commit 7e1e880855f42127f0cfbd742f82613edc8187df Merge: 7ce9d5b f332425 Date: Sat Jul 23 14:40:54 2016 -0700 Merge pull request #1476 from RosettaCommons/everyday847/fix_windows_build Don't look for sys/resource.h on Windows commit 7ce9d5bf5174d497560ce1624761e0c166dc30c3 Merge: c68d507 d11bc3c Date: Fri Jul 22 16:07:06 2016 -0700 Merge pull request #1475 from RosettaCommons/vmullig/aspartimide Add a score term to penalize sequences that are likely to result in aspartimide during peptide synthesis In designing peptides, we're having to throw away or redesign a heck of a lot of designs because of DN, DS, DT, Dx, DG, dn, ds, dt, dX, or dG sequences, which often result in the unwanted aspartimide side-product during peptide synthesis. My Thursday night project will be to add a score term to penalize these two-residue sequences during design, so that the packer simply doesn't put them in. (There are several other things that we're also having to filter for, and each one cuts down our viable designs by an order of magnitude, greatly increasing the number of designs that we have to do in order to get one that we can synthesize. This is the easiest and quickest thing for me to fix with a non-filter-based solution, increasing our good design rate by an order of magnitude or so.) Tasks: - Add the score term. - Have it only apply itself to pairs of residues that are conventionally connected (i.e. residue i is connected to residue j at residue i's C-terminus and residue j's N-terminus). - Have it penalize the sequences in question. X Double-check which sequences should be penalized. (Some also say DC, DD, and DR [and their mirrors]. DP and Dx', where x' is N-methylated, should be immune to aspartimide formation, though.) @gbhardwaj --> If there's a need to tweak what's penalized in the future, or to add general user controls, we can do this when we need it. - Unit test. - Beauty. - Documentation. commit c68d5070724eb4e1b6c1b5ee9c91bc1de6d1dfa2 Merge: 62063d8 dfec261 Date: Thu Jul 21 19:24:29 2016 -0700 Merge pull request #1146 from RosettaCommons/everyday847/rna-dev Cleaning up and troubleshooting ERRASER a bit; also, some non-natural residues commit 62063d837652235ed85a376b5bac0c8f0dc39474 Merge: ef9dd4d 005326e Date: Wed Jul 20 11:23:28 2016 -0700 Merge pull request #1372 from RosettaCommons/jadolfbr/antibodies/fix_h3_ab_protocol Camelid and antibody protocol fix This PR enables camelid antibodies for the antibody protocol, specifically, antibody_H3. I don't think this ever actually worked as the test for camelids was never being checked. This also adds an integration test for camelid antibodies and antibody_H3. commit ef9dd4d294f4310252543e507083cb3c4849d65f Date: Tue Jul 19 18:57:59 2016 -0700 Removing an extraneous file, and taking the opportunity to beautify master while I'm at it. commit 0028baa6259ff5598dcf35623f6782537a4df5c4 Merge: 892dc6f 2f520dc Date: Tue Jul 19 18:52:35 2016 -0700 deleted: source/src/protocols/cyclic_peptide/dVdPN_A.pdb commit 892dc6f7fb355ad662847c82dc6bff29d39e2943 Merge: 3dfda33 19e4da7 Date: Tue Jul 19 16:44:02 2016 -0700 Merge pull request #1472 from RosettaCommons/jadolfbr/jadolfbr/carbohydrates/val_fix Fix simple glycosylation Fix an uninitialized variable in the copy constructor of glycan relax that was causing the simple glycosylation unit test to fail in valgrind. Thanks to @roccomoretti for actually debugging this and finding where the variable was uninitialized in the first place. commit 3dfda3335774295a5053d685bb45c83c4b442446 Merge: fadb0ac 54f14ff Date: Wed Jul 20 07:19:14 2016 +0800 Merge pull request #1473 from RosettaCommons/dimaio/symm_density_fixes Two small fixes for elec_dens_fast with symmetric complexes. commit fadb0ac28d8eddd38c7703ca740510bff901f03e Merge: 2d13982 5c1aaeb Date: Tue Jul 19 14:03:59 2016 -0700 Merge pull request #1470 from RosettaCommons/hahnbeom/fa_intra_elec this is "just adding fa_intra_elec term". commit 2d1398245393eb68d21773cbf8544100146755e3 Merge: 11809c5 97e11b1 Date: Mon Jul 18 19:05:21 2016 -0700 Merge pull request #1469 from RosettaCommons/jadolfbr/demo_scripts add scripts moved from demos. commit 11809c546db6832427f0221e61b93f3201376b3f Merge: 109f0a2 277e4b9 Date: Tue Jul 19 04:43:49 2016 +0800 Merge pull request #1471 from RosettaCommons/dimaio/app_bugfixes Fixing two bugs in hybridize/cartesian_sampler. Thanks @roccomoretti for finding these. commit 109f0a264ed196f738e2583bb1d2b8ca62ccdde9 Merge: 811632d d33e40b Date: Mon Jul 18 10:46:06 2016 -0500 Merge pull request #1467 from RosettaCommons/roccomoretti/valgrind_benchmark_fix More integration.py fixes Fix integration.valgrind -- slightly different flags are needed. (--skip-comparison messes it up.) Also, fix the integration test execution time ordering. (The extra directory in the test name messed things up.) commit 811632d136667bad5c75a65e59bc0ef6faa940a9 Merge: ef059b4 98c2f3b Date: Sat Jul 16 23:07:20 2016 -0700 Merge pull request #1466 from RosettaCommons/tlinsky/constraint_generator_nonglobal Add serialization support to ConstraintsMap commit ef059b4c5486a97789e55fea41a75d0e29d3cc2f Date: Sat Jul 16 15:13:10 2016 -0500 Small change to hts_io integration test. The test doesn't actually produce a screening_features.db3 file, so remove the analysis of that file. commit ad3252184b328423ea6f575ffc06266f144889c0 Merge: ba861e0 8035a40 Date: Sat Jul 16 14:01:05 2016 -0500 Merge pull request #1454 from RosettaCommons/roccomoretti/alignVectorSets Fixes for numeric:alignVectorSets numeric:alignVectorSets() had some edge conditions (zero vectors, co-linear vectors) which resulted in utility_exits. Add special cases to catch these conditions and do something reasonable instead. Unit tests for alignVectorSets() added. There's some integration test changes observed (KIC_with_fragments, density_denovo), which look to be due to changes in optimizations w/r/t this inlined function. (The changes don't happen locally with a debug build.)