commit 8176854bef9d31d8a80d80a3ca97c608c73a70ee Merge: 50e50f6 ce8765d Date: Fri Apr 1 22:23:09 2016 -0400 Merge pull request #1243 from RosettaCommons/JWLabonte/Windows_build fixing PyRosetta build commit 50e50f61d36009f4696505fba965998c913d7589 Date: Fri Apr 1 15:31:26 2016 -0700 Very minor bugfix for SimpleCycpepPredictApplication in a rarely-used mode. Merging without testing. commit fac75af8d55207acc3489f317f31eed7117a2ba1 Merge: c7a4ed7 7ba6dd8 Date: Fri Apr 1 14:11:04 2016 -0700 Merge pull request #1205 from RosettaCommons/everyday847/fix_chi_bug Miscellaneous metalloprotein fixes. - auto_setup_metals now is properly behaved with the new metapatching system - auto_setup_metals now works with cartesian minimization Integration tests will fail due to either: a) changing the level of some tracer output in ResidueProperties b) adding a new score term commit c7a4ed7af970318577287e38cd9f1105885e1e70 Merge: 1951fdb b05c281 Date: Fri Apr 1 14:01:18 2016 -0700 Merge pull request #1240 from RosettaCommons/vmullig/peppredict_setting Fixing a minor bug in the simple_cycpep_predict app When the user set certain residues to have certain dihedral values, the wrong residue was sometimes being set when the pose was circularly permuted. This affected the efficiency of sampling, but would not invalidate the scientific results (so this bugfix need not be pushed to BOINC immediately, @davidekim -- it can wait for whenever the next BOINC update happens). commit 1951fdbd8511a183b62db943ec2991a3d070ad29 Merge: 4be15d4 1cb11c1 Date: Fri Apr 1 13:41:01 2016 -0700 Merge pull request #1242 from RosettaCommons/vmullig/fix_splice_test Attempting to fix the splice_out_L1_L2_longer integration test Changing the random seed for the splice_out_L1_L2_longer integration test. This test's success is highly dependent on the seed value, and for many seeds, it fails to find a solution that passes filters. The switch to lbfgs minimization caused enough of a trajectory change that this test started failing. commit 4be15d410f7cc8470124c3ab38ae08ded1685cb0 Merge: 7f35c29 ebc700d Date: Fri Apr 1 13:20:34 2016 -0700 Merge pull request #1237 from RosettaCommons/tlinsky/virtroot Add c++ setters to VirtualRootMover commit 7f35c293a15a5be744feb81ef0cf390eb7923011 Merge: 0cae309 1d5929e Date: Fri Apr 1 03:21:21 2016 -0700 Merge pull request #1229 from RosettaCommons/everyday847/cleanup Trivial, semantic-neutral code cleanup effort to core/scoring: I think it makes sense to move forward with this PR: even the scorefile scores, in that one integration test that appears to just get optimized differently, end up the same. commit 0cae3092782a6dfc70e10d190cc779187406545f Merge: 4481504 f1a582f Date: Thu Mar 31 18:07:58 2016 -0700 Merge pull request #1148 from RosettaCommons/everyday847/dunbrack_cleanup Clean up core/pack/dunbrack - If I want to do more work on this, I'll do it in a separate PR. May as well get things looking better asap. commit 4481504a3774db214ebda9eecefc40793e34c5aa Merge: c1e8713 f3c30b3 Date: Thu Mar 31 11:44:27 2016 -0500 Merge pull request #1236 from RosettaCommons/roccomoretti/silenttagfile Add support for -in:file:tagfile to SilentFileInputter. he relationship between -in:file:tags and -in:file:tagfile is similar to -in:file:s and -in:file:l -- that is, you can now pass a file with a list of tags, rather than having to list all the tags out on the commandline (and without the length limits doing so imposes). The -in:file:tagfile is a pre-existing flag, only used once in AbrelaxApplication.cc, but with similar semantics. This extends the functionality to JD2 protocols. (Also fixes the option file description.) commit c1e8713c5934f99310f81bccb53b81e3e742b69c Merge: a61ddd9 dd600d6 Date: Thu Mar 31 10:26:56 2016 -0400 Merge pull request #1211 from RosettaCommons/JWLabonte/XRW/HETNAM_records Post-XRW: Refactoring reading, writing, and storage of HETNAM records This merge completes a task having been on my to-do list for a long time — a refactoring of `HETNAM` code in Rosetta to be more general / less carbohydrate-centric. Now anyone should be able to specify using `HETNAM` records the desired base `ResidueType` for a specific three-letter-code at a specific position in the structure. (This was currently only functional for three-letter-codes that are listed in the database as carbohydrate codes.) A clear example is now found in `source/test/core/import_pose/3-letter_code_ambiguity_resolution.cxxtest.hh ` Now, Rosetta-format `HETNAM` records are output by default for all non-AA, non-AA, non-virtual, and non-membrane residues. This will change ~50 integration tests. There is a known issue with `HETNAM` records involved in branched complexes being sorted poorly. I will fix this in a later merge, and it currently only affects sugars. A flag, `use_pdb_format_HETNAM_records`, can be used to have the Rosetta output PDB-format HETNAM records instead, but for this to be truly useful, we need to have the PDB name for each 3-letter code stored somewhere in Rosetta. (Perhaps a future pull request?) This merge also cleans up / simplifies `SFR` code that was a mess because about six of us were working on it at the same time during the ChemicalXRW. (As an extra bonus, it also introduces the (`molfile_to_param.py`-generated) oxidized and reduced versions of flavin into the database.) All unit tests pass. Windows PyRosetta test not completed. (See Sergey's e-mail.) ~50 integration test changes from `HETNAM` records in output files carbohydrates test change from new sorting of `HETNAM` records. number_of_residuetypes test change from adding two more commit a61ddd9803e1c8485377bcb5019304434607c55d Date: Wed Mar 30 12:12:59 2016 -0400 Reverting 6b05687a3e in master to 3501c41d per David Johnson's request commit 6b05687a3e7f2a0690821f6f2fc694db7eb61105 Merge: 16648b4 3501c41 Date: Wed Mar 30 08:35:08 2016 -0500 Trying to merge RRM DNP app changes, having troubles commit 16648b4a1758e9c2453ca7f89d461067f9f20735 Date: Wed Mar 30 08:24:11 2016 -0500 Improved RRM DNP detection app