac (e.g. in match). commit 4344e9fd5f3dc734f94408aaa9e71f916425f8e1 Merge: 5f9f096 136a242 Date: Tue Jul 29 09:02:49 2014 -0700 cleanup/reorganization of stepwise code to prepare for rosetta dev meeting. merge from branch rhiju/swm_cleanup. integration tests checked -- all changes cosmetic or recurrent floating point deviations on my mac (e.g. in match). commit ea3780887273283c13f24f4f6278040574f68854 Merge: 5f9f096 a651f94 Date: Mon Jul 28 20:27:21 2014 -0700 This commit adds a new loop modeling protocol to the Rosetta code-base, KIC with fragments, which combines the power of kinematic closure with sampling coupled degrees of freedom from protein fragment data. In the KIC with fragments protocol, coupled phi/psi/omega torsion angles from consecutive residues in protein fragments are used to sample all but 6 torsional degrees of freedom. Those remaining 6 phi/psi torsions are solved analytically by KIC. This combination allows for rapid sampling of large conformational spaces. The protocol is based on Kale Kundert's refactored KIC code, which provides a more flexible and more easily extendable framework than its legacy counterpart. Our current benchmark results, using the 45 12-residue loops KIC benchmark set, indicate that KIC with fragments retains the sub- Angstrom loop reconstruction accuracy of the next generation KIC protocol, while considerably outperforming previous methods in the sampling of sub-Angstrom models (median fraction of sub-Angstrom models = 33% (without using homologs during fragment generation), compared to only 13% for next generation KIC, 6% for legacy KIC and 1% for CCD). KIC with fragments can be activated for the centroid (perturb) and fullatom (refine) stages using the following flags: -loops:remodel perturb_kic_with_fragments -loops:refine refine_kic_with_fragments Fragment data can be loaded using the standard flags -loops:frag_sizes and -loops:frag_files A comprehensive documentation for KIC with fragments, incl. algorithmic details, protocol usage (such as necessary input files and available options) and a quick-start example can be found at https://www.rosettacommons.org/docs/wiki/application_documentation/KIC_with_fragments This commit also contains a subtle bugfix by Kale in KicMover that was causing chain breaks during initial loop building. That bug only affected the refactored loop modeling framework and in most cases led to reduced performance (in one benchmark case it caused the initial loop build to fail). The newly-added KIC_with_fragments integration test is expected to change. The following integration tests have already failed before and are not affected by this commit: torsion_restricted_sampling centroid_disulfide_scores No other test changes expected. NEWS: Adding a new loop modeling protocol, KIC with fragments, which combines the power of kinematic closure with sampling coupled phi/psi/omega degrees of freedom from protein fragment data. commit 136a2426dafe0cffb540ac7754b2e9a68a9220e8 Date: Mon Jul 28 15:10:40 2014 -0700 fixing namespaces that go with move of rotamer_sampler to stepwise/sampler commit 1146cc61f53b97fbe8f0d2b721125839e4b8f2ef Date: Mon Jul 28 15:00:24 2014 -0700 moving rotamer_sampler/ to stepwise/screener/ -- a good step towards complete unification of all stepwise/ code. commit 3fd8de37b01ac891c5668a3f0ae65127d73f1045 Date: Sun Jul 27 15:06:06 2014 -0700 adding -sampler_silent_file option to create movies for Rosetta developers stepwise talk. Also adding some copy/clone functions to options. I think those might not be necessary, but best to be safe. commit a651f94de66d58571cfd09420c11610065d5dd0f Date: Fri Jul 25 12:44:31 2014 -0700 adding xcode ide project dir to .gitignore commit 9f9966143c6b026f687a48182cbd015bd66f9cb4 Date: Thu Jul 24 18:18:06 2014 -0700 bugfix of previous merge error commit 6fe0ad033893b28fbbb69fed151ab90b944e2010 Merge: c9e965c 0c923ea Date: Thu Jul 24 14:34:15 2014 -0700 resolving merge conflicts commit 1e0df6409d8f49e404400fdc41b1ce4836214ef4 Date: Thu Jul 24 17:15:17 2014 -0400 adding a to-do note to RotamerSampleBase.hh about including a RotamerSamplerDOF_Type for easier addressing, fast-forwarding, and other i/o to RotamerSampler in the future. commit 5c9d734ebeb01dab5c8ff38bc86b01d99f0dc07a Date: Thu Jul 24 17:11:49 2014 -0400 adding nice output from RotamerSampler class, including nested description of each loop and its size and, in some cases, the DOF that is sampled. commit 5be19feb64c37650316f23dadec326967f14a1e0 Date: Thu Jul 24 14:35:59 2014 -0400 get rid of verbose output commit 81d0e7f36ac9a95e7b7b8f24be61c6600b642470 Date: Thu Jul 24 12:34:39 2014 -0400 setup align pose and native pose default to first inputted starting pose -- trying to keep SWM output models with reasonable alignments. commit 6a09aeb1616f3d9325db9e993069a13193c44c36 Date: Thu Jul 24 12:00:15 2014 -0400 fixed up namespaces and tracer names in stepwise/ after util reorganization/ commit 883e0b2dc807cfbe7010fbbcc8f4181ff154858c Merge: 026f09b 6fdbcd5 Date: Thu Jul 24 11:08:13 2014 -0400 merge from master into rhiju/swm_cleanup branch. commit 026f09bdd57a3acf6b85b5ad2590a399689135db Date: Wed Jul 23 17:47:29 2014 -0400 splitting/refactoring stepwise/modeler/rna/util.hh into a separate legacy util.hh commit c9e965c12ef0833bdb339aa307671ca4005a5fb3 Date: Wed Jul 23 13:52:03 2014 -0700 changing name output of LegacyKIC_Sampler to fix Kale's unit tests commit 09134edbb13e18ad0ddff7e70584e1cbdafc366b Merge: 9a025a4 2aadce9 Date: Wed Jul 23 12:17:06 2014 -0700 Merge remote-tracking branch 'origin/master' into rpache/KIC_with_fragments commit 850f1bef29df28b776a0798276937cae1bf7f0cb Date: Wed Jul 23 14:18:12 2014 -0400 trying to align to pose1 by default, if no native is specified. Might eventually be better to keep all poses from -s inside align_pose, and choose to align based on whichever fixed domain is available in the root. commit 55211af835e81d399095c2dbea8a2c016d920248 Date: Tue Jul 22 23:51:09 2014 -0400 massive reorganization of stepwise/modeler/util.hh into mostly separate utils. commit 9a025a441ef9ab1ab831e7283d3dcaa4fc1f7a99 Merge: a0641b5 afcf7f1 Date: Tue Jul 22 20:15:22 2014 -0700 Merge remote-tracking branch 'origin/master' into rpache/KIC_with_fragments Conflicts: source/src/protocols.3.src.settings source/src/protocols/comparative_modeling/LoopRelaxMover.cc source/src/protocols/loop_modeling/samplers/LegacyKIC_Sampler.cc commit a0641b5e25109fb7958838c87b970fef6c775bc4 Merge: 5dccbe3 840a017 Date: Tue Jul 22 19:27:33 2014 -0700 Merge branch 'rpache/KIC_with_fragments' of github.com:RosettaCommons/main into rpache/KIC_with_fragments commit 5dccbe3148ccee1171f076cd304e42af76881555 Date: Tue Jul 22 19:17:33 2014 -0700 adding KIC_with_fragments integration test commit 1e795b7f031a181688c6787cf686ad1fc31e3485 Date: Tue Jul 22 21:56:56 2014 -0400 further refactoring of util.hh throughout stepwise/ code. took this opportunity to put pdbslice into pose/util.hh and also to change names of getPoseExtraScores & setPoseExtraScores to getPoseExtraScore and setPoseExtraScore, since they only get/set one score at a time. commit b5df04bc7127e3168be6f7a95c324f305dcb1cf2 Date: Tue Jul 22 20:19:07 2014 -0400 cleanup of util.hh functions in stepwise/ directories. About halfway through. commit ee05304bd526a238591473a5cd3c338032c99729 Date: Tue Jul 22 18:03:22 2014 -0400 simplification of FoldTree delete_extra_vertices() to not take desired_root; this was needed to fix a bug in slide_jump(), which is now instead fixed internally to that function. Had to create a prepend_edge() function, which is like add_edge() but inserts the desired root-containing edge at the beginning of edge_list. commit 9cc470200d13baa600534ee43eb3629f56809243 Date: Tue Jul 22 13:08:21 2014 -0700 fixes to linux gcc build commit 20fc4a759cb613dbab2be9e8351a7495ead31ac9 Date: Tue Jul 22 16:07:41 2014 -0400 argh yet another fix to alignment, in case where a root atom triad is used to do superposition commit 90c4f29b11bd088bb62041ad470c4bb8b7d8498f Date: Tue Jul 22 12:37:42 2014 -0700 Revert PDBInfo rename in remaining src and test files, part deux. commit b5d3e90931efef9c686488290ab9941854300f0c Date: Tue Jul 22 12:00:16 2014 -0700 Revert PDBInfo and PDBPoseMap rename in remaining src and test files. commit c230d7be9ea248c9dbe39976721bb7b66bb63f42 Date: Tue Jul 22 14:56:53 2014 -0400 for builds from scratch, when outputting movie or final pose, align over all atoms commit 8f829a0219e3d99c7ff08a259315dddcf97f333c Date: Tue Jul 22 11:56:34 2014 -0700 Revert "Fixing the unit test build following Rhiju's renaming" This reverts commit b1fa4fe6eccfcae8e90a481ff51c93679807f469. Conflicts: source/src/core/conformation/Conformation.cc source/src/core/conformation/symmetry/SymmetricConformation.cc source/src/core/conformation/util.cc commit 6e7bacf1f3de7d09ee05c69d9b6d61526e4fc133 Date: Tue Jul 22 14:56:33 2014 -0400 bug fix to alignment when there are multiple domains... commit 8f199f02ea517c35a02dd4f1ae68e686ec11e529 Date: Tue Jul 22 14:56:16 2014 -0400 remove redundant line commit 9f423ddeb88e022aa63aa41e87fa26fa408d3308 Date: Tue Jul 22 11:47:20 2014 -0700 Revert "fixing PDBInfo --> PDB_Info, PDBPoseMap --> PDB_PoseMap, as I think this is Rosetta convention (underscores separating acronyms, for readability)" This reverts commit 020f84b2e5ad0627cf406fbcb73512faab34d448. Conflicts: source/src/protocols/environment/Environment.cc source/src/protocols/features/strand_assembly/SandwichFeatures.cc commit fc18bb36251f2aa867e70ee1a75b0f65f5622a71 Date: Tue Jul 22 00:31:14 2014 -0400 fix to pose aligner in protein terminus case commit 251c86f3f80e97abd3c93fee0cacfdf29204b8a5 Date: Tue Jul 22 00:03:43 2014 -0400 fix to virtual_sugar checks with proteins. commit 6bbd8e2a9e11b5f12dced530a0075245b0828089 Date: Mon Jul 21 23:23:06 2014 -0400 fixing uninitialized variable in ConformationViewer which led to graphics sometimes going off screen. commit 2553ca6934bbf3e5739949ae00e322cc44a12d6e Date: Mon Jul 21 23:22:36 2014 -0400 fixing root choice error -- should always place root in a fixed domain if possible! commit 62d5033399f1c595b3c64b76173292cef4f11fdb Date: Mon Jul 21 22:41:18 2014 -0400 changing namespace stepwise/sampling to stepwise/modeler, which makes more sense now that most of sampling is held in rotamer_sampler commit 2a9daee42682d3d047a52913ecf3f52e44edf2bc Date: Mon Jul 21 22:09:41 2014 -0400 moving StepWiseMonteCarloOptions into options/ subdirectory for consistency with rest of protocols/stepwise directory hiererarchy. commit df0a462911446f5d36df5956def57079a6341c8b Date: Mon Jul 21 21:40:09 2014 -0400 fixing modeler_options/ directory to options/, less verbose commit cdb4b00b111f02d8dfca652215eaa230eacb3c36 Date: Mon Jul 21 21:26:33 2014 -0400 refactoring StepWise options to inherit from a unified options -- removes more copied code, yay. commit cb7204c52a9080c97c1d09555e1594169629ebfd Date: Mon Jul 21 16:13:11 2014 -0400 for final superposition in stepwise monte-carlo/assembly, do alignment over all fixed domains seen in pose, not just the first one. commit 5594804a07ac14bd6de2209b15161fd6ef0dfc00 Date: Mon Jul 21 14:36:51 2014 -0400 major bug fix in cutpoint setup in full_model. oops. commit c651c47827a6f305bb86b217070ee4ecfff36f9b Date: Mon Jul 21 14:36:20 2014 -0400 do not read in DMS potential stats form disk unless we actually end up computing DMS potential -- speed up scoring. commit 22922e2997f943eb50387043f0405c965095d2f3 Date: Mon Jul 21 09:04:03 2014 -0400 trying to prevent a silly phosphate addition error in SWM RNA. commit 9dca2d019d5069db2b0d4c104478973245952bff Date: Sat Jul 19 20:49:57 2014 -0700 fix for chain_connections where one set of docking residues is not contiguous and happens to have some residues before and some after the residues in the other side. commit 840a017b3fe85594872846b111a1d345e054a1f9 Merge: b326bfa c6e4ce1 Date: Fri Jul 18 17:16:13 2014 -0700 Merge commit 'c5e4ce1e050ea86c2bce46609a409a9e2a7d1143' into rpache/KIC_with_fragments commit b326bfa4bfd36dbdce87261b60b16a27c930ea87 Date: Fri Jul 18 16:02:59 2014 -0700 Update LoopModeler unit tests. commit 183cbe257fdde8e3d35ba44c89cc89f8f89b2c35 Merge: 58f672e 0f55db2 Date: Fri Jul 18 13:15:40 2014 -0700 Merge remote-tracking branch 'origin/master' into loops-xml commit 58f672e04d67e6ce117ce65c02260d42a39d9fd3 Merge: 6c3f004 a65064f Date: Fri Jul 18 13:15:13 2014 -0700 Merge remote-tracking branch 'origin/rpache/KIC_with_fragments' into loops-xml Conflicts: source/src/protocols/comparative_modeling/LoopRelaxMover.cc source/src/protocols/kinematic_closure/ClosureProblem.cc source/src/protocols/kinematic_closure/KicMover.cc source/src/protocols/loop_modeling/LoopBuilder.cc source/src/protocols/loop_modeling/LoopBuilder.hh source/src/protocols/loop_modeling/refiners/LocalMinimizationRefiner.cc source/src/protocols/loop_modeling/utilities/LoopMoverGroup.cc source/src/protocols/loop_modeling/utilities/LoopMoverGroup.hh source/src/protocols/loops/loop_closure/kinematic_closure/KinematicPerturber.cc commit 6c3f004d54dd892ddf551c56e2c479e921dee9ff Merge: c16f650 81518f5 Date: Fri Jul 18 09:55:15 2014 -0700 Merge branch 'master' of github.com:RosettaCommons/main commit c16f650b9abd56b44db3d6b651968d1a2d5c47de Date: Fri Jul 18 09:49:37 2014 -0700 Add LoopModeler (with a RosettaScripts interface). The LoopModeler class is meant to supersede the loopmodel application. I had to transcribe the code that reattaches the sidechains between centroid and fullatom mode into the new framework, so I can't be sure that my code works until I benchmark it. The RosettaScripts interface is largely in place, but there are still a few tweaks I need to make. commit 23135abca3b400b7940c4019931279bc637eac6a Date: Tue Jul 15 20:15:10 2014 -0400 Fixing a const-ness issue of the direction argument in a private method. The primart reason for this commit is the close_loop_in_single_direction has now had two virtual methods extracted from it. The more important of the two is actually responsible for updating all of the torsions of a particular residue based on some CCD math stuff. In this flavor of the mover, it iterates over the torsions in the residue and solves for them one by one (i.e. phi then psi). This was done in anticipation of some work being in the Dunbrack lab that might lead to phi and psi being solved for simulataneously. The other method sets the value of the max_per_move and max_total torsion deltas. The reasoning behind making this a virtual method is to provide a mechanism other than the residue's current secondary strucutre assignment to get these values. For example, one could imagine using a vector1< Real > of length loop_,size() where each element specifies the max per move torsion delat for that residue. I hope that this adds to the flexibility of this mover. commit 46a235643a05ee2fdb8e80ea9065d3cec8f1297a Date: Tue Jul 15 17:45:40 2014 -0400 Changing the order of the methods in the header (and in the cc to match). Adding a note about how to properly copy a RamaCheck instance if the derived type is unknown. commit 5fb31799e33c3e9626ce01325f56af1c5292f4cd Date: Tue Jul 15 17:37:25 2014 -0400 Adding a clone method to RamaCheck, removing the rama() method in the derived classes. Also adjsuting some spacing because I want to. commit dfc7e6cb3c33b351f9929deaa6cea1cc1ada5c40 Date: Tue Jul 15 09:13:33 2014 -0400 Comitting my working version of Jason's pilot app thing. commit a65064fa527a0e93e4ad772ec07bd8fb3f05e5ef Merge: 03a6e96 c9199ff Date: Mon Jul 14 18:31:56 2014 -0700 Merge branch 'rpache/KIC_with_fragments' of github.com:RosettaCommons/main into rpache/KIC_with_fragments commit 03a6e969b426bfb000667e6aa091e8ef63086d1c Date: Mon Jul 14 18:29:45 2014 -0700 changing LoopBuilder to respect the max_kic_build_attempts flag commit 08b746014e06bd2273593eee39559bcece074719 Date: Mon Jul 14 18:28:38 2014 -0700 changing KICMover to respect the max_kic_perturber_samples flag commit b278726e6d5cc306336597ed58a8429a66928a12 Date: Mon Jul 14 19:22:22 2014 -0400 Updating Rama check to work better with CcdLoopClosureMover. Writing lots of doxygen, it compiles and runs. commit 9826a4c3153cf8ba4ee95b21c322b4736b9b0f55 Date: Mon Jul 14 19:20:07 2014 -0400 More updates to CcdLoopClosureMover to account for RamaCheck being a thing. commit be09b9866b3e0f801caeb59f1a311f968b8a54f0 Date: Mon Jul 14 17:17:24 2014 -0400 Implementing regiser_options() in RamaCheckBase and calling it from CcdLoopClosureMover. commit 399ff19d43e9c635e904f1bd40b8522dabb2f5f3 Date: Mon Jul 14 17:09:48 2014 -0400 Fixing some silly mistakes that prevented compilation commit c9199ffaec7f98b24668fd37df7158b75943c9ce Date: Mon Jul 14 11:38:07 2014 -0700 Consolidate the MinimizationRefiner hierarchy. commit 563bccf4d09162d13dae1cfa598a2ab3f0e1f2af Date: Mon Jul 14 14:25:50 2014 -0400 Removing the compute_rama_score method from CcdLoopClosureMover commit 9e59de510816c792986629992581758c135911f5 Date: Mon Jul 14 14:19:42 2014 -0400 Making CcdLoopClosureMover use the RamaCheck classes where possible. Removing now useless member variables, methods and options. commit 22b1389935c47216ee890352900e4e54a2c406a6 Date: Mon Jul 14 14:18:51 2014 -0400 Initial commit of RamaCheck classes. These will be helpful for encapsulating all of the RamaCheck stuff that we want to do with CCD. commit 988b780409998638aeac5e7a9e6b188f8287c895 Date: Sat Jul 12 16:27:55 2014 -0400 Initial commit of unit tests for CcdLoopClosureMover. Right now it just closes a loop and makes sure it is closed and that it happened within the allowed number of cycles. commit 393c392cd24a83d99a2fc6071b031ac49f046eef Date: Sat Jul 12 14:05:56 2014 -0400 Moving a comment to a more sensible place commit 541b049057ca83fb38a0686f512171df04a8fd47 Date: Sat Jul 12 13:54:46 2014 -0400 Updating a few comments commit 4c50ce8da8c3b894e941408477f2bca1f16a4d8d Date: Sat Jul 12 13:44:01 2014 -0400 Getting the Rama2B stuff to compile. I thought I was being so clever, but then there was const-ness parade of horribles. For now I've added a second i_var for the rama_2B map, and made both rama maps mutable so they can be initialized lazily in a const method. If this getting to be a bit much in terms of the amount of code dedicated to evaluating Rama, we should spin it off into its own class. Oh, right. This builds and runs and all of that good stuff. commit 5d28a0c0f96fc66dbf7d857b9d07b7266a8f3bf0 Date: Sat Jul 12 12:42:59 2014 -0400 Uncommenting compute_closure_metrics. It was mistakenly commented commit 919b2872c7318271151e9ab0060c304705bf1896 Date: Sat Jul 12 12:34:03 2014 -0400 Fixing a typo in a comment. commit 732edfd61a8f0689e85d67f4bf539ed38f402d40 Date: Sat Jul 12 12:27:13 2014 -0400 Adding a new option to the options system: rama_2b. There is a new member variable in CcdLoopClosureMover that corresponds to this, accessor/mutator, options reading, initialization and copying. I also changed rama_ to a ReferenceCountCOP and made it mutable. There is a new private method called 'compute_rama_score' that handles all the rama_ stuff, including lazy initialization. All calculations of rama scores are routed through this method. Depending on the value of rama_2b, this method will initialize the 2B Rama maps, static_cast the RefCountOP to the appropriate class (either RamachandranCOP or Ramachandran2BCOP), compute the score and return. Rama2B is false by defualt becasue I haven't tested it. commit 6361438732ec749dfbe575c3b3a8fdc09b96ad45 Date: Sat Jul 12 10:47:30 2014 -0400 Changing the defaut CCD tolerance to 0.08 A to match the paper. commit 56ec2b43614d947a7a4958ef3fea9a0d131dacfb Date: Sat Jul 12 10:44:58 2014 -0400 Removing unnecessary headers from CcdLoopClosureMover.hh commit dae1a6d21e62ba8e2347b1652d75bd571bb5f269 Date: Sat Jul 12 10:36:01 2014 -0400 Removing 'Matrix' typedef. Fixinig const-ness and pass-by-value vs pass-by-reference issue in the private copy_data method. commit 121b598d6450c60e7fa7735c32e642812a1981d2 Date: Sat Jul 12 10:25:31 2014 -0400 Removing uneccessary inclusions from CcdLoopClosureMover, adjusting some spacing throughout. commit 5182be4d27e86876955c5f6d767df48969ae14d7 Date: Sat Jul 12 09:38:17 2014 -0400 Changing nearly all of the 'using namespace' calls to 'using' calls. I prefer this, but it makes very little difference. Re-enabling the computation of closure metrics, but now this happens in its own little privatge method that apply calls. Removing unecessary 'using namespace' calls. I think I'll try to figure out which headers can be removed next. commit 0113ce6ad53e2c07a646ae22182e0915d70dd15b Date: Fri Jul 11 23:34:31 2014 -0400 Moving ccd calculations to numeric code, lots of little cleaning things. This seems to work still. A good next step is to make the code in numeric use iterators instead of ints going from 1 to 3. commit b87a1f4663073be722d17e24724a42735f773913 Date: Fri Jul 11 23:28:42 2014 -0400 Whoops, forgot to commit this earlier. this makes it build. commit 8c712d660d9cb95e02518f6fd01c63e69198b4b4 Date: Fri Jul 11 23:27:53 2014 -0400 Adding a function to numeric that calculates the angle and resulting deviation for CCD moves. commit 717111bad0320afdc0b0b9865c434c64b73336a9 Date: Fri Jul 11 18:42:07 2014 -0400 Making deviation a single real and not a vecotr, fixing the various calls to those functions that provide access to it and trying to flip theta_hat instead of alpha. Doens't buuild, have to go home. commit 81599fe418e9af143b13abc914eb5c9096ec109e Date: Fri Jul 11 18:38:50 2014 -0400 Cleaning up Jason's pilot app thing commit 34e8a6fc967303ec3aea3742dbd6227df95e67cc Date: Fri Jul 11 17:50:41 2014 -0400 Making some changes to get CCD to actually close loops. It closes loops! Huzzah! commit 98735f4459773002f0e52ef4d09db1c90a15f797 Date: Fri Jul 11 14:14:13 2014 -0400 CCD Refactor: deleting a crap ton of code; woo! Hopefully, the loop will close now. commit 8547408cd03291d3775cabaa5e8b9f54415f8c36 Date: Thu Jul 10 19:05:34 2014 -0400 Intermediate stage of testing out pose-based CCD moves. It's not looking great right now. commit b324d5d2c692859254b6c0e4ce94aba700be6925 Date: Thu Jul 10 17:12:17 2014 -0400 Eclipse, I hate you. commit 7d033df0976f0e8b5fc9fb061305603e6974b4cc Date: Thu Jul 10 16:55:43 2014 -0400 bug fixes; new M and F seem to work as planned; now we need to deal with 'refolding' commit 48ee5b7fdf97267d5d04a5c5415a1d670c5ba703 Date: Thu Jul 10 14:23:41 2014 -0400 bug fixes commit eded0cf8e0f528266bd4620e2a50a8fbd7bea6ed Date: Wed Jul 9 15:11:35 2014 -0400 CCD Refactor: adding get_anchor_matrix() method to replace get_overlap_positions and tons of other code commit 26c38d9112def80ee634c44c89247c7fcbdda196 Date: Tue Jul 8 19:44:42 2014 -0400 CCD Refactor: clarifying, i.e., trying to understand the math commit c2038dc13b868f32654bef2a38e44fc85049c5d7 Date: Tue Jul 8 18:13:42 2014 -0400 CCD Refactor: deleting what we think is a useless for loop commit 923ed9e1eebe1c3a0193e4ad18b99c5624a0ffb3 Date: Tue Jul 8 17:19:37 2014 -0400 CCD Refactor: removed cutpoint as a parameter from all functions, since loop_ is a private datum commit 56cb0f67f3701961d09390035e45c3b769608f5b Date: Tue Jul 8 16:54:14 2014 -0400 CCD Refactor: removed n_mainchain_atoms/nbb as a parameter from all functions; now it is generated as needed for each use case and renamed to be more clear as to what it actually is in each case commit c4a8b8accd55d56c4eea523806fb5e9ad4fc21a5 Date: Mon Jul 7 19:16:27 2014 -0400 bug fix in a pilot app commit 054b7fe0c802033ae3fc47a7b9686e728b9b014e Date: Mon Jul 7 15:01:44 2014 -0400 CCD Refactor: removed an unused param from the debug_information_during_clousre() method commit 42b7bcd97ea747b922ebc9894529ed5e4ff2cab8 Date: Mon Jul 7 14:58:37 2014 -0400 CCD Refactor: fixed error in how backward deviation was calculated; this should fix all the tests that failed because the loop was claimed to have not been closed, even though the actual results were physically the same commit 029cdf853f8f2481b45952a0379457a5074e5006 Date: Mon Jul 7 14:19:20 2014 -0400 bug fixes commit 47c09a431bd06c9c92041ce7ccc9818977db51b9 Merge: 0eeab62 637f9cf Date: Fri Jul 4 01:02:38 2014 -0400 merging with Brian's changes commit 0eeab6209a632f2e02c6f470cbb2ab786cf698b9 Date: Thu Jul 3 22:07:36 2014 -0400 CCD Refactor: changed all calls to ccd_moves() to use CcdLoopClosureMover; fixed renamed setter calls commit 637f9cfed36dd5cebd75d2dbfef414f2b65dadde Date: Thu Jul 3 21:02:45 2014 -0400 Implementing parse_my_tag, using setters where possible in parse_my_tage and init_options. commit 63d0bd1a54c155417fad789dc4c458b97a49df7c Date: Thu Jul 3 20:39:51 2014 -0400 Requiring three inputs to the max_deviation ccd options, writing an init_options() method in CcdLoopClosureMover. commit 16ce1bfd75440b1679b90757683eec52ee1be96b Date: Thu Jul 3 19:48:01 2014 -0400 Adding a bunch of options to allow commandline customization to the CCD mover. commit ebf237dfb83a586bff935b24b4d318379d81d93f Merge: 30252be 763e97d Date: Thu Jul 3 19:26:36 2014 -0400 merging in changes from Brian commit 30252be217295d4664c6647ba379c41904716d17 Date: Thu Jul 3 19:25:47 2014 -0400 CCD Refactor: deleted the other CCD Mover altogether commit 763e97d24e88c65e170a85c01c1f7726be9b1e34 Date: Thu Jul 3 19:12:08 2014 -0400 Fixing a parenthesis-square bracket misfire. commit 84bdd396b9a988e680031b4da118214924beeefc Date: Thu Jul 3 19:06:36 2014 -0400 CCD Refactor: deleting almost every method from ccd_closure.hh and .cc commit 5623bf56204b23b413da2be1be18ed8967d9dc24 Merge: d0f1eed 86ccb30 Date: Thu Jul 3 19:02:19 2014 -0400 # [ONE LINE DESCRIPTION OF CHANGE] # NEWS: [DETAILED DESCRIPTION OF CHANGE] # ---------------------------------------- # Unit test status: [Pass/Fail/Not Run] # Integration test status: [Number of changed tests / Not Run] # [NAME_OF_CHANGED_TEST_1]: explanation of change explanation of change ... # explanation of change, cont'd. # [NAME_OF_CHANGED_TEST_2]: explanation of change #+BugFix [BUG_NUMBER] [LINK_TO_BUG] # Uncomment and fill in the line above to indicate this commit # fixes a known bug. # On branch weitzner/make-ccd-a-class # Your branch and 'origin/weitzner/make-ccd-a-class' have diverged, # and have 1 and 1 different commit each, respectively. # # Changes to be committed: # (use "git reset HEAD ..." to unstage) # # modified: source/src/protocols/loops/loop_closure/ccd/CcdLoopClosureMover.cc # modified: source/src/protocols/loops/loop_closure/ccd/CcdLoopClosureMover.hh # # Untracked files: # (use "git add ..." to include in what will be committed) # # .directory commit d0f1eedbdf4fd98f04d0c32e5f3ef120401ffedb Date: Thu Jul 3 19:02:12 2014 -0400 I have no idea what I modified on this check in. commit 86ccb305e30e97b67baf6bb808e13e423576d8a3 Date: Thu Jul 3 18:54:24 2014 -0400 const-correcting a bunch of stuff. making things nice, see. commit e90c8ba19cead26707fd6a67c2080cbd024c9eaa Date: Thu Jul 3 18:54:07 2014 -0400 CCD Refactor: moving all functions from ccd_closure to the Mover, Part 3 commit ca5eb9738bed3fbe51e8e132d0ee296315d7882a Merge: 46536ab d667f50 Date: Thu Jul 3 18:35:29 2014 -0400 # [ONE LINE DESCRIPTION OF CHANGE] # NEWS: [DETAILED DESCRIPTION OF CHANGE] # ---------------------------------------- # Unit test status: [Pass/Fail/Not Run] # Integration test status: [Number of changed tests / Not Run] # [NAME_OF_CHANGED_TEST_1]: explanation of change explanation of change ... # explanation of change, cont'd. # [NAME_OF_CHANGED_TEST_2]: explanation of change #+BugFix [BUG_NUMBER] [LINK_TO_BUG] # Uncomment and fill in the line above to indicate this commit # fixes a known bug. # On branch weitzner/make-ccd-a-class # Your branch and 'origin/weitzner/make-ccd-a-class' have diverged, # and have 1 and 1 different commit each, respectively. # # Changes to be committed: # (use "git reset HEAD ..." to unstage) # # modified: source/src/protocols/loops/loop_closure/ccd/CcdLoopClosureMover.cc # modified: source/src/protocols/loops/loop_closure/ccd/CcdLoopClosureMover.hh # # Untracked files: # (use "git add ..." to include in what will be committed) # # .directory commit 46536ab48945e52cedc9bc96026721633d94d5ec Date: Thu Jul 3 18:35:23 2014 -0400 CCD Refactor: moving all functions from ccd_closure to the Mover, Part 2 commit d667f5021303877fa54fb228933fc8a12ca28d1c Date: Thu Jul 3 18:32:19 2014 -0400 Const-correcting the shit out of 'debug_information_during_closure', which happens to have the ugliest signature ever. commit 32559d5f418ba6e077df671ad06414c4e6fb4b82 Merge: 98e9437 352527e Date: Thu Jul 3 18:24:53 2014 -0400 resolving merge conflicts commit 98e9437e19675bec196710f41deffe2335e6ba54 Date: Thu Jul 3 18:20:36 2014 -0400 CCD Refactor: moving all functions from ccd_closure to the Mover, Part 1 commit 352527ea35011aba1c2d0ee4187bec57a8120adc Date: Thu Jul 3 18:17:50 2014 -0400 Cleaning up the interface to CcdLoopClosureMover. Setters and getters no longer have a 'set' or 'get' prefix. Added a static map to go from chars to enums to represent secondary strucutre. Made a lot of things that should never be negative unsigned. commit 265ddc6fca7950a87061f9752bf5c5e889952c04 Date: Thu Jul 3 18:15:40 2014 -0400 Making some numbers that should never be negative unsigned. Added a check to prevent underflow. commit a28950073d90146c9f5ae6f1aeff5d65cc536e28 Date: Thu Jul 3 14:39:56 2014 -0400 Alering CcdLoopClosureMover's show() to use the movemap data member directly to avoid copying a movemap as a part of printing... because that is absurd. commit 50b8bed05949809a251f4b0390d05e4ba6abd012 Date: Thu Jul 3 14:31:24 2014 -0400 Removing useless functions from CcdLoopClosureMover (loop_start() is unnecessary -- just get the loop and ask it whatever you want!) and updating show() to call Loop's show(). commit 53f6f7147af5dfd9ccf39569bacc9b48a71df018 Date: Thu Jul 3 14:24:21 2014 -0400 Adding a show() method to protocols::loops::Loop. Now the streaming operator (<<) calls this public method. I've added a little additional detail to the string representation of the loop (e.g. labeling what the various numbers represent), so this will change any integration tests that printed a Loop. The << operator is no longer friended (hooray!) because it can simply call the public method show(). commit 85dc07993cffbe1c2391ed93fb411ce40364b005 Date: Thu Jul 3 14:04:43 2014 -0400 fixed MoveMap bug in StepWiseProteinCCD_Closer commit f48a9c78d4cb95630197fae09db3c8eb81c79890 Date: Tue Jul 1 18:00:20 2014 -0400 pointer bug fixes commit 91fafdf63679e2add15c22776b48edca69dbb2e4 Date: Tue Jul 1 13:45:02 2014 -0400 Adding a few more useful TODOs and making the copy constructor deep copy data to which we are pointing. commit fa3453015296c6d8517102e5f7377a5631831e44 Date: Tue Jul 1 10:34:14 2014 -0400 More comments. It took me a while to understand why the atom number was called “torsion” but I get it now… I get it now. commit 9e4a159076b2718972d6ba4615322fb88e9f06ce Date: Tue Jul 1 09:33:03 2014 -0400 Adding a couple of comments to note some functions that could be moved to core. commit 8f798bd4761e9aea32f667621fec150b5c2d5f86 Merge: 80ef402 7f54625 Date: Mon Jun 30 17:37:07 2014 -0700 Merge branch 'rpache/KIC_with_fragments' of github.com:RosettaCommons/main into rpache/KIC_with_fragments commit 80ef4024a5f5c85acc5474c419e37cbd655dc24e Date: Mon Jun 30 17:35:33 2014 -0700 changing format to tabs instead of spaces commit 25c2c469cc6d005c8e4867ed412ba00adc54dc62 Date: Mon Jun 30 18:16:36 2014 -0400 Making comment about old vs new rama scores a FIXME so we can find it more easily. commit 362b416eab571a09c8f3d21c0cd53fad9c6b91ad Date: Mon Jun 30 18:08:41 2014 -0400 Tagged some functions to be moved to numeric, comments about simplifying the interface to CcdLoopClosureMover commit feb4db8e3bdeecdc1a67db3fe296a1645519c87b Date: Mon Jun 30 17:56:27 2014 -0400 Tiny spacing cleanups, using Loop::size() instead of computing it when needed and adding some TODOs commit bf74a569b1edb33ed913894fdeffb6b49f242e52 Date: Fri Jun 27 22:37:58 2014 -0400 CCD Refactor: replaced call to fast_ccd_loop_closure() with CcdLoopClosureMover.apply() in StepWiseProteinCCD_Closer commit 5683cafcfdcedb523ce29222287b818326b122c9 Date: Fri Jun 27 22:24:25 2014 -0400 CCD Refactor: replaced call to fast_ccd_loop_closure() with CcdLoopClosureMover.apply() in WobbleMover commit 9c4252a7cf40211bdcfe9d947751c8f11b6a4f50 Date: Fri Jun 27 22:16:52 2014 -0400 CCD Refactor: replaced call to fast_ccd_loop_closure() with CcdLoopClosureMover.apply() in LoopMover_QuickCCD commit 02bbfaa5d9eef6e098f742c5135bcae8816bd863 Date: Fri Jun 27 22:09:45 2014 -0400 CCD Refactor: replaced call to fast_ccd_loop_closure() with CcdLoopClosureMover.apply() in Phil's test1 pilot app commit 029fff16f4d332877579f8a17023843e14d6d268 Date: Fri Jun 27 21:58:42 2014 -0400 CCD Refactor: replaced call to fast_ccd_loop_closure() with CcdLoopClosureMover.apply() in LoopRebuild commit 6566abea7803b5f3c500a48e5a21bfb00671e8df Date: Fri Jun 27 21:40:29 2014 -0400 CCD Refactor: replaced call to fast_ccd_loop_closure() with CcdLoopClosureMover.apply() in loops/loops_main.cc commit 9be31668805aa50cf4e56cc060a25b543a82962c Date: Fri Jun 27 21:16:46 2014 -0400 CCD Refactor: replaced further calls to fast_ccd_loop_closure() with CcdLoopClosureMover.apply() in devel/inv_kin_lig_loop_design/Protocol.cc commit ca4be2a0c362b7ad71a398a46329a13881761cbd Date: Fri Jun 27 20:49:33 2014 -0400 bug fix commit bf2e8254fcca5d97d8939b0d482a9a507a7d3d41 Date: Fri Jun 27 20:40:26 2014 -0400 accidental commit of nothing commit 5c8982ca0797aa94be3953a2b11e1c64a1e56ea5 Date: Fri Jun 27 20:37:47 2014 -0400 CCD Refactor: replaced call to fast_ccd_loop_closure() with CcdLoopClosureMover.apply() in devel/inv_kin_lig_loop_design/Protocol.cc commit be4022534d559081461141e0b5243622f6342d9f Date: Fri Jun 27 20:08:36 2014 -0400 CCD Refactor: replaced call to fast_ccd_loop_closure() with CcdLoopClosureMover.apply() in CCDLoopCloser commit b32969fc44b99efa616f852064908ffb2a1e81f9 Date: Fri Jun 27 19:50:08 2014 -0400 CCD Refactor: deleted fast_ccd_loop_closure() from ccd_closure.cc; now I will changed all calls to it to use CcdLoopClosureMover commit ab291dba0a78404483c7ce17ea5555243f42a437 Date: Fri Jun 27 16:10:44 2014 -0400 bug fix commit e5767124836b2d0ed8d7d3e59507b1eb341373c2 Date: Fri Jun 27 14:49:14 2014 -0400 bug fix commit 3fc3b1937aa8af4f483e993fb8df5b49318b4adc Date: Fri Jun 27 14:06:19 2014 -0400 CCD Refactor: clarified confusing variable names; cleaned up code more commit 5fee5f90201056e508bce2c12148cbe584bc09bf Date: Fri Jun 27 10:30:22 2014 -0400 CCD Refactor: more private data added; new enum to simplify things; added const STEP_SIZE indexed by ChainDirection commit e67d76e68c7c4322c14cad473ae383a63863c0b8 Date: Fri Jun 27 09:03:16 2014 -0400 fixed linker error commit 8aa7067d9315d9cb59d90c41df6cea8fdc71f04d Date: Thu Jun 26 23:30:29 2014 -0400 CCD Refactor: removed fast_ccd_loop_closure() method, having moved everything into apply() commit 281455e7881d3f676712736c2362a78e777e006d Date: Thu Jun 26 19:05:03 2014 -0400 CCD Refactor: copied over fast_ccd_loop_closure() to CcdLoopClosureMover commit 91a53e6fe670e4b46d987db85ddf76401b179b8c Merge: 556b9ba a90e2a7 Date: Thu Jun 26 18:03:09 2014 -0400 resolving merge conflict commit 556b9ba1cd9287cb8c56fc458403a440f0683c0d Date: Thu Jun 26 18:01:04 2014 -0400 bug fix commit 2926c542f7bd003e199cfd6470c0d130c6dcb419 Date: Thu Jun 26 16:00:54 2014 -0400 CCD Refactor: moved code from .hh into .cc commit a90e2a7d90d4a5377a2635910c486950c5e5e145 Date: Thu Jun 26 16:00:54 2014 -0400 CCD Refactor: moved code from .hh into .cc so we can #include a fwd.hh commit 04b7e7d91b4d7bad463a23dbb8991f4269f067e1 Date: Thu Jun 26 14:51:30 2014 -0400 CCD Refactor: finished reformatting CcdLoopClosureMover.cc, including adding new accessors commit 3b35620096233b54857c0beae4cbdbec2b193119 Date: Thu Jun 26 11:01:52 2014 -0400 bug fixes commit 6c97d3633c47f8ff5a0e2611ceefe7b1b685876b Date: Wed Jun 25 21:58:59 2014 -0400 CCD Refactor: updated/cleaned/fixed 'boiler plate' code in CcdLoopClosureMover.cc commit 99cd24037ee37904973ceb8696eeb17935eee093 Date: Wed Jun 25 21:10:03 2014 -0400 CCD Refactor: updated/cleaned/fixed CcdLoopClosureMover.hh commit 29ef5534ebbcc0f3f148addbc0137badc6387b04 Date: Wed Jun 25 20:26:08 2014 -0400 CCD Refactor: updated/cleaned/fixed CcdLoopClosureMover.fwd.hh commit cf710800ad70b3b647278616f4ed96f29a7f4899 Date: Wed Jun 25 17:27:36 2014 -0400 CCD Refactor: fixed tests commit 3cb8ebb6e24787c21a059319a97886537b6afb63 Date: Wed Jun 25 07:48:43 2014 -0400 minor tweaks commit 43773b422633e6b603d3970b5dae1c80d8ea0ffc Date: Tue Jun 24 20:48:26 2014 -0400 removing warnings: who the @%!* turned off Werror? commit 5721dec742b9268b5acabaf01dcd1e54f39a48b9 Date: Tue Jun 24 20:09:33 2014 -0400 bug fix commit aafee8a3881ef177778ecf12b0e49d87cb9f649e Date: Tue Jun 24 20:07:20 2014 -0400 bug fix commit d85d67bbce0f62ecb2c342c4422db62538fc4910 Date: Tue Jun 24 20:05:11 2014 -0400 bug fix commit fce3c66c94f2e7a9c77bdfebb5949a8bce69f69b Date: Tue Jun 24 19:31:01 2014 -0400 CCD Refactor: before swapping out a for loop with a cleaner one commit 7ada20ef7086b7dcd3a203f9c39d4246a556c2b1 Date: Tue Jun 24 19:13:36 2014 -0400 CCD Refactor: cleaned up copy_torsions_to_pose() method commit 4949deccb656a6a2827719704a52eb49f6038cef Date: Tue Jun 24 19:01:10 2014 -0400 CCD Refactor: cleaned up load_coords_and_torsions() method commit bf019a3f7c96be0bec699bec2d72b630f07cda7a Date: Tue Jun 24 18:22:56 2014 -0400 CCD Refactor: cleaning up cc file; moved enum def to hh file commit 8340b8d6a33b660351142c8893787b71d6426303 Date: Tue Jun 24 17:38:30 2014 -0400 CCD Refactor: cleaned rest of hh file and changed all types to better typedefs commit 472a6e6d7e2eec5fe3459fe1f9fa6e8fb5796060 Date: Tue Jun 24 17:27:49 2014 -0400 CCD Refactor: cleaned up #inclusion commit bb99c838d616c6ac22ad4ce3a83ab269590d661c Date: Tue Jun 24 17:21:25 2014 -0400 CCD Refactor: fixed file header Doxygen lines commit 3ca7572a5099d69e32c4b559a34e103a8c0b1617 Date: Tue Jun 24 14:56:53 2014 -0400 Changing "direction" to be an enum instead of an int. Changing a few types to be more detailed -- i.e. Real -> Angle when appropriate. Creating another small function to reduce nearly duplicated code in the get_deviation funciton. This code really isn't all that complicated -- a couple of days of work in earnest and we'll be all set! commit 7f546254bec2d1d7f86d180cb697cecdc7439d1c Merge: 8bae369 a776c06 Date: Mon Jun 23 16:20:58 2014 -0700 Merge branch 'rpache/KIC_with_fragments' of github.com:RosettaCommons/main into rpache/KIC_with_fragments commit 8bae36914286fcef42f4c623c0bd477647a0551a Date: Mon Jun 23 15:42:39 2014 -0700 Make it easier to use fragments for loop building. commit 236b68e32284cb3240aaa97903f5d20ba1f43d4f Date: Mon Jun 23 13:12:07 2014 -0700 Make the minimizer settings easier to control. Amelie pointed out that legacy KIC uses different minimizer settings in centroid and fullatom mode. This commit adds code to copy that behavior in refactored KIC. commit 68d4e2c54e132df8fbc427a8d3e8e8dde6a509ba Date: Sun Jun 22 19:38:12 2014 -0700 Fix a closure bug in refactored KIC. This commit fixes a bug in KIC that was causing chain breaks for perturbers that set either omega or a bond angle for the first residue in the loop. These dofs are basically ignored by KIC because they are outside the pivots, but they were still being improperly applied to the pose. This bug was only noticeable when the IdealizePerturber was being used, because no other perturber set omegas or bond angles. commit a776c062cf73f4f2dff3605e88b997f988b0386a Date: Thu Jun 19 16:49:12 2014 -0700 removing tracer debug output from ConstantLengthFragSet::overlapping_with_region function; this eliminates the need to mute that tracer to avoid long runtimes due to writing to the terminal; tracer output in the FragmentPerturber class has been adapted to also provide the frame length commit db2e4863477d8664c5b90b3b59958e4c9609c58e Date: Wed Jun 4 17:58:58 2014 -0700 changing max KIC perturber samples default value back to 2000 commit 8fb3caf284b4d596c2b6292f226acfaba88be5fd Date: Tue Jun 3 12:11:24 2014 -0700 adding the standard Rama perturber before the given custom perturber during initial loop build (in LoopBuilder class); this ensures that the initial loop build is not biased towards the starting structure by discarding all starting loop torsions and replacing them with random values from Rama space; the given custom perturber can change those torsions afterwards commit 6faa1799d3244a759e7fd6c01ee13f758160e9cf Date: Tue Jun 3 12:05:08 2014 -0700 restoring max KIC perturber samples to 2000 commit 6fbd6ecbc0ef4bfe5aa374655500f03a832df875 Date: Tue Jun 3 12:01:47 2014 -0700 checking if requested min_overlap is too large for the given region in ConstantLengthFragSet commit 85a60cb22610a0422829e222e8934f0292d1e46e Date: Wed Apr 23 15:30:33 2014 -0700 fragment libraries are now passed to the FragmentPerturber as const reference commit 536998ebe44f9b864fa883479ed66f25ed9ea8fb Date: Tue Apr 22 14:11:20 2014 -0700 implementation of the FragmentPerturber class; this finally enables sampling using KIC with fragments commit 1c022533998d7fd1d4bb5dac5d23724de635c4ce Date: Tue Apr 22 14:07:50 2014 -0700 throwing a BadInput exception if KIC with fragments is enabled, but no fragment libraries are provided; also fixes a bug where the refine stage would still use standard KIC even if KIC with fragments is set commit 6b448e257801d9401feb9483bb0ae52791cb3982 Date: Wed Apr 16 17:05:16 2014 -0700 adding the function overlapping_with_region, which returns the number and list of all fragment alignment frames that somehow overlap with the given region (also allows those frames that start before the region and reach into it); currently only implemented for ConstantLengthFragSet (the FragSet parent class simply calls the region method by default) commit 521d913b7fbb79a427840754c8d241df089a2d3c Date: Tue Apr 15 14:45:42 2014 -0700 including Frame.hh (instead of Frame.fwd.hh) in FrameList.hh to fix compilation; this is needed due to FrameList inheriting from vector1 commit 1749f18b9fa9b5e7a30656ec40d1e2c894b140d1 Date: Thu Apr 10 00:40:05 2014 -0400 remove all all.hh files except for FArray and options system commit 9e5f4e2f50d3ff7e8019a728d334f718795fb925 Merge: 48a76c0 7f238cc Date: Thu Apr 10 00:23:57 2014 -0400 merge master into branch commit 48a76c06b9f5f125c05625695ddf3cb58e140691 Date: Thu Apr 10 00:05:32 2014 -0400 Remove version comments from fa_standard residue_types commit f19e6e9cf57eaf187fb0693aca3bc33d673ddf9d Date: Thu Apr 3 20:01:02 2014 -0700 fixing compilation of LoopRelaxMover commit ece27a314a01c4b132ecf33e88d2b08c20f01fbb Date: Thu Apr 3 18:57:18 2014 -0700 adding FragmentPerturber class and registering it in protocols.3.src.settings; still requires implementation commit 46b10661476e12e30a113295b615a1a134fb5d9d Date: Thu Apr 3 18:44:24 2014 -0700 adapting the LoopRelaxMover to execute KIC with fragments when the given flags are set (currently in debug mode for testing purposes) commit ed2b6dd992dddadeb1849677694be8f9f309967e Date: Thu Apr 3 16:38:49 2014 -0400 Carbohydrates & Lipids: updating centroid database files commit 587028ad198510514c7bcc8e9abac0a52392e8f1 Date: Tue Apr 1 14:32:26 2014 -0700 refactoring LoopBuild main function to load fragment data whenever fragment files are given on the command line; this implicitly enables fragment loading for KIC with fragments commit 0451f4d76a5e6369d64f853b41d619537f5f0518 Date: Mon Mar 31 18:19:09 2014 -0700 fixing compilation of LoopBuilder with custom perturber constructor; the given custom perturber can overwrite bond lengths, angles and omega torsions after idealization if so desired commit 519296b4d636b8705180e619aa14a5083907fe3d Merge: d3a113c 5f747a3 Date: Wed Mar 26 18:41:39 2014 -0700 resolving conflict in options.settings when merging-in master (rev. 56584) commit d3a113ce5af8057b633f56828a3d880584680787 Date: Wed Mar 26 18:31:44 2014 -0700 making perturb_kic_refactor and perturb_kic_with_fragments report when initial kinematic closure failed commit f825821e85255ca7a441cb6f40aefa534db9e342 Date: Wed Mar 26 18:29:40 2014 -0700 added clang 5.1 to option settings commit 304eceee4d01b196bc56e65659dc5e8e93865327 Date: Tue Mar 25 18:54:22 2014 -0700 adding custom-perturber constructor to LoopBuilder; this allows to use a custom perturber for picking phi/psi torsions during the initial loop build; bond lengths and angles, as well as omega torsions are still idealized commit 0a8dd8eeb1b1191acd4eeb62a860cc1231a577a1 Date: Fri Mar 21 17:04:44 2014 -0700 adding perturb_kic_with_fragments and refine_kic_with_fragments options commit 34671a5cc851b32c0035e48a457446b7c31ef1f0 Date: Fri Mar 21 17:03:10 2014 -0700 adding user-specific xcode IDE files to .gitignore commit c2423b1a01a623a69b4e1452b6615e7b04673257 Date: Tue Nov 19 18:05:50 2013 -0800 add clone() method to UpdateEnzdesHeaderMover commit 0a8e899de7bcceb4ff2cbd498a778c6232df0c4e Date: Tue Nov 19 17:34:47 2013 -0800 fix typo in new updateEnzdesHeaderMover commit b2d858dfe4d66693c8e27291ae153ac7cb8cf0fe Date: Tue Nov 19 17:06:26 2013 -0800 Add mover to update the enzdes header block in case the enzdes residues change