commit 08f28fd12288855fa014eca4893f6b97b329db09 Merge: 6f59738 e622184 Date: Mon May 23 13:49:40 2016 -0700 Merge pull request #1358 from RosettaCommons/vmullig/design_cycpep_app Add filtering for oversaturated hydrogen bond acceptors to simple_cycpep_predict app. This allows the simple_cycpep_predict app to automatically throw away sampled conformations in which more than the allowed number of hydrogen bonds are being formed to a hydrogen bond acceptor. It pains me to split that infinitive. commit 6f597384488f5a91383a9026b1968084a7e86388 Merge: 9ef7ab3 b00646d Date: Mon May 23 11:54:52 2016 -0700 Merge pull request #1350 from RosettaCommons/tlinsky/tlinsky/hb_cst_gen_update Minor constraint generator updates commit 9ef7ab3ee934639c1531c8cd7a18cc4a4c101815 Merge: 54ede79 146fd6c Date: Sun May 22 21:09:27 2016 -0700 Merge pull request #1349 from RosettaCommons/vmullig/oversatisfied Add a filter for hydrogen bond acceptors with too many hydrogen bonds Rosetta's scorefunction poorly accounts for cases in which too many hydrogen bond donors are trying to bond to a single hydrogen bond acceptor (e.g. three amide protons hydrogen bonding to a single carbonyl oxygen). This is largely because of the pairwise-decomposible hydrogen bonding score terms, which can't be aware of any other interactions the residues in question are making with a third body. This filter is intended to flag these cases. Tasks: - Create the .cc, .hh, .fwd.hh, and Creator.hh files (using Jared's handy script). - Write the parse_my_tag: - Private member var (core::Size), initialization, getter, and setter for allowed number of oversaturated acceptors. - Private member var (bool), initialization, getter, and setter for whether we're just counting backbone. - Private member var (core::Real), initialization, getter, and setter for the energy threshold for counting something as an h-bond. - Private member vars (ResidueSelectorCOPs), initialization, getter, and setter for two optional selectors for the hydrogen bond acceptor residues and hydrogen bond donor residues. - Write the apply() function. - Peripheral functions -- report() and whatnot. - Unit test. - Debug. - Integration test. - Documentation. - Beauty. commit 54ede79e2366aad779cd9b7601e6af98ec95e95b Merge: cf2629e aa101d1 Date: Sun May 22 21:04:04 2016 -0700 Merge pull request #1355 from RosettaCommons/vmullig/update_rosettascripts_talaris2014 Switching some more defaults to talaris2014 from talaris2013. Certain utility functions in RosettaScripts still default to talaris2013, and some default to score12. Updating to "commandline", so that they always stay in sync with whatever the default Rosetta behaviour is. commit cf2629e7612fa4ef4e1cd9cb52c19d13032fdc1b Merge: 9a69209 f6e7934 Date: Sat May 21 23:59:02 2016 -0700 Merge pull request #1329 from RosettaCommons/vmullig/peppredict_blugene Modifying the simple_cycpep_predict application to play nicely on Blue Gene. I need to do this to allow it to be run on large-scale clusters while BOINC is tied up during CASP. This will also be my test-bed for writing a multi-level job distribution and collection hierarchy (and, ulitimately, adding multi-threading to it). It does NOT replace jd3 in any way; on the contrary, it's a convenient place to test features that we might want in jd3. Tasks: - Add -cyclic_peptide:MPI_processes_by_level flag to let the user specify how many processes will be devoted to each level of the hierarchical communications scheme. - Add option to control size of batches being distributed at each level. - Modify the simple_cycpep_predict app to set up MPI options. - Add a SimpleCycpepPredictApplication_MPI class to the protocols level that handles the multi-level communications. - Revise the job buffer size to a list of job buffer sizes, and remove the requirement that the job buffer size be at least the number of slaves per first-level master. - Add hooks to SimpleCycpepPredictApplication to let it be set up by SimpleCycpepPredictApplication_MPI, and to suppress its disk I/O. - Finish implementing all of the functions marked //TODO WRITE ME in SimpleCycpepPredictApplication_MPI.cc. - Have this class actually distribute jobs down the hierarchy. - Have the slave nodes call the SimpleCycpepPredictApplication class for sampling. - Option to return only the top n% of jobs. (Job return is two-step: first, send list of scores up the hierarchy to the emperor; have emperor determine and request top n%; second, send only top poses up the hierarchy.) - Send results summaries UP the hierarchy. - Sort sent results as they propagate up the hierarchy. - Unit tests for sort functions. - Send requests for poses DOWN the hierarchy based on sorted results. - Have the SimpleCycpepPredictApplication_MPI class collect results UP the hierarchy. - Write out silent structures from the emperor node. - Add integration test to MPI test suite. - Documentation. - Test on jojo. - Test on Blue Gene. commit 9a69209e4e20a15f3a46fd25c9fbef9f5169c305 Merge: 0f2f818 47f479a Date: Sat May 21 12:20:01 2016 -0400 Merge pull request #1354 from RosettaCommons/smlewis/Extender_pilot_app_bitrot trival bitrot repair on a senescent pilot app (CAP->COP); This is a noncompiling pilot app that was useful for generating starting structures for FloppyTail. As a noncompiling app it didn't get fixed when the smart pointers were updated and CAPs went away. This app remains disabled in scons (although it does compile now), so there oughtn't be test changes associated with it (and so I'm not loading the test server with it, either). commit 0f2f8187e12709a8d25e31a3c84354a811b13d1e Merge: b969d5d 27f356c Date: Sat May 21 11:17:12 2016 -0400 Merge pull request #1352 from RosettaCommons/JWLabonte/sugars/docking This merge improves a private pilot app I used for glycan docking. It also includes the following fixes/changes: more sugar patches and .params 2-deoxy- another rhamnose more H-placement fixes adding output to notify a user if input rings are not chemically believable fixes rotamer sets for substituted sugars (I had planned to add ->6-beta-D-Manp, but it looks to be already in the database....) All tests pass. Integration test changes expect because of .params file/patch changes and/or new output. commit b969d5d2401a8ce8a19ce50858048606183d69ec Date: Fri May 20 18:03:07 2016 -0700 Beautifying master, so that I can see what's ACTUALLY changed in my beautified branches. commit fe624004f6ba21931392f896b7e32a0ce14bcb61 Merge: 56e169b 6bc23a1 Date: Fri May 20 15:45:18 2016 -0400 Merge pull request #1351 from RosettaCommons/kimdn/sew_DN added comment to Hasher.cc in SEWING to show which part was changed by Doonam commit 56e169bb82a5b71cf75a2779314a93b7f458b1e4 Merge: 4846dc5 b1cf8f9 Date: Fri May 20 11:19:05 2016 -0700 Merge pull request #1347 from RosettaCommons/bfrenz/reorder_foldtree Removed a debug statement from the previous merge and added a check f… commit 4846dc50718b267fa7e72ab9cf921a93893087db Merge: 8834591 d0b0a48 Date: Thu May 19 01:28:25 2016 -0700 Merge pull request #1346 from RosettaCommons/bfrenz/reorder_foldtree Fixed an issue in reorder fold tree where only the start and end of e… commit 8834591a5136e41bef7bdf7c0a1892012d3e0e4a Merge: 4a23313 07089e8 Date: Wed May 18 23:16:13 2016 -0700 Merge pull request #1344 from RosettaCommons/tlinsky/fix_utility_join Fix segfault in utility/string_util.cc::join() with empty vector commit 4a2331335b9587c0647ca9d6947b84662d62a20a Merge: 57afddf 930c4c2 Date: Tue May 17 13:36:32 2016 -0600 Merge pull request #1340 from RosettaCommons/sergey/binder Fixing various PyRosetta issues commit 57afddfdecde1cb3f89075a78ee568a62154a6de Merge: 5f0d389 b2a54a8 Date: Tue May 17 01:19:59 2016 -0700 Merge pull request #1343 from RosettaCommons/tlinsky/sheet_remodel_cst_gen Fix fldsgn::topology bug(s) and wrap SheetConstraintGenerator commit 5f0d389d9c0c99da8ac6b173ec5be12c6a9c454f Merge: 15b290e ff8bec2 Date: Mon May 16 14:28:22 2016 -0700 Merge pull request #1327 from RosettaCommons/vmullig/tweak_fdes Minor tweaks to FastDesign and to the ReadResfile TaskOperation -- Adding support to FastDesign for clearing the pose if it contains D-amino acids. -- Adding an explicit copy constructor to the ReadResfile TaskOperation that clones the ResidueSelector, if one is present. -- Adding explicit set_residue_selector() and residue_selector() functions to the ReadResfile TaskOperation.