commit 9184a652bc35c3c1cd2a77d1f9c77d580d0c209b Merge: ecf9ce8 dba492c Date: Fri Sep 25 03:42:27 2015 -0700 Merge pull request #831 from RosettaCommons/revert-830-revert-829-vmullig/clang_fix_master Re-merge "Fix library levels and Mac clang builds" Reverts RosettaCommons/main#830 commit ecf9ce868e516c82c7618a1c8b6c75dffbfc5c9f Merge: 21af408 c6d19d2 Date: Fri Sep 25 03:25:14 2015 -0700 Merge pull request #830 from RosettaCommons/revert-829-vmullig/clang_fix_master Revert "Fix library levels and Mac clang builds" Reverts RosettaCommons/main#829 Blargh -- I was too quick on the merge. commit 21af408d3374a577d84871e2a2439bd6b59182a2 Merge: 6842695 96a3344 Date: Fri Sep 25 03:18:01 2015 -0700 Merge pull request #829 from RosettaCommons/vmullig/clang_fix_master Fix library levels and Mac clang builds @davidekim: Please use the test server next time. Your merge messed up the library dependencies. Restoring by moving cyclize_peptide() and fixH() functions from protocols/forge/methods/util.cc to protocols/relax/util.cc. In the process, I'm rewriting fixH() to use the proper functions in core for rebuilding polymer bond-dependent atoms (rather than manually placing the atom named "H" at a hardcoded position). commit 684269596b1a88146e87337f659832c326457e1d Merge: fd66021 ea2bdc4 Date: Fri Sep 25 01:31:40 2015 -0400 Merge pull request #808 from RosettaCommons/everyday847/more_ring_work Pack with ring conformers commit fd66021f71d2e80c60c7ea4ee4896cc00cd11c46 Merge: 8070d21 84a79d1 Date: Thu Sep 24 12:43:57 2015 -0700 Merge pull request #828 from RosettaCommons/davidekim/gaurav_cyclic_peptide_stuff Adding in Gaurav's cyclic peptide code for ab initio. commit 8070d21e80be50aed58d4daf8f1aa658105e78d7 Date: Thu Sep 24 10:28:50 2015 -0700 Added a torsions only vall for the older vall 2001 version. commit c9daadbe3fa6919b7b91a9118aaf3d7d79d28704 Merge: 60a7a14 6d13d56 Date: Wed Sep 23 14:25:29 2015 -0700 Merge pull request #771 from RosettaCommons/kylebarlow/general_dev Fixing cmake cppdb linking errors in 2013-onward linux g++ versions Committing fix suggested by Tom Linsky on rosetta-devel@googlegroups.com on Fri, May 8, 2015. Solution also referenced at: http://stackoverflow.com/questions/20369672/undefined-reference-to-dlsym This doesn't break the Clang builds on my machine, but I'll be testing that, and the behavior of other g++ versions, on the test server shortly. Linking error fixed by this: libcppdb.so: undefined reference to dlsym' libcppdb.so: undefined reference todlclose' libcppdb.so: undefined reference to `dlopen' collect2: error: ld returned 1 exit status commit 60a7a14b4718b00f4f4875752d0201397384bc2d Merge: 1a50248 e66ef97 Date: Wed Sep 23 13:33:43 2015 -0700 Merge pull request #804 from RosettaCommons/vmullig/peptide_predict Adds a pilot app to predict structures of backbone-cyclized peptides This is basically one of my RosettaScripts converted to C++ and enhanced with tunable parameters that can't be adjusted easily in RosettaScripts without rewriting the script. Tasks completed: -- Add simple_cycpep_predict.cc in apps/pilot/vmullig. -- Read in sequence and build peptide. -- Cyclize. -- Circular permutation. -- Add constraints. -- Read native. -- Set omega and randomize mainchain torsions. -- GenKIC closure -- GenKIC filtering by rama and total hbonds. -- Added rama filter to GenKIC. -- Documentation for new rama filter. -- Integration test for new rama filter. -- Added scorefxn option to HbondsToResidue filter. -- Documentation for this option. -- FastRelax with high hbond strength of each GenKIC solution. -- FastRelax top GenKIC solution, updating cyclic O and H. -- Re-filter by total hbonds. -- De-permute (undo the cyclic permutation). -- Calculate RMSD to native. -- Dump pose and filter results. -- Repeat nstruct times. -- Add integration test. -- Add internal documentation. commit 1a502488edd6566290db2fa7b5f04191a86f7c1d Merge: 551a664 84ac553 Date: Wed Sep 23 13:29:10 2015 -0700 Merge pull request #820 from RosettaCommons/vmullig/mac_clang_issue Trying to fix Mac clang unit test build Removing the "#define private public" and "#define protected public" lines from unit tests. Updating LoopModelerTests and DsspDesignOperationTests to be friend classes to the classes that they're testing. commit 551a6648e43bcdb0bf6bbca430333c5b26713e24 Merge: 0209414 6e2fd85 Date: Wed Sep 23 14:37:09 2015 -0500 Merge pull request #823 from RosettaCommons/roccomoretti/fix_dna Fix for dna_interface_design test Convert the debug_assert() which is failing to an if(){ utility_exit_with_message() }, with extra debugging output to (possibly) assist users, and increased output levels on dna_interface_design integration test. Also, fix the underlying issue with the triazolamerN patch, which is related to deleting the H atom when it's used for the internal coordinates of the base residues types. Instead, just make the H virtual, like N. This may or may not be the long-term fix for this patch. commit 0209414da0bc1eedff43ede717fae47258a5e205 Merge: ecc3369 928c7ee Date: Tue Sep 22 20:38:07 2015 -0700 Merge pull request #822 from RosettaCommons/davidekim/indexed_fragment_dev Davidekim/indexed fragment dev commit ecc3369e2f7c3596dc4611d0e74a7c90885003bb Merge: ef0ed1c c2df409 Date: Tue Sep 22 18:23:51 2015 -0500 Merge pull request #821 from RosettaCommons/bazzoli/ppi-weights Updated PPI_discrimination.wts commit ef0ed1cdfdbd5ccd64b8a43b44802ac72f2ee7fe Date: Tue Sep 22 16:12:10 2015 -0700 add crued residue-pair-motif scoring pilot app commit 562bba3f5b43e9a366c69d69475e182f4b599c86 Merge: 37fcd29 ec92a57 Date: Tue Sep 22 15:49:53 2015 -0700 Merge pull request #819 from RosettaCommons/vmullig/tweak_bettercluster Small tweaks to bettercluster pilot app Small tweaks to bettercluster pilot app. No test changes expected. commit 37fcd291840346f4a86a780e4ebbe9301cd00e7f Merge: 45d2d62 a6ff0f9 Date: Tue Sep 22 14:46:11 2015 -0700 Merge pull request #814 from RosettaCommons/revert-813-vmullig/unfustercluck Revert "Vmullig/unfustercluck" Reverts pull request #813. This restores: -- Merge of pull request #798 ("Use SSBOND records, if available...") -- Merge of pull request #793 ("Remove exception from annotated sequence") -- Commit 68a6a18 ("Fixing library levels build") -- Commit 36de51b ("Fixed unused variable") -- Merge of pull request #807 ("Exclude PNA from chirality checks...") -- Commit d475d31 ("Using two vectors... ugh.") commit 45d2d6299afa7e97169b7136edf3f55deab97387 Merge: 4c3e326 03adf56 Date: Tue Sep 22 09:59:56 2015 -0600 Merge pull request #818 from RosettaCommons/PyRosetta Adding PyRosetta binding for RotamerVector commit 4c3e326484b53e1061a1d77427e00ef88c9afc6a Merge: ab66592 e94a399 Date: Mon Sep 21 23:45:51 2015 -0700 Merge pull request #817 from RosettaCommons/vmullig/mac_clang_issue Fix the Mac clang 3.7.0 issue Mac clang 3.7.0 has thread_local as a C++ language keyword, albeit one that throws an error if used in the absence of c++11. This means that our attempts to define thread_local when not using c++11 throw an error. This is an attempt to remedy this. Instead of defining thread_local, we define THREAD_LOCAL as: -- nothing if we're not using c++11 -- thread_local if we are Then we replace all instances of thread_local in the code with THREAD_LOCAL. Note that there's still an issue to resolve in one unit test (ResidueGraphTypesTests), which has the following lines in it: // Unit Headers #define private public #include #undef private This is still preventing the Mac clang unit tests from compiling. I can see why someone would do this to expose the private functions in the class that they're trying to test, but I also think it's important that the compiler flag attempts to redefine language keywords. commit ab665922d6a1494d0443a7e1b4dbd0c7f435a3f2 Merge: 17f845e a62fd7f Date: Mon Sep 21 11:17:27 2015 -0700 Merge pull request #816 from RosettaCommons/hpark/beta adding beta_july15_cst.wts for cst usage with the energy function commit 17f845ee9e12ca5b286594aafa51e8e3c1ef6296 Merge: d475d31 263deb1 Date: Sun Sep 20 22:07:16 2015 -0700 Merge pull request #813 from RosettaCommons/vmullig/unfustercluck Vmullig/unfustercluck Rolls master back to Sergey Lyskov's commit 1da8a4c, before a whole lot of stuff was broken. @everyday847, @rhiju, I'm going to create a branch and a pull request for reverting this pull request (i.e. restoring all of the broken stuff). IN THAT BRANCH please fix all the broken stuff, test the branch, then re-merge with master. commit d475d31a34bcce75565e04ec7665a91adbb4e6dd Date: Sun Sep 20 17:53:28 2015 -0400 Using two vectors... ugh. commit aafd27f0b141606896785df14148c5a8cd1beefd Merge: 36de51b be07da8 Date: Sat Sep 19 19:27:36 2015 -0700 Merge pull request #807 from RosettaCommons/rhiju/fix_pna_integration_test exclude PNA from chirality checks to determine D- or L- amino acids, … Fixes PNA integration test. commit 36de51b986fd4efb3a21054529f719db3766368b Date: Sat Sep 19 17:51:00 2015 -0400 Fixed unused variable I had intended to cut down on having too much warning output per annotated sequence read-in that I left half-implemented. So sorry! This should be it for now... :-( commit 68a6a189e8cbe3dd267cd65d0b3004ea7eb37697 Date: Sat Sep 19 14:54:57 2015 -0400 Fixing library levels build; sorry! commit 791ade228547653e8dc189c8eb851113b4381ead Merge: 450d750 dc32015 Date: Sat Sep 19 14:47:43 2015 -0400 Merge pull request #793 from RosettaCommons/everyday847/deprecate_disulfide_exception Remove exception from annotated sequence commit 450d75095dfa6bb8ebca173cd77ef5190b5423e5 Merge: 1da8a4c dac22cf Date: Sat Sep 19 09:32:01 2015 -0400 Merge pull request #798 from RosettaCommons/everyday847/ssbond_input Use SSBOND records, if available, to prompt conformation::detect_disulfides. Integration test changes are all cosmetic/reflect that NtermConnect and CtermConnect are no longer silenced by CMDLINE_SELECTORs. commit 1da8a4c0bcd967364f2acc107fa553b147a4a786 Date: Fri Sep 18 18:58:17 2015 -0400 Updating HPC ‘execute’ so it uses test working dir for logs by default commit 0184b0529438399008749f63994991f4cc59bfa6 Merge: dbcf6ff 01efea3 Date: Fri Sep 18 14:54:21 2015 -0400 Merge pull request #799 from RosettaCommons/everyday847/branching_in_centroid Rudimentary centroid mode for branching commit dbcf6ff6e9024aa6ed2e280ff5ed6eac7f3b655f Merge: c0e92cf 08414b5 Date: Fri Sep 18 09:26:02 2015 -0700 Merge pull request #806 from RosettaCommons/rhiju/fa_stack_updates Rhiju/fa stack updates all changes are OK: +broken tests are the 'usual' ones in integration (pna, inverse_rotamer_remodel), which I'm fixing in a separate branch. + also saw a 'cosmetic' line ordering change in integration.release_debug for mm_params. + last, dna_interface_design is also broken, but only in integration.release_debug (not integration). seems to be affecting everyone.