commit ce60b79f128a9a7bf3c3b2b01d72082742f8e54c Merge: 06c605e 492e35b Date: Wed Dec 24 01:07:49 2014 -0500 Fixing Windows PyRosetta build commit 06c605ef0d6fd02fd405215406233d29615289c6 Date: Wed Dec 24 00:57:52 2014 -0500 Fixing Windows PyRosetta build commit a28f972f7ad965e0d01c7c3fb949314a75bcb75b Merge: d51c974 eabb558 Date: Thu Dec 18 19:46:39 2014 -0500 Merge pull request #228 from RosettaCommons/jkleman/mp_updates MP_UPDATES: * compute_structure_based_membrane_position: makes sure the embeddings show in positive z direction * EmbeddingDef: = constructor now takes a boolean whether the embeddings should show in positive z direction = implemented invert function that inverts the normal * Embedding: = constructor from pose and topology makes sure total embedding normal always shows in positive z direction = implemented invert function that inverts the normals of all EmbeddingDefs * AddMembraneMover: = debug check_pdb_for_mem to read in MEM in PDB file; it now goes through every residue in the pose to identify the MEM residue and matches that up with the user input; this means that reading in a membrane residue from the commandline works now * Types: = created core/conformation/membrane/types file that contains all membrane default values = replaced (hopefully) all instances with the default values in types * moved membrane_axis from docking into protocols3/membrane/geometry/util * MEM.params: = for fullatom, changed normal to length 15 * Conformation: = update_membrane_position now normalizes first and sets the points from the vectors - this is correct behavior: this function should now always be called with the vector for the normal and not with the point Unit tests: pass Integration tests: expected changes commit d51c974cbb38679a0f8050352463c258cf7c7cc6 Merge: 44cad4d d0404ce Date: Thu Dec 18 11:13:36 2014 -0800 Merge pull request #235 from RosettaCommons/hahnbeom/patchs warning error removed commit 44cad4df7eef20f865c5586f2dae4039fb893d13 Merge: 0a6378a 7313f5f Date: Thu Dec 18 20:22:40 2014 +0200 Merge branch 'nawsad/flexpepdesign' merged nawsad/flexpepdesign branch into master. made a small change to task factory to allow design of the peptide if -design_peptide flag in on commit 0a6378ad7d75e99af89f17383e9b399524149065 Merge: eb3c0d8 fd7782d Date: Thu Dec 18 20:17:22 2014 +0200 Merge branch 'master' of https://github.com/RosettaCommons/main commit eb3c0d8aaa3358ae2c063c7950b99ed3038457cc Merge: a5f1a5d dec0fe5 Date: Thu Dec 18 20:16:27 2014 +0200 resolved merged conflict in FlexPepDockingProtocol.cc commit a5f1a5d48d892bb145e22d7df9976c95f8b9f489 Merge: ddd7049 0771986 Date: Thu Dec 18 12:27:31 2014 +0200 Merge branch 'master' of https://github.com/RosettaCommons/main commit ddd704923c9470058b97e9ff0846cc838bbfc0cf Merge: 37e5c15 61ccb38 Date: Wed Dec 17 12:53:30 2014 +0200 Merge branch 'master' of https://github.com/RosettaCommons/main commit 37e5c159280813e9c6fb0d955a46013aeab64990 Date: Mon Dec 15 19:16:27 2014 +0200 Made some changes to fix Real type error seen during testing. commit 1ee143c26231d598544626c8e670ca9579b71f34 Merge: 01c5a01 33ad70f Date: Mon Dec 15 12:59:31 2014 +0200 Merge branch 'master' of https://github.com/RosettaCommons/main into nawsad/peptide_placement commit 01c5a01b3464b57e2cecc37f7ce6078deca42302 Date: Thu Dec 11 11:19:22 2014 +0200 Modified default value of flag -sample_pcs commit e0d0a351189b2ea8daad4fd4cf9fd12edaf501bc Merge: dbac149 d947955 Date: Wed Dec 10 11:33:44 2014 +0200 Merge branch 'master' of https://github.com/RosettaCommons/main into nawsad/peptide_placement commit dbac149f13cf8d5daff1524be78d163341c9945f Merge: 290248d 7722efe Date: Wed Dec 10 11:11:02 2014 +0200 Merge branch 'master' of https://github.com/RosettaCommons/main into nawsad/peptide_placement commit 290248d54adf36f93a0d01faee7c477ad3578336 Date: Wed Dec 10 11:09:24 2014 +0200 Made some changes to the place_peptide_on_binding_site function, like changing variable name to match coding convention. Also changed the order different function call in the apply function commit b9acfb97fc64e8fa4af9fef50f1df94950614ffb Merge: 0afa959 a54b378 Date: Mon Dec 8 16:39:24 2014 +0200 Merge branch 'master' of https://github.com/RosettaCommons/main into nawsad/peptide_placement commit 0afa959f4f06e9929b2e45e6cd409198a08e29b0 Date: Mon Dec 8 16:35:09 2014 +0200 Added new function place_peptide_on_binding_site to the FlexPepDock code to allow placement of peptide on the binding site using SiteConstraints and PCA. Also added SlideIntoContact function to remove inter-chain vander Waals clashes commit f205ba596fc07172e2e00dce75e7633f588295c6 Merge: e000a67 2940cba Date: Mon Nov 3 10:16:10 2014 +0200 Restored Splice_out_generic integration test commit e000a67083963c6868f1f63ee1e70e27ec00a2de Date: Mon Nov 3 10:16:10 2014 +0200 Restored Splice_out_generic integration test commit 4ed7b930e8111b02ae5b66b8afffb52140fc63f5 Date: Fri Oct 31 13:59:42 2014 +0200 Deleted faulty Splice integration tests commit 5c29b695adf6a12e2320eb07a71787b9e61d860c Merge: 339943e 5bfc4aa Date: Fri Oct 31 05:17:53 2014 -0400 Adding benchmark script for 'source' rosetta release commit 339943e07bdd1e4d34650247425f2199156ae5dc Date: Thu Oct 30 14:54:35 2014 -0700 A few changes to electron density scoring and the density_tools application. - Reduce the number of times rho_calc is computed in density_tools - Mask used by density tools is always bandlimited - Better treatment of mask radus for high B factor atoms - Fix a small bug in scattering factors where they were always integers - Fix incorrect S scattering and add P scattering params commit cd5061af73a4bb3badd5d40d15e092fc5d281afc Merge: 702b448 43885df Date: Thu Oct 30 13:05:37 2014 -0500 Merge pull request #149 from RosettaCommons/roccomoretti/exception_fix Fix a few places where we were throwing exceptions which wouldn't be caught by the standard top level EXCN_Base catch. I also changed option system behavior such that running with -help will exit successfully, rather than with an exception. commit 702b4483488d6dd931958670798d0fbe9a36296c Merge: 415e7b9 6063b17 Date: Thu Oct 30 13:41:20 2014 -0400 Merge pull request #153 from RosettaCommons/dougrenfrew/remove_redundant_suck_scoretype Removing redundant "suck" score name from ScoreTypeManager.cc. SnugDock had a slight trajectory change when I ran the tests locally. commit 415e7b96eda3377008be5144ffee42cc96f4d05d Merge: 7c66196 c44ad84 Date: Thu Oct 30 08:33:11 2014 -0700 Merge pull request #151 from RosettaCommons/nollikai/coupled_moves_update Making some minor changes to coupled_moves protocol output Changes include: 1) adding output_prefix option 2) outputting starting sequence / score prior to Monte Carlo simulation 3) dumping scored pdbs instead of unscored pdbs commit 7c661966a99b102f1cfa31b7167cc73b31713b6e Merge: 5808cf8 5955413 Date: Thu Oct 30 17:04:17 2014 +0200 integration test for fuzzy logic design commit 5808cf8d582e7fe94e6cd91903a61892d33d913a Date: Thu Oct 30 17:04:17 2014 +0200 integration test for fuzzy logic design commit a71179feac2030667e031f5932b500b4ad507a46 Date: Thu Oct 30 09:56:44 2014 -0500 Fix instance of shared_from_this from stack object LoopRelaxMover was allocating a sub-mover on the stack. The problem is that in the apply of the submover, shared_from_this() was being called, resulting in an error under our new pointer scheme. Allocation was changed to be on the heap rather than on the stack. Thanks to @schaarj for pointing out this issue. commit 4d1eaeb0e65fae677b0814727559f8165be0f0fa Date: Wed Oct 29 17:27:03 2014 -0400 Adding new release_debug_no_symbols build. Adding '-g' flag to release_debug builds. Adding integration.release_debug_no_symbols test. commit 40819eec387bb69430d0ea2cf3ab57ad140f8f82 Merge: 83377b0 440b27d Date: Wed Oct 29 10:28:34 2014 -0700 Merge pull request #145 from RosettaCommons/kalekundert/abbrev-fragments Add support for abbreviated fragment libraries. commit 83377b0311ffe5793fbe480414b9015900043b96 Merge: 20dd532 88c2f24 Date: Tue Oct 28 15:46:49 2014 -0700 Bugfix in extract_symm_unit with waters. commit 20dd532566ae4299058a0f1a6bd9f0580e2a4e60 Date: Tue Oct 28 15:43:33 2014 -0700 Bugfix in make_asymmetric_pose for poses with explicit solvent commit b313e383e5a571e32803fc1c0c4e0f8147ce16d9 Date: Tue Oct 28 12:25:02 2014 -0700 Fixing small bug in make_asymmetric_pose introduced during pointer rewrite commit 4c966ee5d5f5c46068be2d09aa10f730047440a5 Merge: 1ce893a 8343ddd Date: Tue Oct 28 10:07:06 2014 -0700 Merge pull request #77 from RosettaCommons/calebgeniesse/cmake_speedup Matching CMake build to SCons build for graphics, release, & debug modes commit 1ce893a212c99cd96bed6429b5af9b749227fd44 Merge: 0cea9b6 d00f6ca Date: Tue Oct 28 16:21:24 2014 +0200 Merge pull request #143 from RosettaCommons/sjf/AddFoldUnit_new Sjf/add fold unit new commit 0cea9b60179832a56fc0e26f93dc64d4e12a1a5d Date: Fri Oct 24 16:32:41 2014 -0500 Added support for opencl build with clang on macos commit 8a689c70810c042997c57b433bbd971df9bf6efb Date: Fri Oct 24 14:38:02 2014 -0500 Make clang the default compiler for os x 10.10 Yosemite commit a86c2bba0789806e2f1beb36b901515ad71ef57b Merge: 584ce81 c5db489 Date: Thu Oct 23 14:32:35 2014 -0700 Merge pull request #141 from RosettaCommons/rpache/fragment_perturber_speedup commenting out debug tracer info to speed-up the fragment perturber commit 584ce815df46d09509cc69fa61283eabbb207aa6 Merge: 776c644 13221d4 Date: Thu Oct 23 13:41:08 2014 -0700 Merge pull request #142 from RosettaCommons/nollikai/coupled_moves_ligand_weight Fixing missing input file in coupled_moves integration test This change should allow the coupled_moves integration test to run properly. commit 776c644a04b3e8a6c9a60479f7a4b773f20b6876 Date: Thu Oct 23 13:26:31 2014 -0400 Updating release script, adding branch name to git repository path commit dcdb41ae2d92fab5b8bc00a78cca56c04d2a97e2 Merge: 093501d 7243d8b Date: Thu Oct 23 01:01:21 2014 -0400 Merge remote-tracking branch 'origin/master' into benchmark commit 093501ddaa822ae5e5f5c334afd613258c22985f Date: Thu Oct 23 00:54:12 2014 -0400 Updating release.PyRosetta test commit 039361131ad4ff4000ec7e2ccbb1ba9b6e50b2ef Merge: cd436ca f60cd00 Date: Mon Oct 20 08:09:58 2014 -0600 Merge pull request #139 from RosettaCommons/PyRosetta Fixing sub-classing in PyRosetta commit cd436ca758a4849cd6e80fa0b02cc620089d8521 Date: Sun Oct 19 22:29:06 2014 -0400 Removing unused test blocks. Should hopefully fix the ninja build commit 437bcf6f08c63ca48822bde7b043de64480ebcfa Merge: 3c8c743 c64bd36 Date: Sat Oct 18 13:51:16 2014 -0400 Merge pull request #121 from RosettaCommons/rfalford12/rosetta_membrane3 Rosetta Membrane Framework Updates (October 2014) -------------------------------------------------------- This merge includes a series of bug fixes, updates, and new Rosetta membrane framework applications. Summary of Changes: (1) Loading in Membrane Models: Add capability to load in a membrane PDB. This could be a PDB output by another framework application or something created manually. Two ways to do this: (a) Search the PDB for a membrane definition (pass -in:membrane) (b) Specify the position of the membrane residue on the command line (2) Membrane residues: (a) Adding residue property MEMBRANE for EMB and MEM residue types. (b) Similar to (a): adding back Is_membrane() methods in residue type (c) Updated membrane and embedding residue param files (defaults) in fa_standard and centroid (3) Library reorganization: Moved io (resource manager) and geometry (utilities) code to the protocols level (protocols/membrane). (4) Changed default membrane fold tree behavior: Adds membrane residue by jump to the center of mass residue of the protein instead of just appending to the end. (5) PyMOL Viewer: Fixing a ton of bugs, making the implementation more generalizable (a) Removed old membrane planes class (not needed) (b) Computing plane positions on the python side (more lightweight, flexible with other Rosetta protocols) (c) When the membrane position changes, pymol will now dynamically redraw the planes. (d) Removed the extra -view_in_pymol flag. If the framework is on and pymol viewer is on, membrane planes will automatically be drawn during visualization. (6) Updating score_jd2: Score_jd2 compatibility with the membrane framework. Can score a new membrane protein or rescore a pdb output from another framework application (7) Rosetta scripts hooks for all membrane movers. (a) AddMembraneMover (b) MembranePositionFromTopology (c) SetMembranePositionMover (d) VisualizeMembranePlanesMover (e) SetupForMembraneSymmetry (8) Membrane Relax Protocol: Application for refinement of membrane protein structures using membrane min cycles. Still in pilot apps. (9) Symmetric Membrane Protein-Protein Docking Protocol: Application for symmetric protein-protien docking with the membrane framework. Includes a generic SetupForMembraneSymmetry mover. Still in pilot apps. (10) Integration tests for load time, symmetric membrane protein-protein docking, and membrane relax (11) Support for demos (in Rosetta/demos directory) for all 5 membrane framework applications Test Status ------------------- Mac build: All Pass Unit Tests: All pass Score Regression: Expected changes due to PDB info for MEM residue updates (no numerical changes, just PDB differences) Integration Tests: - mpframework integration tests - changed due to add - membrane_relax - changed due to deprecation message in old membrane energy methods - assemble_domains_jd2, broker, metalloprotein_broker, others - fixing rms print in scorefile with Luki's patch - score_jd2 - change due to adding membrane functionality in this application The linux tests have not yet completed on the test server - seems backed up quite a few commits. If there are any concerns or issue I will be sure to watch out for them and address as they come up. Please let me know if you have any concerns. commit 3c8c743c51d1a9cb847610937d122e83ddb26784 Date: Fri Oct 17 17:10:30 2014 -0500 Remove unused function with highly questionable logic. commit 9f50d761f17abd4a31dc63008a739629ea3af022 Merge: fba416c aa6c839 Date: Fri Oct 17 07:58:02 2014 -0700 Merge pull request #135 from RosettaCommons/calebgeniesse/cmake_debug Fixed slowdown in cmake + ninja build commit fba416cb10a490b1a1fff7e2849f53228dd9be0e Date: Thu Oct 16 21:42:15 2014 -0400 Adding the correct version numbering for OS X Yosemite (10.10) to setup_platforms.py commit d8959f0c8e898b6a89d0c963ad8778723e69639f Merge: 4ec565f 41ed454 Date: Thu Oct 16 21:28:27 2014 -0400 Merge pull request #133 from RosettaCommons/weitzner/unit-test-cleanse Weitzner/unit test cleanse Removing the #define private public. Get ready for me to get on my high horse! commit 4ec565f267b8c5f1b3e94acacb7ef24fa4ad5c15 Merge: c80b26b abb103e Date: Thu Oct 16 01:10:42 2014 -0400 Merge pull request #136 from RosettaCommons/JWLabonte/molfile_to_params Minor Improvement to `molfile_to_params.py`: one can now specify the root and neighbor atoms from the command line. This merge also includes some rider changes related to carbohydrates and lipids in the database: * corrections to bond order in lipid topology files * expansion of `dock_glycans.py` carbohydrates integration test expected to change due to corrections in lipid bond orders. molefile_to_params integration test expected to change due to output change. commit c80b26bd20dc66447d9fc3f86443d359ed6787ae Merge: c677712 d6c9c08 Date: Wed Oct 15 12:38:47 2014 -0700 Merge pull request #130 from RosettaCommons/daslab Daslab -- minor bug fixes in stepwise the 9 integration test changes are expected. (match_1n9l is always changing.) commit c6777126e7a2cacc73da884f72ac9249d375ca74 Merge: 376e5ec d4c69c4 Date: Wed Oct 15 12:30:12 2014 -0400 PyRosetta. Adding special handling for classed derived from utility::SingletonBase so bindings for them could be created. commit 376e5ec90e29717a2ee0510e66dff8c9388b8af5 Merge: 25f6f82 36112d2 Date: Tue Oct 14 14:32:45 2014 -0700 Merge pull request #134 from RosettaCommons/indigogo/imm_pub Indigogo/imm pub commit 25f6f82642395c05c95e540eeb24766ab4f4a9a0 Merge: 6b76f86 1ebad79 Date: Tue Oct 14 15:26:28 2014 -0400 Fixing PyRosetta imports, this should fix most of the PyRosetta unit tests. commit 6b76f86d40819cae9f47a65316eea343f05a561b Date: Tue Oct 14 15:09:00 2014 -0400 Fixing PyRosetta imports, this should fix most of the PyRosetta unit tests. commit 6e9972b47fddd88703b138eabad7022fb4dd3f17 Date: Mon Oct 13 11:33:05 2014 -0400 Adding explicit cast from unsigned integer to shared_ptr commit c5a65301340ae7eba78a61048f4ffab3c1dc91dc Merge: 8adbc7b 2ec65c0 Date: Fri Oct 10 20:29:28 2014 -0400 Merge remote-tracking branch 'origin/master' into PyRosetta commit 8adbc7b3f8957698351036c663b4ef9271a45c88 Date: Fri Oct 10 20:24:06 2014 -0400 Fixing Rosetta Windows builds. Fixing minor bug in MinMover. commit ff2ab9a0a3343e2f9f6f81a9306c9934306962b3 Date: Mon Sep 29 19:53:03 2014 -0400 Setting memory requirements as 2Gb per cpu for PyRosetta tests commit 7521ce14f2c0766ac28719da9ae479375f152d93 Merge: a666d19 62697b3 Date: Mon Sep 29 19:31:15 2014 -0400 Adding Ninja builds commit a666d19d28ff41f80e33d77a957f5f93c9a1883b Date: Mon Sep 29 15:23:25 2014 -0400 Adding Ninja builds commit 9c3c22c4c817f391d29705a223679c009a1c4e0e Merge: 48a3482 3e18672 Date: Mon Sep 29 14:41:34 2014 -0400 Merge remote-tracking branch 'origin/PyRosetta' into benchmark commit 48a34826eeeffade03053c085423f0c718cb518a Date: Tue Sep 23 23:45:49 2014 -0400 Fixing PyRosetta unit test script commit 3be102f7d81efc09f9b7c12606edeb20f63fde1d Date: Tue Sep 23 20:47:16 2014 -0400 Refactoring PyRosetta tests. Redirecting all test output to special directory commit 3caedf578a9cffed2ab7a7fcf35d3ed01bf6bd6b Date: Fri Sep 19 23:39:46 2014 -0400 Fixing typo in release and PyRosetta tests commit 60b4f77d511f00659c6482737486ca14d80fbc7c Date: Fri Sep 19 23:34:12 2014 -0400 Adding PyRosetta TestBindings self-test commit a4a692eb88c90b4b7dda6aa411331878aa303000 Merge: d88ba24 7ef848f Date: Fri Sep 19 22:20:23 2014 -0400 Merge remote-tracking branch 'origin/master' into benchmark commit d88ba24be9c2c1f9660701f6d7371f5de1b9eb0f Merge: 71d44dc 9ee6d4a Date: Thu Sep 18 23:42:24 2014 -0400 Merge remote-tracking branch 'origin/master' into benchmark commit 71d44dc6e820b59eaa85c6fba53b60a9f9340278 Date: Thu Sep 18 16:42:25 2014 -0400 Dummy commit C commit 684802ebc8d05a162ead0fb8ea65e5df4685271c Date: Thu Sep 18 16:38:53 2014 -0400 Dummy commit B commit 8986ffa2b3e1da7264ccf8f75a8ee3b34c9b1688 Merge: 66f203e 713772c Date: Thu Sep 18 16:27:56 2014 -0400 Merge remote-tracking branch 'origin/master' into benchmark commit 66f203e1bfbc2142fad4dc289bc687e49bbbd170 Date: Thu Sep 18 16:23:51 2014 -0400 Dummy commit A commit aaac78373532e68a6f8de9531f1651a4dcd004a7 Merge: 1823fd7 71c4441 Date: Mon Sep 15 00:16:52 2014 +0300 Merge branch 'master' of github.com:RosettaCommons/main commit 1823fd7ed8a5a4f3f1b263ed2f57feb793442bae Date: Mon Sep 15 00:07:27 2014 +0300 Fixed problem related to loop length change when using tail segment when deleting residues commit 712dc9dec81c98f356c95ba6c54d4087d80b63bb Date: Wed Sep 10 19:27:38 2014 +0300 Bug fix in splice to allow splice out of H3. Splice out integration test should change. Bug fix in splice to allow splice out of H3. Splice out integration test should change. commit d4e2060cfb0aac41a888e143cbdefc4b90022ce4 Date: Wed Sep 10 14:32:49 2014 +0300 Corrected problem related to splicing out longer tail segments, and added lambda specific PSSMs and profilematch files for splice out. So far the AbDesign and AbPredict protocol has not worked with lambda light chains. Here I'm adding PSSMs and profileMatch info to enable this. At the same time I'm also fixing a bug in LoopLengthChange which did not allow appending of more than one residue to tail segments when used with splice.cc. commit 361238303037a2ba727aec57209cb8ca27ef2f49 Merge: 16fb7dc d1459b6 Date: Wed Sep 10 10:31:54 2014 +0300 Merge branch 'master' into chnorn/lambda commit 16fb7dcfb84a29d8ece7cc3f872512353189cedc Merge: 4c37ba1 7e6567e Date: Tue Sep 9 11:06:38 2014 +0300 Merge branch 'master' into chnorn/lambda commit 4c37ba1f3c306c9442fb3cb5e3b68a6e555a2595 Merge: 84a40a5 e19b80b Date: Mon Sep 8 19:16:03 2014 +0300 Merge branch 'master' into chnorn/lambda commit 84a40a5dda782108e20c75f9f921f067ae9aa932 Date: Mon Sep 8 19:12:23 2014 +0300 fix pssm database names and adding profile match info commit 4750e3946f10726dfc414e359e4612200bb5bd65 Date: Sun Sep 7 15:47:21 2014 +0300 adding lambda information to pdb_profile_match files commit 4bf3869e4eb5d11917d79c17047daa59cdf9a16b Date: Sun Sep 7 15:32:29 2014 +0300 changing the location of pssm files for lambda splice commit 96cc4fb60815c5db59fdeb075b9fbd7ac8c84ead Date: Sun Sep 7 14:39:36 2014 +0300 adding pssms for lambda antibodies commit 500500a1bf7ac86d4f60ce0274275e0b372d5654 Merge: 4c62520 5d03eaa Date: Sat Sep 6 02:20:33 2014 -0400 Adding configuration file for benchmark script. Updating PyRosetta unit test script so it now use boost_python_library config option. commit 4c62520477e8e3b59243f49015ed3544ad9ffbee Merge: 5b03965 93d24c3 Date: Fri Sep 5 17:48:55 2014 -0700 Merge pull request #76 from RosettaCommons/nollikai/CoupledMover Adding CoupledMover to protocols/simple_moves Created a new mover that performs coupled side chain / backbone moves. For ligands, this mover performs a rigid body rotation and translation coupled with ligand rotamer optimization. This mover currently uses ShortBackrubMover for backbone moves, BoltzmannRotamerMover for side chain and ligand rotamer moves and RigidBodyPerturberMover for rigid body moves. This mover is compatible with PackerTasks that allow positions to be designed, making it easy to incorporate backbone flexibility into sequence design. Since ligand moves can also be performed, this mover is particularly useful for the design of ligand binding sites. In the near future I will commit a protocol that uses this mover to predict the set of tolerated sequences for a given design problem by keeping track of all the sequences that are accepted during a Monte Carlo simulation. commit 5b03965b6d65725e7492a8dc60be34bbc0850399 Date: Fri Sep 5 19:04:51 2014 -0400 fixing tests (My text editor erased two needed spaces again; grr.) commit d73c67d70eca28e9f66806c0184eac6ca3173523 Merge: 08479a8 6abef29 Date: Fri Sep 5 15:51:19 2014 -0400 Carbohydrates: mostly database updates This merge includes some addition of ATOM_ALIASes, a new sugar topology file, (so that I can load in sialyl-Lewis X,) and some sugar pilot app updates to reflect the recent options system clean-up. It also adds a formal +1 charge to all lower terminus peptide residues. ---------------------------------------- Unit test status: Not Run (no C++ code changed) Integration test status: 1 test change carbohydrates: expected, due to the +1 on peptide lower termini commit 08479a8cfe3f0600b26f20172eddc37994970972 Merge: ffba37b f0cf9ae Date: Thu Sep 4 21:52:57 2014 -0400 Adding PyRosetta unit tests commit ffba37bbf059ce928d854b854b92294c1c1c98aa Merge: 148d91b a65850b Date: Thu Sep 4 15:28:24 2014 -0700 Merge pull request #75 from RosettaCommons/nollikai/ClashBasedRepackShellSelector Adding ClashBasedRepackShellSelector to core/pack/task/residue_selector Created a new ResidueSelector that identifies residues that clash with any possible rotamer of all designable positions in a given PackerTask. This solves a problem I routinely encounter with distance-based repack shells, which never include the same residues I would have chosen from looking at the structure. Instead, this ResidueSelector can be used to define a repack shell that only includes residues whose side-chains clash with any rotamer of a design position, resulting in the selection of residues that I actually want to be repacked. This code was co-written with Roland Pache @rpache commit 148d91b4d8be3329448da7f88d69ad468d14270f Merge: 58bb206 3dd13ad Date: Thu Sep 4 16:13:34 2014 -0400 Atom Typing: fixing two bugs related to atom typing NEWS: The following bugs have been fixed: - The patch system failed to correctly set chemical::Atom's MMAtomType name, so so any variant ResidueType had mismatched MMAtomType names and indices. - The patch system failed to correctly set new Elements when an AtomType changed. This was primarily an issue for cases when virtual atoms were changed to real atoms and vice versa. - The Gasteiger atom-typer failed to correctly assign GasteigerAtomTypes in those cases, because it relies on having the correct Element. (As an aside, I have also add a miscellany of my own glyco-PyRosetta pilot apps for tracking in Git.) ---------------------------------------- Unit test status: Pass Integration test status: 1 test changed carbohydrates: now showing correct atom typing commit 58bb206579dcbc60949cf54fc4468f48e6084456 Merge: a8269ab c23363c Date: Thu Sep 4 16:12:22 2014 -0400 pulling master commit a8269abe30aa6c6a5a02403a934f2a224e21f65b Date: Thu Sep 4 10:51:10 2014 -0400 Carbohydrates: adapting dock_glycans script to work with new version of PyRosetta commit c3db849628780733605bd5f4e4c847208fc88c69 Date: Wed Sep 3 14:37:41 2014 -0400 Carbohydrates: tracking PyRosetta pilot apps with Git commit c393763e50da0ad450dc495b9579b8b20e78175c Merge: 303d972 e6a2d55 Date: Wed Sep 3 14:04:51 2014 -0400 merging in master commit 303d97226f3e6cc29652eb7248053525acd4a329 Date: Thu Aug 29 13:25:52 2013 -0400 Carbohydrates: adding PyRosetta application for generating ring conformation relative energy surface tables/plots