commit 6c1c48a0a0a4a28eecdc4ad885342c91b6b7cf93 Date: Thu Jul 3 15:54:16 2014 -0700 small fixes to get rna puzzle 12 jobs to run commit 3ebb32087cab3b400e89a64cdfb3f431c4b807f6 Date: Thu Jul 3 15:54:16 2014 -0700 small fixes to get rna puzzle 12 jobs to run commit 3acc540c8b09bd0a040306494b52de9f8ef4648c Date: Thu Jul 3 15:22:46 2014 -0700 Refactored ReportToDB to always store job input/output tags Member variables already existed for these tags, but were usually null strings, unless set by an outside piece of code. Only one piece of code currently does this. Tags will be set to the current JD2 tags unless a custom tag has been set (new bools store whether or not this is true). As ReportToDB always has these tags now, I removed superfluous code in StructureFeatures to get tags from JD2. commit c396a62a2598b7c6f1b1f473a99ccd9e45a46b67 Date: Thu Jul 3 18:03:49 2014 -0400 Updating rosetta scripts hooks in all protocols/membrane movers commit feef80a7cf4e459816a577f8f5c19f0baff435b2 Date: Thu Jul 3 17:35:39 2014 -0400 Adding new movers to hook into rosetta scripts init files and will test build next commit f4cc3cb68ec91f5db2a97ce7b698a343aa84b5aa Date: Thu Jul 3 17:31:00 2014 -0400 Fixed parse my tag for rosetta scripts in visualize membrane mover - not doing in show planes mover quite yet commit 568d3c8b912cf9aeb8f24dd74e0ff10c1ce3228e Date: Thu Jul 3 17:28:27 2014 -0400 Implementing parse my tag in all protocols/membrane package movers commit 0fe1b8e1e1a770ceba230d73fe922033b53ba75e Date: Thu Jul 3 15:56:58 2014 -0500 Updates to replace_residue-related helper methods. commit 554ed64a59203ec694dd0589f209684810aea21e Date: Thu Jul 3 16:50:10 2014 -0400 Implemented parse my tag in membrane normal perturb movers commit 34bbd48d62761139c6a4b39260c802a2a621f8c8 Date: Thu Jul 3 16:41:34 2014 -0400 Implementing full parse my tag method in add membrane mover commit cd473899d42601f35e0b70736d3a5c0e31134d7a Merge: f8a38da 3d56141 Date: Thu Jul 3 16:20:11 2014 -0400 Resolving merge conflicts - adding initial membrane orientation code, anchoring code, fold tre emodifications, multibody setup, etc into parallel devel commit e2a0d7ba5406326ab719692e821714fd6cf3f419 Date: Thu Jul 3 15:11:12 2014 -0500 Override second replace_residue function in ProtectedConformation; create general sandboxing method for doing replace_residue. commit 9f482edeef60ec075d7645c79668d2e2658fa7f9 Date: Thu Jul 3 15:55:42 2014 -0400 add creators for GraftMover classes commit f8a38dae69ccc865e5d40e4f427bfafbfef3c9f6 Date: Thu Jul 3 15:37:41 2014 -0400 Removing use incorrect derivtive option - not sure why this skipped the merge. Mirrored from master branch commit ac799d104fa30cc9c0157a1538f248ccc8933e53 Merge: 7577a37 2884d93 Date: Thu Jul 3 15:29:57 2014 -0400 Fixing rhiju's merge conflict of rna features and dna test pilot app commit 657924002d7eea86bce1f20d74506f389340abed Merge: 2ea9a6b c50299c Date: Thu Jul 3 12:28:43 2014 -0700 Merge remote-tracking branch 'origin/master' into kylebarlow/general_dev commit 2884d9310b9904d89c4ed606c0039210b6b6fabf Merge: 6b41774 c50299c Date: Thu Jul 3 15:27:49 2014 -0400 Merging ninja local with remote master branch: = PyRosetta build is currently broken. Will not be due to membrane changes commit 3d5614198e745682e3576d5ccd989ce756f30e00 Date: Thu Jul 3 15:19:00 2014 -0400 Quick compile fixes in membrane position perturb movers commit 7ffd960df80b364932330de3ecd0f83975cc5e6e Date: Thu Jul 3 12:14:42 2014 -0700 Added an overloaded operator= in SymmetricConformation with an 'other' of type Conformation. This fixes a bug where copying a symmetric pose used Conformation's operator= instead of SymmetricConformation's, and failed to copy its symmetry type. commit 75db96a4be5f6d8855e9ac5fcc8024cda67cb37c Date: Thu Jul 3 15:13:29 2014 -0400 Implementing the rest of position perturb movers - not tested yet, but going to put this on hold until I can get the pymol communications going for testing commit c21fee82ef4f9442a06de0aeac19540e030bf1d5 Date: Thu Jul 3 14:59:38 2014 -0400 Applying center and normal perturb moves in position perturb mover - just needs to implement the rest of the apply methods commit edb982d64c947539c1a86ac4ffa15fbbd67050bf Date: Thu Jul 3 14:44:39 2014 -0400 Perturb movers compile without apply or parse my tag commit c50299c3dec5fc4a6815da01d10badd9bbbefb5f Merge: bb493f0 f1f7794 Date: Thu Jul 3 14:41:28 2014 -0400 Merge master in to bug fix branch Fixing a bug in the PyMolMover. Also fixing the mac clang build. Also fixing all the builds. commit 5da1a765726cbcfc3bf961062c082126f5aed03a Date: Thu Jul 3 14:09:20 2014 -0400 All of the shell code for perturb movers should be present commit 10d32a6800a7093df22ea5255d0c3b23f5830384 Merge: 603053c f1f7794 Date: Thu Jul 3 14:08:23 2014 -0400 Merge master into branch commit f1f7794c5bf889936ec0458cc67422a2c7ee7551 Merge: d738aca 2eee5bf Date: Thu Jul 3 14:06:36 2014 -0400 Add option to FastRelax RosettaScripts to disable design by default if passed TaskOps as discussed. Please note that in order to design within FR using RS and TaskOps now, one must pass disable_design=false to RS. commit 2eee5bf77d8fee4b7039ef1cecd232b9da3c71e6 Date: Thu Jul 3 14:06:14 2014 -0400 fix commit bb493f011c0c3cae8ab72777af4c6d1328aeb769 Date: Thu Jul 3 14:02:53 2014 -0400 Fixing build commit ef550ba622da53d196696010bc187fedceec8474 Date: Thu Jul 3 14:02:27 2014 -0400 Implementing membrane center and normal perturbation mover shells - everything but the apply mehtods commit 8afa8bcf6fd0f3068a26debb3e3487c4bd7b4c71 Date: Thu Jul 3 13:57:12 2014 -0400 fix commit fa64d7a86857a906fcab75acd44ba3657be44e3b Date: Thu Jul 3 13:48:05 2014 -0400 Updating implementation of small gaussian perturbation movers for membrane position commit 5ed848dda5bc20d956f239359de4069949930a77 Merge: 519c40d d738aca Date: Thu Jul 3 13:35:50 2014 -0400 Merginf master i to bug fix branch commit a6f236b861c3c0b0c3bff7babffe8909a4d5a8a3 Date: Thu Jul 3 10:28:39 2014 -0700 adding RNA_DMS_Potential for scoring DMS. Code compiles but not tested yet. commit 761476c5e579eeb60a52e197677e577abf1c28c2 Date: Thu Jul 3 11:44:57 2014 -0400 Finished implementing membrane normal perturb mover commit 3bcbf84798a87162b3721777629855145b24a0ef Date: Thu Jul 3 10:42:27 2014 -0500 Improve failed DoF access error message. commit 283d30f901d6264bd6f967f2a5739313c082c550 Date: Thu Jul 3 11:41:13 2014 -0400 Implementing membrane center perturbation mover header commit e971a6b6280d93d5fdcb24a8448f9039c0d45795 Date: Thu Jul 3 11:27:38 2014 -0400 Starting to implement the basic parts of membrane psoition perturb mover commit 43b1f4acda7a8c72c4cda594b49f1ec40b52038b Date: Thu Jul 3 10:13:48 2014 -0500 Fix a bug where loops built from selections were claiming cuts at the first or last residue. commit c22a2523dce77cf2829b5918bd2a3df4073d8a3c Date: Thu Jul 3 10:13:13 2014 -0500 Comment clarificatin. commit 121036f1c60d562be3ad6a11a34d486814c5bb47 Date: Thu Jul 3 11:10:01 2014 -0400 And we are good - needs 2 separate movers for protein and membranes - one that will move to an exact position specified, and another that will move relative to an existing position. The absolute vs relative is important for preserving membrane coordinate frames commit f7f3179ade768a55aa5740df2cff762a7772727c Date: Thu Jul 3 10:55:07 2014 -0400 updating membrane position rotation translation mover to not normalize input at constructor (makes a mess) and needs to think about those input checks to prevent crazy things from happening. Also starting to implement backbone of the perturb mover commit d738aca5d10f3b422fbe65e5b5212d75f60caced Date: Thu Jul 3 17:47:28 2014 +0300 adding AlignedTHreadOperation to thread a sequence based on a FASTA formatted pairwise sequence alignment. commit e42dc997e8bbc13791c523ad59cb90d80ace7a19 Date: Thu Jul 3 17:46:23 2014 +0300 fixing uninitialized variable in ThreadSequenceOperation commit 4e3ae178f0659eb45ca85113bd704e7c77ef0e7b Date: Thu Jul 3 10:45:00 2014 -0400 Adjusting membrane position rt mover for generality - can apply to other jumps besides the membrane jump, whose number should now be specified in the constructor commit e84e2121547210872367d82c90c6c9d924897f7c Date: Thu Jul 3 09:56:14 2014 -0400 Making a quick adjustment to membrane posiiton RT mover to show the move generalizes to moving both the protein and the membrane position" commit b56818cc8663344625fad6698d5c594ba2293360 Date: Thu Jul 3 09:31:31 2014 -0400 Updating core.3.src.settings commit 47ed87c07cec2781d2f62c5e8afea58e2f205d59 Date: Thu Jul 3 00:58:27 2014 -0400 Getting rid of an old method in core for depth no longer used - now lives in membrane info commit 2995799f4718b5e3410a2acc0a32af293c3775d5 Date: Thu Jul 3 00:55:54 2014 -0400 No longer allowing explicit setting of xyz coordinates in the membrane virtual - moves are occuring reliably - use those instead. Also getting rid of the embedding_methods class not in use and used to rely on ability to set xyz commit 8c4edaea9a950f7e17d39ebd9882bb0452fcd44c Date: Thu Jul 3 00:49:01 2014 -0400 Deleting random files that were added once... commit d4c48e9a546f87f1341b2363990235de88c1ae7e Date: Thu Jul 3 00:44:37 2014 -0400 Transform into membrane mover - also behaves reasonably now. Will add an additional unit test for this later commit 219a79f54346246e1da964c76d0edcf3ed6bdfac Date: Thu Jul 3 00:12:35 2014 -0400 Updating transform into membrane mover commit d675721d58d953d01bab4433cea7397bffebad09 Date: Thu Jul 3 00:07:17 2014 -0400 Membrane normal now derived from directionality of local coordinate frame commit 9f98fa97b443a24dfe89cde8960ac4bb3fd93ac3 Date: Thu Jul 3 00:06:12 2014 -0400 updating membrane conformation to return a sin inverted normal vector from the local coordinate frame - this ensures correctness just in case of transformations commit 6183e235449d21711104870ab77eb60a5aa67965 Date: Wed Jul 2 23:56:24 2014 -0400 Benchmark scripts: Updating build.levels test so it now automatically run update_options.sh and version.py scripts before checking library levels. commit 9a6b9ba1cba9df0e13910337d78867c4993c77b3 Date: Wed Jul 2 23:49:03 2014 -0400 Just for the commit history, global frame rotations are randomnly in the visualize membrane application commit e587121581f0b5bd1a66e4e88fe6c15fef7396fd Date: Wed Jul 2 23:45:42 2014 -0400 Membrane position rotations working in the global coordinate frame - great ;) commit 50bfea5a76876f2ad51e4a8861c28589702f08e1 Date: Wed Jul 2 22:18:06 2014 -0400 Getting rid of initial orient mover, too hacky and detemrinistic commit 7f3c10192a3a8cd03240195eabbbd74fe6bef8ea Date: Wed Jul 2 21:44:29 2014 -0400 Fixing initial orient mover starting coordinates for a, b, c from stub. Had a and b reversed by accident commit caf28e211ee58e2278823e0a3408e2866f7fe160 Date: Wed Jul 2 21:39:59 2014 -0400 Adding a membrane initial orient mover - will ensure that the normal axis of the membrane planes is pointing upwards along the z direction, also making the remaining computations more predictable and numerically reliable. In the future, the params file should just be setup to create a good default membrane stub but I am currently uncertain of the steps to do this commit e3c90338d1853de40e0256f27347fb7c896c1c05 Date: Wed Jul 2 20:50:28 2014 -0400 Updating membrane position and initial position mover to use the updated rotation move commit 650a0e47a90215fa32a43b7035881ddfb4b86843 Date: Wed Jul 2 20:40:46 2014 -0400 Updating membrane position mover - should make the correct rotations now commit 1331beabbc7510b1c05a304bafd5d5fbccc7da0f Date: Wed Jul 2 18:51:27 2014 -0500 Fix build Remove unused variables commit 22c058e66b956395946b2df1db99747d3130c446 Date: Wed Jul 2 19:06:44 2014 -0400 Fixed rotations - working all good now :)" commit 6cec188f3d165bd8a387ffe721a47e7df6d1a0ce Date: Wed Jul 2 18:51:03 2014 -0400 Ok - just like we explicitly set the center, I am going to explicitly create and set a new stub with my desired normal. It doesn't look like rotation about some arbitrary axis is a good approach - it will not guarantee the deterministic result. This follows the idea of a uniform and guranteed way of working in absolute coordinates when things in Rosetta are mostly relative commit 525244f7e5cde536ee032217f0a198fe03c1f02d Date: Wed Jul 2 18:39:21 2014 -0400 Warnings as Errors: An integration test will now fail if -Werror is off. commit e528875470e16e35c84e6e3fba02c1ea92112531 Date: Wed Jul 2 18:16:33 2014 -0400 Hacking stubs...one way to get the correct result but it still feels wrong... commit 616300da71034ec97714aa9a1624e006d395a75f Date: Wed Jul 2 17:49:27 2014 -0400 Fixing default membrane params to give the proper stub orientation from initial positioning commit 61fd819bb433e8d81d8fa969b133ca2fe09f1817 Date: Wed Jul 2 17:23:03 2014 -0400 Working on initial stub orientation and deterministic move commit 519c40d01c3afee0ef0cd4adab542ae59b5f717c Date: Wed Jul 2 16:13:20 2014 -0400 Cast a numeric::size to a boost::unit64_t to fix clang build commit fcba7ca6d7f75550eef45a12d68afb3007c60fe4 Date: Wed Jul 2 15:54:24 2014 -0400 Some compilers are picky about what gets added to the global namespace or standard namespace when it comes to math.h vs. cmath commit 2e6083ba707d3f6f34c3009f6769d08514787ff2 Merge: 0eb84b0 ab0c89c Date: Wed Jul 2 14:54:15 2014 -0400 Merge master in to bug fix branch commit ab0c89c11dbbc7bcf28fe8db45ec2565b58202f1 Merge: 546ee74 b5dfcc2 Date: Wed Jul 2 13:31:49 2014 -0500 Promote ensemble_generator_score12_sidechain_ver2 to public It's mention in the Kellogg et al. paper supplemental, and has been requested on the forums. (Liz says that there's no reason it can't be public, but still recommends against its use.) New integration test for the application commit 546ee7412693bdaa0258b19005b23f844b8b2e63 Date: Wed Jul 2 13:31:40 2014 -0500 Add integration test commit 6678fc299dd1101deae4d68d7738bc327272b288 Date: Wed Jul 2 14:20:20 2014 -0400 Updating initial mover to make transformation instead of a position rt transform commit b5dfcc224caf5b7218c06405af629b7ca62830b7 Merge: 4a4cd2b ebd13a8 Date: Wed Jul 2 11:15:50 2014 -0700 Merge branch 'master' of github.com:RosettaCommons/main Resolve Conflicts: source/src/protocols/protein_interface_design/filters/RmsdSimpleFilter.cc Merging master to commit fixes that break pyrosetta and clang builds commit 4a4cd2ba2417c32ca6f8b5233ffc696049a04156 Date: Wed Jul 2 11:07:58 2014 -0700 Fixes to compilation errors for OSX clang and pyrosetta. Several fixes of stuff broken by my last commmit: http://benchmark.graylab.jhu.edu/revision?id=57001&branch=master It is quite possible that there are still things to fix. commit c9e9a08db800eb7b7aebcd998a4bd20908c80d82 Date: Wed Jul 2 13:04:48 2014 -0500 Fix compilation commit 41b007fa60e8f01f5c9a5ad8940b89006d14f9a0 Date: Wed Jul 2 12:55:57 2014 -0500 Move ensemble_generator_score12_sidechain_ver2 to public commit 9440f92c9a3be82667caf6ebcbd5130780164d0b Date: Wed Jul 2 13:34:07 2014 -0400 Membrane moves and protein transform moves are occuring consistently - will add initial orientation mover now commit ca0ebbb3ea4fe15585b05128e0e054b8877fd22f Date: Wed Jul 2 13:27:33 2014 -0400 Updating membrane position RT mover to set 2 as the default membrane jump. Also fixing check reasonable membrane fold tree method to check valid jump point but not the specific jump number. Scheme seems to work out pretty well commit bc867666f1b8a37f58ba13ea0465d277328c5745 Date: Wed Jul 2 12:48:17 2014 -0400 Adding anchoring virtual residue to protein and changing the default membrane jump number to 2. This now also being explicitly set in the add membrane setup mover. Not going to track protein jumps - that is protocol specific commit 0eb84b0ac2cb5e3ae6324a34a08cbf820e1099f9 Merge: 898bc82 ebd13a8 Date: Wed Jul 2 12:41:34 2014 -0400 Merge master in to bug fix branch commit 898bc82f1aee1ad1faa8a78fb79c54e0bfdea46f Date: Wed Jul 2 12:28:59 2014 -0400 Adding additional checks in PyMolMover to the length of the object name before sending strucutre to pymol commit ebd13a8a4322be08c8e8f13ef2813e135c46bde5 Date: Wed Jul 2 12:11:53 2014 -0400 Adding an option to MinPackMover::parse_my_tag to activate the off-rotamer packer. Also fixing indentation in the RMSD filter as well as a Size initialized with NULL warning / error. commit 15e42a8dae33c045ad81441ecdb8a08f483f7e19 Date: Wed Jul 2 11:33:45 2014 -0400 Adding code for rotating about the jump commit f5d7f8b9f9dd58affc5413bc7e6ba224a34e79e8 Date: Wed Jul 2 10:53:19 2014 -0400 Lots of things to commit: Starting files for membrane orient perturb mover, work on the fold tree, some outlines for needed modifications to the pymol mover and add membrane mover modifications commit a03a82f4d36cc9f132026d870ccde98fade47424 Date: Tue Jul 1 22:53:10 2014 -0500 Fix a bug where Claims did not have access to PDBInfo object during claiming. commit 3cba4126d3c9656a68bce81c65afb7ed468f7920 Merge: 6b828d5 cf36209 Date: Tue Jul 1 21:38:39 2014 -0500 Merge mystery remote changes and LooCM mover registrator fixes. commit 6b41774e3e321a4a15c1b8a08535a41b4bdf30ca Merge: a9312e5 5ae4a79 Date: Tue Jul 1 22:38:23 2014 -0400 Merging in branch master from remote into ninja local commit 6b828d5c9eee323c9dd545ffc40fdb96094945c6 Date: Tue Jul 1 21:35:32 2014 -0500 Fix Registrator bugs and bug relating to Loops creation from selector commit e7b8398f2f0a6b4d04b2d011845ca2c26734cc41 Date: Tue Jul 1 20:29:18 2014 -0500 Add LoopCM to Mover registration system. commit cf3620931c7d90defa54813d4991f6708ff3f2fb Date: Tue Jul 1 20:29:18 2014 -0500 Add LoopCM to Mover registration system. commit cab6dc6c3cccdcba85371952c673b3c6b55fc0b7 Date: Tue Jul 1 17:28:42 2014 -0700 refactoring RNA_Data stuff a little to allow read in of actual DMS values and scoring. commit 7577a37dce0fa6a4aca95467569eb899a3da902e Date: Tue Jul 1 18:17:27 2014 -0400 Fixing a bug in the linux.gcc.debug build - did not explicitly declare the namespace required for use of core types in MembranePositionRotation mover. This should fix it commit 0ddd30c51ee465cf7bf56e3c8e965e1f1a5096f1 Date: Tue Jul 1 18:06:22 2014 -0400 Membrane Framework Updates: = Membrane Position RT Movers - Apply explicit rotations & translations to the membrane residue without modifying the fold tree. Rearranges the current fold tree - so there will be expected integration test changes for membrane_relax and load_mpframework (and anything else that prints the fold tree in it's show statement) = Fixed unit test build = Added MembranePosition rotation/translation mover unit test. Should be more rigorous in the future, but the basic test is present = Adding shadows of pymol mover code from a previous merge. This is not the most up to date version, and will be merged in at a later date commit fbd698e9ed8b7ab7d3b96d84ddc46160bfa21800 Date: Tue Jul 1 17:57:02 2014 -0400 updating membrane position movers to take a general membrane jump, no longer hard coded to position 1 commit e198d432d8956a42e77411e02fedc10569e5b0f8 Date: Tue Jul 1 17:51:14 2014 -0400 Rotation code and unit test behaving reasonably - merging basic code into devel next commit 8df0cdd47d556136336c86dddbca49b53ff387ee Date: Tue Jul 1 17:16:57 2014 -0400 Adding current version of the code commit 3857fb1b2e51f1878fee831766ff6a45a84cb499 Merge: 96e9119 0aa4dfe Date: Tue Jul 1 10:51:57 2014 -0700 quick merge from swm_general to dms_score branch. commit 0aa4dfea662065327bf1826a3de02f5abfb36f77 Date: Tue Jul 1 10:51:41 2014 -0700 getting linux to compile with Vector, which has a name conflict with some system library. commit 96e91196d648ca97d8fb3c4408c158e4d3159215 Date: Tue Jul 1 10:49:56 2014 -0700 fix to constraint setup in SWM when reference pose has crazy numbers. commit 88b90c671b6b0b3a0e4b5de4d30cc6ca4589a5af Date: Tue Jul 1 10:48:43 2014 -0700 getting rid of a compiler error due to wrong order of initialization of variables commit ebce9c942cec7d3736ffcbe06e82797531f5a55d Date: Tue Jul 1 10:48:13 2014 -0700 updates to get pseudomethyl energies for DMS/RNA modeling commit 8c31e19b544cdc91aab9726a18809923f53c22c9 Merge: 77a2ea3 9c4f067 Date: Tue Jul 1 10:22:22 2014 -0700 merge from master. commit 88df09526ac577b4d6b8daa02a0e27ed121cc77d Date: Mon Jun 30 23:16:39 2014 -0400 Currently has reasonable rotation code - will document tomorrow commit 310cb74b1ccbb89bfa645ac75275ede5e105226e Date: Mon Jun 30 22:46:17 2014 -0400 Oh that's beautiful, finally doing rotations :D And I'm not kidding this time commit 04f4c2b0bd0110e2e0b8de92b836699d54702c37 Date: Mon Jun 30 21:53:36 2014 -0400 Trying rotation with new representation of the normal from Justin's suggesiton about handling deterministic rotation moves commit 8f798bd4761e9aea32f667621fec150b5c2d5f86 Merge: 80ef402 7f54625 Date: Mon Jun 30 17:37:07 2014 -0700 Merge branch 'rpache/KIC_with_fragments' of github.com:RosettaCommons/main into rpache/KIC_with_fragments commit 80ef4024a5f5c85acc5474c419e37cbd655dc24e Date: Mon Jun 30 17:35:33 2014 -0700 changing format to tabs instead of spaces commit 5ae4a7914a7d96164249a3964096f764db10941b Merge: 571cd77 c3ac9dc Date: Mon Jun 30 16:59:44 2014 -0700 Merge branch 'master' of github.com:RosettaCommons/main Update/merge in order to commit Fragments/Epigraft update to origin. This merge will provide the next filters: 1. FragmentLookupFilter 2. SSamount 3. RmsdSimple Plus updates to MotifGraftMover (see Web Documentation) commit 85d45557e305f719696345a95efee4efc1409acf Merge: 430fd49 481fb5a Date: Mon Jun 30 18:50:20 2014 -0500 Merge justinrporter/env_claimscript in anticipation of removal of that branch. commit 481fb5aa54687675230ec8be99b27f1bfb302d45 Date: Mon Jun 30 18:49:15 2014 -0500 Add LoopCM Client-based mover to make KIC and CDD perturb and refine movers claim. commit 8511cb57c0b05a28f895dfc029333f20b79ff6c8 Date: Mon Jun 30 18:48:11 2014 -0500 Add selector based constructor for TorsionClaim. : commit c3ac9dc6bc71d6907a7e5032620112b0c60a0e36 Date: Mon Jun 30 19:45:40 2014 -0400 [minor update of sequence_recovery] - removed 'database path' comment ('database path' will be automatically assigned) [update of SandwichFeatures] - added 'exclude_sandwich_that_is_suspected_to_have_not_facing_2_sheets' - better tracers - should not change any integration tests other than (expected) features and features_database_schema (if any) commit 571cd77f7cfc3d0cd80576d07aa3254e5e70cc38 Date: Mon Jun 30 16:18:09 2014 -0700 Merge master into fragments Epigraft. Merges sucessfully master into Epigraft and Fragments branch commit 430fd491a0d9439e80c29db9a5ffb6b001761621 Date: Tue Jul 1 00:44:33 2014 +0200 Remove unimplemented EnvLabelSelectorCreator to fix PyRosetta build. commit 7bcca9a2fc6c6d3fcb559e58cb1db64766d2f1c8 Date: Mon Jun 30 16:18:04 2014 -0400 added SpanningTopology test, compiles, doesn't run; fixed bug in geometryUtil test commit 16fc02e658cee1438e372a3cb0007efb175fbc9e Merge: 6f0277f a8db437 Date: Mon Jun 30 21:39:13 2014 +0200 Add scriptable claiming and bug fixes to Environment. Also add some new mover supertypes ("MoveMapMover" which is a mover that respects movemaps and "MoverApplyingMover" which is a mover that contains a single other mover that it applies). No (new) integration test changes expected, no (new) unit test breakages expected. commit fed1249aed37ad894c4b276f5e21834435ca1f6f Date: Mon Jun 30 14:29:17 2014 -0500 Add vector1< bool > initializer for IndependentLoopMover. commit a8db43726825ad7e33027ec85c9e90339422882d Date: Mon Jun 30 20:41:46 2014 +0200 Fix a use of the ! operator on vector1< bool >. commit a5638d44173fce2551526a09b2ab92a44cf7db66 Merge: dac4b73 6505c5b Date: Mon Jun 30 14:06:06 2014 -0400 Merging in membrane stub moves which should become useful in the show planes viewer commit 6505c5b57e607f92ca1d01d5ea9303308ce2a602 Date: Mon Jun 30 14:04:58 2014 -0400 Still bugs in rotation... commit 3aa5456cbd83327eb6fc71463f112b482194fffc Merge: 0d5365b 6f0277f Date: Mon Jun 30 10:37:12 2014 -0700 Merged master fixed conflicts commit 0d5365b46fb05df832a55df7a75aa3635d775ce8 Date: Mon Jun 30 10:25:38 2014 -0700 Merged Lucky changes to fragments epigraft This commit has the merge of Lucky's changes to JD2 that affect nstruct by adding the multiplepose mover commit a3f80fd9c82f97bff74abcecdb4c18a33c67327e Date: Mon Jun 30 10:07:55 2014 -0700 Working version of merging fragments to Epigraft This version is before merging to master's Lucky changes to nstruct. commit 6daaef26bee8a5df7f291dcda252db4de7ac3538 Merge: e83bacf c447e2c Date: Mon Jun 30 18:38:50 2014 +0200 Merge branch 'justinrporter/env_devel' into justinrporter/env_release commit e83bacf6eca8f5a32a02ea47ae8282b772731b2c Merge: 3bdeb7f 6f0277f Date: Mon Jun 30 18:05:04 2014 +0200 Merge branch 'master' into justinrporter/env_release commit baf3b213deb13f151e84dc549b7268ae2a28fed6 Date: Mon Jun 30 11:56:46 2014 -0400 Updating mover creator and forward headers to relfect the actual state of the mover commit 261403fea5c5c075d95ea9b557f0a4a888e771cd Date: Mon Jun 30 11:51:17 2014 -0400 Implementing translation and rotation move as separate rb moves that can be composed in a top level mover - the reason these need to be separate, is because one is acting upon the actual RT in the jump, whereas the other deals with the actual coordinate position in the stub. It fixes the non-coherence issue with center being a point and nomal being a direction. finally commit 3a18942a849b0870be57eebe8c5f94765639b3c8 Date: Mon Jun 30 10:36:04 2014 -0500 Modify FragmentMover to implement MoveMapMover interface. commit 54332a1c339750e28fe3ff75a7f4bc550ad03122 Date: Mon Jun 30 11:34:54 2014 -0400 Has the independent moves that work - will just compose into 2 separate moves and things should be good commit 112ded1edb668fb957a1c29efeb54447b8a65af1 Date: Mon Jun 30 10:53:33 2014 -0400 Membrane rt still has bugs, taking code to merge into another branch commit c447e2cba11769cc3dd109ece332bac4f985ae76 Date: Mon Jun 30 09:51:54 2014 -0500 Add PDBInfo persistence unit test. commit ef8b9a8c74113ab0b88ca03a9f1da900e58b9be2 Date: Mon Jun 30 10:40:21 2014 -0400 Removing an errant std::cout statement; this code looks like it's ready to me. commit 9c8543c8f708f6ab52874a4bc070dcb53b899304 Date: Mon Jun 30 10:27:37 2014 -0400 Adding unit tests for the CDF code in Ramachandran2B commit dbab01fe587376df44875039fc9c3bc055e97be3 Date: Mon Jun 30 10:08:01 2014 -0400 Unit test finally doing something reasonable - going to implement the rest commit 635d59852dde641e70fd692d12b19a8c937c377b Date: Mon Jun 30 10:03:25 2014 -0400 Implement corrected rotation & translation in membrane position rt mover commit 5e0bcae795a71bd8b932d00c834448caef81a4fb Date: Mon Jun 30 09:52:42 2014 -0400 Finally got translations working - code in the unit test and needs to be back generalized to the mover, but got something working ;) commit 6f0277f02d8a44453fe85f779b0854303ba70ba8 Date: Mon Jun 30 13:37:11 2014 +0300 changed 2 chain assert to warning. commit 42c57e703d5d36feed2366d42be9def075d401d0 Merge: ec1d24e 82a2c17 Date: Mon Jun 30 10:44:49 2014 +0300 Merge branch 'master' of github.com:RosettaCommons/main commit ec1d24e3c5414672ba008414b81696e0b797cfc4 Date: Mon Jun 30 10:43:27 2014 +0300 added (and commented out) statement to print all files Rosetta is trying to open. Useful for nacl commit 804486aeb1c0663d0f56147baedaec298e79bc23 Date: Sun Jun 29 22:57:47 2014 -0400 Same orientation problem in setting the jump - code looks more reasonable now though commit 2aab4ea6a199e9a96ba1c5d53f54cc701d9a56d1 Date: Sun Jun 29 22:48:29 2014 -0400 Updating membrane position mover - rotation matrix is correct, but trying to set it in the stub is more complex commit 99515cce3e6e98bb8d53e1393e647b8b1d518460 Date: Sun Jun 29 22:37:21 2014 -0400 Correcting rotation move, things should hopefully work now commit e8a5b6b22e14b1d3e5eaf371efcea25531cebe04 Date: Sun Jun 29 22:18:55 2014 -0400 Right now, I am explicitly setting the rotation matrix equal to the stub matrix which is flat out wrong so the test will not pass. Getting there though ' commit e1d75c6fb4e31d147640fb1c5b786835f4cbd7fe Date: Sun Jun 29 21:12:03 2014 -0500 Fix a bug where PDBInfo-less poses would cause an Environment crash. commit b99647e6a689b0536ff45fa97214f816354a8c41 Date: Sun Jun 29 22:11:04 2014 -0400 Consecutive translation test passes - still doesn't check for this strange is_stub edge case that seems to be often relevant for membranes. The thing, is that its not invalid for the normal to be along the same axis as the center, which can happen. Will look into it commit 02bc0022d8793d5c2c8a4bdd03804ed57521683e Date: Sun Jun 29 21:59:39 2014 -0400 Forgot to add spanfile to protocols test settings - recompiling and copying over to default bin now commit fa82db66f054bd5d0e63327e81216ea098e702ab Date: Sun Jun 29 21:54:50 2014 -0400 Membrane rotation/translation position unit test compiles with just consecutive translation test implemented commit 3644b4efd684b14547b209b624ca3e3606f262cc Date: Sun Jun 29 20:42:46 2014 -0500 Fix a bug in ScriptCM where it would fail if it doesn't have a passport. commit 423ea0a41b6b220f8e5167c12d63da0a7c455a54 Date: Sun Jun 29 20:42:20 2014 -0500 Fix a bug where the Environment was destroying PDBInfo objects. commit 30e26ce98e7eee37e06d67d2c331d6ac1c7c7c54 Date: Sun Jun 29 20:41:36 2014 -0500 Update 'allow_dupiclates' setting algorithm in virtual residue creation to be claim-order independant. commit f34c677a0200d5920f5dd74ab81871e15a91afad Date: Sun Jun 29 20:40:51 2014 -0500 Add more useful name output to UniformRigidBodyCM. commit 3a089b9437a19e2cd2e7bf338043d53394aa6e95 Date: Sun Jun 29 20:40:26 2014 -0500 Add more useful error output when Pose object going into ChainSelector has no PDBInfo object. commit 5d8ad5624f175c362f2acdd4f7509eccca680f0c Date: Sun Jun 29 20:39:49 2014 -0500 Add debug output to FoldTreeSketch. commit cb173b56002e3c551a324d5c0920eb3c682e2809 Date: Sun Jun 29 21:33:07 2014 -0400 Adding bacteriorhodopsin pdb and spanfile for membrane pos rt unit test commit 9c0c406d9418d46bb98ba5085c82a1edd91fe862 Date: Sun Jun 29 21:27:35 2014 -0400 Starting to implement membrane position RT test commit ce96da913d4475dc1fab57472ce15707f32b28fe Date: Sun Jun 29 21:23:31 2014 -0400 Remedied current unit test situation - everything commented out except for unit tests I know will work commit 0194b6f04e8e9cb39756261b97c23755b4b6f376 Date: Sun Jun 29 21:18:06 2014 -0400 Getting rid of check_trans pilot app - code now implemented in the mover commit 7a7a5938651a71c5eaabeec5b00a2d2025482f03 Date: Sun Jun 29 21:16:15 2014 -0400 Adding uniform RT to membrane stub to its new home in the mover commit e44c4f7e3454bdbd38c44b34dd38c58a2b4fde4a Date: Sun Jun 29 21:11:04 2014 -0400 Check trans now contains code for valid Uniform RT of the membrane stub - also reads pretty logically which is pretty exicting commit c0213115dd2c8b2682ffa544c1215a61177e7cb6 Date: Sun Jun 29 21:07:12 2014 -0400 Downstream and upstream positions were flipped - does the translations correctly :) commit b0a36e768c27422abb444ced62378d97baea86dc Date: Sun Jun 29 21:02:04 2014 -0400 Check trans code contains some probably more acurate code for moving the membrane stub...still not perfect though commit 39146cc9253a4d9af2749cea8289870958452ad2 Date: Sun Jun 29 21:01:17 2014 -0400 Check trans code contains some probably more acurate code for moving the membrane stub...still not perfect though commit d1b8e9b7899444aeda67e087c5ffd8c92a85585f Date: Sun Jun 29 19:19:21 2014 -0400 Translations are occuring correctly - now to just figure out rotations commit 8968b8a6c9ff65f20d7521e43f1075b12a71e6a0 Date: Sun Jun 29 16:00:52 2014 -0400 Fixed a lot of bugs related to making rotations/translations but its still not doing what I need...working on it commit 354bd82af40f9992c55e0e053e6d32731f1d6246 Date: Sun Jun 29 15:36:44 2014 -0400 I have no idea what is going on...pymol shows that the translation/rotation are occuring appropriately but the output in my check trans begs to differ commit 9a50ca1331480cf58e048f6a404debc6991f61f6 Date: Sun Jun 29 15:14:32 2014 -0400 Adding pilot app as a check for this commit 7f9661ef984932f9c5e823d6b02f43f4a0a52522 Date: Sun Jun 29 15:14:10 2014 -0400 Committing current work trying to fix moveable membranes commit 883b889195bf1265092e83bd2b5dcbca689e4e78 Date: Sun Jun 29 13:33:40 2014 -0400 Implementing uniform rotation/translation move from the membrane stub commit b9648fbfc0f0a22e65e4bd02a0f1db3638c6aa6f Date: Sun Jun 29 13:18:31 2014 -0400 Dropping the requirement for membrane residue to be the root of a reasonable membrane fold tree (much more generic) and making the check fold tree method take a const reference for correct pose binding commit 82a2c17d2cf6e3254a656b759bae9626b074e25c Date: Sun Jun 29 12:40:05 2014 -0400 Fixed Cterm_amidation hydrogen naming Many residues have hydrogens named e.g. 1HE2/2HE2, which rendered the atom names in Cterm_amidation problematic sometimes. C-terminal glutamine with this patch applied would see protons flying all over the place, potentially affecting pose scoring, for reasons incomprehensible. Additional advantage: the new names, 1HN and 2HN, are the Correct Names according to PDB style and don't conflict with anything but mutually incompatible patches like Cterm methylamidation. commit 5fde101a64707d77f8d7f26d2fa1f4222748e46d Date: Sun Jun 29 19:06:51 2014 +0300 Addeed if conditional to handle case where Splice.cc deals with one pose. commit 3381ceb3af7ea1192288203708a08870eeb497e0 Merge: 86530c6 cc425be Date: Sun Jun 29 17:31:34 2014 +0300 Solved conflict in Splice.cc Conflicts: source/src/devel/splice/Splice.cc commit 86530c66958fbb80df562771eecc21ad7253f847 Date: Sun Jun 29 17:12:24 2014 +0300 Minor corrections to Splice.cc. Will cause integration test changes to Splice_out and Splice_in commit dac4b73c4f8241dcff164ee907d30375c2ee3c0e Merge: 8e28e36 ea08a10 Date: Sat Jun 28 22:28:53 2014 -0400 Merging branch mpframework devel into pymol mover viewer branch commit 895f05a8af0c7840a07c15154a1bbafccbbed946 Date: Sat Jun 28 22:26:13 2014 -0400 All of the code compiles...except the move ;) commit ffb8aa5f93054be6e3f27370d2a1f10d98c2aa56 Date: Sat Jun 28 22:02:22 2014 -0400 Implemented everything in the membrane uniform rt mover except the apply - going to need to do this one interactively commit baf2009fc5ab1b3a9e80e02dbc8141893854002d Date: Sat Jun 28 21:56:05 2014 -0400 Implemented mover creator header and forward header - also working on cc file commit fe34ba207e49c8b7de0d9dde01e9989fff685204 Date: Sat Jun 28 21:51:00 2014 -0400 Making a shell for the cc file for membrane position RT mover commit ec56f4c7e187469c1432827fa523c2a7ebbd7995 Date: Sat Jun 28 21:37:08 2014 -0400 Membrane residue cannot be the root for the move to work - changing this temporarily in teh code commit 7b824ff1de2c73a812270f50fc4c091ec35aca0b Date: Sat Jun 28 21:31:52 2014 -0400 Implemented header file for membrane position mover commit 76c0f1ce33ec4e9239e85bc02d59d50d9c0a28a3 Date: Sat Jun 28 21:20:09 2014 -0400 Starting to think about how this move will actually work... commit 3132a360d8a6e72e07e903c493725f5c689b69e7 Date: Sat Jun 28 21:05:23 2014 -0400 Initial add of files for Membrane Position RT mover commit ea08a10921c15608485d1f2f24ab8d3eb8ba2dd3 Date: Sat Jun 28 18:38:58 2014 -0400 Membrane Framework Updates: - Added enum MembraneParams.hh for referencing atom indicies more cleanly in the membrane residue - Added arguments in the membrane info constructor for specifying the membrane jump number. Also added these methods to the copy constructor of MembraneInfo - Added a check_membrane_fold_tree method that users should run - this will let them know if their fold tree is reasonable for use with things like the atom tree minimizer. - Fixing ~20 files broken by the spanning topology updates - most due to lack of #include membrane info and incomplete type definitions. Includes resource manager code, energy term #include declarations, etc. - Formatting fixes in Embedding classes for coding conventions commit cc425be2fbc9a5caf43e948cb1f5eb8bbba00eab Date: Sat Jun 28 17:56:42 2014 +0200 Add information to 'option not found' error in utility::tag::Tag. commit 2a04d0531503164bd3b45900431afa4e1eb40a87 Date: Sat Jun 28 18:15:10 2014 -0400 Membrane Framework Updates: - Added enum MembraneParams.hh for referencing atom indicies more cleanly in the membrane residue - Added arguments in the membrane info constructor for specifying the membrane jump number. Also added these methods to the copy constructor of MembraneInfo - Added a check_membrane_fold_tree method that users should run - this will let them know if their fold tree is reasonable for use with things like the atom tree minimizer. - Fixing ~20 files broken by the spanning topology updates - most due to lack of #include membrane info and incomplete type definitions. Includes resource manager code, energy term #include declarations, etc. - Formatting fixes in Embedding classes for coding conventions commit a27bc70465980e884372d478a13c3aa5bb0e65f1 Date: Sat Jun 28 17:48:51 2014 -0400 Membrane Framework Updates: - Added enum MembraneParams.hh for referencing atom indicies more cleanly in the membrane residue - Added arguments in the membrane info constructor for specifying the membrane jump number. Also added these methods to the copy constructor of MembraneInfo - Added a check_membrane_fold_tree method that users should run - this will let them know if their fold tree is reasonable for use with things like the atom tree minimizer. - Fixing ~20 files broken by the spanning topology updates - most due to lack of #include membrane info and incomplete type definitions. Includes resource manager code, energy term #include declarations, etc. - Formatting fixes in Embedding classes for coding conventions commit 765af5251fc43898a200d82910211bfecf5b345e Date: Sat Jun 28 17:40:46 2014 -0400 Fixing lots of bugs resulting from julia's spanning topology commit commit e62dfaba315da82989b9ee1fc8d55252ca6e388c Merge: 3ad1d10 1c743fa Date: Sat Jun 28 12:28:12 2014 -0700 merge of SWM phosphate-pack fix to master. Checked integration tests of this fix - changes to swm tests and apparent floating point changes in inverse_rotamer_remodel and match_1n9l commit 46cab0fe5772297ef901a5164b77f0c62206f604 Date: Sat Jun 28 16:41:08 2014 -0400 Debugging some additional namespace and scope errors introduced in conformation and embedding-methods (even though that class is going away in less than 5 seconds... commit a92913b9a23c88fac6965b57712ee95707d5ea69 Date: Sat Jun 28 16:39:48 2014 -0400 Adding the membrane jump constructor to conformation commit 3ec9b571779f0ccfd6024588b907a9cfd7dd9a5c Date: Sat Jun 28 16:35:23 2014 -0400 Implemented check membrane fold tree method in membrane info to check for a reasonable membrane fold tree commit 6093934d784fb579e4bdf3d9de5f8d67ae5a0276 Date: Sat Jun 28 16:32:08 2014 -0400 Adding default argument to membrane info - can specify the membrane jump number. will become useful when fold trees become more sophisticated. All code & copy constructors changed accordingly commit b2b5cbe1ae62f9d9fe577876b4a1ea8d40be42f0 Date: Sat Jun 28 16:13:40 2014 -0400 Cleaning up conformation with a beautiful enum, never did i think enums could be so awesome commit f770b34cc7171ee1785609ad8c0ce61402dcb3c6 Date: Sat Jun 28 16:10:08 2014 -0400 Updating conformation #includes - also removing hacky set thicnkess method commit 8b8f50b7c6a49a644c19af810ef391ca4e0e6945 Date: Sat Jun 28 16:03:56 2014 -0400 Adding membrane params enum for better index refereincing in conformation.hh commit 93c6a8a534aebc2fa47f321d650df37210e642f3 Merge: d528bec 506873b Date: Sat Jun 28 15:38:57 2014 -0400 Merging in most recent version of mpframework devel into membrane code fixes branch - accepting Julia's params files changes for now but will not accpet in flex sampling branch commit 3ad1d10016df9ba94a86eadbccf24ea483ba2324 Date: Sat Jun 28 12:26:16 2014 -0700 fix up apps compilation commit 506873bd12edc57838167492d96c3337a9adb633 Date: Sat Jun 28 15:23:35 2014 -0400 Framework Updates: Adding Integration Tests for Membrane Framework Application Development (for Rebecca's apps): - load_mpframework: Load and initialize a membrane protein using the framework with add membrane mover and initial membrane position mover. - membrane_ddG: Run C++ adapted version of membrane mutate, relax and compute total score ddGs - memrbane_relax2: New custom membrane protein structure refinement/relax protocol. Currently just minimizes - translate_membrane: Membrane pose translation mover - used often in visualization Updatng Objects: - SpanningTopology: Fixed show method to override ReferenceCount#show( ostream ) and trace with output. Also added copy constructor and assignment operators and removed unnecessary cc guards - Conformation: Added show_membrane() method - show method used temporarily for showing membrane output. Composes MembraneInfo - MembraneInfo: Added membrane_info.show() method to show base information in the object. commit 28627e0d3e93963d04eeab0e8165c850fe70a0c4 Date: Sat Jun 28 15:21:58 2014 -0400 Framework Updates: Adding Integration Tests for Membrane Framework Application Development (for Rebecca's apps): - load_mpframework: Load and initialize a membrane protein using the framework with add membrane mover and initial membrane position mover. - membrane_ddG: Run C++ adapted version of membrane mutate, relax and compute total score ddGs - memrbane_relax2: New custom membrane protein structure refinement/relax protocol. Currently just minimizes - translate_membrane: Membrane pose translation mover - used often in visualization Updatng Objects: - SpanningTopology: Fixed show method to override ReferenceCount#show( ostream ) and trace with output. Also added copy constructor and assignment operators and removed unnecessary cc guards - Conformation: Added show_membrane() method - show method used temporarily for showing membrane output. Composes MembraneInfo - MembraneInfo: Added membrane_info.show() method to show base information in the object. commit bf0716cab75601e34e1694294f756e0bd0b41bed Date: Sat Jun 28 15:12:53 2014 -0400 Updating membrane ddG command file to locate teh right executable commit 4df3b8bf3522f95c0863d4594729813718f3c655 Date: Sat Jun 28 15:12:24 2014 -0400 Adding membrane ddG integration test inputs commit 2a37434c7136ffc7d700716f0a84432a5b11bff3 Date: Sat Jun 28 15:11:21 2014 -0400 Adding starter files for membrane ddG integration test commit 78abe0f15b0fdadda3858f26099ebf4c288ce710 Date: Sat Jun 28 15:03:47 2014 -0400 Adding test starter files for membrane relax integraiton test - just doing integration min right now commit 5ee0d57a84079f9de838a1ed81efed7e0611e427 Date: Sat Jun 28 15:02:33 2014 -0400 Updating membrane ddg, membrane relax and translate membrane pose integration tests. Relax should compile now and will try setting up the next 2 integration tests commit 38e74c25ba063ee22112502f1f4f8c6fdff5b36d Date: Mon Jun 23 18:11:35 2014 -0700 fixing swm to not pack terminal 5' phosphate at root residue. its because the phosphate holds the root atom, and its not easy to move the root atom elsewhere. eventually we'll fix this by including a virtual residue as another root, and have a jump into the RNA root residue. commit 843246dfcd5a98e7583501cf41e9095de6b0a6e4 Date: Sat Jun 28 14:34:41 2014 -0400 Adding extra space to spanfile integration output commit a5f9330f75227b59bd8990d9293948b9fc6f1535 Date: Sat Jun 28 14:32:04 2014 -0400 Updating command file for translate membrane integration test commit 066a14917bf12cad9db0a97d92c4f91fefdd0667 Date: Sat Jun 28 12:58:53 2014 -0400 Updating translate membrane command file commit cb31f93727d7f994591559b81ae054bdf539b33f Date: Sat Jun 28 12:58:04 2014 -0400 Quick fix to load mpframework integration test - all tests pass ' commit 2d2cb62e93d61dbc34a31eeceef888e004a091cd Date: Sat Jun 28 12:53:57 2014 -0400 Adding integration tests as a temporary add - still needs to add the executables for these guys commit c1a2ed118455cd9b57263df75366258a99cc6759 Date: Sat Jun 28 12:52:49 2014 -0400 Commenting out membrane ddg test for now commit 6ef8d6693b22140f33e7b98845676f77362576c3 Date: Sat Jun 28 12:38:25 2014 -0400 Adding membrane ddG and translate membrane pose integration executables to build settings commit d1e5b2fb3194b96d11e1a6b14232aea5b4cad919 Date: Sat Jun 28 12:36:13 2014 -0400 Adding translate membrane integration test commit eed4911d3fd55b71b991e6e4b86275b0d74e0f71 Date: Sat Jun 28 12:35:31 2014 -0400 Adding translate membrane pose application to be used in integration test commit 70f9ecb987ed2fba4b4931baf5239a44a535826b Date: Sat Jun 28 12:26:41 2014 -0400 Adding starter shell for membrane ddG application commit a7a79a67ae60bc916f5e485ec06d5c3f246b1b09 Date: Sat Jun 28 12:26:20 2014 -0400 updating load membrane pose application - hopefully can fix the bug I was seeing with implicit cout construction. Also updated the conformation show_membrane method signature to take this required reference commit 36417af23350c8a226db3062707f32255c3922c0 Date: Sat Jun 28 12:10:13 2014 -0400 Bug fixes in load membrane pose pilot application commit 36d74c408e5a8d60eb27bf196ad624f8dae06a30 Date: Sat Jun 28 11:57:26 2014 -0400 Now its added to build settings commit ff1e943b73c48f35b8977fa98d52c68592355fbb Date: Sat Jun 28 11:38:13 2014 -0400 Putting together a full show_membrane method in conformation to display the information in both membrane info and derived from coordinates. Might want to do this differently since it requires an unintuitive composition of methods commit a4c4e6559db6ade13f8e869376c14cf32980c8a8 Date: Sat Jun 28 11:31:27 2014 -0400 Implementing overrided show method in membraneInfo commit 05e98271e61f14fb0af999d6001b05077587dfd5 Date: Sat Jun 28 11:29:39 2014 -0400 Implementing required assignment operator and deep copy constructor methods required by Rosetta in SpanningTopology - will do a doxygen update later commit 4b343e71fe8f095abc5935ffbb2c0be8435a81d3 Date: Sat Jun 28 11:24:17 2014 -0400 Starting to write show method in membrane info and membrane conformaiton (haven't decided how I'm doing this yet) and fixing spanning topology object to conform to coding conventions and override base reference count methods where required commit 877d4129c7c3bdd88085978c163b2bd072bdc8af Date: Sat Jun 28 11:13:41 2014 -0400 Adding integration test files for load mpframework integration test - incudes bacteriorhodopsin pdb (1C3W), spanfile, bare minimum flags file and command file loading the load_membrane_pose executable commit 57b8418fc57d04fbc4edb55ad922b1147dd63761 Date: Sat Jun 28 10:58:41 2014 -0400 Ammending the commit message: Integration tests expected to change from the previous commit are UBQ_E2_thioester_two_ubiquitins app_exception_handling broker_membrane buried_unsat_kinemage membrane_relax, These were broken in a previous version of the framework - the top 4 are currently broken in the pulled thread in master and membrane_relax is changed due to Rebecca's current development of the membrane relax applicaiton commit 8e28e36456d812e43bc519a3608923425aa56186 Date: Sat Jun 28 01:49:47 2014 -0400 Adding a bookmark in the pymol mover for membranes commit 26ba29767e1dc0c47794389aa9b0f805ce439d54 Date: Sat Jun 28 01:42:13 2014 -0400 Compiling version of show membrane planes mover - not yet tested, needs some work and checks. Might also need to make some changes to get this to work in the visualization pipeline. In genera, the mover computes 3 points for the upper and lower planes such that pymol can draw 2 triangular planes from these points. These points are special virtual residues - they are connected by jump to the central membrane point. This means that if in the pose's conformation the membrane moves, the planes should move according to the viewer as well. This might be unintuitive to frames at first - but will show how you can sample the membrane position around the pose commit 1b18aae09382c31deb9230a21f5d0fea3a7baf19 Date: Sat Jun 28 00:20:10 2014 -0400 Added options reading in mover construction, also adding ShowMembranePlanesMover to build settings commit 44ffb8f68c17cef40ee91f0624277c99fbfefc42 Date: Sat Jun 28 00:19:09 2014 -0400 Implementing options reading in show planes mover and adding new visualize option for plane radius commit 1a1bb5e3b6437f8530e8d6ce71ad98c315f3a137 Date: Fri Jun 27 23:54:10 2014 -0400 Adding mover creator header for show membrane planes mover rosetta scripts hook commit 3c24615bdd87ab44a569b5ca268a1a67f2d4f648 Date: Fri Jun 27 23:51:25 2014 -0400 Implementing most of the body of show membrane planes mover - making progress commit 8144345b4a06a9494292f6ee20b388769393d406 Date: Fri Jun 27 23:08:23 2014 -0400 Adding header and forward header for show membrane planes mover commit 61930f9be2651a11c67dade5217aa03154e7824a Date: Fri Jun 27 23:05:52 2014 -0400 Initial add of mover files - adding show membrane planes mover which will add 6 points for an upper and lower triangular membrane plane commit f50d75cfb648daa9f170de5f833f761845171c1b Date: Fri Jun 27 22:58:53 2014 -0400 fixed bug in spanfile_from_pdb commit 5b34dc2c64fbac1769c0f0a453a4fd6b4d4da5d2 Date: Fri Jun 27 22:10:46 2014 -0400 added SpanningTopology unit tests, needs to be tested commit af9b740da9aaa55c74522fa4ab603dc06e3f4b0f Date: Fri Jun 27 22:10:16 2014 -0400 moved pose_info function from pilot app to core/membrane/geometry/util commit cf24e7e158e0ad93bc76c6d6c560efce386c2084 Date: Fri Jun 27 22:09:00 2014 -0400 SpanningTopology: took function out of constructors and made them private commit 3a91f944e4f0a997832d87fbcac373eb13a18760 Date: Fri Jun 27 22:07:03 2014 -0400 added testfiles for unit test commit 1c743fa41ebc5883787e75397c5a47db928c1371 Date: Fri Jun 27 17:03:26 2014 -0700 Temporarily removing some pilot apps from pilot_apps.src.settings.all which are causing the debug compilation to fail due to errors-as-warnings. Kevin, please check these: several have unused variables, and sasa_buns.cc has a typo. These also seem to be causing the app_exception_handling integration test to fail. commit 6304b71d6f69138f98e3cc5d5f394662cb09d146 Date: Fri Jun 27 16:24:39 2014 -0700 Removing unused var in a pilot app of Kevbin's to get debug build compiling. commit aa7d00aef0721c1035c4ca0bc5809e4afd066c19 Date: Fri Jun 27 18:35:43 2014 -0500 Fixing some bugs with VirtualResidue creation. commit 1397ac93680b2530ae0c950a90ec26518c418072 Date: Fri Jun 27 18:35:19 2014 -0500 Add MoverApplyingMover archetype to moves, modifying GenericMonteCarloMover to have this archetype. commit da5ca0c50f3b6b5514415e310e11a2772212357b Date: Fri Jun 27 19:04:29 2014 -0400 added spanfile_from_pdb pilot app, compiles, runs commit 40b9c7c11dc8ee5be3c6c8785c15e3021759d362 Date: Fri Jun 27 19:03:26 2014 -0400 implemented show function for Span commit 1cbc262dd9c615bbfb9ef375f3fbf8b8b6f66a8c Date: Fri Jun 27 19:02:41 2014 -0400 fixed bug in Embedding commit 7e5550f4030dc6f580bc20d6268e5fdf1e4bcbc3 Date: Thu Jun 19 16:27:37 2014 +0200 Change pose->set_new_conformation() to take a ConformationCOP rather than a ConformationOP since it clones it anyway. commit 07e58db0ad7e8d60162ca32a843135ac8591be76 Date: Fri Jun 27 18:48:41 2014 -0400 add disable_design tag to FR parse_my_tag. Will wait a day or two to merge commit 5bc54c29905db1caad703921e681011c11f7d350 Date: Fri Jun 27 18:16:25 2014 -0400 bugfix to finally allow SnugDock to work on antibodies with any antibody numbering scheme and cdr definition commit 2ea9a6bb4aaaf02c621f45d4610c7120199b7c22 Merge: 7404c21 fab252a Date: Fri Jun 27 14:39:31 2014 -0700 Merge remote-tracking branch 'origin/master' into kylebarlow/general_dev commit fab252a69192138bd20a4730a6c5234ffe798e77 Date: Fri Jun 27 14:59:34 2014 -0400 Modifying the Symmetric rotamer set functions to enable symmetric pose that contain peptoids Peptoids use a different orient_on_to_residue function to properly align the first side chain atom. This commit updates the symmetry code to call the alternate function when the targe tresidue is a peptoid backbone. Unit test status: All pass except the two DdgFilter test Integration test status: All pass except app_exception_handling and buried_unsat_kinemage commit 7c6cd5ff8570f054dc6a67724b08de92deebc894 Date: Fri Jun 27 11:15:44 2014 -0700 Added an option to HSSTriplet filter which ignores the direction of the strands and helix (default false). If set, the helix-sheet angle is normalized to a value between -90 and 90. HSS Triplets that score 180 degrees without this flag set are parallel to the sheet but pointing the wrong N->C direction, creating confusion among users who don't expect the filter to fail in that case. If this flag is set, these parallel sheet-helix triplets will pass the filter. commit 41fa52bdf0e5ff5c9885f9519a4a71d4d623df6f Date: Fri Jun 27 14:42:48 2014 -0400 More progress with the Ramachandran potential Fixing a bug in how entries in the CDF array are drawn if the CDF is meant to hold the exclusive cumulative sum. I shoudn't pick the first entry with a given value, but instead the last entry with a given value. commit 9fa1256bd581e4ce0623e0d3ca429ee4f1fbdccc Date: Fri Jun 27 13:09:06 2014 -0400 Progress in testing the Ramachandran potential commit 7776ee3cf0151c7c6e0b8a34c855f9aae448ca7d Date: Fri Jun 27 10:51:33 2014 -0500 Add ScriptCM to Mover Factory system. commit 0ba99f15f4e4dacc9d8bad096fe7b1d9e8f2d562 Date: Fri Jun 27 09:36:35 2014 -0400 Getting rid of a penalties class that should have not been present due to merging commit d528becf0df786b559e4b7dca498fc2f97d82c8b Date: Fri Jun 27 09:30:34 2014 -0400 Adding some quick notes into the params files and conformation commit 76bff8bed10d3b5fb185b06edd24b7b6a771fdec Date: Thu Jun 26 22:42:32 2014 -0700 Removing ORNX.params from the database. This was a residue type that I started to add but never got around to testing; I hadn't meant for it to make its way into master quite yet. No integration or unit test changes expected. commit ff30a2c40909b87cc33c596cca8140ad0a51f3d8 Merge: 7ff2ab4 04ec940 Date: Thu Jun 26 18:34:59 2014 -0400 Merging mpframework_devel into here commit 04ec940daa960e15d0d27695d2822274e93bab0a Date: Thu Jun 26 18:33:46 2014 -0400 fixing library level build commit 7ff2ab4b25075e3eaccf62553278767e7696ca9b Date: Thu Jun 26 18:13:16 2014 -0400 mpdocking: changed back to dock_mcm_protocol commit 603053ce6d0741070cd5ace1a6a0f1fbb6a03c09 Date: Thu Jun 26 17:32:30 2014 -0400 fix syntax commit bc535ebbf30cfb65f27eec77d633cd8a801b4c2b Date: Thu Jun 26 17:28:29 2014 -0400 add parse_my_tag to the main GraftMovers, add has_branch function to RS util, add function to load movemaps into the datamap, then call separately from the parse_movemap functions commit 41c8b8368ab7c720f080d1a89c740a41db3992d2 Date: Thu Jun 26 17:25:45 2014 -0400 Adding a unit tests for the CDF in the Ramachandran class, and providing read access to data of the Ramachandran class in order to make sure that the CDF is being calculated correctly. commit 75cdccb6a2f3b05000eaa3064ce8f69623f1fac0 Date: Thu Jun 26 14:50:37 2014 -0500 Modify MinMover to implement the MoveMapMover interface. commit a6e9a90053c5ec6df237ce1bea398dd53b28674a Date: Thu Jun 26 14:47:49 2014 -0500 Reenable warnings-as-errors in scons. Also fix warnings-as-errors issues with gcc and clang under linux. Hopefully the test server doesn't pick up any additional ones. commit 44a69d861f4926e8b99e94f8c3bc5b06807ccd63 Date: Thu Jun 26 15:46:38 2014 -0400 binary search over the CDF now works commit d5ecc25980fc62c8c8a0e7daf79eed7c3ac90d67 Date: Thu Jun 26 14:41:16 2014 -0500 Add constructors to MoveMapMover to allow easier subclassing. commit c3b0e1842a1048d6418cf1a1265de0449611890e Merge: d96d03b a790a63 Date: Thu Jun 26 15:27:45 2014 -0400 Pulling from mpframework_devel commit d96d03beb12d0e4df4ac88a79764a8c3e54bf4e4 Date: Thu Jun 26 15:25:22 2014 -0400 put scores for MC simulation into -mc:log_scores_in_MC flag; should reverse 83 integration test changes in commit 5d88106ee718c5b0; the 2 scoring changes in this commit are fine. commit 885811348e0cfcd92474c1bf445952bd2ea3924e Date: Thu Jun 26 15:02:40 2014 -0400 debugging commit 06289ea3a2c0d6e53d31d7992e37863e72f86f2c Date: Thu Jun 26 14:00:59 2014 -0500 change option name in TorsionClaim tag parsing. commit 39a24d8d8a3159d967a2085a9e864a485991101d Date: Thu Jun 26 14:44:57 2014 -0400 added pilot app spanfile_from_pdb commit 543ed882e887f106d3409d395e786c1428c4ebe4 Date: Thu Jun 26 11:57:10 2014 -0400 OK. The refactoring now compiles. commit a790a63464897ebcacbdf9ccde383ccd6dd71151 Date: Thu Jun 26 11:02:19 2014 -0400 Adjusting spacing. commit ab61ddee0a3648715fd27f1ee41012be21e7c98b Date: Thu Jun 26 10:05:55 2014 -0400 Separating out the ppo_torsion_bin into its own files; adding more functions for working with ppo_torsion_bins commit 5f30fdb2d92e5d0cd4b161140ea6e07e32aa1005 Date: Thu Jun 26 09:42:50 2014 -0400 fixed bug to display thickness correctly, adjusted MEM and EMB params files for that commit a11ace3d79ca3579f92d3ea015895fbea4635283 Date: Thu Jun 26 09:00:58 2014 -0400 progress in refactoring the remainder of the loops code that used strings to describe the torsion bins -- replacing these strings with utility::vector0< core::conformation::ppo_torsion_bin > commit 91cb4665dbd0bee7a5bc32cf68d3be13ea794268 Merge: f992045 faa9455 Date: Wed Jun 25 23:10:50 2014 -0700 Merging vmullig/cycpep into master. This tweaks GeneralizedKIC a bit, as well as fixing a problem in setting the position of atoms dependent on non-polymer connections on PDB import. (This might fix the problem with the UBQ_E2_thioester_extra_bodies and UBQ_E2_thioester_two_ubiquitins integration tests on the test server -- I'm not sure. I haven't been able to reproduce that failure.) Unit test status: All pass except the two that have been failing (protocols:DdgFilter:test_filter_parsing and protocols:DdgFilter:test_use_filter) Integration test status: No changed tests; two were already failing (app_exception_handling and buried_unsat_kinemage). As mentioned, the UBQ tests that fail on the test server don't fail when I run the integration tests. Changes to be committed: (use "git reset HEAD ..." to unstage) modified: source/src/core/chemical/AtomICoor.cc modified: source/src/core/chemical/AtomICoor.hh modified: source/src/core/conformation/Conformation.cc modified: source/src/protocols/generalized_kinematic_closure/GeneralizedKIC.cc modified: source/src/protocols/generalized_kinematic_closure/util.cc commit 17c4888bba07ba68a19c00899fadf4f978e3242e Date: Thu Jun 26 01:14:48 2014 -0400 added mpdocking files commit 3b8c58b8b0189c15d3fc7dad2c31cec869c16727 Date: Thu Jun 26 01:13:27 2014 -0400 added regular docking protocol to mpdocking commit d3a76bbb51768fdf803caa96a0d0c22848db18df Date: Wed Jun 25 23:33:56 2014 -0400 forgot to add wts files, adding them now commit ee5e31dbd00e31038cd94736fdb03353d9c9299a Date: Wed Jun 25 23:33:11 2014 -0400 setup docking weights for centroid and FA, just quick and dirty, needs to be benchmarked commit 2a978ea0e6295c20470f0e223d3df143d654cefc Date: Wed Jun 25 22:48:17 2014 -0400 MPdocking: took code out of protocol into pilot app for faster compiling commit faa945503291e794c88e7a7abef5717a4f851449 Merge: 7d93244 f992045 Date: Wed Jun 25 19:39:53 2014 -0700 Merging master into vmullig/cycpep in preparation for integration testing and the reverse merge. commit 5d88106ee718c5b0aab6e049fc65bcc84e8e71d3 Date: Wed Jun 25 22:10:01 2014 -0400 fixed thickness in params files, both for centroid and FA commit 7d93244cb2392cd07c0caeb474f5589a1190dd69 Date: Wed Jun 25 18:51:45 2014 -0700 Turning off bettercluster in pilot_apps.src.settings.all in preparation for merge with master. commit 1327e95b394f6a315b25f672344bc3fa19755846 Date: Wed Jun 25 21:47:50 2014 -0400 Massive refactoring of the taboo perturbers eliminating just a ton of duplicated code. commit e5043e5998e158ff7bcd543bf53c397ac70bfa29 Date: Wed Jun 25 18:28:07 2014 -0700 Trying to fix a problem with loading PDB files containing residues with atoms that must be rebuilt which have connection-dependent stubs. commit 7c9d51ce1b5b67cf5fe9eadc66a6a837a403ec0b Merge: 9266d88 2f42fb8 Date: Wed Jun 25 21:27:58 2014 -0400 Updated SpanningTopology Also added MPDocking, runs, but needs fixing commit 2f42fb8efe5fe01a4bd8cae04db4b238f386c908 Date: Wed Jun 25 21:05:27 2014 -0400 MPDocking runs, but needs fixes commit edaf14a542322a3cd9e242b48ac00a124a182729 Date: Wed Jun 25 19:08:56 2014 -0400 compiled commit b43b92b7421a57d2302cbcef5911c03bf54df5d3 Date: Wed Jun 25 15:00:35 2014 -0400 First stab refactor of the KinematicPerturber and the KinematicMover so that they aren't using strings but are instead using arrays of core::conformation::ppo_torsion_bins commit f99204541fe1636f5bf42b25d8c3300cbef1a341 Merge: 630ab01 7733d83 Date: Wed Jun 25 10:59:34 2014 -0500 Add atom mapping facility to PDB file loading. -- Gemetric Remapping. The core of this commit is to allow Rosetta to remap atom names when loading PDB files, specifically in the case where you may have renamed the atoms. (Main use case was for sdf file loading, which don't have atom names.) For example, if you have a ligand params file with one set of atom names, but want to use it to load a PDB with different atom names for that residue, you can do that in one of three ways: * Call ResidueType::remap_pdb_atom_names( true ) in the code * Add the line "REMAP_PDB_ATOM_NAMES" to your params file. * Add the commandline flag "-remap_pdb_atom_names_for LG1 LG2", specifying one or more three letter names of the residues you wish to remap Then when that ResidueType is used in PDB loading, remapping will happen based on the percieved geometry of the input residue, matching up the elements and bonding as best as it can between what's in the ResidueType and the percieved geometry in the PDB residue. Each input residue of the same name3 can get different name mappings, although the name remapping occurs after the detection of the best ResidueType, so geometric remapping will not help with distinguishing between two residues with the same name3. -- Atom Aliases As part of the name remapping, it was simple to add atom aliases. That is, params file can now have an ATOM_ALIAS line, which tells Rosetta about alternative names for atoms. (Again, this happens post ResidueType decision.) For example, we could now add the line: ATOM_ALIAS 1HH1 HH11 To the ARG.params file to tell Rosetta that HH11 is a valid alternative name for the hydrogen it normally calls 1HH1, allowing direct coordinate loading for that atom from PDB NMR structures. Note that while I've added the facility to Rosetta, I haven't yet added any ATOM_ALIAS lines to the database, as I was seeing conflicting information about how to map PDB-typical atom names to Rosetta atom names. Specifically, depending on source I saw different chiralities for atoms. (e.g. do the ALA methyl protons HB1->HB2->HB3 go clockwise or counter-clockwise when viewed along the CA->CB vector?). -- Bug Fixes In PDB file loading there were issues with atom recognition. Specifically, coordinate assignment went via whitespace-stripped name, whereas missing atom detection went by whitespace-preserved name. This causes Rosetta to rebuild things like "OXT " atoms, which occur in a number of integration tests (the expected name is " OXT"). This commit now attempts to use the whitespace stripped version for coordinate assigment, and then bases the missing atom detection on which atoms had coordinates assigned. (This difference accounts for the bulk of the test changes.) Also, there was a chain-termini adjustment finalization which updated the residue type with the new terminius variants, but didn't attempt to assign coordinates to new atoms if there were (otherwise) ignored atoms with the appropriate names (e.g. " OXT"). This resulted in atoms that didn't get coordinates assigned, but that weren't necessarily annotated as missing atoms. This commit attempts to detect that somewhat, and assign coordinates if the atom is present. (But not as well as if the termini is detected originally.) -- Integration test changes expected: Extra Trace-level output ---------------- FAIL fold_and_dock Whitespace stripping issues on atom name loading -------------- FAIL contactMap FAIL database_jd2_compact_io FAIL grid_scores_features FAIL kinemage_grid_output FAIL ligand_database_io FAIL ligand_dock_7cpa FAIL ligand_dock_grid FAIL ligand_dock_script FAIL ligand_water_docking FAIL residue_data_resource FAIL sdf_reader FAIL startfrom_file FAIL write_mol_file Termini fixup coordinate related changes ---------------- FAIL zinc_homodimer_design Also silently affects: AnchorFinder motif_extraction rs_flexbbmoves zinc_heterodimer Cosmetic tracer changes ----------------------- FAIL AnchorFinder FAIL gen_lig_grids FAIL jd2test commit 7733d83fe7c7bab75baa34ee269288ad84dc5482 Date: Wed Jun 25 10:57:39 2014 -0500 Add atom name remapping annotation to sdf-loaded atoms. commit d3d3d8e7419f582db82fad040503b1e74126c234 Date: Wed Jun 25 10:34:06 2014 -0400 Now both Ramachandran and Ramachandran2B implement the low-memory, CDF-based methods for drawing phi/psi bins randomly, biased by their probability. I still need to remove the use of strings from the Taboo kinematic perturber. *sigh* commit a5d01784838abf7e60a66ec64a2743052574de75 Date: Tue Jun 24 21:42:30 2014 -0700 Removing duplicate function definition in Conformation.cc commit 630ab01e3eb6f910a1063ac3d85ea5eabd45215b Date: Tue Jun 24 20:33:34 2014 -0700 Removing debug output from DeclareBond.cc. commit 5a5da912c9091b1ee31be2c2d378c498e26db091 Merge: 0aa4707 14f7ffb Date: Tue Jun 24 20:30:48 2014 -0700 Merging master into vmullig/cycpep to get latest fixes to core (removing i+1/i-1 assumption about polymer residues). commit 14f7ffb27bbb224f37be03e748352cc2e3c1ffc4 Merge: 8ac66a34 ce123ca Date: Tue Jun 24 19:02:42 2014 -0700 Merging vmullig/ncaas into master. This changes some core functionality in a way that should reproduce the old functionality exactly, except in cases where terminal residues have backbone-backbone or backbone-sidechain connections (e.g. cyclic peptides). I'm trying to take out some of the instances of Rosetta assuming that each residue is connected to the i+1 and i-1 residues, so that terminal residues with connections will score properly. Unit tests: All pass Integration tests: 2 are failing to run in the master branch already (app_exception_handling, buried_unsat_kinemage) 2 expected changes; 13 others that seem to be random, small changes: UBQ_Gp_LYX-Cterm and UBQ_EZ_thioester: expected changes since the C-terminal glycine that's bonded to a sidechain should now score properly with p_aa_pp and omega. Small random changes: remodel_disulfides inverse_rotamer_remodel antibody_H3 relax_w_allatom_cst antibody_H3_legacy antibody_legacy -- NOTE: This one is producing bizarre output, both before and after this change (see the output PDB file). KIC_vicinity hotspot_graft rs_flexbbmoves antibody_designer antibody_graft jrelax Additional notes: --This change updates the way that residue backbone torsions are computed in Conformation.cc. Instead of assuming that each residue is connected to the i-1 residue at its lower connection, and the i+1 residue at its upper connection, Rosetta now checks what the residue is actually connected to and uses that for calculation of mainchain torsions. --This should not change torsion calculation or scoring in any usually-encountered case. --This should not affect the CTERM_CONNECT or NTERM_CONNECT types that were added when the peptoids branch was merged into master, recently. Those are still handled as special cases. --If anyone notices any aberrant functionality as a result of this change, please e-mail me (vmullig@uw.edu). I've tried to be as thorough in my testing as possible, but with a deep core change, it's always possible that something was broken. commit ce123caa20b33051ab71799b7eeebafdc86a6d74 Date: Tue Jun 24 18:56:54 2014 -0700 Taking stdio.h back out of Conformation. (I was just using it for debug output, temporarily.) commit b0ec683df639ae016c703711d2507ee903b43c6b Date: Tue Jun 24 21:16:10 2014 -0400 work on simple movers commit ea046423e1178235fadfab3b0f98b3f57b19c12c Date: Tue Jun 24 17:50:48 2014 -0500 Termini change name fixup commit 8445d389fe8b3b929634886b2a20ff80ca475542 Date: Tue Jun 24 17:17:47 2014 -0400 added Pymol observer to MPDocking commit 6dca3f30df5739e132727f89dac963b50abf6a32 Date: Tue Jun 24 17:05:41 2014 -0400 added MPDocking protocol, compiles, not tested commit 77a2ea36ed8b83a6fc717e38215dd3df512430fc Date: Tue Jun 24 14:03:51 2014 -0700 updates to rna_features to capture DMS data. commit 8ac66a34b8a8b5c0155d3170f41bb2f21d79991d Merge: ee2354b 1b58093 Date: Tue Jun 24 16:03:12 2014 -0500 Fix raw pointer use in core::util::add_cutpoint_variants() Meilerlab Powercoding with Alyssa Lokits This addresses the core of bug 0000336 - removing the raw pointer use in core::util::add_cutpoint_variants() and remove_cutpoint_variants(). It also starts in on the comments made by Justin Porter, replacing core::util::add_cutpoint_variants() use with core::util::pose::correctly_add_cutpoint_variants() Attempts to fold in some of the other add_cutpoints/add_chainbreaks were made, but we ran out of time prior to debugging them. No test changes (aside from currently failing ones) expected. commit cd52d7753e913a0c29c8325091f88910a076432c Date: Tue Jun 24 15:01:57 2014 -0500 NamedAtomID_Map for assigned coordinates, to account for terminus patching. commit a76ec18a0fd6221d7aa1406c55d6ce69a7e0bdec Date: Tue Jun 24 15:43:31 2014 -0400 Progress in reimplementing the Rama2B table-shrinking code. commit ee2354bfc04423e07472aa3a0155e7e8172cbe08 Date: Tue Jun 24 15:36:45 2014 -0400 commit 1b5809369726cb3dd7b6629b68df4dfb87e1c0ad Date: Tue Jun 24 14:24:54 2014 -0500 Remove commented out items. commit 94f6d8c616557ef111bec264b2b022246a8aaa45 Merge: a064e86 c815293 Date: Tue Jun 24 14:21:16 2014 -0500 Merge remote-tracking branch 'origin/master' into cutpointfix2 commit c8152937db8610d4f1755fdd21d9946201cf4309 Date: Tue Jun 24 14:40:20 2014 -0400 PyRosetta. Fixing monolith build imports order. commit 01c97092352bb7408dc21056d55113d250aec5fe Merge: 8047629 5a3bcf7 Date: Tue Jun 24 13:55:29 2014 -0400 fixed merge conflict commit 5a4bf0e914a55fdd72a161cd9aaa36b5d1f78508 Date: Tue Jun 24 13:38:27 2014 -0400 Extrapoliate Ser/Thr HBond parameters to H2O HBond Parameters Make HBonds involving water compatable with Talaris2013 by extrapolating the parameters derived from Ser/Thr to HBonds involving H2O. Accept utracets to resolve change with HBondsTest:test_hbond_compute_energy2 Expected integration test differences relative to d45953f: app_exception_handling buried_unsat_kinemage -> broken in trunk dna_interface_design geometric_solvation ligand_dock_script readin_dna_rna_protein sdf_reader swm_protein_move_inside_coiledcoil_by_bond commit 821a429205ffe98dbb24f1433073947c57d659ae Date: Mon Jun 23 23:48:29 2014 -0400 add NetBeans IDE template class files. commit 91ee33139fd1ec24e4a2570fdbf0544bafe2c9a5 Date: Mon Jun 23 23:02:29 2014 -0400 change name of file commit cbf7b870b7386d1ec246d45a7784e7c4df639b8b Date: Mon Jun 23 18:11:35 2014 -0700 fixing swm to not pack terminal 5' phosphate at root residue. its because the phosphate holds the root atom, and its not easy to move the root atom elsewhere. eventually we'll fix this by including a virtual residue as another root, and have a jump into the RNA root residue. commit a9312e5bb6189844a78aff8fc163a2fefd621fcf Merge: b739ef4 d9f84f8 Date: Mon Jun 23 20:26:09 2014 -0400 Merging in master commit 9266d88d6a2ad57aeb68c4d4991b2203671e134e Date: Mon Jun 23 20:15:29 2014 -0400 Bug fix patched from membrane perturb and score branch for old update of embedding cordinates upon scoring. Taking this out - should fix crazy coordinate errors commit 8047629d0d6da8bc42193b509402a617b39f74b6 Date: Mon Jun 23 19:33:58 2014 -0400 Added length check for spanfile Compiles, took out SpanfileLoader stuff needs to be updated so it takes cmd line input and not resource manager commit ae0ca4da072f3f7f6360c61b177faaa765bbd44c Date: Mon Jun 23 16:25:51 2014 -0700 I was overzealous in last merge of master with this branch. Restoring some code that I had deleted for cyclic peptides with the cyclic variant types. commit 7f546254bec2d1d7f86d180cb697cecdc7439d1c Merge: 8bae369 a776c06 Date: Mon Jun 23 16:20:58 2014 -0700 Merge branch 'rpache/KIC_with_fragments' of github.com:RosettaCommons/main into rpache/KIC_with_fragments commit 8bae36914286fcef42f4c623c0bd477647a0551a Date: Mon Jun 23 15:42:39 2014 -0700 Make it easier to use fragments for loop building. commit 7e3c6137379ea7276a096447c9cd514f8ff411f0 Date: Mon Jun 23 16:45:47 2014 -0400 Fixed flags to match single spanfile Compiles, fingerprint energies are the same except membrane center has moved Old location is 0, 0, 0, new location is different Thickness is still off (is on y-axis instead of z-axis) commit aeb805e976c128ae002f5a4d9afca4c03d5354b6 Date: Mon Jun 23 16:27:15 2014 -0400 Shortened reading in of spanfiles in AddMembraneMover In AddMembraneMover: replace all arrays of spanfiles with a single spanfile commit 2e43b3c4dbf70b2cb597c500328c3d39a38af950 Date: Mon Jun 23 15:53:07 2014 -0400 removing chain dependence in SpanningTopology doesn't compile yet. We need to propagates changes into AddMembraneMover commit 236b68e32284cb3240aaa97903f5d20ba1f43d4f Date: Mon Jun 23 13:12:07 2014 -0700 Make the minimizer settings easier to control. Amelie pointed out that legacy KIC uses different minimizer settings in centroid and fullatom mode. This commit adds code to copy that behavior in refactored KIC. commit 5a3bcf703efe97a120ea3b79b31dd4ccff65feeb Date: Mon Jun 23 15:53:07 2014 -0400 removing chain dependence in SpanningTopology; doesn't compile; propagates changes into AddMembraneMover commit d9f84f8b723e8028e70180315987e2c93ef65533 Merge: a34d684 045a855 Date: Sat Jun 21 11:25:43 2014 -0500 Fix CA_rmsd warning message Meiler lab Powercoding with Alyssa Lokits Make it such that CA_rmsd(pose1,pose2) doesn't print a warning message for missing CA atom (e.g. ligand residues or virtual residues). Explicit range CA_rmsd will still print a warning. Also fix/remove bb_rmsd_*() functions, which weren't actually using all their parameters. Fixes bug 0000337 Integration test changes expected as warnings are no longer printed: membrane_relax relax_w_allatom_cst mr_protocols hybridization density_refine metalloprotein_abrelax density_refine_symm readin_dna_rna_protein commit a34d68470e53a56e60571ed931a79c68fd5044fe Merge: c82dbf4 5eec14d Date: Mon Jun 23 14:37:19 2014 -0500 Add a cxx_ver option to test/run.py Also remove the default for cxx, so hopefully Mac users will now be able to better autodetect that they're using clang. This fixes bug 0000335 No test changes expected commit 5eec14d9669611f4f70e49dc5c8e6cfa8c70f28f Date: Mon Jun 23 10:23:15 2014 -0700 Add some API docs on the nb_list minimizer option. Specifically, I added doxygen comments to certain methods of MinMover and MinimizerOptions. I wrote these comments because I just had to read a bunch of code to figure out what nb_list did. I'm not an expert on the minimizer, so these comments may not be perfectly complete or accurate. But I don't think they're totally off-the-mark. commit f39d0cc5a897a1731089d0eba4310fa0da01477d Date: Mon Jun 23 11:46:32 2014 -0400 resolve merge conflicts, run fingerprints commit ce5b73c2ab370b4fd6ab0fca5b3a8591ca629e34 Merge: 8724870 3e52d93 Date: Mon Jun 23 11:04:12 2014 -0400 resolved merge conflicts commit 87248709d2e4040ecba927d936bb2ffa175b3852 Merge: 54b4234 e435904 Date: Mon Jun 23 10:49:36 2014 -0400 resolve merge conflict commit 51caecff65e4e3cfb19d66c2c4183de09c8fa214 Merge: c63c6d1 2a3c16b Date: Mon Jun 23 13:34:48 2014 +0200 merge master into local commit c63c6d114e1b3c733450ab430ab6e7f635689bae Date: Mon Jun 23 13:28:43 2014 +0200 adding a new RotamerSetOperation and TaskOperation to selectively oversample rotamers that interact well with one or more specified target residues. no test changes expected commit d45953f07f86e57c598d3bf7022cbb56143d3e79 Date: Sun Jun 22 23:39:47 2014 -0400 Fix broken H-Bond polynomials in Talaris2013 ISSUE The AHdis polynomials for Trp donor -> Gln/Asn acceptor H20 donor -> protein backbone H-bonds in the sp2_elec_params HBond parameter set (used by Talaris2013) were not being evaluated because the xmax was set to -1234. RESOLUTION To resolve the issue, this commit 1) extends the hbpoly_ahdist_aASN_dTRP_9gt3_hesmooth_min1p6 up by 2% and sets the xmin/xmax appropriately 2) replaces the polynomial poly_AHdist_ah_dOH_1 (used by hbdon_H2O,hbacc_PBA bonds) with hbpoly_ahdist_aGLY_dSER_9gt3_hesmooth_min1p6 (used by hbdon_HXL,hbacc_PBA bonds). This new polynomial is compatable with Talaris2013 where the old one is not. 3) adds consistency checks to numeric::Polynomial_1D constructors and error handling to HBondDatabase::initialize_HBPoly1D() 4) adds unit tests polynomial.cxxtest.hh testing the consistency check code 5) accepts all unit test utracers RAMIFICATIONS Hydrogen bonds between Trp donor -> Gln/Asn acceptor H2O donor -> protein backbone have been completely ignored in Talaris2013(!). This commit allows these interactions to be scored. Note, the HOH residue type is by default not recognized, so HBonds involving water won't appear unless you ask for them. ANTICIPATED TEST FAILURES No unit test failures Note, the following utracers have changed/been updated: Modified source/test/core/scoring/hbonds/hbond_compute_energy.u Modified source/test/core/scoring/hbonds/read_polynomials_from_database.u -> These are changes are clear Modified source/test/protocols/docking/DockingProtocolFunctions.u Modified source/test/core/pack/RotamerTrials.u Modified source/test/core/pack/SymmetricRotamerTrials.u -> These are presumably because new HBonds are being evaluated Modified source/test/core/scoring/fa_atr.data Modified source/test/core/scoring/fa_intra_atr.data Modified source/test/core/scoring/fa_intra_rep.data Modified source/test/core/scoring/fa_rep.data Modified source/test/core/scoring/symmetry/fa_atr.data Modified source/test/core/scoring/symmetry/fa_intra_atr.data Modified source/test/core/scoring/symmetry/fa_intra_rep.data Modified source/test/core/scoring/symmetry/fa_rep.data -> These shouldn't have changed, but by inspection they look to be due to platform specific rounding Integration test failures with $ uname -a Linux contador 3.2.0-60-generic #91-Ubuntu SMP Wed Feb 19 03:54:44 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $ clang --version Ubuntu clang version 3.0-6ubuntu3 (tags/RELEASE_30/final) (based on LLVM 3.0) Target: x86_64-pc-linux-gnu Thread model: posix relative to revision 2a3c16b ///////////////////////// app_exception_handling buried_unsat_kinemage -> broken in master docking_ensemble enzdes geometric_solvation hotspot_hashing kinematic_looprelax ligand_water_docking mpi_multistate_design mr_protocols pocket_relax readin_dna_rna_protein swa_protein_prepack swm_protein_move_inside_helix_by_bond UBQ_E2_thioester_extra_bodies -> After inspection, these all look like trajectory changes NOTES Thanks Phil Bradley for the bug report. commit 68d4e2c54e132df8fbc427a8d3e8e8dde6a509ba Date: Sun Jun 22 19:38:12 2014 -0700 Fix a closure bug in refactored KIC. This commit fixes a bug in KIC that was causing chain breaks for perturbers that set either omega or a bond angle for the first residue in the loop. These dofs are basically ignored by KIC because they are outside the pivots, but they were still being improperly applied to the pose. This bug was only noticeable when the IdealizePerturber was being used, because no other perturber set omegas or bond angles. commit 2a3c16b32ed952da9074dd35da9a6e57dde7856f Date: Sun Jun 22 13:39:42 2014 -0400 Add support for passing additional arguments to profile tests commit ceafa67369e078c9113c344f4e2552f1aae904ff Date: Sun Jun 22 13:38:59 2014 -0400 Add relax_native profile test This test runs relax on a set of (35 suggested) structures five times each. It is used in the (O'Meara et al. H-Bond/Electrostaics paper). commit a064e868a8465931d7af0b24bcfbf51699f5ffd0 Date: Sat Jun 21 15:05:57 2014 -0500 correctly_add_cutpoint_variants(Pose) commit fb15776998862c753d11bbf55e72a30a4228423c Date: Sat Jun 21 14:53:59 2014 -0500 Fix a problem where TorsionClaims would claim their inverse. commit 23c83df26eb056af85a5419ea005aae961148fb3 Date: Sat Jun 21 14:23:49 2014 -0500 Remove pointer in src/core/util/kinematics_util.hh commit 3e52d93b3c5959efd23e421083d2c49c1d95a304 Date: Sat Jun 21 15:07:31 2014 -0400 Updating membrane framework - adding rosetta scripts hooks to all movers and updated documentation dox throughout. Vector parameters still not working in rscripts, but will ask for help commit fff27760f272f348560fb6aa15f547ec48e59249 Date: Sat Jun 21 14:49:10 2014 -0400 Adding all 4 movers now hooked into Rosetta scripts commit 191d19b523b51ac32cf12b2cae0f01c33720e4fa Date: Sat Jun 21 14:39:25 2014 -0400 Adding rosetta scripts hooks to initial membrane position mover commit 27a3cdd1e2154fd71319d4e9ad3f6ed9f5d286ae Date: Sat Jun 21 14:35:27 2014 -0400 Adding rosetta scripts hooks in add emmbrane mover but no parse my tag yet because of vectors commit 61cd28f1d1013d7bb0a24b56761a66b02904bfea Date: Sat Jun 21 14:27:54 2014 -0400 Adding mover creator headers for add membrane mover and initial membrane mover position commit 5dd800b8fd6af545c6aa5b385eab23ff197ba01f Date: Sat Jun 21 13:48:47 2014 -0400 replacing calles to embeddingMover with calles to InitializeMembranePosotionmover commit 5f16ce7e6de5bda55e13c6e1aebd68242ab13ed5 Date: Sat Jun 21 13:47:30 2014 -0400 Updating documentation in conformation and replacing calls to update_embedding with calls to update_membrane_position commit 2b3ceab5f547af8c1762f3251c78841ccc35bd8a Date: Sat Jun 21 13:19:20 2014 -0400 Updating doxygen in membrane info object and adding required assignemnt operator commit 6f3416c842048d2ae0c6b439bce3e4f337c72563 Date: Sat Jun 21 12:57:32 2014 -0400 Renaming embedding mover to initial membrane position mover - will eventually take sequence and structure based but for now just structure - also adding docuemntation to this mover and updating it in the build settings. I have not yet fixed upstream changes - will fix when I compile apps commit ade097ccf8ad5de888f323f0cf128e4d16d0d01a Date: Sat Jun 21 12:36:53 2014 -0400 Updating doxygen tags in AddMembraneMover commit 045a85505e09ada9efcb5ee5da1396b372ab1cdc Date: Sat Jun 21 11:25:43 2014 -0500 Fix CA_rmsd warning message Meiler lab Powercoding with Alyssa Lokits Make it such that CA_rmsd(pose1,pose2) doesn't print a warning message for missing CA atom (e.g. ligand residues or virtual residues). Explicit range CA_rmsd will still print a warning. Also fix/remove bb_rmsd_*() functions, which weren't actually using all their parameters. Fixes bug 0000337 Integration test changes expected as warnings are no longer printed: membrane_relax relax_w_allatom_cst mr_protocols hybridization density_refine metalloprotein_abrelax density_refine_symm readin_dna_rna_protein commit 2fe0eafce356a753eff717e990b7d1b62283b6b5 Date: Sat Jun 21 09:46:21 2014 -0500 Better handling of the output differences issues. commit 972655fd04f0543ec57f05b444b93c860fce01a1 Date: Fri Jun 20 18:05:51 2014 -0500 Clean up source/ide/ directory from old xcode items The new way of doing xcode is in source/xcode/ If you were still using the old xcode setup, see https://wiki.rosettacommons.org/index.php/Tools:XCode for details on the new way, or email the developers list for help. commit b22819ea688ce988c58f7af3c1976bc00c7aca54 Date: Fri Jun 20 18:04:14 2014 -0500 Fix warnings in BuriedUnsatisfiedPolarsCalculator2 commit 146372f64acbe1b583df9a1f89339a1dcb15823c Date: Fri Jun 20 18:31:25 2014 -0400 Merging membrane translation rotation into uniform mem mover, membrane visualization mover, and applications for executing these operations plus their respective cmd line options into mpframework-devel commit 780d1433b38e31aac804bff62d34299941032b11 Merge: 2f21214 83bb025 Date: Fri Jun 20 16:56:57 2014 -0500 merge commit 9c9bbae9cf686308918fd4eaa390eb60185fbb38 Date: Fri Jun 20 17:28:48 2014 -0400 Beginning the refactoring to bring down the memory use for the Rama2B and Rama sampling done by next-generation KIC. commit 5f19fbd7c7a8dd49c6f94b407624b4d664936044 Merge: 2a3b3c5 ea19c10 Date: Fri Jun 20 16:59:34 2014 -0400 Merging in the gcc fix I made this morning on crumb into ninja's remote commit 2a3b3c50c62764a6d3dc80aca7d11667c913205b Merge: fc1b5b0 a11ade7 Date: Fri Jun 20 16:56:23 2014 -0400 Resolving merge conflicts in my pilot app build commit a11ade77e70c5a62a8fe10024d9a8083028f5ffa Date: Fri Jun 20 16:42:13 2014 -0400 Fixing crazy thickness problem commit dc6dd1a24629564a31d2d63ae964e66766b580c2 Date: Fri Jun 20 16:32:17 2014 -0400 Working transform and visualize pipeline commit 90b986120caa79ec2f7267bc3cd33338dc69a14b Date: Fri Jun 20 15:29:23 2014 -0400 Fixing residue labeling order in membrane params file commit b14b6602b93458d24860454e2e067774035b7f44 Date: Fri Jun 20 15:25:15 2014 -0400 Adding output tracers commit 54b4234bf6ed0fac1450237a2265eb7255c3fc5e Date: Fri Jun 20 15:16:14 2014 -0400 SpanningTopology: added spanning method commit 31957a5f68f6d62d7bf52bd9a07a28c01168d542 Date: Fri Jun 20 14:44:40 2014 -0400 SpanningTopology correct commit 6a5a9af3dbdb6932b8db246cbc5950f1f2601034 Date: Fri Jun 20 14:31:30 2014 -0400 Updating membrane thicnkess method in conformation to print the correct thicnkess and set correctly in the virtual residue commit 7b257f498273cfa320b667828d56498a968e8127 Date: Fri Jun 20 14:30:32 2014 -0400 Updating membrane thicnkess method in conformation to print the correct thicnkess and set correctly in the virtual residue commit 92594661baba74587b99577ca802df309c87e6bf Date: Fri Jun 20 14:12:36 2014 -0400 Adding more documentation to transform into membrane mover commit 83bb025090925c0ebcaf07c73ed8af369f94bd4a Date: Fri Jun 20 13:08:51 2014 -0500 Fix termini naming issues. commit dcee8c467184ae953d4c353c5e234bc5746636ec Date: Fri Jun 20 14:02:25 2014 -0400 Updating rosetta scripts and full hooks in transform into membrane mover - will hook into registrators later this afternoon commit 2f21214d87ffc5192be98bef0fbb573ddd375367 Date: Fri Jun 20 13:47:12 2014 -0400 [update of SandwichFeatures] - much better (accurate and catching more) 'fnIII' topology identification - should not change any integration tests other than (expected) features and features_database_schema (if any) commit f60bd26506e216452db9ff72491c835e34cd3391 Date: Fri Jun 20 13:04:45 2014 -0400 Pulling direct rosetta scripts hooks out for now - will reimplement with the rest of the movers commit 74de6a6242e04cf78939e0bcec87b3033f4cc3ac Date: Fri Jun 20 12:32:50 2014 -0400 Implementing rosetta scripts and full mover requirements in transform into membrane and visualize membrane mover creators commit 12e0399450683a29d32e29f5af181f86154bd40f Date: Fri Jun 20 12:12:18 2014 -0400 Fixing quick rscripts plug in compiler error commit 1a5b11b32ecd383cefd2d8b9ef1bf215c52814cc Date: Fri Jun 20 08:45:33 2014 -0700 removing undefined function to restore Pyrosetta build. commit f8c1cc92fb8bf6e005025841b63c18e8b6a82dfc Date: Fri Jun 20 11:34:45 2014 -0400 implementing the remainder of rosetta scripts tags commit ee0e0085abffe3878a4066afdcfd8cac0d340e9c Date: Fri Jun 20 10:53:37 2014 -0400 Continuing to implement rosetta scripts hook for visualize membrane mover and adding 2 new command line options and an option group to the membrane new keys for visualize:spacing and visualize:width commit bdbd9ca4fd042a51ce5fc59648b2c3e7b2a4c88c Date: Fri Jun 20 10:43:41 2014 -0400 Implementing mover creator header for visualize membrane mover and fleshing out the rest of the required mvoer methods commit 1ad8d710673aa9128803dadc5d70ee566fd665fe Date: Fri Jun 20 10:06:40 2014 -0400 work on simple movers, add comments to AlignChainMover and AddJobMover commit ea19c1065b1a85ee4349ddf87a97c7688b7ab4c7 Date: Fri Jun 20 09:25:57 2014 -0400 Fixing bug introduced in residue energies breakdown application for membrane proteins - this fix should fix the linux gcc compile commit e4359041dc658f5da4a59ce84b7d23a7354b70e2 Date: Fri Jun 20 08:29:53 2014 -0400 Fixing initialization order in julia's refactoring branch commit fec941e9fd22ba22687febb2e6638c035de75801 Merge: 9e6af7d f827cfa Date: Thu Jun 19 23:48:14 2014 -0700 Merging master into vmullig/ncaas to get Rhiju's fix that fixes a unit test. commit 9e6af7d03697cb278fb4deb6b6ef9c11d299c5bf Merge: 450698b b6e0207 Date: Thu Jun 19 21:44:22 2014 -0700 Merging master into vmullig/ncaas for integration tests. commit 450698bf993baf348f749d96c39c97e340dd7de4 Date: Thu Jun 19 20:55:32 2014 -0700 Fixed (?) a bug in recent changes to Residue.cc. commit daa1a7d72e334c42f893412c967e67287e00d871 Date: Thu Jun 19 20:21:21 2014 -0700 Reverting temporary changes to a unit test. commit 53ed390818a5df4217498b30c62185c138b23cc8 Date: Thu Jun 19 20:13:54 2014 -0700 This should fix a major bug in Conformation and Residue: when a residue was replaced with a variant with a different number of connections (e.g. an N-terminal type being removed), the connections within the residue would be updated properly, but the connect_map_ in the residues to which it was connected would not. For example, if residue 1 had an N-terminal type, and residue 2 were attached at that residue's upper connection (which would be connection 1), residue 2's connect_map_[1] would store residue 1, connection id 1 -- and would continue to do so even when the N-terminal type was removed from residue 1, which would cause the connection id in residue 1 to switch to 2. Any code that interrogated residue 2 for the atom in residue 1 to which it was connected would return the nitrogen, rather than the carbonyl carbon. This was masked since most code relied on the assumption that polymer residues were connected at their lower connections to the seqpos-1 residue's upper connection, but that's an assumption that I'm trying to remove. Now, this problem should be fixed. commit 3ea390b4d7a3296c357214057c1c2bd1e5ada75c Date: Thu Jun 19 22:13:11 2014 -0400 Adding jd2 compatibility to visualize membrane app commit 857378016c95096c4655e24a027f9078ba508a22 Date: Thu Jun 19 21:55:28 2014 -0400 Updating pilot apps settings - should work more reasonably now commit 3f07fc30711795899fa1dd5c24755ead5b98ded2 Date: Thu Jun 19 21:48:33 2014 -0400 Updating translate view membrane application which should translate all structures into a uniform and display the membrane planes as virtual residues. Works with jd2 to take a list of PDB files commit 869981a17876b8ee09f2c81e44bce2b18a45bc3e Date: Thu Jun 19 21:41:03 2014 -0400 Adding top level membrane visualize executable to build settings commit fc1b5b04721c6a3fb7a166e309f43263777471ec Merge: 0e3e231 d9bfb8b0 Date: Thu Jun 19 21:14:07 2014 -0400 Merging gcc fixes with mpframework devel local on ninja commit 0e3e231146a38f0b77d6629afa90e3ee15b7b3e0 Date: Thu Jun 19 21:12:34 2014 -0400 Updating scoretypes enum to corectly list cd2b types commit a776c062cf73f4f2dff3605e88b997f988b0386a Date: Thu Jun 19 16:49:12 2014 -0700 removing tracer debug output from ConstantLengthFragSet::overlapping_with_region function; this eliminates the need to mute that tracer to avoid long runtimes due to writing to the terminal; tracer output in the FragmentPerturber class has been adapted to also provide the frame length commit f827cfaa4c4d712bc2a7d8bbc40d0321d7e91419 Date: Thu Jun 19 16:46:05 2014 -0700 fix to unit tests for hbond_type_manager. commit 4908734b19214f40c6e0becd8e282cf04bc0e5b4 Date: Thu Jun 19 16:46:05 2014 -0700 fix to unit tests for hbond_type_manager. commit 2605101766840f95a6b28ca78ead9d8468b66038 Date: Thu Jun 19 19:27:07 2014 -0400 Membrane residue energies app compiles commit 43ebca3e2a6853fc3bf49bef106607dfef04f90d Date: Thu Jun 19 19:10:33 2014 -0400 fingerprint ref folder correct now, still missing the corrected app that prints all the scores commit ad040643d0ba96bae1d8e02dd11f1b76e6032762 Date: Thu Jun 19 16:09:29 2014 -0500 Adjust log printing for remapping. commit 28ffa954e43dac4d469aa7c069795171b6d904f5 Date: Thu Jun 19 16:39:27 2014 -0400 fixed spacing commit 6f426273cca9f0beb0284211c3f474c776f2268a Date: Thu Jun 19 16:33:44 2014 -0400 Adding membrane per-residue and per-atom energies breakdown applicaiton - addapted to take add membrane mover on the pose commit 61b2da19475c89605210865b01ebe2eea964e849 Date: Thu Jun 19 16:28:16 2014 -0400 Updating visualize membrane mover and pilot app for transforming a set of structures into a signle app using pdb lists in jd2 commit 34bda2a913fd3895d4b2f28e0e3e0d8b1354ca85 Date: Thu Jun 19 16:25:13 2014 -0400 fixed indentation in Span commit 6b09da1d2068d9ff2e08a7462b4b20415d8d9c73 Date: Thu Jun 19 15:19:17 2014 -0500 Fix ATOM_ALIAS parsing commit ab636e1fb28731e39265f38cdc6d8e58980fe1a0 Date: Thu Jun 19 16:02:22 2014 -0400 fixed constructor in Span.cc commit 1af1b516a37e7fdb1fc11fad7fc45c6f23fcfbaf Date: Thu Jun 19 22:42:28 2014 +0300 Splice is now closing VH and VL commit fc6e4ce1b1d323811b32c31934babf7180e4d02a Date: Thu Jun 19 15:36:13 2014 -0400 adding pdb files to ref commit 903f96b9c8d3229d191d3d540840ff787970ffa1 Date: Thu Jun 19 15:34:25 2014 -0400 comparing fingerprint tests, MPFAEnv changes, probably numerical precision errors commit b31d51c2c2ef90e01587673f200e7fc25e5215c3 Date: Thu Jun 19 15:07:48 2014 -0400 Starting to work on a pilot app that will enable me to translate all structures into a single membrane and them move that membrane position commit f9060bbf8a0d00594d64d31a52ac0295c1c018f9 Date: Thu Jun 19 15:07:05 2014 -0400 Applying center shift move in visualize membrane mover. Also commenting back in rotation of membrane residues move - after looking into this deeper I think what it is doing is correct, but will test a bit more commit f774d2032581f661614cbb140084d65454f92ec3 Date: Thu Jun 19 13:25:16 2014 -0500 Add atom aliasing commit a07c2e57b4ed3b5aa79051ffaf7190721cfbafb0 Date: Thu Jun 19 11:19:52 2014 -0500 Add limits on the number of remappings to consider commit 8849c2d344a1d71727904d0071627c64334b8039 Date: Thu Jun 19 11:19:30 2014 -0500 More name remapping in PDB loading commit 48a79f664d4636e8f6b208519501b41a4f68e704 Date: Thu Jun 19 10:56:05 2014 -0400 Applying center shift move in visualize membrane mover. Also commenting back in rotation of membrane residues move - after looking into this deeper I think what it is doing is correct, but will test a bit more commit 51a2df1d81ed22c944e5448194a14c6d147934da Date: Thu Jun 19 10:43:45 2014 -0400 pilot_apps.src.settings.all change and make_ctags script commit 72c3fbd843d61a262bd9895ca92a0a7390d7ec12 Date: Thu Jun 19 16:18:16 2014 +0200 Fixing warnings-as-errors. commit 9c6f97b19949a5b32000fdcea76e67b4ea7dc263 Date: Thu Jun 19 02:20:36 2014 -0700 REVERT ME LATER!!! Temporarily adding output to this unit test to make it easier for me to find the reason that it's failing. modified: test/protocols/forge/build/SegmentInsert.cxxtest.hh commit 88a537d28e0041bea21f431f0aca062be4f1120b Date: Thu Jun 19 02:19:38 2014 -0700 Adding a note to Conformation.cc. I think I've found where I need to fix it. commit b2469020b8472295e34110e99e9230100b19c92e Date: Thu Jun 19 00:20:52 2014 -0400 Updating implementation of visualize membrane mover - still missing center shift and not rotating correctly commit d9bfb8b0c0d87c75a5f9dc63339375199a5e22a9 Merge: 4e90b0c bd6c66f Date: Wed Jun 18 22:59:38 2014 -0400 Merge branch 'master' into rfalford12/mpframework_devel commit b6e020788fe44a927ae5df8addf42c1cfecec75b Date: Wed Jun 18 19:40:19 2014 -0700 Adding a pilot app commit 033a9966ca2a2dc8cbf154368540d457e18e7606 Date: Wed Jun 18 21:26:14 2014 -0500 Modify EnvLabelSelector to be a legacy-only LocalPose caching object for support of Claims. We'll see how this works out. commit 9c4f06769543ff500378af9d36a19dc3f44b034c Merge: fa9a3fe 5b65c19 Date: Wed Jun 18 19:09:50 2014 -0700 Merge of several important changes from personal branch: (1) fix to geom_sol derivatives, needed for RNA, (2) removal of 'incorrect_deriv' options from hbonds, not in use anymore, (3) code to allow parsing of residue chains and numbers from tags like 'A:5-20', used now in stepwise assembly/monte carlo to read in 'conventional' chains and numbering from FASTA files, (4) cleanup of directory structure in protocols/stepwise/, including combination of all legacy/ subdirs into one subdir. Integration tests checked, and only RNA and swa/swm tests change, except maybe for order of tracer output from match tests. commit 06e1c1867ee7f19ab96163fd8e3f7880dcace3ea Date: Wed Jun 18 19:08:23 2014 -0700 Adding a check at the upper connect for badly-connected residues (in Conformation.cc). commit 99bdc141d9b332994045eb60e05b9fb0f94fdb5a Date: Wed Jun 18 19:02:03 2014 -0700 Taking out debug output added while working on P_AA.cc and Conformation.cc. commit fa9a3fed392c46932fbbf81b50932e031a3a078f Merge: 1f9489b 9e74d58 Date: Wed Jun 18 19:01:27 2014 -0700 merge from master in preparation for geom_sol derivative fix merge back to master. commit 1f9489bc15d4c3666b05959dd2dc24d6dffaa82d Date: Wed Jun 18 18:59:58 2014 -0700 important fix to derivative calculation in hbonds after my geom_sol derivative updates -- my bug caught by integration tests. commit bd6c66f7e5e685e0c675290051bf8f69abbcf441 Merge: f2b2788 5b65c19 Date: Wed Jun 18 21:14:40 2014 -0400 Fixing master mege conflict - merging master branch into mpframework devel to ideally fix pyrosetta build commit 0945c80e3060b119ca1535ccbaa0f62373fb9c8f Date: Wed Jun 18 20:08:39 2014 -0500 Update claim script changes to current state of Environment development. commit f2b27883443d510744b0090f6fc469ad74586341 Date: Wed Jun 18 21:08:20 2014 -0400 Updating overwritten change to some master merge conflict commit 4e90b0c2ff4c36a40fa2b5b2abf30d5bec0dca88 Date: Wed Jun 18 21:05:09 2014 -0400 Adding sfxn fingerprint reference results - contains full list of residue-atom scores for 1bd, 2bd, and wsd energies - this includes the low resolution and high resolution energy functions commit 5b65c197ffbe10fc7e9ab7c6e9359f30af7543c9 Date: Wed Jun 18 20:59:26 2014 -0400 [typo corrected at ProteinResidueConformationFeatures] [update of SandwichFeatures] - change from 'fn3' to 'fnIII' because 'fnIII' seems more correct according to '2008_Manipulating the stability of fibronectin type III domains by protein engineering' - should not change any integration tests other than (expected) features and features_database_schema (if any) commit 90ec06be999f7f177172cc5cf1a99a3c8bc10db7 Date: Wed Jun 18 20:57:32 2014 -0400 Fixing initialization order build error in Span. - note, base class should always be initialized prior to the member data commit f845af0647dc829bc47f1f770382116921ea53cb Merge: 9e74d58 54f8735 Date: Thu Jun 19 02:47:25 2014 +0200 Modify ResidueSelectorLoader to obey the 'name' RosettaScripts tag option. No expected integration or unit test changes. commit 9e74d580d91b7b4161c0ce33a6938720d12071e2 Date: Wed Jun 18 17:15:54 2014 -0700 fixing endianness check in BinarySilentStruct to handle RNA properly. only change to integration tests are in inverse_rotamer_remodel, match, match_1n9l in tracer output order; bet they will not reproduce on the testing server. commit 5b59cfb8898902ede36a571adc317a0569481743 Date: Wed Jun 18 17:15:54 2014 -0700 fixing endianness check in BinarySilentStruct to handle RNA properly. commit 5b55b5708312d52794ef1626f1b026b337e123a2 Date: Wed Jun 18 16:34:58 2014 -0700 Trying to fix a problem in Conformation.cc that's breaking unit tests. Adding a check for deformed resiudes in the function that gets mainchain torsions. commit 77bc5df2de7a6971d8c91305d039391cf0057b86 Date: Wed Jun 18 19:19:55 2014 -0400 Fixing Windows build commit 426d1a95b1d6d6a8c9cd58d18218c4592157de0b Date: Wed Jun 18 19:06:55 2014 -0400 added gitignore back commit e0a89b79eabcdb03318acb8bb4238bfdc74cb182 Date: Wed Jun 18 19:05:01 2014 -0400 fixed compiler errors, membrane fingerprints fail, but the tests are wrong commit 126b62ba2ab763670e60033dab32eaf4a89ffd27 Date: Wed Jun 18 19:02:02 2014 -0400 Made a quick change, but rotation is still not working and shift not even present. Visaulize mover still needs some work commit 2bb6b521b443b04d33da618077d6c9d841eac3a8 Date: Wed Jun 18 18:43:26 2014 -0400 Adding visualize membrane app, has a relatively working version but would like to capitalize on the jump I can use commit 3e2514ba2a80e574211314f6bc4b06a6f6a9f635 Date: Wed Jun 18 18:42:57 2014 -0400 Quick fixes to transform into mem commit 4b47ba6c01ea970c61e11538c560acff03f2d4b9 Date: Thu Jun 19 01:25:51 2014 +0300 removing throw exception for native client commit 4f810f0d55a91f56de42499953bcd13881f41e81 Date: Wed Jun 18 18:07:53 2014 -0400 Implementing visualize membrane mover, hope it works commit 0a92196e354a7dcac27a78f7174f629a04601c2b Date: Wed Jun 18 14:58:58 2014 -0700 Tweaking Conformation.cc commit 952afc42300a754465ec5a892c9d6880787aec08 Date: Wed Jun 18 17:50:49 2014 -0400 Adding visualize membrane mover - at least the pieces for it. probably won't compile yet commit b108d13e8b8dc4a8f267033cc1dc5c926aaf4ce2 Date: Wed Jun 18 17:50:02 2014 -0400 Quick updates to transform membrane mover commit 99c75aa408ceec3c0ba36e69212502bec0a0f167 Date: Wed Jun 18 16:04:10 2014 -0500 Convert to bimap usage commit 2a7a61500869b0d29ead8f33721157c13a499e3d Date: Wed Jun 18 16:28:35 2014 -0400 Updating transform mover to apply and set jump, was missing those lines in the previous commit. COmpiles commit 7086bba9abab43fbdcd250404078cf02921740c3 Date: Wed Jun 18 16:23:37 2014 -0400 removed ignored files from git index commit da639d3d2dc46681628100545bbe6d4b3d4366a5 Date: Wed Jun 18 16:23:15 2014 -0400 Implementing rotation move about normal commit ad387b82117e2df49a6ade44277f4833ac4b640b Date: Wed Jun 18 16:13:56 2014 -0400 Removing crazy debug trancers from trans memb app - I know my center shift is reasonable, correct not sure. I also know from my quick tracer test that conformation.update_embeddding, soon to be renamed, is also working reasonably commit f4b922e11e4080cf7a2891c8c7a07c9efeeaf167 Date: Wed Jun 18 15:57:53 2014 -0400 Fixing typos in transform into membrane mover forward declaration, also declaring a tracer in the pilot app to check if the update embedding method is working commit c2e4f01e8d034125f84593cb7b3839484e215d0a Date: Wed Jun 18 15:51:57 2014 -0400 Implementing membrane transform mover pilot app commit a5ff2446eb0aa3ea52336c6e2aff0dbe2ba6ba9a Date: Wed Jun 18 15:45:32 2014 -0400 Adding transform into membrane pilot app commit 87d07d71b77abda9280b20bc4a4759772719242a Date: Wed Jun 18 15:45:15 2014 -0400 Fixing compiler errors in transform into membrane mover, added to build settings too in protocols.3 settings commit de227d4f833818a93027988fea088d20d38eef16 Date: Wed Jun 18 15:42:34 2014 -0400 remove generated files in basic from tracking commit 54f873507a8d4599a2fe1732a9407addb1c58417 Date: Mon Jun 16 14:27:42 2014 -0500 Add 'name' tag option or ResidueSelectors for controlling the name of the Selector in the DataMap. commit 5b50902e286d694c56e5fe0f49269dd00fc787ed Date: Wed Jun 18 15:30:43 2014 -0400 Implementing center translate move in transform into membrane mover commit 13f7df7e9a211523f880b7fc87cda30a96a89aa2 Date: Wed Jun 18 15:23:23 2014 -0400 sasa unit test expected value parameters commit 2c8338e061034a896892c83cfac7154f3a1aeebd Date: Wed Jun 18 14:27:15 2014 -0400 Fixing typo in the name of the transform into membrane mover commit 31965ccf31d8ed78234b880ac66b618d964bf2b2 Date: Wed Jun 18 14:20:03 2014 -0400 Adding starting files for transform into membrane mover and implementing forward header and header file commit 264f41577ae5c3fa8e04781c810d78cb5352e438 Date: Wed Jun 18 14:11:14 2014 -0400 Removing new results directory from sfxn fingerprint tests - only ref should be committed commit e66eab8a91b291ff49d499008097a15b45c56ea3 Date: Wed Jun 18 13:33:16 2014 -0400 fixing build, removed ref for fingerprints, compiles commit 45e020767179c616d1156bb10b97b88012233305 Date: Wed Jun 18 12:04:07 2014 -0500 Remove superflous resid commit b6c74288acce5d935eb3c19f1a62b10723b6c6d9 Date: Wed Jun 18 12:49:06 2014 -0400 fixed sasa unit test parameters for real... why does this "unit test" test so many units??' commit d1df21ad57aea3f5c1d12993aafaf201125e67d3 Merge: a67d06e 0e47167 Date: Wed Jun 18 10:08:05 2014 -0500 Merge env_devel changes into env_claimscript. commit 0e47167e05a75f85ce7f72e3963a15ba80909349 Date: Wed Jun 18 10:00:55 2014 -0500 Add MoveMapMover interface for interfacing with ScriptCM. commit 960fbf1c77ca2e58591d255bcd9b8e886155b109 Date: Wed Jun 18 17:12:51 2014 +0300 Added code sanitation to indicate that number of chains in pose is smaller than the xml flag. This was added to the following task operations: PreventChainFromRepackingOperation.cc, ProteinInterfaceDesignOperation.cc, RestrictChainToRepackingOperation.cc, SelectResiduesWithinChain.cc commit 0aa4707b64cf12679eb8e5894978a2ba48b81104 Date: Wed Jun 18 03:48:47 2014 -0700 Adding bettercluster.cc back to the list of pilot apps in pilot_apps.src.settings.all. commit 5a71999b3135ad514dd6b667e7751a33868b3c0e Merge: d1192c5 baff9ea Date: Wed Jun 18 03:30:34 2014 -0700 Merging master into vmullig/cycpep to get changes to bettercluster (taking out Alglib and replacing it with internal principal component analysis). commit baff9eaaa9a7f86716b139db65bb7489b543cdac Merge: 10fa6db 6fe82a9 Date: Wed Jun 18 03:02:59 2014 -0700 Merging vmullig/betterclusterfix into master. I think I've successfully replaced the PCA analysis that I was doing with the Alglib library with something cobbled together using the Eigen library. No unit or integration test changes expected. commit 6fe82a9735c9e59049ba448c7f49aa53e9acfd8e Date: Wed Jun 18 02:50:56 2014 -0700 I think that bettercluster.cc is now working properly with the new PCA analysis machinery. commit 7d966013df1d10b70556ea1f5310b7f16dcc8ffd Merge: a7ebab5 10fa6db Date: Wed Jun 18 12:50:27 2014 +0300 Merge branch 'master' of github.com:RosettaCommons/main commit a7ebab5ac9ba7768e1fb9659cf7165fe3b03efd9 Date: Wed Jun 18 12:16:07 2014 +0300 Added more PSSMs for Splice commit ab2e134724d529fed4643350519ad428cd430580 Date: Wed Jun 18 02:12:30 2014 -0700 Bloody Eigen matrices are 0-based. Of course. Fixing bug in PCA.hh. commit 1d9dde679430600bee2881dded9577b93d1ce6c0 Date: Wed Jun 18 11:12:53 2014 +0300 Removed unnecessary dump_pdb and removed unused variable that caused an error commit 34c1dc894ebadec228515b404036fbbdafff09f7 Date: Wed Jun 18 01:00:25 2014 -0700 Options.dox is reported as having changed -- I'm not sure why. commit a6bade4d55aa563b389e3608576f4e969783a1d9 Date: Wed Jun 18 00:58:42 2014 -0700 Forgot to initialize a variable in PCA.hh. commit 38855be5f0d538491dde104d9d3825a353d8f198 Date: Wed Jun 18 00:19:08 2014 -0700 Trying to fix bugs in the new function in PCA.hh. commit b3d17403520dafdeb253c6c8487c475b8f197de2 Date: Tue Jun 17 22:02:18 2014 -0700 Ready to test new PCA analysis code. commit 236a93f515b10ec868784296c2674c5b55700baa Date: Tue Jun 17 21:16:05 2014 -0700 Working on n-dimensional PCA analysis. commit dd66302f27b242ad34e9c8c25799d40d5e14b4fb Date: Tue Jun 17 20:54:21 2014 -0700 Working on general n-dimensional pca analysis. Blargh. commit 0a733a30bcd8093def2d93fb36a39cecbb32b723 Date: Tue Jun 17 20:08:33 2014 -0700 Changed my mind. Leaving this inlined, for now. commit 96ca0df0fc49bb81160be53d9de1878ca3d8cc11 Date: Tue Jun 17 20:07:59 2014 -0700 I don't think the n-dimensional PCA analysis code should be inlined... Maybe it should. I'm not sure. commit 17c43dbbec8ea9d0c87d3db306dc8ebeae5c0897 Date: Tue Jun 17 20:04:32 2014 -0700 Initial commit of PCA_internal_test app, and beginning of implementing a general n-dimensional PCA analysis function in numeric. commit 2019ea48a049b8fdce653c218d5c291e592c7607 Date: Tue Jun 17 21:21:23 2014 -0500 Add in-place version of DofPassport::render_movemap. commit 10fa6dbe83eb1589c6e99f8a91698fb4775e4c49 Merge: 6b790d2 a3aecaa Date: Tue Jun 17 19:05:27 2014 -0700 Removing alglib from pilot apps; bettercluster.cc pilot app now broken. (I'll have to add something to numeric to do PCA analysis in more than three dimensions). commit a3aecaac3b09504eab91df3d997eb5a76f07d82f Date: Tue Jun 17 21:31:43 2014 -0400 Fixing PyRosetta build commit 9e23e600da072b87991fb778ea8a2594640944aa Merge: 1b0b267 84955eb Date: Tue Jun 17 21:31:21 2014 -0400 Merge remote-tracking branch 'origin/dougrenfrew/pyrosetta_dunbrack_constraint_fix' commit 6b790d272db961fd201cfcfb219d4fcb9eb6e0dc Date: Tue Jun 17 17:02:23 2014 -0700 Deleting alglib from pilot apps. This will break the bettercluster.cc app for now. I will switch this over to use Rosetta's internal libraries for principal component analysis. commit a497b9a22e340149126fa5c57dde7fc5c0e3eff4 Date: Tue Jun 17 17:13:14 2014 -0400 resolving conflicts, 2 remaining commit 2c07276e6027808650f76271780100d18117fe80 Merge: 6f7fbc2 1b0b267 Date: Tue Jun 17 15:12:46 2014 -0700 attempting to merge master into rhiju/swm_general branch. commit 6f7fbc2c8f1348503f21db192ada1d334525822b Merge: d9a7537 cc13434 Date: Tue Jun 17 15:11:13 2014 -0700 attempting to complete merge from master commit d9a753735c8c918ddb12c2e73ba1f2b1675d9e30 Date: Tue Jun 17 15:10:31 2014 -0700 attempting to complete merge from master commit 1b0b267f31cbc92ace16455558f3453a196db66b Date: Tue Jun 17 18:08:36 2014 -0400 Update unit tests for reduce SASA radii as default commit a3dc62713275f5d731d9e2ce061e533a69b1ffce Date: Tue Jun 17 15:07:08 2014 -0700 attempting to complete merge from master commit 37fe02ceffd5f7f83bb2533c6a4ee3dfc17497c2 Date: Tue Jun 17 15:05:45 2014 -0700 attempting to complete merge from master commit 5c40e0a485e9e285b6d658cef483f7a09e3f4cf9 Date: Tue Jun 17 15:22:30 2014 -0400 added core/membrane/geometry/Embedding.*, doesn't compile, need to add EmbeddingConfig commit f97769918c6e7f71c0e44f1152d963ae7067ffa3 Merge: ddefea1 28abab5 Date: Tue Jun 17 17:25:22 2014 -0400 resolving conflict in settings file commit ddefea12c47fd47137cd9c7638e3c426577ea55e Merge: 894225c 6d00d1d Date: Tue Jun 17 17:22:36 2014 -0400 pulling from devel commit 4528ba1d8d3f12450becaad2847e8b3f4ddf55d2 Date: Tue Jun 17 16:45:47 2014 -0400 WaterFeaturesReport TackOperationFeaturesReporter vsasa stuff kevin pilot apps commit 28abab5113bee4b214b8238bac9f29f295af352b Date: Tue Jun 17 15:21:26 2014 -0400 added core/conformation/membrane/Span.*, compiles, fingerprint tests pass commit 6fef135cd8e788a6e0e7c8b73adb218449d6bfef Merge: 93da2bb 120dc26 Date: Tue Jun 17 14:37:10 2014 -0400 pull from master commit 93da2bbb3d6f55f2170fe32d7a517c2e62421ce3 Date: Tue Jun 17 14:34:37 2014 -0400 database checkout from master, looks like a bunch of new stuff was added commit b6c6a72125426e76f82df3970048eadf49c32f3b Date: Tue Jun 17 14:21:12 2014 -0400 added new files to fingerprint tests commit df900a33a33221fdd3449374b1f407affb4e6322 Date: Tue Jun 17 14:20:30 2014 -0400 fingerprint tests finally run commit 84955ebf6954da3dad26c749b1b247b88194abd8 Date: Tue Jun 17 11:19:08 2014 -0400 Adding an additional header to try to fix the PyRosetta Windows build commit 8156ff92566bac90bf5bc1c4f8441a0fbac57995 Date: Tue Jun 17 09:29:40 2014 -0500 Fix bug in stage id parsing where IVa and IVb would map to IIIa and IIIb and improve clarity of error reporting. commit 6d00d1d63a631150ab4e08e254dd94f22b30260d Date: Tue Jun 17 09:28:53 2014 -0400 Getting rid of non-relevant unit tests and fixing header only build commit 120dc26826178629a2de401f1512058a5e4bbd32 Date: Tue Jun 17 15:26:29 2014 +0300 fix TR commit 796791a16cf4f24a7cf6df755ab30adc9d884be3 Date: Tue Jun 17 07:41:07 2014 -0400 Fixing gcc build commit ea02d49b2f3214d2bf3d478c5e63dcb523d48931 Merge: ce2b71c f0f5842 Date: Tue Jun 17 13:06:37 2014 +0300 Merge branch 'master' of github.com:RosettaCommons/main commit ce2b71ceb6f9283f8681f8f709479251c38889be Date: Tue Jun 17 13:04:45 2014 +0300 Added new PSSM files to protocol data used by Splice mover. Added tail segment mover to Splice.cc commit f0f58426ee6cebdee7a25ec88f63dc3ec965584e Date: Tue Jun 17 00:45:03 2014 -0400 Fixing PyRosetta namespace build commit 40a6eb7978367b1183cb6e6937ab6601fe1379a4 Date: Mon Jun 16 23:14:51 2014 -0400 FINGERPRINT TESTS RUN :) commit d637a35f6bde116edc8d7cdcb794d4c62d99bd2c Date: Mon Jun 16 20:02:01 2014 -0700 VICTORY! Conformation.cc now properly calculates backbone dihedral values of nonstandard connections (e.g. N-to-C terminal peptide bonds). Now for extensive testing. commit 6e8b58aca89de1e4ce8ed4ed92eaefd0d0d1aece Date: Mon Jun 16 22:59:40 2014 -0400 Removing extra resource manager file support commit 375962ee617cfdd63f9d50dcac93d76de4778cc8 Date: Mon Jun 16 22:57:44 2014 -0400 Still deleting old files commit fce662961223db21c14720b63e7c41b3ac399393 Date: Mon Jun 16 22:56:04 2014 -0400 Getting rid of more old unused files commit 343c3175f03aa5bfcff134cf3f62f56c03530e81 Date: Mon Jun 16 22:55:02 2014 -0400 Removing more old files commit 5b575c4076a6201e03e8a68e344eede867238b77 Date: Mon Jun 16 22:54:42 2014 -0400 Removing old config code, will not be used commit 9cf59d227e329072eba48f64bb8911513d0f9338 Date: Mon Jun 16 22:49:38 2014 -0400 Updating flags files in membrane cen and membrane fa sfxn to correct sfxn fingerprint tests commit 0cc0c81f1869be83de4126f3b6c384afcec080f3 Date: Mon Jun 16 19:14:53 2014 -0700 Adding more debug output to Conformation.cc commit dc69ec5b8f495c99c3fd435fe6aa8cb772673446 Date: Mon Jun 16 21:26:40 2014 -0400 Updating local minimize app - will minimize after structure based embedding update commit 066c4d9e4b79e7b7b2879f0ba10c0ccf8a0bbc4c Date: Mon Jun 16 18:30:53 2014 -0500 Attempt to get PDB reading working. commit 99381b28053e0bb6c9c55e97515c57d12eef2819 Date: Mon Jun 16 19:12:34 2014 -0400 Updating local minimize pilot app, added to build settings and it compiles commit 87574333ec091ca6cd23d5346c57c35934193d06 Date: Mon Jun 16 19:02:28 2014 -0400 Updating structure based embedding mover so it compiles and local minimize app commit 7d159955cff9ed95f846c372536d665ede12a60b Date: Mon Jun 16 18:35:46 2014 -0400 Updating embedding mover to make structure based computation commit a2ef3141a59be07a5b80610c6e412b857f016ede Date: Mon Jun 16 18:34:02 2014 -0400 Updating optimize membrane mover commit 28a05de1c1650c557289866a49818567d2d4783d Date: Mon Jun 16 15:12:04 2014 -0700 Update BuildPackagedBindings to stage static and database files. Adding staging of static files in packaged bindings package directory, as opposed to module directory. Modifying packaging script to accept target package directory instead of module directory. Adding symlink-based staging of database files. Adding initial nose-based binding tests, to be staged and run as component of binding package. Adding configuration for nose-based tests. commit b3881976ea8fcfdf2a5a8bc277d1e125ed9632c4 Date: Mon Jun 16 15:03:17 2014 -0700 packaged_bindings binding bug fixes. Fixing core.pose import via addition of core.pose.datacache abstract base class wrapper. Removing dead code from core.pose and core.import_pose byhand bindings. Updating logging support path names. Updating module import order. commit 6273b1054c08f86a9d05f6623fe247c719c36d93 Date: Mon Jun 16 18:17:41 2014 -0400 Adding ‘--skip-comparison’ command line flag to sfxn_fingerprint.py script to reduce confusion in testing server runs commit 9a538c68dfea7c9ab9dfd3aa74971514ba03f7b6 Date: Mon Jun 16 16:53:25 2014 -0500 Renaming. commit 894225cdf361d35e59e033f11bfa385b4cff48af Merge: 167e012 e3aa166 Date: Mon Jun 16 17:41:32 2014 -0400 pulled from mpframework_devel commit 167e012d56a918799fe528b96dbe6e301b27a3e3 Date: Mon Jun 16 17:39:04 2014 -0400 added ref for fingerprint tests commit e4cf7c7155543964f3ae5b3f165d883316ca222c Date: Mon Jun 16 16:18:46 2014 -0500 Hook mapping in to PDB loading commit 6e341f3ad3fb60d9af69528aa9c1680e5e8725ea Date: Mon Jun 16 16:40:11 2014 -0400 Writing my own custom membrane optimization mover - uses slightly different approach and scoring from previous monte carlo. Because my mover is essentially inside out allowing me to do a true monte carlo search isntead of a score vs. score search. hopefully this can smooth out minimization commit ff32fbbb633c5387c756bd22c1c75936d2b7586a Date: Mon Jun 16 15:14:08 2014 -0500 Clean up file_data_fixup code. commit ba2b70a14021ad667101377cb9a69172b1878dbc Date: Mon Jun 16 14:58:43 2014 -0500 Replace distance hack entirely commit 124efce17465929c4005d2ddfaf6dad091d7e726 Date: Mon Jun 16 14:51:07 2014 -0500 Compute bonding based on element covalent distance commit 169d009415443f5ab22ccbfc3bf046fa8e6c29ec Date: Mon Jun 16 15:36:24 2014 -0400 Filling in optimize membrane mover - but ran into a scorefunction bug commit edf3703dbcbb766f98d5ad5be6526ed666f579bc Date: Mon Jun 16 14:27:42 2014 -0500 Add 'name' tag option or ResidueSelectors for controlling the name of the Selector in the DataMap. commit c83f54ac212e9266f35604d55e1aa3b1a58f03f8 Date: Mon Jun 16 15:13:47 2014 -0400 local_minimize.cc: pilot app for minimization of membrane proteins with the new framework. checking out optimization of mp moves, etc commit 62acc5be86e0c3e873b2197f882938358201f178 Date: Mon Jun 16 14:48:17 2014 -0400 Adding local minimize app - just getting started, it won't compile yet without the opt membrane mover I am currently working on commit 92c12f0bacf18cf7801f8768d0be5f6d59b2cd0e Date: Mon Jun 16 14:40:11 2014 -0400 Starting to implement optimize membrane mover helper methods, taking a short break to outline the local minimize app that is the goal of this entire refactor commit a26dd4c822b70f7e48be860cb830d223bfff741d Date: Mon Jun 16 14:26:11 2014 -0400 Starting to implement optimize membrane mover header - still figuring out what options should or shoould not be user controlled. Will set defaults and allow command line/rscripts access anyway commit 941e9759135f289d5e1dd0afe97a4545ac365a3c Date: Mon Jun 16 14:16:53 2014 -0400 Adding starting files for optimize membrane mover and implementing forward header - should take the place of the old monte carlo protocol commit c472d832e122b40faef5edb907f90fc9b901706a Date: Mon Jun 16 13:50:19 2014 -0400 Well that is weird - scores match when I recompile the executable with a change. Must have just needed a force recompile to link the libraries commit 8816695fd520a2f4ef27a7de25fbf7b99e3a504d Date: Mon Jun 16 19:28:10 2014 +0300 Added seqeunce threading from source pdb to current pose commit 69fd0e46b24589fe89564d2a6fb02a4c0337adaf Date: Mon Jun 16 12:27:07 2014 -0400 add creators for the movers, finish DeleteRegionMover commit 419fa36f69843d7522a585392ef2dd6c98d92411 Date: Mon Jun 16 12:02:33 2014 -0400 Trying to debug the introduced discrepancy in the membrane fullatom env term. Added debugging tracers to both base classes commit 4d73eccae199f245bc86124c189f22c4cd0ff2b9 Date: Mon Jun 16 10:48:25 2014 -0400 Ok, just kidding. something crazy is happening with the old term, possibly in applying penalties, but that isn't so much a concern here commit 967266ed068408005a29adad5d95a994a59af7da Date: Mon Jun 16 17:17:09 2014 +0300 Added more tracer variants to control Splice output. Minor changes to add_coordiante_constraint function commit 1739668f193fb91f0af284bd07692ec41c9492ee Date: Mon Jun 16 09:52:08 2014 -0400 Adding back membrane and membrane_fa executables to test sfxn differences between new and old - fa mpenv and cen env terms are the only ones not working in the new refactored code and I'm not sure why commit c58e7b5761a6a9318938b8b49e4ef29c53860195 Date: Mon Jun 16 16:47:46 2014 +0300 Add a new function to sPLice that finds a cut site on antibodies that is on the oppsite site from the CDRs commit 29f495a79c28eaa60d54d209f58afc0ec670dc06 Date: Mon Jun 16 12:14:24 2014 +0300 Added copy dihedral angles after ccd to chainbreak residue and two adjacent ones. also does minimization afterwards commit 08998f73879d1c9519e8b9310699858ec7a4b0e2 Date: Mon Jun 16 00:37:03 2014 -0700 Trying to get Conformation.cc working with torsions defined by atoms that are covalently connected, but not in the AtomTree (e.g. N-to-C terminal linkages). Something isn't working properly right now, though, in get_torsion_angle_atom_ids. This is a problem for tomorrow. commit 2fca137ea03f2795c9f540eaa1353f821197ad34 Date: Sun Jun 15 23:57:50 2014 -0700 Fixing typos in Conformation.cc commit 3430fa3a79c3d6df46ba738e74a59a6665f7fdaa Date: Sun Jun 15 22:47:47 2014 -0400 Removing debug tracers from add membrane mover - solvation term working fine, environment term needs work commit 20e61330580e9aecd39deb8fd48e7e013b4c1702 Date: Sun Jun 15 19:29:56 2014 -0700 Finished adding atoms_are_bonded functions to Conformation.cc and ResidueType.cc. commit 08bed203a2981fb375c5ed3b2226577537d2e423 Date: Sun Jun 15 22:21:28 2014 -0400 Removing extra debugging tracers commit 18206509bd947c929d429a7c86d3c3f090e72a4b Date: Sun Jun 15 19:16:26 2014 -0700 Working on Conformation.cc -- adding function to check whether two atoms are bonded. commit 486574abed882008893af0ddf389824d908b1f51 Date: Sun Jun 15 21:45:12 2014 -0400 Starting to update fingerprint apps based on the new refactor commit d7b5a70edbdb6a58af0d92e1685d8fcfc6d2cee5 Date: Sun Jun 15 14:23:46 2014 -0700 SymmDocking will now always use the correct jump(s) to determine interfaces to repack commit f060e668f820bbae2d51474f67f1d1b06045c31f Date: Sun Jun 15 17:09:41 2014 -0400 Adding membrane framework integration executable, integration test not yet setup and the unit tests are probably in mass disarray commit 4ac4c37cb04f0ebee24bf5c91f07411decbb975f Date: Sun Jun 15 17:08:39 2014 -0400 Add membrane mover works - and that is a beautiful thing commit 36716637949dbdf98ab6163765082adf59a5d3d2 Merge: 74de4b4 e0ed3b0 Date: Sun Jun 15 13:24:06 2014 -0700 Merging in a few bugfixes to symmdocking: don't reset unmovable translational dofs, proper transforms for multicomponent symmetries. commit 7a9467db33c8a6f61eb9acf400d08e289bde241d Date: Sun Jun 15 16:24:03 2014 -0400 Adding framework integration test app commit 7b36243002737291f470b7b94c487c0b892bda36 Date: Sun Jun 15 12:22:44 2014 -0400 Updating mover registrator, creators and resource loader creators to not depend on the old cpm movers commit b53ff5d7644c1005a492cf3e8889154890ab77ec Date: Sun Jun 15 11:41:34 2014 -0400 AddMembraneMover compiles :) commit cf26dd2031a198abcd6287c7ddb9edee8ca40047 Date: Sun Jun 15 11:35:28 2014 -0400 Initial bug fixes in AddMembraneMover - trying to get it to compile would be good commit ebb0f7d217c0c9c6e15853e64860f3a97596bec9 Date: Sun Jun 15 01:06:28 2014 -0400 Tiny build error in the .hh is breaking compilation in the .cc. Will figure this out tomorrow commit 1b8ce0352fa3d1ebd999c276b6896b49407febef Date: Sun Jun 15 01:05:29 2014 -0400 Initial build fixes to AddMembranemover, and removing CreateMembranePoseMover dependencies from FastRelax commit a9e0b6fedb49cc9fca9d687dc1219b2c5e1432d9 Date: Sun Jun 15 00:34:13 2014 -0400 Removing an old dependency on EmbedDefOptions, IO and fallback from a previous iteration of the membrane code. This code is kept in an old branch but no longer in main development commit 81589a4b857ba7b60ce6ea1a477e3d31d1e63136 Date: Sun Jun 15 00:25:30 2014 -0400 Fixed embedding methods dependency on membrane info, now to conf pass through method commit 6bd12e662edb1d1a3e71cb1efd124495feba319f Date: Sun Jun 15 00:21:38 2014 -0400 Updating hbond energy correction with new changes commit 729eff76eebbfc5950c87e04b905dabc6707b10b Date: Sun Jun 15 00:18:37 2014 -0400 Introducing mutability of fa derivatives into fa solv and fa env energy methods - intendend use here is ok and overcomes coupling problem mentioned before commit 22c8f2f815e7339cf2a68c47f8d8aaebc83fab0f Date: Sun Jun 15 00:14:09 2014 -0400 Adding add membrane mover setup options to options_rosetta.py in membrane_new setup group commit 6b3bbe88c0894a6a48a07ab6e6bce1e5d94ab518 Date: Sat Jun 14 23:36:59 2014 -0400 ARGH CONST CORRECTNESS commit 16d1e5a52a5009c04bd7cce3bca835dc91cef065 Date: Sat Jun 14 22:28:32 2014 -0400 Killing the old membrane penalites class commit c85179bb72d27718ef10848087672f3eb228bf87 Date: Sat Jun 14 22:24:21 2014 -0400 Low resolution energy terms compile, still waiting on fullatom commit 31a02573995ceae399efd4e53c9ce781f13c5d31 Date: Sat Jun 14 22:14:56 2014 -0400 Fixing constness issue, trying to get energy terms to compile again and praying I haven't started any fires here commit a92e0378902f82b66b3e4bdf5dd5fca062105914 Date: Sat Jun 14 21:55:50 2014 -0400 Woohoo - core.2 compiles with the changes commit 22eda2fa0e9738792c78df586d5559eca9cf0a06 Date: Sat Jun 14 21:45:45 2014 -0400 Updating conformaiton object with quick fixes commit 5fd26857bad0813f608229bf52a43bdea754f288 Date: Sat Jun 14 21:15:54 2014 -0400 Getting rid of the corresponding un-needed data members fa_proj_deriv and fa_proj_deriv_coord commit c147962ed05c77fabb61e0f879a507355a99b4c7 Date: Sat Jun 14 21:14:22 2014 -0400 Removing un-needed computing of derivatives in fambsolv commit d957ca6bce25d5c1e4b6ce971594fe955a0341c5 Date: Sat Jun 14 21:08:28 2014 -0400 Ok - all of the derivatives live in their respective energy methods now, but still need to clean up the solvation term commit 4ec2ea45439732a34d19b0849875a3dff6d5c93f Date: Sat Jun 14 20:59:16 2014 -0400 ok, i've decided to initialize this stuff twice - mostly because I think this is the best way to guarantee the pose derived data is correct. if I find another way, I can always change it commit 92e1bba014fe05aa7b320c9abd7e4519b1beeb7a Date: Sat Jun 14 20:02:10 2014 -0400 Just kidding - what a mess. scoring needs fa projection, derivatves need their derivatives, but all of this data is derived from one another. what happens first. crazy setup collision commit c9ac90fedc45eff133e6f96677b5b9f87f166efc Date: Sat Jun 14 19:58:09 2014 -0400 In theory, fampenv will now compute its own derivatives as it should have originally, but the game only ends when it compiles... commit 739a49f753f0b26cdd6dfb20a16251d047d06d5d Date: Sat Jun 14 19:41:00 2014 -0400 Moving dE/dz derivative pre calculations into their respective energy methods - even though it means the methods will be duplicated, the operations are not slow and it will be more clear to the user what the energy method and gradient method actually entails commit 15373a42cb284840469add9bbd695682d6ad3c99 Date: Sat Jun 14 19:12:55 2014 -0400 More updates to membrane info, still trying to figure out what to do with the derivatives, introducing an old problem commit 61b3fb0e56ff202b29ea94e5f82c6af5b2ac3eb7 Date: Sat Jun 14 16:31:30 2014 -0400 Removing references to un-needed methods I deleted - but now membrane info is unhappy becasue it has derivatives it cannot compute - might just be doing this on the fly outside? not sure yet commit 3c4054121d300ada6118023a0851fa24700c96ed Date: Sat Jun 14 16:28:22 2014 -0400 Implemented update embedidng method which talks directly to conformation's copy of residueOPs which are mutable if you are an insider commit aeded9dc9a2f682e7d1a4f0ca560baade7b0a128 Date: Sat Jun 14 16:19:08 2014 -0400 Implementing residue and atom z position method relative to the membrane in Cofnormation - easist way to separate derived coordinate responsibilities - will need to do this similarly with the fullatom derivatives supplied commit e132d8f0ad7e915d97a6355d1a2cfd86ba8586c3 Date: Sat Jun 14 16:11:29 2014 -0400 Updating methods in conformation to play nicely with membrane info and AddMembraneMover - includes atom z position, residue z position, overloaded setup_membrane methods to match membrane info constructors but respect method constness, and updated getters that will eventually but not yet pass through to pose commit 46df5c468b491de3f6bf7756576b341d33718fc3 Date: Sat Jun 14 14:05:25 2014 -0400 Updating protocols.3.src.settings to get rid of other code and use only add membrane mover (and some other movers I will add a bit later commit 5b53087593de154fd1bb4a62a208f5689edd572e Date: Sat Jun 14 14:03:17 2014 -0400 Removing old crazy code for creating membrane proteins - starting fresh commit 0a9db00d98615315b2fd86c4d935a4282142e2cb Date: Sat Jun 14 14:00:54 2014 -0400 Getting rid of lots of old dead code - starting fresh, starting from scratch. This commit gets rid of core files not used any more - will be doing the same with protocols files soon commit bdeff62d2ed77e4eddab11593774c14bc90ba7f9 Date: Sat Jun 14 13:55:01 2014 -0400 Killing old un-needed code, adding membrane mover creator for rosetta scripts compatibility but not yet implemented commit 920f0346d805f5a3f58efbc85a07898942795c66 Date: Sat Jun 14 13:52:17 2014 -0400 Adding a simplified membrane info interface - will break everything under the sun commit 696b405c78da84a2c50cd383208a68cdde343de2 Date: Sat Jun 14 13:46:50 2014 -0400 Updating author info in AddMembraneMover commit 01414419a2d06fd791ca949156978aa42e265e39 Date: Sat Jun 14 13:23:01 2014 -0400 Starting to kill the old membrane info conf internal containment scheme - working on one that separates knowledge of coordinates from position commit c1b07428a3541dc008d4818b111bdae3de0b1bde Date: Sat Jun 14 13:05:06 2014 -0400 Alright - we have reasonable version of the cc and hh for add membrane mover as well as an expected API from conformation and membrane Info. going to set those up next commit 2331f61f245d9c91c01b9155039a90ca5e17471b Date: Sat Jun 14 12:53:02 2014 -0400 Implemented default, custom/pyrsetta and copy constructors in AddMembraneMover commit e9f307a35bd5d93eb5450314751a290344f90d03 Date: Sat Jun 14 12:32:47 2014 -0400 Got all of the pseudocode there for membrane protein setup - killing it commit dc373fb4fae01388d3661e3e3f719200e88624de Date: Sat Jun 14 11:06:33 2014 -0400 More updates to add membrane mover commit 918df7883af310ad7d152c1d7adfe97a7607b356 Date: Sat Jun 14 17:27:36 2014 +0300 Saving changes to Splice that I know work before adding more changes commit 57f97522ff82ace966fb0bdb42fdb78c5c73162c Date: Fri Jun 13 22:08:58 2014 -0400 Starting to implement new AddMembraneMover - will need to also modify membrane info constructor, ensure PyRosetta and Rosetta Scripts friendliness commit 9e0b24667feaa818b3abfc3b37b34f52ef23ec0b Date: Fri Jun 13 21:49:46 2014 -0400 Adding code for a new lightweight membrane protein setup - minimal and only creates the objects we need while maintaining a good API commit 86514bd5d685cf867235cbbb164031d9ef577350 Date: Fri Jun 13 18:40:28 2014 -0700 I've figured out what's going wrong and how to fix it, I think: --Mainchain (and side-chain) torsions in Residue are set by a function in Conformation, which relies on the AtomTree. --If a torsion is sensibly defined by covalent connectivity, but isn't in the AtomTree (e.g. a C-terminus-to-N-terminus peptide bond), it gets reported as 0.0. --I need to add a way for Conformation.cc to measure torsion angles in this case. Look for TODO in the code; this is where I'm adding this. commit 7c62269fd727afe1e5d2bb2e85000880292d925d Date: Fri Jun 13 18:11:21 2014 -0700 Adding some debug output to DeclareBond mover. commit 4af19b409fac7d3bebfaa371d43c82971efc5525 Date: Fri Jun 13 18:10:57 2014 -0700 Adding an update_residue_torsions() to Conformation.declare_chemical_bond(). commit e3aa16647ddf00f103630313be5b7702b82af4b7 Date: Fri Jun 13 21:03:45 2014 -0400 Updating pilot apps commit 5f833f7caa3d055434c50b2f596de5f75dd95d45 Date: Fri Jun 13 18:11:02 2014 -0500 Add McGregor fall back, deal with naming issues. commit 0bb3138bd64c3f23bd2eeacdba5c814294f2a1d9 Merge: 8a4d4a4 b739ef4 Date: Fri Jun 13 18:03:41 2014 -0400 merging devel in local devel commit 8a4d4a480ed517ae2c829dc25339e181bb1d5e24 Date: Fri Jun 13 18:02:12 2014 -0400 setup scorefxn fingerprint for MPs commit e0ed3b0916fc77d236bbbfe18de2d53c14ffa288 Merge: 8a551c7 dac5110 Date: Fri Jun 13 17:55:06 2014 -0400 Adding peptoids to Rosetta Despite the short commit title, this commit has been a long time coming. Most of the work was done by myself but it also includes contributions from Tim Craven and from Glenn Butterfoss. It was recently published in JACS (http://pubs.acs.org/doi/abs/10.1021/ja503776z). **A Rotamer Library to Enable Modeling and Design of Peptoid Foldamers. P. Douglas Renfrew, Timothy W. Craven, Glenn L. Butterfoss, Kent Kirshenbaum, and Richard Bonneau, Journal of the American Chemical Society, Article ASAP It contains... -- more 100 residue type parameter files (and various patches) for peptoid side chains (only 2 are enabled by default as they are used in integration tests) -- 2 peptoid rotamer libraries (there are more but they are large and can be downloaded separately) -- updates to MM atom types and params to suport peptoids -- updates to MM atom type names in metal ions -- code and some basic movers to create score and minimize cyclic peptides and peptoids (this was done independently of the cyclic work Vikram has been doing and the 2 functionalities should be resolved at some point) -- updated UnfoldedStateEnergyCalculator to work with peptoids and simple sequence profiles rather than only random fragments -- added unfolded state energies for peptoids -- updated and basically rewritten MakeRotLib protocol that works peptides and peptoids, and can distribute jobs via the MPI jobdistributors -- added an assortment of pilot apps to work with peptoids -- refactoring some of the rotamer library code to separate large classes in to multiple files -- added a new rotamer library class for peptoid rotamer libraries which are dependent of the preceeding-omega, phi and psi torsion angles -- some random little code clean ups Unit tests: All pass Integration tests: Expected changes: cyclization make_rot_lib ncaa_fixbb unfolded_state_energy_calc number_of_residuetypes Cosmetic changes: splice_in splice_out fold_and_dock splice_seq_constraint Saw some rounding changes on linux/gcc commit 8a551c759512e3619bac46bae723b7db5b962686 Date: Fri Jun 13 17:50:45 2014 -0400 Update to cyclization flags commit 4801d6550e284bc15671ec52ec28ef3ca2f84f3c Date: Fri Jun 13 17:44:10 2014 -0400 Forgot one return value commit fa60682fcb90e6974dae10423a142f950049abb0 Date: Fri Jun 13 17:33:43 2014 -0400 Adding try/catch block and/or proper return values for apps commit dac5110e026b030e164f79866e8620a222f3d3cc Date: Fri Jun 13 17:09:56 2014 -0400 PyRosetta. Fixing Windows build. Upgrading source files dependency calculation. commit 574998257da103a7648c096612c67f01defd0c04 Merge: def7add 33d9f07 Date: Fri Jun 13 17:04:11 2014 -0400 Merging master in to peptoid commit 6278064df214b1669c535251f9ecb838a4401205 Date: Fri Jun 13 17:03:27 2014 -0400 added site.settings.wiggins commit e1064ebfc67dcaaf3af1f36b5837611e02eca1bd Date: Fri Jun 13 16:46:07 2014 -0400 begin adding simple_movers to namespace for use in RS commit 33d9f075ab893697c2812f472e39b6afadbbeba5 Date: Fri Jun 13 15:43:36 2014 -0500 Commenting out test_assert_exit unit test. commit 2a99e43be16a8962325d2a4f687d089cd5c153fb Date: Fri Jun 13 15:36:52 2014 -0500 Testing Benchmark server utility script. Adding dummy unit test that just raises an assertion error. This should fail on the test server. commit def7add7fd1a486aca189508078cdffc49260c3d Date: Fri Jun 13 16:32:57 2014 -0400 Turning off some pilot apps commit 59b5d75504b5ddd8dda7e5f41ea4124ee9850e0b Date: Fri Jun 13 15:15:13 2014 -0500 Test for mapping, including scoring pairs commit 19a616a3a6080869796f4a2d83f6f72ad57c298b Merge: cc13434 6409d4a Date: Fri Jun 13 14:33:10 2014 -0500 Add text parsing to BOND_TYPE lines Instead of SDF-based numerical values, you can now use text designations (like ARO or DELOCALIZED) to specify bond types in params files. Database files have been updated to use the new scheme, but molfile_to_params.py will still output the old numeric values. No substantive test changes expected. (Standard numeric variablilty with ligand_dock_script encountered.) commit 6409d4a27998111914f3c7eebcb75f16ea425aaa Date: Fri Jun 13 14:33:10 2014 -0500 Add text parsing to BOND_TYPE lines Instead of SDF-based numerical values, you can now use text designations (like ARO or DELOCALIZED) to specify bond types in params files. Database files have been updated to use the new scheme, but molfile_to_params.py will still output the old numeric values. No substantive test changes expected. (Standard numeric variablilty with ligand_dock_script encountered.) commit b739ef41f73bff20a44db49cb19029360506823f Date: Fri Jun 13 12:56:18 2014 -0400 updating sfxn fingerprint tests for membrane centroid and fullatom energy functions commit e4372e571cffc2fd288ac87ec855736ff0b59c8a Date: Fri Jun 13 11:45:20 2014 -0500 Make errors for unrecognized stages and stage ranges more friendly. commit 3b1eb9ecb4df5559ef4ba656d9b3edbeb6f96bbb Merge: 3d6f10b 3bb14a0 Date: Fri Jun 13 11:54:14 2014 -0400 Merging commit 2e3ecdaa6954daeb95d82137af115480cd6bf6ce Date: Fri Jun 13 11:35:24 2014 -0400 Adding membrane unit test fixes commit 3bb14a07538fbc469a98c82f136b626f282f2569 Merge: e8603e4 cc13434 Date: Fri Jun 13 11:12:49 2014 -0400 Merginf master in to peptoid commit e8603e4a4f186406b07e017008613c870a11d0e5 Date: Fri Jun 13 11:10:17 2014 -0400 Commenting out all peptoids except those used in integration tests commit 566f738c09886fc7132d1f133b2483bbdb102c3f Merge: 1eedcea cc13434 Date: Fri Jun 13 09:48:32 2014 -0400 Merging remote master into ninja local master contianing mpframework devel branch commit cc1343434beaa895b082d40a84b6507aba62baf4 Date: Fri Jun 13 01:14:28 2014 -0400 Fixing PyRosetta Windows build commit ea9d6ee2efcbaac494f3bce2ea946a712f85b258 Date: Thu Jun 12 22:03:02 2014 -0700 Fix erraser commit f7775220c158f2a4553264628791bc6fc61de338 Date: Thu Jun 12 20:55:04 2014 -0700 More debug output. commit 564d585dd5c22a3f84f3725329d81aadfd3d8dc3 Date: Thu Jun 12 20:33:25 2014 -0700 Forgot .h? commit 4853aad78d63a25e98b019b814fb5a18598e4d00 Date: Thu Jun 12 20:24:45 2014 -0700 Adding stdio to Conformation.cc temporarily. commit 158a11f1130255b09efde4ab787f2688c14ad723 Date: Thu Jun 12 20:02:47 2014 -0700 Still more debug output. commit 984a392fe3ecf915678f2746fd99708587ad01bf Date: Thu Jun 12 19:26:52 2014 -0700 More temporary debug output. commit 1eedcea0140327b1001d8ba930d1c3e372df0223 Merge: a541608 d9a7f83 Date: Thu Jun 12 21:47:00 2014 -0400 continuing to merge remote master into ninja local master commit 0d7be482e61fc453912699ed5204a508dadc6a0c Date: Thu Jun 12 18:39:09 2014 -0700 Adding debug output to P_AA.cc commit a447dc61f247f2375bee277a59f0367df262f4b1 Date: Thu Jun 12 18:36:03 2014 -0700 Taking out a check in P_AA.cc that introduced a bug. commit f6e1e031c3e405a87bc90e599db6b0234ee693f3 Date: Thu Jun 12 20:30:05 2014 -0500 Remove std::cout call from FragmentCM. commit 940194540a5ff35ad4c4f360d6a759d8cab5ea24 Date: Thu Jun 12 20:26:28 2014 -0500 Modify FragmentCM to automatically determine fragment length from options when appropriate. commit 5adafba1c0c5585c5fd7109d1833312f3ad3e386 Date: Thu Jun 12 20:09:54 2014 -0500 Add FragmentCM to RosettaScripts parsing archetecture. commit d9a7f8374230a60a966ff73f469100585faedbc8 Merge: 1b4dfd6 25e9638 Date: Thu Jun 12 17:59:10 2014 -0700 Move packaged binding generation scripts into packaged_bindings submodule. Moving egg-packaged binding generation scripts into standalone packaged_bindings submodule to support independant modification of package-oriented bindings. Updating packaged binding script to support unix-like platforms. commit 1b4dfd6968b3916b8c30822417326f1a3448311f Date: Thu Jun 12 17:33:10 2014 -0700 Update pyrosetta import initialization and strip __init__ module. Updating pyrosetta import initialization to perform boost module imports without polluting module root namespace. Updating imports to attempt to load, but gracefully fail if target modules are not available. Enables support for core binding generation without protocol level bindings. Removing extraneous code from rosetta.__init__. commit 8bcf3c1533b6f4fe9f054276f998b8949a29539c Date: Thu Jun 12 17:31:28 2014 -0700 Adding alpha-amino acid check to P_AA.cc. commit 545cbbfe3f4afa48f2950c8066daf7118ad87106 Date: Thu Jun 12 16:58:22 2014 -0700 Remove cross compile and unused options from packaged_bindings. Removing unused build options from BuildPackagedBindings.py and windows-based cross compilation options. Adding "target" option to build script specifying a build target level. commit aaa6cf2311008fbb17fbff62483e012e75828345 Date: Thu Jun 12 16:32:17 2014 -0700 Tweaks to Conformation and DeclareBond mover to help the rebuilding of connection-dependent atoms. commit ff0e5cb5f8e9defcc4995b1014a9b4f0f5deff48 Date: Thu Jun 12 14:44:05 2014 -0700 Tweaking DeclareBond mover. Currently doesn't compile -- need to fix. commit 5c17889419fe7e8735eb3cdfa033493f74b7dd2e Date: Thu Jun 12 16:38:54 2014 -0700 geometric solvation: found a major bug in setting pseudo-base atom for acceptor, even though I thought that I had previously corrected this issue. found this while testing option to not compute derivs if unnecessary (which did not actually result in a speed up). commit d1192c56852326dcff5d29af1bdb6e56c447a45f Date: Thu Jun 12 16:32:17 2014 -0700 Tweaks to Conformation and DeclareBond mover to help the rebuilding of connection-dependent atoms. commit 25e9638f1ecc093830c66b76cccde14a6476cce4 Date: Thu Jun 12 16:02:23 2014 -0700 Output to pdb commit f48563fd8dcb73f3aa29446d6a6e754312cf820c Date: Thu Jun 12 18:55:16 2014 -0400 Adding new app and integration test that prints the number of ResidueTypes in the default FA_STANDARD and CENTROID ResidueTypeSets. Integration test status: [1] The new number_of_residuetypes test will "fail". commit de24a1bc9348f7ae547e83bb29821b6c15e0b224 Merge: d560b25 77c49f0 Date: Thu Jun 12 15:17:41 2014 -0700 Merge branch 'master' of github.com:RosettaCommons/main commit d560b25f5e19f5b3aa3224fcca69501e8a831482 Date: Thu Jun 12 15:17:27 2014 -0700 add a quick-and-dirty pKa calculator in rosetta scripts commit 9de77bab1d7ee2f5c088a230232717d3d040ced1 Date: Thu Jun 12 14:44:31 2014 -0700 Modifying Conformation.cc to remove seqpos-1 and seqpos+1 assumption. commit a4815f1261f4a5ced48eb3e8342f84d4d2e010f5 Date: Thu Jun 12 14:44:05 2014 -0700 Tweaking DeclareBond mover. Currently doesn't compile -- need to fix. commit 77c49f0b3893ee92ac323110a72f25f104a52d8e Date: Thu Jun 12 16:36:14 2014 -0400 Fixing PyRosetta build commit 7ba9d2ce74bf873917506cb26af4528a70c51a66 Date: Thu Jun 12 15:28:09 2014 -0500 Add missing braces around if block for ShapeComplementarityFilter Thanks to Luki for catching this. commit b29966c72c4d7015366d43b0a7ae3c30e73fdaac Date: Thu Jun 12 12:41:12 2014 -0700 Updating some comments on some of the methods in Residue, since the Doxygen documentation is currently misleading. commit 69e7a70a7a6013011c63c7b22630bb39d08d47d1 Date: Thu Jun 12 14:52:33 2014 -0400 fixing intra derivatives for geom_sol commit 464e40e6a36c8b44b76314c6116a1a885c03c010 Date: Thu Jun 12 14:50:15 2014 -0400 allow vector1 has_value() and index() to accept numbers like 5, not just variable names commit 26d3fbc0fdc453b219cdd9e43604baebaaf94137 Date: Thu Jun 12 14:48:39 2014 -0400 Changing the ignore_list to ignore changes to the number of MM paramerters and and ResidueTypes Unit test status: [Pass] Integration test status: [210] 210 tests will fail as a result of the cosmetic changes. commit 76d7d27b31db22984f858534f7d2258a0e444428 Date: Thu Jun 12 13:43:14 2014 -0500 Modify AbscriptMover to use FragmentCM's build-in CutBias claiming instead of its own. commit 1ff1499a72a41ad27a8cd3e79dbab30203f2ec57 Date: Thu Jun 12 13:40:08 2014 -0500 Modify FragmentCM to use ClaimingMover::state_check and allow FragmentCM to claim cut biases. commit fc7bb6b23c7d0573c99a8dd57e90ecb2db37ef3e Date: Thu Jun 12 13:31:17 2014 -0500 Add ClaimingMover::state_check to help with failing attempted changes to claiming-involved member variables after claiming. commit 80632092164512300121816cabecd683e6fde5f5 Date: Thu Jun 12 13:07:50 2014 -0500 Add basic unit test. commit 0ba2dcbac8c0ae2a5ec8ea67192ecd50cef81dbb Date: Thu Jun 12 13:23:47 2014 -0400 unifying context_independe and context_dependent geom_sol calculations. Wish these weren't different files that require maintenance, but that's the way ScoringMethods work now. Most of the work is in the shared Evaluator class, and there are comments at the top of these file to apply updates from one to the other. commit c693d1015d6c33ed8477f87597ca5352fa07b140 Date: Thu Jun 12 19:10:15 2014 +0200 Fix a few bugs in FragmentCMTest. commit 1ebe689c33c93431b0e6b99ea533d9e0d9f1a73a Merge: e5c42e2 a118c71 Date: Thu Jun 12 19:58:14 2014 +0300 Merge branch 'master' of github.com:RosettaCommons/main commit e5c42e2591ff4acc8caaa63f44b331132fefff86 Date: Thu Jun 12 19:55:08 2014 +0300 Corrected fold tree in Splice commit d268c0706a79ec27954a7644df710d634428783f Date: Thu Jun 12 19:53:47 2014 +0300 Added new PSSM files to Rosetta splice database commit 3d6f10bdc7174f368abf62c518aae567767de644 Merge: c695541 a118c71 Date: Thu Jun 12 12:18:25 2014 -0400 Merging master in to peptoids commit 1841747bf872b336fd7eb6caf534e7e0f3a01db4 Date: Thu Jun 12 11:02:58 2014 -0500 Add FragmentCM::apply testing function, fix fragment loading bug. commit c69554146ee9d8313728d876733ee6d239a4142a Date: Thu Jun 12 11:23:56 2014 -0400 AtomICoor connection check assumed only one connection and issued a warning if there was more than one. Change != to > to support multiple connections without warning. commit a541608b7f583e2e33c1640092f1df8ea00b2345 Merge: e296f5f a118c71 Date: Thu Jun 12 08:37:32 2014 -0400 continuing to merge msater into this "pre-merged" branch while I wait for a broken pyrosetta build commit e296f5fddf740b77dc9d4c0a17e9a8d68165a602 Date: Thu Jun 12 08:31:02 2014 -0400 Stripping out mp apps and scripts from master merge commit a118c710bed1eefea916e9d7db63282c69f3d208 Merge: 6115db3 6155036 Date: Wed Jun 11 20:44:13 2014 -0700 Merging vmullig/ncaas into master to alter the way rama handles nonstandard connections. --Eliminated the rama_score_nonstandard_connections option. This is now the default behaviour. (That is, if a residue is connected to something that is not the i+1 or i-1 residue, or if the connection is not a traditional C->N connection, rama can still score the residue). --Fixed a few problems with Ramachandran.cc that were causing unit tests to fail with the new behaviour. --Added connect_map_size() method to the Residue object (useful for a quick check in Ramachandran.cc to fix one of the afore-mentioned bugs). Unit test status: All pass (EXCEPT for DdgFilter:test_filter_parsing and DdgFilter:test_use_filter, which were failing before.) Integration test status: 4 changed tests --These are all expected changes, due to backbone-to-sidechain connections in which the terminal backbone residue is now scoring with rama. --The changed tests are: UBQ_E2_thioester_extra_bodies UBQ_Gp_LYX-Cterm UBQ_E2_thioester UBQ_E2_thioester_two_ubiquitins --Note that some of the above tests seem to be failing to run sometimes. I couldn't reproduce this on my system, but it seems to happen on the test server, and might be related to my earlier changes to the CYX residue type. I'll try to diagnose and fix this at some point in the future. On branch master Changes to be committed: (use "git reset HEAD ..." to unstage) new file: source/src/apps/pilot/vmullig/ncaa_notes.txt modified: source/src/basic/options/options_rosetta.py modified: source/src/core/conformation/Residue.hh modified: source/src/core/scoring/Ramachandran.cc modified: source/src/core/scoring/methods/RamachandranEnergy.cc commit 6155036e55b2d46fa6cfc1db7ce685b7d2d17eca Date: Wed Jun 11 20:17:55 2014 -0700 Hacky fix to a problem with the changes in Ramachandran.cc that only crops up in weird situations. commit 3d3d74d57e73131ee20d0ef35ad3a1a6ff8a0584 Merge: 8d5e88e b35da3d Date: Wed Jun 11 21:36:24 2014 -0400 mergning in ninja naive docking application and membrane framework relax starting copy into mpframework devel commit 8d5e88e35da7cdde33bdbe3e917eae1dabc37ba8 Merge: 6a00b07 f6d8ff4 Date: Wed Jun 11 21:35:39 2014 -0400 merging ninja mpframework devel with ninja master pulled on 6/11/14 commit f6d8ff43f424a08f33cb2aba1716460935abac48 Merge: 21e17b8 6115db3 Date: Wed Jun 11 21:34:56 2014 -0400 merging branch master on remote into ninja master 6/11/14 commit c4ca07d5bc754fa89a8b821daa920948ac04575c Merge: 19fd6cb 6115db3 Date: Wed Jun 11 18:27:37 2014 -0700 Merging master into vmullig/ncaas for integration testing. commit b35da3d1e4889928ae3d9e1f585fcf2cb2b3a7f0 Date: Wed Jun 11 21:24:16 2014 -0400 Compilation fixes to embedding methods commit 34d6e032318ed06d6cee491b28f4de33fa71d325 Date: Wed Jun 11 21:00:31 2014 -0400 Bug fixes, should compile and do embedding update from structure. Downside is that scoring is still caling the shots, and should be done via lazy update from pose commit de0eec40082b5d47b98d0aa11f177a980fadd090 Date: Wed Jun 11 20:46:31 2014 -0400 removing hacky embedding update methods - moving into a static methods class commit 19fd6cb3a8d0369a6ba222e03430749cbdb16110 Date: Wed Jun 11 17:43:42 2014 -0700 Fixed problem with Ramachandran.cc that was causing unit tests to fail. commit 28c06d6bd87176a371fb5fd712d4daed8135d0b6 Date: Wed Jun 11 20:15:25 2014 -0400 Adding a reasonable version of relax, and starting files for separated embedding mehtods and new mover class commit a2477f8d92363306183e23b7452f8e3c8200427a Date: Wed Jun 11 18:55:57 2014 -0500 Initial trials on the graph mapping cases. commit 6115db35f773a6443d76c32c986c513286eb004e Date: Wed Jun 11 18:58:48 2014 -0400 remove unused variable commit 495349a0274d1b89fb1414f9e531209eb8c94ddb Date: Wed Jun 11 17:26:54 2014 -0500 Initial pass for heuristic atom matchups. commit 366e1afe84f77f942eb969e707d7ab248dc0f9d1 Date: Wed Jun 11 23:56:49 2014 +0200 Remove cout calls from FragmentCMTest. commit 1410f704da378ee994e7c8da48b9b3a7915de3a4 Date: Wed Jun 11 16:01:09 2014 -0500 Add multi-chain and fragment shift unit test to FragmentCMTest. commit 2c9dac8adb3fed8b423fb45a2792ce698375d33d Date: Wed Jun 11 15:14:17 2014 -0500 Fix a bug where FragSet::min_pos and FragSet::max_pos would read out double-offset values. commit 36b93d065bc363c884c9d87ce617422425a6e981 Date: Wed Jun 11 11:41:32 2014 -0500 Update set_selector and set_mover in FragmentCM to complain if its already issued claims. commit 3f720b61057420fd054626e9bec511ccf45d88c1 Merge: fba86c3 49f0648 Date: Wed Jun 11 16:55:04 2014 -0400 Refactor GraftMover classes Refactor GraftMoverBase, AnchoredGraftMover, and utility functions in protocols/grafting to be more extendable. Separate logic for cartesian-space fixed insert protocol into its own class, CCDEndsGraftMover. This logic of this GraftMover's apply is as follows (Based off of AnchoredGraftMover): /// 1) superimposes the insert onto the scaffold using any overhang residues, /// 2) Inserts the pose piece into the scaffold pose, deleting any overhang residues. /// 3) Cycles of: /// a) SmallMover for sampling (Can be disabled)) /// b) CCD of both terminal ends of the scaffold using flexibility settings or movemap /// to close the graft. /// c) MinMover to help close the graft through chainbreak terms /// d) Closure check - will return if closed (Can be disabled) /// d) MonteCarlo Boltzmann criterion /// /// 4) Repack flexible residues, insert residues, and neighbors (can be disabled) Make smooth centroid scoreterms default in both classes Have AnchoredPDBCreator use dfpmin_armijo_nonmonotone mintype Update unit tests, add unit test for RestrictToMoveMapChiOperation. Rename two antibody design movers ---------------------------------------- Integration test status: [ 2 ] AnchoredPDBCreator: Will fail from change in mintype and centroid scorefxn antibody_designer: Will fail from a number of changes, but this is fine. commit 49f0648bab56773efa8d859842eed96a55e96419 Date: Wed Jun 11 16:54:42 2014 -0400 fix tab commit cbf1ab0462b92fc9c6135cd0c4d0a4d2732b7872 Date: Wed Jun 11 16:51:47 2014 -0400 update output and doc strings commit 289bfb3f84893fdeca37e387bf63d075437683cb Merge: 7cc89e5 fba86c3 Date: Wed Jun 11 14:21:00 2014 -0400 Merging master in to peptoids commit 7a66604fa8a56299f4b2fa09c6789b6f001d0b95 Date: Wed Jun 11 13:56:30 2014 -0400 finish debugging graft refactor commit fba86c316bc84dfbbcc3197baef4baad21365933 Date: Wed Jun 11 12:44:54 2014 -0500 Attempt to fix UBQ integration tests I'm not entirely sure why this issue just recently started showing up. (It looks like it should have occured a long time ago.) commit 12f07fd8cf2e858ddc755385742b6451208c9f56 Date: Wed Jun 11 11:39:12 2014 -0500 Fix build commit 8a5209aa604ea0d671dfb6611e6b5582e3bc142a Date: Wed Jun 11 18:18:04 2014 +0200 Fix bugs in FragmentCMTest commit 9eb764e53ac2505b0caad33cff6cf92e21afc111 Date: Wed Jun 11 11:44:19 2014 -0400 fix restrict mm chi op unit test commit 11b5a41ce71bbf64c1ae4abbd8e5012f7684a6ab Merge: 1f2b7cb 6981795 Date: Wed Jun 11 10:26:30 2014 -0500 Surface complementarity error handling Small changes for better handling of sc error conditions. Shouldn't affect non-error sc pathways. commit aa142ac72c9b21606617480352e97a6fe498f998 Merge: 66d0b76 3bdeb7f Date: Wed Jun 11 16:53:24 2014 +0200 Merge branch 'justinrporter/env_release' into justinrporter/env_devel (update to master.) commit 3bdeb7f0c3b1ac90c13e87d98fc1f40ef4038103 Merge: f6d3a2b 1f2b7cb Date: Wed Jun 11 16:52:33 2014 +0200 Merge branch 'master' into justinrporter/env_release commit 1cf7a0e23d8d87459f37bda254eb2fd6627d1762 Date: Wed Jun 11 10:50:34 2014 -0400 Making some multithreading fixes without much luck commit 1bc04b3504b2e106ee92ea2cc3c54b2defe56b1a Date: Wed Jun 11 10:09:12 2014 -0400 Killing internal creation of a membrane pose in fast relax protocol - not the right way to go commit 6eb14d55e07d91de20783a92039f6a9afb7a51b5 Date: Wed Jun 11 09:10:26 2014 -0400 Trying to get the framework relax version to run in parallel with jd2 - temporarily removing conformation warnings...wait not a good idea hold on commit 2708bbc72ed14ad36b2a267458fecffd7bd4e82d Date: Wed Jun 11 01:23:38 2014 -0700 Blargh -- still have the same bug in GeneralizedKIC.cc. When trying to close a particular loop, I'm getting the terminal residue pulled out of the backbone by its sidechain connection... Will track down tomorrow. commit f03fa0c95b5586dbcf25ffe3d2d1af9be13e5b0b Date: Wed Jun 11 00:42:45 2014 -0700 Trying to track down a bug in GeneralizedKIC that's causing a loop to tear apart... commit 212859d9123a42d43494ef01d94e3e81656a1234 Date: Wed Jun 11 00:11:28 2014 -0700 OK -- I think I fixed the bug just introduced into GeneralizedKIC.cc commit f2e0b0aeddec32e1a54a98c65594df8f348f7410 Date: Tue Jun 10 23:59:18 2014 -0700 Trying to remove the requirement that the first pivot atom be in the first loop residue in GeneralizedKIC... but I've introduced some weird bug. commit afa1f79ea1437b24b782ad66102da9a4eb66f362 Date: Tue Jun 10 21:56:21 2014 -0700 Trying to get changes to Ramachandran.cc working with all unit tests. Currently, about 10% fail, all for the same reason (which I don't fully understand yet, but will work out). commit ffa8a64fd3bd91e6a6ca83efd0d8ed71de120434 Date: Wed Jun 11 00:44:52 2014 -0400 add unit tests for more grafting utility functions as well as RestrictToMoveMapChiOperation commit 66d0b76c835c8f6db1d358980611b94298f7789d Date: Tue Jun 10 22:18:54 2014 -0500 Add FragmentCM unit test and helper fragments. commit 37613ef6f8c29fc046fec1bfa3b52722ca8251df Date: Tue Jun 10 22:18:04 2014 -0500 Add an initialize option to turn off FragmentCM and FragmentJumpCM initialization. commit 6a83c2636fc270cf5cbebcc5a58ab381f59c2e01 Date: Tue Jun 10 22:17:18 2014 -0500 Fix a bug in managing end-of-chain nonexistant DoFs. commit 5079e72fb5cac4af6edfa13f04400325c88921c2 Merge: 7b6b2ce 1f2b7cb Date: Tue Jun 10 18:48:18 2014 -0700 Merging master into vmullig/ncaas commit f6af48ce78f2fc419e0bccfee94c1807cbdb7225 Date: Tue Jun 10 17:54:48 2014 -0400 commit 7cc89e5059a9efc0fbbc6d9e6fef95ea37f113e0 Date: Tue Jun 10 16:54:11 2014 -0400 Updatig MakeRotLib unit test to work with new lower case namespace name. commit c61c47afa1570111927eaecc2ac0746e03f48af6 Merge: 7e7612f 1f2b7cb Date: Tue Jun 10 14:55:43 2014 -0400 Merge master in to peptoid commit 7e7612f8e2d1691a3e83e3c8d2b1eb645b0b0929 Date: Tue Jun 10 14:52:29 2014 -0400 Fixing warnings commit 1f9bf2e059d3d24c64429efd693f42fab595af3c Merge: 99e6f89 9fa4440 Date: Tue Jun 10 10:21:06 2014 -0400 Merging in mprelax branch into mpdocking branch so I can get the mp solvation term fix commit 768e05b672a0822d11d075361c61bdc894604aad Date: Tue Jun 10 00:20:02 2014 -0400 debugging commit 1f2b7cb69f67d2dc95961a94eaef405a83b7bf85 Date: Mon Jun 9 20:35:17 2014 -0700 Minor changes to GeneralizedKICfilter.cc. No integration test or unit test changes expected. --Also made changes to the design_cycpeptide_MPI.cc pilot app. --This commit turns off an app in pilot_apps.src.settings.all; the previous one is the actual merge commit. commit fe609029de5d1470e67705f14e2da8a1bf92896a Merge: a1f2ca2 915f13c Date: Mon Jun 9 20:33:22 2014 -0700 Merging vmullig/cycpep into master to make a minor fix to GeneralizedKICfilter.cc. commit 915f13ce63d9a55608473ca9bf39f7e5d8ea5219 Date: Mon Jun 9 20:25:03 2014 -0700 Fix to GeneralizedKICfilter: the greater than option now works for the distance filter. commit b14c74911296ec74409ea1863fb07975dd593e7b Date: Mon Jun 9 22:49:14 2014 -0400 work on debugging commit 7fb076205989e1b0dc0fc0b5a386ad23853ff811 Date: Mon Jun 9 17:58:26 2014 -0700 The design_cycpeptide_MPI app now correctly handles initialization of the sequence with the in:file:fasta flag. commit 9fa444010ca041061daf6515cbc81190cfdb0971 Date: Mon Jun 9 19:57:08 2014 -0400 Adding penalty terms to fullatom membrane weights commit 0e9a6cc6d4cb9f758e6bd1c8093df44ba70a6ea1 Date: Mon Jun 9 18:22:11 2014 -0400 Updating fullatom energy terms to do a hacky structure-based embedding update for now - also added an update method in conformaiton becasue it seems like the OP in membrane info isn't really talking to conf very well commit 3b71936caa458f8925b8cc2a213a87672a87fd68 Date: Mon Jun 9 14:47:55 2014 -0700 Trying to fix a problem with design_cycpeptide_MPI.cc: if the user specifies that a position isn't to be mutated, but sets it to something different than the input file with the -in:file:fasta flag, that position isn't being initialized properly. commit a1f2ca27bb9b3d59d5a61f589931ba4866103aa4 Date: Mon Jun 9 22:04:14 2014 +0200 Implement unimplemented method (fixing PyRosetta build error)." commit d1a6b9aaf49e1f0260d15f608b03dc826a8be1b5 Date: Mon Jun 9 14:36:56 2014 -0400 Commenting out test_utility_exit unit test commit 050e0b43be8d617b3ceddf6afbc0e161581f376a Date: Mon Jun 9 14:08:33 2014 -0400 added missing classes commit ce0240182107ef6004a75c90abe00e01c489ed5d Date: Mon Jun 9 14:01:51 2014 -0400 renaming GeometricSolEnergy to ContextDependentGeometricSolEnergy, and some code cleanup in there. commit 9a9def49d420f5901266b7dfa185e2bb674d1493 Date: Mon Jun 9 13:38:56 2014 -0400 Testing Benchmark server utility script. Adding dummy unit test that just call utility_exit. commit d68fffe38fae92fc41bbeedc91c12c975ff8a56c Date: Mon Jun 9 12:30:10 2014 -0400 in geom_sol code, getting rid of pass_check() function that was used for debugging. commit 15fd6013f4e9eac450b81ec473dd073ebc3f0026 Date: Mon Jun 9 12:25:10 2014 -0400 removing copied/ugly code from geom sol derivative setting by combining into reused functions. commit c4ff0304e6eb955c620477bb1940b062ec2c53c8 Date: Mon Jun 9 12:16:10 2014 -0400 Making temporary updates to membrane relax protocol - will make fixes later to the actual runtime events" commit 08726482faf20fb7d755c55a682a69f7222cd718 Date: Mon Jun 9 18:15:01 2014 +0200 Fix several 'TagCOP const' calls. commit 8a5cd4243312206462a614cd7804f2988ceaa7c9 Date: Mon Jun 9 12:05:23 2014 -0400 continuing simplification of geom_sol derivative calculations, including removal of redundant sign flips. commit 54a7aa0045c244fde2d48578f6b18b3f2b139777 Date: Mon Jun 9 11:56:47 2014 -0400 setting abase2 atom properly for geom sol. allowing for input/output of HBEvalTuple from core geom_sol calculation, to maintain consistency. Some cleanup of comments. commit 1ca27dbe85dcccc709f6e5879c2471672ab8698d Date: Mon Jun 9 11:17:49 2014 -0400 deprecating use_incorrect_deriv option -- no more use cases since geom_sol derivative calculation is fixed. commit 0a779b8b6e7171d4ba1355eaca9cdd4385226283 Date: Mon Jun 9 11:12:12 2014 -0400 updating names of HBDerivType from hbderiv_ABE_GO_NO_xD and hbderiv_ABE_GO_NO_xH to hbderiv_ABE_GO_GEOMSOL_OCC_ACC and hbderiv_ABE_GO_GEOMSOL_OCC_DON, to clarify that they are in use (only) for geom_sol derivatives. Getting rid of deprecated code block with incorrect hb derivatives. commit 369aed8149e1767758c5d644999eae9481bf484e Date: Mon Jun 9 10:56:21 2014 -0400 Derivatives work for geom_sol_fast! Code needs cleanup, though commit c1e180cdfb1bae2e0ab9e5720cd1d3d8ded7dba8 Date: Mon Jun 9 10:52:27 2014 -0400 update to hbonds derivative calculation to give exact derivatives for geom_sol. commit 5ca2221834caa7903533111d9cc283d57af7f24f Date: Mon Jun 9 10:45:58 2014 -0400 Updating gitignore to ignore the Xcode project .oirig file. For some reason we have both .orig and .template, but the project file generation script only looks for .template. This should help with some confusion. Also, removing project.pbxproj.orig commit b5945c0daf8e4b7ed929433ecf241acf943fa86c Date: Sun Jun 8 22:00:42 2014 -0400 update unit tests for refactor commit e3ec57513e51e1af29f47ff2e42d67a7bd284235 Date: Sun Jun 8 21:43:52 2014 +0200 Fix header build actually, and fix next error in PyRosetta build. commit 774b40161fa4935ee0bb40f2393d165252206a24 Date: Sun Jun 8 15:11:27 2014 -0400 update to geometric sol evaluator to allow rigorous derivative calculation even if bond lengths/angles move at atoms. commit 0f93d9ca42cb489c2afe3f38357b0f16c4f37bd3 Date: Sun Jun 8 15:10:23 2014 -0400 updating hbonds deriv computation to work properly with geom_sol commit 218ec5466029698e806bfedf58325813287d095d Date: Sun Jun 8 19:56:04 2014 +0200 Fix header build and (second try) to fix PyRosetta build. commit 99e6f89112cc21ada2eebefe155eec3957a99e24 Date: Sun Jun 8 12:20:04 2014 -0400 Adding a ridiculously naive version of a membrane protein-protein docking application commit f48684e52552b04490c8395ba559c17b723f93c4 Date: Sun Jun 8 11:03:30 2014 -0400 fix ab naming changes botched in cherry pick commit c4bb9586546d2db65f67b0a5141371bb9a59abdd Date: Sun Jun 8 10:34:41 2014 -0400 start testing commit e381e51f8663520374cec901ecc14470d99b8b71 Date: Sat Jun 7 18:41:33 2014 -0400 cherry_pick graft refactoring commit 27000816fcf05d26ed099a8203deff33eeffcb0a Date: Sat Jun 7 11:23:45 2014 -0400 cherry_picking commits for graft refactor commit 57f738073b3bbd78e59340cffe25df6ad431ec7a Date: Thu Jun 5 14:33:22 2014 -0400 add new constructor for GraftMovers commit 759f5a0aa9580b5477c9245cad7f2b745902f3e5 Date: Tue Jun 3 14:58:29 2014 -0400 cherry_pick graft refactoring commits commit 6a00b07c11d04ad92c7d94b53add6da85f231c6a Date: Sun Jun 8 10:42:56 2014 -0400 Adding warning boxes for deprecated old membrane scoring code commit a5d58f42f8a602f8f8fa88066e468d6bba9e8cc0 Date: Sun Jun 8 04:27:20 2014 +0200 Fix memory output causing repeated integration test differences. commit 859829d44047db089afcd9600cc691b69c61c652 Date: Sat Jun 7 18:31:20 2014 -0400 Adding dissulfide fix commit e890106d29ecf5b9ed6bab835f196cb21d4e3f34 Date: Sun Jun 8 00:27:08 2014 +0200 Attempt to fix PyRosetta build. commit 23664bdfce27cf35017ccf85f242280ad88c6977 Date: Sat Jun 7 22:03:43 2014 +0200 Fix build. commit 64a7a9c02f1c3856c432f1ac51aded93155869a1 Merge: 24f5aad ca6e89d Date: Sat Jun 7 15:19:35 2014 +0200 Including latest updates to Environment system, including improved unit test coverage, improved virtual residue handling, residue selector use, and numerous bug fixes. Trivial log integration test changes expected in all rosetta scripts applications. commit 2b15e4c7a0cbae2c5fd71d3f132078a5494490ac Date: Sat Jun 7 00:23:48 2014 -0400 Updating membrane fullatom weights file commit c82dbf4638cd277c50d802ed5012bd33280af451 Date: Fri Jun 6 21:57:54 2014 -0400 Add cxx_ver to test/run.py commit 954149a2eabe36aec46dc184b1a3937578209b56 Date: Fri Jun 6 19:46:02 2014 -0400 Turning fullatom solvation energy back on for membranes - going to start debugging what's wrong commit 00ddb3c7daba957409e6a035b97cb424370e66de Date: Fri Jun 6 16:55:12 2014 -0500 Modify FragmentCM to use a ResidueSelector rather than the label system. commit 24f5aad67914dbba6ce7e1a4f20253b548dfa145 Date: Fri Jun 6 17:15:09 2014 -0400 Fixing unit tests that were affected by the MAX_RESIDUE_TYPE limit. Nine core unit tests and one protocols unit test have actually been "silently" failing due to the new max residue types limit. The patches.txt file has recently been edited to cut down on the number of ResidueTypes created and a limit of 3000 ResidueTypes has been set on the size of the ResidueTypeSet (limit is controllable from the options system). Only the fa_standard/patches.txt was edited however. Tests that call the -restore_pre_talaris_2013_behavior flag don't observe the changes to fa_standard/patches.txt were affected by the limit on the ResidueTypeSet. They hit the limit and then utility_exit. For some reason, they not register as failing. Unit test status: [All Pass except for DdgFilter on linux gcc] Integration test status: [No test changes expected] commit 53541aecd8ee0d69214c1f05f7259473256aaa93 Date: Fri Jun 6 16:29:43 2014 -0400 Membrane relax plus JD2 - up and running. Now to just make structures work commit cd31a2f40ad0aa87bc1e8635a664e1ecf8994f3e Date: Fri Jun 6 11:57:52 2014 -0400 fixing tracer names throughout stepwise code commit 2f47e83059232d8a1e7d5b7331204f7b5411c0a3 Date: Fri Jun 6 10:57:15 2014 -0500 Add parse_my_tag to FragmentCM. commit 97262cc70b6599faa6f5d27e1f8b6354c40cb8e0 Date: Fri Jun 6 11:57:09 2014 -0400 Removing duplicated virtualBB.txt patch from patches.txt This should fix the rotamer recovery unit test. I am not sure why the unit tests did not skip the patch like the integration tests do. I suspect the ResidueTypeSet is construcutred differently in the unit tests. Unit test status: [All test pass except DDG tests that are currently failing still fail] Integration test status: [11] 10 cosmetic integration tests changes relating to virtualBB.txt no longer being skipped. What looked like rounding differences in the ligand docking integration test occured on my system. commit 3b609a2377ffc483ac4e79b147ee4014c81dd158 Date: Fri Jun 6 11:56:03 2014 -0400 a little more cleanup of namespace definitions throughout stepwise and RNA code. commit 1f7ad7ba6d0bcbaf6ae2d2972de978a896136654 Date: Fri Jun 6 11:49:14 2014 -0400 fixing namespaces throughout stepwise/ commit 37c8896a28bd343aca51246dedf1a63f179c4399 Date: Fri Jun 6 10:17:55 2014 -0500 Remove mutable updateMM parameter from FragmentCM. commit 244efedb010d63ce22ef9108fa1a439b00672a5c Date: Fri Jun 6 18:05:06 2014 +0300 Changed fold tree in Splice.cc commit 1f73f055cbc9c4bf8b0251676480a8cfe26cb7d7 Date: Fri Jun 6 09:23:04 2014 -0400 fixing up namespaces throughout stepwise/legacy/ commit 88c2bf6dbef6de880ab05ba86dab220d8ae70518 Date: Fri Jun 6 09:12:27 2014 -0400 Bug fix for residue com method - used to be ambiguous when moved to protocols commit 6fd34da806ccbdce8457e1e74b67ee57370fe8ae Merge: 75687f6 9d8fff5 Date: Fri Jun 6 15:54:19 2014 +0300 Merge branch 'master' of github.com:RosettaCommons/main commit 75687f674c99e479f0d2475db36a1f35be30df12 Date: Fri Jun 6 15:51:20 2014 +0300 Updated PSSM library for splice commit 0e0c236af10db006d11ed19dc3ca5314e9c91d67 Date: Fri Jun 6 08:47:49 2014 -0400 collating all stepwise legacy/ subdirs into one directory commit 41653162d43858daa1d278f2d0c7abb5e757ed94 Date: Fri Jun 6 15:47:32 2014 +0300 Corrected fold tree definitions commit d47ef09342df78e5863d6cfb150ba516f6bb0190 Merge: 004fc5d 21e17b8 Date: Fri Jun 6 07:58:25 2014 -0400 Merging master into mpframework devel in test branch commit 21e17b840f5c97c6ac10ba50141a9d3874c1b642 Merge: 063af32 9d8fff5 Date: Fri Jun 6 07:56:35 2014 -0400 Merging remote master into ninja local master commit 74de4b4ff39e8a814a75e42783628d88751faf35 Date: Thu Jun 5 19:57:14 2014 -0700 Small bugfixes for multicomponent symmetry commit 77bfd958d3bc466e12d95d06db52e202ece9efcc Date: Thu Jun 5 22:47:10 2014 -0400 Updating membrane relax app with some quick debugging changes commit 0b3a360e9dcaaa54f28f5224228d2b48309fe562 Date: Thu Jun 5 19:28:17 2014 -0700 Removing a few redudant pilot apps. Small update to setup_for_symmetry commit f2345bb694382d0e98e184809d3831a8a1a60c71 Date: Thu Jun 5 18:06:57 2014 -0700 Re-adding bettercluster in pilot_apps.src.settings.all. commit 9d8fff56b394f5f9751f8f5ca412c3f881a78e37 Merge: 11dbf77 6123a80 Date: Thu Jun 5 17:52:36 2014 -0700 Merging vmullig/cycpep into master to bring in a number of important changes: --Certain residue types have been updated (sidechain-conjugation types and crosslinker types) and new ones added. Note that the new residue types are OFF by default in residue_types.txt (as they should be!) --Wendao's BBG mover is a part of this branch. --Improvements to the logic for adding residues by bond, jumps, etc., needed for building complicated cyclic peptides. --Improper dihedrals added to residue types. --Considerable improvements to the PeptideStubMover, GeneralizedKIC, and other tools for modelling complicated cyclic peptides. --Support added to SilentFilePoseInputStreams for loading poses in the order in which they appear in a file, instead of in alphabetical order of tags. --Added a flag to force big-endian/little-endian flipping on binary silent file read (for cases in which automatic detection fails). --A few pilot apps have been added, including bettercluster.cc, design_cycpeptide_MPI.cc, and PCA_visualizer.cc. Unit test status: ALL PASS (prior to merging master -> vmullig/cycpep, since the current master already has three broken unit tests) Integration test status: 6 changed tests, all with expected changes FAIL UBQ_E2_thioester_extra_bodies --Uses the sidechain-conjugation residue types, which have been updated. FAIL ligand_dock_script --Seems to be a numeric precision issue, not a true failure. FAIL UBQ_E2_thioester --Uses the sidechain-conjugation residue types, which have been updated. FAIL UBQ_Gp_LYX-Cterm --Uses the sidechain-conjugation residue types, which have been updated. FAIL broker --Trivial change to output messages when binary silent file big-endian/little-endian flipping occurs. FAIL UBQ_E2_thioester_two_ubiquitins --Uses the sidechain-conjugation residue types, which have been updated. modified: database/chemical/residue_type_sets/fa_standard/patches/N_acetylated.txt modified: database/chemical/residue_type_sets/fa_standard/residue_types.txt new file: database/chemical/residue_type_sets/fa_standard/residue_types/crosslinker/1.2_bisbromomethylbenzene.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/crosslinker/1.3_bisbromomethylbenzene.params new file: database/chemical/residue_type_sets/fa_standard/residue_types/crosslinker/1.4_bisbromomethylbenzene.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/crosslinker/BoronateLDopa.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/sidechain_conjugation/ASX.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/sidechain_conjugation/CYX.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/sidechain_conjugation/LYX.params new file: source/src/apps/pilot/vmullig/PCA_visualizer.cc new file: source/src/apps/pilot/vmullig/alglib/alglibinternal.cpp new file: source/src/apps/pilot/vmullig/alglib/alglibinternal.h new file: source/src/apps/pilot/vmullig/alglib/alglibmisc.cpp new file: source/src/apps/pilot/vmullig/alglib/alglibmisc.h new file: source/src/apps/pilot/vmullig/alglib/ap.cpp new file: source/src/apps/pilot/vmullig/alglib/ap.h new file: source/src/apps/pilot/vmullig/alglib/dataanalysis.cpp new file: source/src/apps/pilot/vmullig/alglib/dataanalysis.h new file: source/src/apps/pilot/vmullig/alglib/diffequations.cpp new file: source/src/apps/pilot/vmullig/alglib/diffequations.h new file: source/src/apps/pilot/vmullig/alglib/fasttransforms.cpp new file: source/src/apps/pilot/vmullig/alglib/fasttransforms.h new file: source/src/apps/pilot/vmullig/alglib/integration.cpp new file: source/src/apps/pilot/vmullig/alglib/integration.h new file: source/src/apps/pilot/vmullig/alglib/interpolation.cpp new file: source/src/apps/pilot/vmullig/alglib/interpolation.h new file: source/src/apps/pilot/vmullig/alglib/linalg.cpp new file: source/src/apps/pilot/vmullig/alglib/linalg.h new file: source/src/apps/pilot/vmullig/alglib/optimization.cpp new file: source/src/apps/pilot/vmullig/alglib/optimization.h new file: source/src/apps/pilot/vmullig/alglib/solvers.cpp new file: source/src/apps/pilot/vmullig/alglib/solvers.h new file: source/src/apps/pilot/vmullig/alglib/specialfunctions.cpp new file: source/src/apps/pilot/vmullig/alglib/specialfunctions.h new file: source/src/apps/pilot/vmullig/alglib/statistics.cpp new file: source/src/apps/pilot/vmullig/alglib/statistics.h new file: source/src/apps/pilot/vmullig/alglib/stdafx.h new file: source/src/apps/pilot/vmullig/bettercluster.cc new file: source/src/apps/pilot/vmullig/design_cycpeptide_MPI.cc modified: source/src/apps/pilot/wendao/test_bbmc.cc modified: source/src/basic/options/options_rosetta.py modified: source/src/core/chemical/ResidueType.cc modified: source/src/core/chemical/ResidueType.hh modified: source/src/core/conformation/Conformation.cc modified: source/src/core/conformation/Conformation.hh modified: source/src/core/conformation/Residue.cc modified: source/src/core/import_pose/pose_stream/SilentFilePoseInputStream.hh modified: source/src/core/import_pose/pose_stream/util.cc modified: source/src/core/import_pose/pose_stream/util.hh modified: source/src/core/io/silent/BinarySilentStruct.cc modified: source/src/core/io/silent/SilentFileData.cc modified: source/src/core/io/silent/SilentFileData.hh modified: source/src/core/io/silent/SilentStruct.cc modified: source/src/core/io/silent/SilentStruct.hh modified: source/src/core/kinematics/FoldTree.cc modified: source/src/core/kinematics/FoldTree.hh modified: source/src/core/pose/Pose.cc modified: source/src/core/pose/Pose.hh modified: source/src/pilot_apps.src.settings.all modified: source/src/protocols/cyclic_peptide/CreateAngleConstraint.cc modified: source/src/protocols/cyclic_peptide/CreateAngleConstraint.hh modified: source/src/protocols/cyclic_peptide/CreateDistanceConstraint.cc modified: source/src/protocols/cyclic_peptide/CreateDistanceConstraint.hh modified: source/src/protocols/cyclic_peptide/CreateTorsionConstraint.cc modified: source/src/protocols/cyclic_peptide/CreateTorsionConstraint.hh modified: source/src/protocols/cyclic_peptide/PeptideStubMover.cc modified: source/src/protocols/cyclic_peptide/PeptideStubMover.hh modified: source/src/protocols/generalized_kinematic_closure/GeneralizedKIC.cc modified: source/src/protocols/generalized_kinematic_closure/GeneralizedKIC.hh modified: source/src/protocols/generalized_kinematic_closure/filter/GeneralizedKICfilter.cc modified: source/src/protocols/generalized_kinematic_closure/filter/GeneralizedKICfilter.hh modified: source/src/protocols/generalized_kinematic_closure/perturber/GeneralizedKICperturber.cc modified: source/src/protocols/generalized_kinematic_closure/perturber/GeneralizedKICperturber.hh modified: source/src/protocols/generalized_kinematic_closure/selector/GeneralizedKICselector.cc modified: source/src/protocols/generalized_kinematic_closure/selector/GeneralizedKICselector.hh modified: source/src/protocols/generalized_kinematic_closure/util.cc modified: source/src/protocols/simple_moves/BBConRotMover.cc modified: source/src/protocols/simple_moves/BBConRotMover.hh modified: source/src/protocols/simple_moves/BBGaussianMover.cc modified: source/src/protocols/simple_moves/BBGaussianMover.hh commit 6123a806b80c1d4dd2e3ba047ee16e3bac871ccc Date: Thu Jun 5 17:31:08 2014 -0700 Commenting out bettercluster.cc in pilot_apps.src.settings.all prior to merge with master. Will uncomment later. commit d23fbe5f1df2e875cedee14304f1da90681d9710 Merge: f657f25 11dbf77 Date: Thu Jun 5 17:09:57 2014 -0700 Merging master into vmullig/cycpep in anticipation of the reverse operation. commit 41e08ff9c56c747aa637489c1d70e29545c1263f Date: Thu Jun 5 15:41:15 2014 -0700 Randomizing a jump translation no longer resets nonmovable dofs to 0 commit 7b6b2cec89d5bf16da7fd17622cfd915830092ba Date: Thu Jun 5 15:28:49 2014 -0700 Taking out the rama_score_nonstandard_connections option, and making this the default Rosetta behaviour. commit f557261cfee4e8791f32652b4d7dcd69502ecc6b Date: Thu Jun 5 18:05:40 2014 -0400 Starting to debug crazy twobody energy bug commit b4bc35b89d3f28f920eff133dcdd6b64e9e29d98 Merge: 50d60a3 11dbf77 Date: Thu Jun 5 17:39:20 2014 -0400 Merge branch 'master' into khouli/buns 'merge from master' commit 50d60a3601b0f3f64b7dc8b3f91b8dfea4b950ee Date: Thu Jun 5 17:31:53 2014 -0400 commit 7ef0a1efa58d4c89d14eb3c40c33e1a3f695e349 Merge: b92b7b0 004fc5d Date: Thu Jun 5 17:22:50 2014 -0400 Merging mpframework_devel updates into membrane relax branch commit 004fc5df82f7020b05ba445758718043e02f4a2c Date: Thu Jun 5 17:02:13 2014 -0400 Turning on hbond correction in fullatom scoring function fingerprint test commit 0ed0183c1795910bffcaccab64ce78a6f506347a Date: Thu Jun 5 16:02:41 2014 -0400 Adding sfxn fingerprint tests to use version mpscorefunction app extending from andrew's original score fprint app commit be2b444ddb0d98f977238f5c94ad37c8b94eadce Date: Thu Jun 5 16:00:48 2014 -0400 Adding membrane scorefunction fingerprint application commit f6d3a2b0e1fd318ff5249bd155bba125e2bd0494 Date: Thu Jun 5 14:58:41 2014 -0500 Fix a mistake in RosettaScripts registration of UniformRigidBodyCMCreator. commit 8af54caa58e9ecc45a4aaa1555d99bd80497f256 Merge: c8170c6 11dbf77 Date: Thu Jun 5 12:50:49 2014 -0700 Merging master into vmullig/ncaas prior to doing some tinkering. commit 8041edfdbf97962934ae86ccc462666a1f2be3db Date: Thu Jun 5 11:14:45 2014 -0700 In Bfactor fitting mover, create PDBinfo if it doesn't exist in the pose commit 6628681d576c6f77d4db8144ac2ebc13ad8319f0 Merge: 06d37f3 11dbf77 Date: Thu Jun 5 13:34:05 2014 -0400 Merge master in to peptoid branch commit 0fd6f7231dc59e5296dda63ac1e533fff395dd66 Merge: b289af3 11dbf77 Date: Thu Jun 5 13:01:17 2014 -0400 merge from master to rhiju/swm_general branch. commit 15bad3057f57791b30d615a1830773eae97859b8 Date: Thu Jun 5 09:49:26 2014 -0400 Updating centroid membrane sfxn fingerprint test - now runs commit bfab09df18cffb514b2d97790ffc74ffed81458d Date: Thu Jun 5 09:25:22 2014 -0400 Updating fullatom weights and command file to correct sfxn fingerprint test commit b84e247ca6e777e86448248d7ec31937c480eb38 Date: Thu Jun 5 09:05:19 2014 -0400 Adding readme in membrane directory commit 5af6265389ac9a52c241a40fffb3427f27edf3e2 Date: Thu Jun 5 09:03:53 2014 -0400 Organizing pilot/ralford apps directory and commenting old apps from the build commit b92b7b04278a23f86ccf987d8556b3bf2e65e992 Date: Thu Jun 5 08:51:13 2014 -0400 Adding membrane fullatom weights commit 07a0d31e55bdafb15b84788f24cdbe8dc40d9596 Date: Thu Jun 5 08:48:55 2014 -0400 Updating membrane relax application - uses fullatom 2014 terms for membranes but crashes on number of 2 body energy types - most likely due to readable CA mismatch commit f657f25d799e127e6ff85473ddc9b8d0c186e500 Date: Thu Jun 5 05:24:15 2014 -0700 The in:file:force_silent_bitflip_on_read flag now works to force big-endian/little-endian conversion on binary silent file read. Removing some debugging output. commit c0e97579f9c25e7bc6df18dc56b0895fcf9adac5 Date: Thu Jun 5 05:18:15 2014 -0700 Still trying to get force bitflip flag to work. commit 263757685667c53e77fc277ebf93c65a792f74a6 Date: Thu Jun 5 05:05:34 2014 -0700 Still trying to get the flag working. Making new functions in SilentStruct virtual. commit d7a89479d12183dcdd0840111d6f64bc7958a0a1 Date: Thu Jun 5 04:35:01 2014 -0700 Trying to get flag to force binary silent file endian flip to work. commit ec362bba62705c48160d19ddf55bbd3d9c027d64 Date: Thu Jun 5 03:57:39 2014 -0700 Tweaking output message in BinarySilentStruct.cc trivially. commit 11db3077983a33224a4bf1d9f5576084dab69adc Date: Thu Jun 5 03:50:53 2014 -0700 Trying to get flag forcing bit flipping to work. commit c75434d9d24480e35efb02bc8c26d823644be05d Date: Thu Jun 5 02:58:50 2014 -0700 Trying to add a flag to force bit-flipping (little-endian to big-endian or the converse) on binary silent file import, WITHOUT bit-flipping when binary silent structures are used for other things (e.g. pose transmission between processes). commit 9ca1ab28e4b4ab455891a3e772a51d958ea72c3a Date: Wed Jun 4 20:22:06 2014 -0700 Trying to fix a bug that's cropping up with binary silent file read on the big-endian Blue Gene/Q system. --Blue Gene uses big-endian architecture, unlike the little-endian architecture of the DIGs. --Binary silent files produced on the DIGs must be bit-flipped for Blue Gene. This is done automatically, BUT the detection rule is not a very good one. About one time in a hundred, a structure gets though without being flipped. --I'm adding an explicit flag to force flipping. I should probably add one to suppress flipping, too. --BUT I don't want this flag to trip up the internal generation of structures from silent file data (e.g. when I transmit silent file data between processes), so I need to ensure that it ONLY affects structures on file load. That's not the case right now. commit e351d253aa70bd32385813d57467736169fb8702 Merge: 0ca087b 2fb87d6 Date: Wed Jun 4 21:22:19 2014 -0400 Merge branch 'master' into khouli/buns merge from master commit db2e4863477d8664c5b90b3b59958e4c9609c58e Date: Wed Jun 4 17:58:58 2014 -0700 changing max KIC perturber samples default value back to 2000 commit 06d37f3fc569d45cd251e2bac7773cf69f1563cb Date: Wed Jun 4 16:58:56 2014 -0400 namespace changes to get peptoid design to compile commit ca6e89d6db6040c9eec6b9bd740d5a2839296faf Date: Wed Jun 4 22:41:21 2014 +0200 Fix a bug in UniformRigidBody.cxxtest.hh causing a bad pose to get passed in to test methods. commit 815df0a1640cc5d9992ab49910c2709d5459e84f Date: Wed Jun 4 16:22:30 2014 -0400 Turning off old membrane terms in relax and turning on new membrane framework compatible terms commit 11dbf778159fe409f03a88a8543ff56f88c2b14a Merge: 2fb87d6 382f68d Date: Wed Jun 4 16:07:20 2014 -0400 Updating LoopAnchorFetures and related scripts. The features integration tests will change because both the schema and what is being computed has changed. commit b240a2a0aea36f0608f4781b5853e14add991585 Date: Wed Jun 4 14:59:18 2014 -0500 Fix a bug in BrokeredJumpData comparison. commit 8cdd0aee27293ee6586c28fb3020d8ab448b7559 Merge: 21ef565 2fb87d6 Date: Wed Jun 4 15:35:17 2014 -0400 Merge master in to peptoid branch commit cf56e909a079495baaf5cb8c5cc7719a73f4371c Date: Wed Jun 4 12:53:28 2014 -0400 Updating membrane info, pilot apps and fast relax to include new membrane relax corrections commit 2fb87d63b6521c8013b863d83645c40d2bd0d24b Date: Wed Jun 4 02:41:23 2014 -0400 Fixing PyRosetta Windows build commit 57dd28cb726ad94540137038085fd6878201ad4a Date: Wed Jun 4 02:28:03 2014 -0400 Benchmark. Updating regression tests comparison scripts. commit e7a0ede225bf999787a49807f8582f96f6b3ef3b Date: Wed Jun 4 01:29:04 2014 -0400 Benchmark. Updating regression tests comparison scripts, fixing bug when comparison log is omitted if brief and full comparison results are equal. commit a8e8a7b8956b2b0c345d318d7fd837769b73fd53 Date: Tue Jun 3 19:31:30 2014 -0700 Added support to design_cycpeptide_MPI.cc for an additional list of atoms to be used in the RMSD calculation. commit 930c5a90b5c3c4681f282b8ed0cdacc7e3aedd1b Date: Tue Jun 3 18:17:25 2014 -0700 Success! I have design_cycpeptide_MPI working properly with silent files, now. commit 5ef9efd7b72a1bc5bec4f336c892920bc66165aa Date: Tue Jun 3 17:36:49 2014 -0700 Pose ordering now fixed in design_cycpeptide_MPI.cc, but it looks like there's a problem with RMSD calculation and maybe with energy calculation. commit 082a3a369ff9eb59c141decbfd59511f78e05079 Merge: d067025 4a0df20 Date: Tue Jun 3 16:12:00 2014 -0700 # [ONE LINE DESCRIPTION OF CHANGE] # NEWS: [DETAILED DESCRIPTION OF CHANGE] # ---------------------------------------- # Unit test status: [Pass/Fail/Not Run] # Integration test status: [Number of changed tests / Not Run] # [NAME_OF_CHANGED_TEST_1]: explanation of change explanation of change ... # explanation of change, cont'd. # [NAME_OF_CHANGED_TEST_2]: explanation of change #+BugFix [BUG_NUMBER] [LINK_TO_BUG] # Uncomment and fill in the line above to indicate this commit # fixes a known bug. # On branch master # Your branch and 'origin/master' have diverged, # and have 1 and 8 different commit(s) each, respectively. # # Changes to be committed: # (use "git reset HEAD ..." to unstage) # # modified: database/chemical/residue_type_sets/fa_standard/patches.txt # modified: source/src/apps/pilot/awatkins/hbs_creator.cc # modified: source/src/apps/pilot/blivens/disulfides.hh # modified: source/src/apps/pilot/chrisk/domain_assemble.cc # modified: source/src/apps/pilot/dgront/JumpSpecificAbrelax.cc # modified: source/src/apps/pilot/doug/rotamer_prediction_benchmark.cc # modified: source/src/apps/pilot/jadolfbr/antibody_design/graft_design_cdrs.cc # modified: source/src/apps/pilot/james/dp_align.cc # modified: source/src/apps/pilot/johnk/constellation_list.cc # modified: source/src/apps/pilot/kale/examples/kick_with_balance.cc # modified: source/src/apps/pilot/kale/kic_refactor/original/KinematicMover.cc # modified: source/src/apps/pilot/kale/kic_refactor/original/apply.KinematicMover.cc # modified: source/src/apps/pilot/kale/kic_refactor/original/simple_apply.KinematicMover.cc # modified: source/src/apps/pilot/kdrew/ld_converter.cc # modified: source/src/apps/pilot/kdrew/oop_creator.cc # modified: source/src/apps/pilot/kdrew/oop_dock_design.cc # modified: source/src/apps/pilot/kdrew/scaffold_matcher.cc # modified: source/src/apps/pilot/neil/enumeration_test.cc # modified: source/src/apps/pilot/neil/matdes_dock.cc # modified: source/src/apps/pilot/olli/r_assign_clusters.cc # modified: source/src/apps/pilot/parin/parin_test.cc # modified: source/src/apps/pilot/ralford/mpframework_integration.cc # modified: source/src/apps/pilot/rhiju/coarse_rna_test.cc # modified: source/src/apps/pilot/rhiju/easy_target_test.cc # modified: source/src/apps/pilot/rhiju/legacy/stepwise_test.cc # modified: source/src/apps/pilot/rhiju/pack_phosphates.cc # modified: source/src/apps/pilot/rhiju/rna_graft.cc # modified: source/src/apps/pilot/rhiju/rna_test.cc # modified: source/src/apps/pilot/rhiju/screen_phosphates.cc # modified: source/src/apps/pilot/rmoretti/ligand_rpkmin_jd1.cc # modified: source/src/apps/pilot/sergey/PDBTest.cc # modified: source/src/apps/pilot/smlewis/FloppyTail_loop.cc # modified: source/src/apps/pilot/wendao/cenrot_jd2.cc # modified: source/src/apps/pilot/wendao/general_pair_counting.cc # modified: source/src/apps/pilot/will/options_will.py # modified: source/src/apps/pilot/will/smhybrid.cc # modified: source/src/apps/public/ligand_docking/arls_impl.py # modified: source/src/apps/public/ligand_docking/ligand_rpkmin.cc # modified: source/src/apps/public/ligand_docking/pdb_to_molfile.py # modified: source/src/apps/public/noncanonical_backbones/hbs_design.cc # modified: source/src/apps/public/noncanonical_backbones/oop_design.cc # modified: source/src/apps/public/rna_util/rna_thread.cc # modified: source/src/apps/public/stepwise/enumerate/rna/legacy/swa_rna_util.cc # modified: source/src/apps/public/stepwise/monte_carlo/swm.cc # modified: source/src/devel/denovo_design/ConnectJumps.cc # modified: source/src/protocols/rotamer_sampler/JumpRotamer.cc # modified: source/src/protocols/rotamer_sampler/rigid_body/RigidBodyRotamer.cc # modified: source/src/protocols/stepwise/monte_carlo/rna/RNA_AddDeleteMonteCarlo.cc # modified: source/src/protocols/stepwise/monte_carlo/rna/RNA_O2PrimeMover.cc # modified: source/src/protocols/stepwise/sampling/StepWiseConnectionSampler.cc # modified: source/src/protocols/stepwise/sampling/movemap/util.cc # modified: source/src/protocols/stepwise/sampling/rna/checker/RNA_ChainClosureChecker.cc # modified: source/src/protocols/stepwise/sampling/rna/checker/RNA_ChainClosureChecker.hh # modified: source/src/protocols/stepwise/sampling/rna/legacy/StepWiseRNA_PoseSetup.cc # modified: source/src/protocols/stepwise/sampling/rna/legacy/connection/StepWiseRNA_ConnectionSampler.cc # modified: source/src/protocols/stepwise/sampling/rna/sugar/StepWiseRNA_VirtualSugarSampler.cc # modified: source/src/protocols/stepwise/sampling/rna/sugar/util.cc # modified: source/src/protocols/stepwise/sampling/util.cc # modified: source/src/protocols/stepwise/screener/AnchorSugarScreener.hh # modified: source/test/core/chemical/carbohydrates/CarbohydrateInfo.cxxtest.hh # modified: source/test/protocols/match/ProteinUpstreamBuilder.cxxtest.hh # modified: source/test/protocols/rotamer_recovery/RRComparer.cxxtest.hh # modified: source/test/run.py # # Untracked files: # (use "git add ..." to include in what will be committed) # # source/a.out # source/external/boinc/ commit d067025a163d0cba8f7096a2418ca868dbb026c0 Date: Tue Jun 3 16:11:07 2014 -0700 Fixed build error caused by trying to access environment variables in basic.settings. commit 4a0df201677c8a06f5df83e65b4f6be9aa912159 Date: Tue Jun 3 16:07:47 2014 -0700 Fix recently introduced bug in ConnectJumps were A was not recognized as a valid ABEGO type commit f2279b540a047e999c7e16bcfb87562a91f1831b Merge: 8ec7b7b fd4b98d Date: Tue Jun 3 18:31:42 2014 -0400 comming fix to find/replace of general to align. Thanks, Doug, for catching this. commit 8ec7b7b52e8c526ba89e0d41b72537db9105959e Date: Tue Jun 3 18:30:53 2014 -0400 additional minor fix for fixing my silly general-->align find/replace. commit fd4b98d729ba7a621691e10a1b9b12767b2163cf Date: Tue Jun 3 17:54:12 2014 -0400 Updating run.py script so it now print scons output for cases when platform could not be found commit 6037a56f022d9bc0e97b7ee6aa5cd732cb60e8ed Date: Tue Jun 3 14:28:33 2014 -0700 Modifications to support android_arm 9 platform. There are some manual steps for a successful build: 1. You must install the android ndk and run android-ndk-install-dir/build/tools/make-standalone-toolchain.sh to create the 'androidarm-tc' toolchain directory. 2. You must set environment variables NDKROOT, TOOLCHAIN, SYSROOT 3. The final link command must be manually run to dynamically link -lz. I couldn't figure out a way for scons to run the correct link command. commit 84d59aef9d318fb068229464e48a5e52dbb206b6 Date: Tue Jun 3 15:53:28 2014 -0400 reverting outlandish find/replace of 'general' to 'align'. commit 8fb3caf284b4d596c2b6292f226acfaba88be5fd Date: Tue Jun 3 12:11:24 2014 -0700 adding the standard Rama perturber before the given custom perturber during initial loop build (in LoopBuilder class); this ensures that the initial loop build is not biased towards the starting structure by discarding all starting loop torsions and replacing them with random values from Rama space; the given custom perturber can change those torsions afterwards commit 6faa1799d3244a759e7fd6c01ee13f758160e9cf Date: Tue Jun 3 12:05:08 2014 -0700 restoring max KIC perturber samples to 2000 commit 6fbd6ecbc0ef4bfe5aa374655500f03a832df875 Date: Tue Jun 3 12:01:47 2014 -0700 checking if requested min_overlap is too large for the given region in ConstantLengthFragSet commit 8021bfeeffcdfe826ffe0d000063f2b12cf16583 Date: Tue Jun 3 14:50:58 2014 -0400 Removing annoying time consuming tracer from membrane fa_embed code commit a99752e3f0e0576813be39f177709a7bb6c66c6f Date: Tue Jun 3 13:39:54 2014 -0400 Adding membrane relax executable to build settings commit af29c4c4d3a190f6429dcbb2cbdaae48367934cf Date: Tue Jun 3 13:36:41 2014 -0400 Adding membrane scorefunction corrections for relax protocol in new if option for protocol setup commit 2a082927f8ec88a11cacd816ea4da81c4379ec4a Date: Mon Jun 2 23:34:22 2014 -0400 Still needs to add the executable commit b8102f868e5462c9002d0846b28f1a038c917596 Date: Mon Jun 2 23:34:03 2014 -0400 Adding starting files to membrane relax application commit f5e157592ec0d7816aab90bc2fe17bdc74578e71 Date: Mon Jun 2 17:29:25 2014 -0700 Trying to fix the state sorting issue in design_cycpeptide_MPI.cc. Not yet successful. commit 290cbcf0dcb01bfc2d070d29d5e4f99a2537be46 Date: Mon Jun 2 16:40:11 2014 -0700 Fixed a bug in design_cycpeptide_MPI.cc that was preventing user-defined constraints files from working properly. commit 73934256782aabe6ae760a1a2bea4cf0b62ee22a Date: Mon Jun 2 15:38:19 2014 -0700 Improved parsing of motif in connectjumps commit 56637f09bf95903c6ecbf049c927b15369479a42 Date: Mon Jun 2 15:13:59 2014 -0700 I've got design_cyceptide_MPI.cc working now with silent files and noncanonical linkers, with one caveat: the order of states in the silent file is not being respected, for some reason. The states are being sorted in alphabetical order of tags, which isn't what I want. I need to fix this. commit 0ca087b1f46d7edecf331268ee38829af2a0192d Merge: 87f2de3 f3fa76a Date: Mon Jun 2 16:38:41 2014 -0400 merge from master commit d2dd53e39bff1ea26cccd1ca49888ac5090f9b71 Date: Mon Jun 2 16:27:59 2014 -0400 Adding relax:membrane scorefunction modifications for mpframework relax mode commit f3fa76a8732c9dcaf98d92e3e963089147facbe6 Date: Sun Jun 1 18:46:17 2014 -0500 commenting out new residue types to test relative performance changes commit 792acf483dd5cd3db2ca045c1b8e406f75b5e365 Date: Sun Jun 1 01:04:46 2014 -0400 Adding ResidueType::has(const char *name) as workaround for what seems to be MSVC bug (thanks to Luki for suggesting it!) commit 3bedf81726c9aa1a4a13b867f4920ba0565aac95 Merge: ce4e0cf 582b3b9 Date: Sat May 31 20:12:40 2014 -0500 Merge branch 'master' of https://github.com/RosettaCommons/main commit ce4e0cf93d71b496f47a77f9348c92a8a4f25742 Date: Sat May 31 20:12:08 2014 -0500 Adding two new complex glycans that are built on HIV epitopes as ncaa. It does change integration tests as it changes the number of rotamers that are hardcoded in some tests commit 582b3b9373b26c9f2244dbc9f3861322c5a3e7c2 Date: Sat May 31 13:27:08 2014 +0300 Adding option extreme_value_removal to DdgFilter. If set to true and repeats>=3 then in computing the average of several repeats the filter will remove the values at the bottom and top. For instance, if repeats=5, 5 evaluations will take place but only the 3 values at the middle will be used to compute the average. This should reduce the sometimes quite significant extreme values observed when 1000s of ddG evaluations are made in a single trajectory. Log change expected in ddG using integration tests. See wiki for details. commit 56d4992eb1ba1e7b4ed302d4f51c24076e06d2f1 Date: Sat May 31 02:47:06 2014 -0700 Adding some debug output to design_cycpeptide_MPI.cc to confirm that the positive states are being loaded properly. TODO: --Correct tag loading when loading negative states. --Try to figure out state ordering issue, since that will affect PCA files. --Test everything! commit 04713eea08764d94d083e895ecb85d4833b13556 Date: Sat May 31 02:40:12 2014 -0700 Positive pose import now works fully in design_cycpeptide_MPI.cc. commit 93fedb424e4ff908fa22f0d7683cebdbeac6dd8e Date: Sat May 31 02:19:42 2014 -0700 Blargh -- trying to get nth import to work in design_cycpeptide_MPI.cc is turning out to be a pain in the next. New plan: import by tag option instead of import nth option. commit 045c0101cb90a5e8924d34351b013106bdcdb6ce Date: Sat May 31 01:37:54 2014 -0700 The design_cycpeptide_MPI.cc app now properly loads a native pdb when the -v_silent_native option is used with -in:file:s or -in:file:l. TODO: make it work with silent files\! commit 396a841058b35989a53d198637ad5d42ff71fc6a Date: Sat May 31 00:37:02 2014 -0700 Possibly (?) fixed the current problem with design_cycpeptide_MPI.cc commit 21a0263c16cfe0ae2df48f21efc565064378ded6 Date: Sat May 31 00:22:43 2014 -0700 Trying to figure out why design_cycpeptide_MPI.cc hangs at the start of the Monte Carlo search... commit 6671e58922c2490ef4b18967f5afacef38425e0b Date: Fri May 30 22:17:07 2014 -0700 Deleting some debug output from design_cycpeptide_MPI.cc commit 90b462d69c2eebe30ca05835bbc9e0f4b66a0ac6 Merge: 31d2b13 3253108 Date: Sat May 31 07:57:58 2014 +0300 Mreged with master, solved conflicts with Splice.cc Merge branch 'master' of github.com:RosettaCommons/main Conflicts: source/src/devel/splice/Splice.cc commit ab9e1ef1dd9e4730d1f78c4884ca8345466a419b Date: Fri May 30 20:13:04 2014 -0700 Success! The design_cycpeptide_MPI.cc app now transmits structures by way of silent file data properly! commit 5128b434c7ad13073c4824bb972c9a4837e84a73 Date: Fri May 30 19:53:18 2014 -0700 OK -- in design_cycpeptide_MPI.cc, the silent file data are being transmitted properly now, including the header line that is not included by default in the steam but which the read function expects. commit da7a4a05d7253ffab54ba08db9b7b5fefa33e48d Date: Fri May 30 19:06:05 2014 -0700 Transmission of binary silent file data now works in design_cycpeptide_MPI.cc, but reconstruction of pose isn't working yet. commit c9ff641689670528d35ab2f09e4cff396683bfce Date: Fri May 30 18:51:53 2014 -0700 Found transmit/receive problem in design_cycpeptide_MPI.cc. (MPI_Bcast must be used for both sending and receiving; MPI_Recv does nothing with MPI_Bcast. Duh.) commit 441c841154d64896f7d64aaebe66545f216a502f Date: Fri May 30 18:16:32 2014 -0700 Fixed final bug in design_cycpeptide_MPI.cc, but slave procs aren't properly receiving positive state. Adding debug output to try to figure out why. commit 2771354663fb603704886ca1a57f8a382e506025 Date: Fri May 30 17:41:16 2014 -0700 Fixed all but one of the compile errors in design_cycpeptide_MPI.cc. Working on the final one. commit a5ddeaba5d751ab2108507d293cb4e9bbad669c5 Date: Fri May 30 14:23:23 2014 -0700 A few fixes for symmetric docking RigidBodyTrans mover no longer resets all dimensions if one dimension slides out of the boundary. SwitchResidueTypeSetMover is quieter with symmetric poses. commit 9f295974d21f56034c8ee888b89318c0ee796e5a Date: Fri May 30 11:21:54 2014 -0700 Fixing Windows build project files make script. commit 063af324d3aa8d3eff6c0dd8f3b961841f6f4d7c Merge: 0a5903b cc89ba4 Date: Fri May 30 10:09:11 2014 -0400 Merging branch remote master with lcoal ninja master commit cc89ba4f88e9d69d5860d709adf8e14892c5fe1d Merge: 6efc58f 1b54bb2 Date: Fri May 30 15:17:30 2014 +0200 add temperature level based interpolated sampling weights for 2d Hamiltonian Exchange fixed a bug for docking metric Fnonnat calculation in /protocols/docking/metrics.cc' commit a25a35cd90aebb855b2c39795991c0ab4e154755 Date: Fri May 30 13:02:32 2014 +0200 Update unit tests for new interface. commit e958a1d0bf4d3763654eaebfab352cda2a72b497 Date: Fri May 30 12:42:12 2014 +0200 Fix warnings-as-errors. commit 1b54bb240f121dbd7e8bfbb494679eb5ef00caa2 Merge: 98e46d1 6efc58f Date: Fri May 30 12:06:00 2014 +0200 Merge branch 'master' into zhezhang1986/changes_to_commit commit 922cd92299c2790228539845116f8e98dffe5294 Date: Fri May 30 02:46:47 2014 -0700 In the process of adding support for silent file input to design_cycpeptide_MPI.cc. Currently, there are a number of bugs in the new code that I need to debug. I'm just setting this commit as a checkpoint before I go to bed. Done: --Added new functions to transmit and receive a pose as a silent structure (converted to a string). --Added import of positive state by proc 0 only; transmission to all other procs. --Added debug lines to dump a PDB from each proc immediately after positive state import. TO DO: --Debug the current code! It's very buggy (i.e. it currently won't compile). --Confirm that poses are being transmitted from proc to proc properly. --Add an import function where the positive state is loaded for the case in which the positive state is specified as the Nth structure. Note that since we want the Nth structure, it might have to look through more than one file. commit 98e46d197a02ec66123518584a8d003a23042d60 Date: Fri May 30 11:11:35 2014 +0200 debuging rename commit e8cae42426018c1d851c59bc4581ae7d3b8898c5 Date: Fri May 30 11:03:18 2014 +0200 rename ThermodynamicRigidBodyMover to UnbiasedRigidBodyMover which will better describe the difference from original RigidBodyMover commit 439a7f3c73f171f10169fa9d999b10e6eb21b1eb Date: Thu May 29 20:39:05 2014 -0700 Adding support for importing the positive design state from silent files to design_cycpeptide_MPI.cc. In progress. commit 560ad2f08defc4ebd3dcb9691e787d783f62e46c Date: Thu May 29 20:24:51 2014 -0700 Fixed a problem with PCA file counting in design_cycpeptide_MPI.cc commit acc66d3d78285c224b210554defa7ba7a57cf3ef Date: Thu May 29 17:29:11 2014 -0700 Fixing a comparsion between an owning pointer and NULL in PeptideStubMover.cc. (Now compares the raw pointer, fetched using get()). commit 84be810d142eef6f61db0e708c55b556198e3eef Date: Thu May 29 17:28:32 2014 -0700 Fixing a warnings-as-errors issue in design_cycpeptide_MPI.cc commit 6efc58f8abb54611ace5a6cdd7e69e6c970a01ef Date: Thu May 29 18:05:10 2014 -0400 Fixing PyRosetta monolith build commit 6362a4d45c1a3a96412490423db77f45933d51a6 Merge: ea183f5 2343f77 Date: Thu May 29 11:47:00 2014 -0700 merged with master commit ea183f52c497953c1dba8a77f81710421133992e Date: Thu May 29 11:36:10 2014 -0700 Added back the use of boost thread for multi-threaded fragment picking. commit 2343f77c8c7cd8ebdf88dd218c3bfcaacc016922 Date: Mon May 12 20:05:30 2014 +0200 Modified std::cout and std::cerr calls to use the Tracer object. Expect trivial integration log changes. commit baee3822ea1bd41f1066a6627da3f86561218076 Date: Thu May 29 18:40:28 2014 +0200 add final test to CoMTrack test. commit 93c856c0757181ee36db17df6f869e05b139fd79 Date: Thu May 29 18:40:00 2014 +0200 Fix bugs in topo driver rb/com test function. commit e43afcd7f90057b4ee713dbdbe18758f457e4800 Date: Thu May 29 18:39:34 2014 +0200 Don't allow EnvClaimBroker to call initialize() in Claimers with empty passports. commit daf5c318438176f98d311433effaa241e21a5855 Merge: d8b63da 49b85ef Date: Thu May 29 17:32:28 2014 +0200 Mergin gin CoMTracker beautification. commit d8b63dabe84c8c3b633b7bc68773c2bb83dbd641 Date: Thu May 29 17:30:04 2014 +0200 Clarity updates to CoMTracker commit ab8df64161d9efc226eff4ef7aeb94bb1b96d481 Date: Thu May 29 03:11:43 2014 -0700 Removing some debug output from protocols/generalized_kinematic_closure/GeneralizedKIC.cc and protocols/generalized_kinematic_closure/util.cc commit 32f369ec9dfefb5973acb8448c6bb39d0e893de5 Date: Thu May 29 03:05:24 2014 -0700 I seem to have tracked down and fixed the first angle problem in GeneralizedKIC, now. commit bf9ea1d9257a83391ed85c3ae212cfa1146dbafa Date: Thu May 29 02:00:13 2014 -0700 I caught a serious bug in GeneralizedKIC pointed out by Yifan. The atom indices of the last three atoms in the loop to be closed (forming the terminal anchor) were based on the FIRST residue, rather than on the last. This created problems in rare cases in which, for example, the first anchor was a nonstandard residue and the last was an alpha-amino acid. I still have a bug remaining, though: the first torsion angle in the chain to be closed is not being set properly (or, rather, it's being set to something new when it ought not to be). commit b289af352c0e34cc0febca3c17077156462055ce Date: Wed May 28 22:53:17 2014 -0700 for stepwise modeling & full_model_info object, allowing for specification of chains & resnum, tested carefully on cases with two chains with similar resnums. commit fdc7a3c75f6c265d61f2aa9fb119ccc17e4eb15c Date: Thu May 29 00:38:02 2014 -0400 Fixing PyRosetta build commit 6044ec251a0d740672ec47bef8e77183d50dc0ef Date: Wed May 28 19:28:48 2014 -0700 fix debug build commit 94d700a958ba8d44e692e1e1463ae989ecab87d4 Date: Wed May 28 17:06:33 2014 -0700 prints out the size of search space commit cf26c79d8c24ac2e6e4a1ecf43c02f7388922c57 Date: Wed May 28 14:58:25 2014 -0700 Adding option to output the score file in JSON format (concatenation of valid JSON objects), and a python utility script to parse and extract data from such score files. To output score files in the JSON format, use the option -out:file:scorefile_format json. The utility script scorefile.py in main/source/tools can convert the JSON score file to the legacy format or CSV, extract selected fields, and compute some quick stats. Further, scorefile.py can be imported into your python scripts and provides the ScoreFile class for easy access to score data. Unit Tests: All Pass Integration Tests: Cosmetic changes to score term order and naming in scorefiles; output is now consistent for silent and PDB files. Affected tests: assemble_domains_jd2 fold_and_dock membrane_relax score_only_silence score_jd2 ThreadingInputter commit 6c211eeb791097c732fc4991726c07ca7023e578 Merge: c8714be a936a4e Date: Wed May 28 14:56:51 2014 -0700 Merge branch 'luki-mbi/json_scorefile' commit 809787d071ac3ab9a0b0af812fba0dddd0081b0e Date: Wed May 28 14:00:01 2014 -0700 updating -terminal_res, -calc_rms_res, etc. to be ResidueChainVector options. Changing the option to emit a pair of residue numbers and chains as utility::vector1 not std::vector. commit c8714bee185ea03bd780476a629abc3977ace9dc Date: Wed May 28 16:47:44 2014 -0400 Fixing Windows build commit 93b4dec1b6c6c555eca719064953665ebee8adb5 Date: Wed May 28 16:41:09 2014 -0400 [update of SandwichFeatures] - allow to exclude sandwiches that have S-S bond since those having S-S bond in core tend to have big holes (bad packing score) - should not change any integration tests other than (expected) features and features_database_schema (if any) commit bea7e7b78285be2e097007ae5ae782b5c36f2d6e Date: Wed May 28 13:27:05 2014 -0700 softening warning in cart min commit cb94f04c964db21b97d0bd7a780c32c8d76abb4c Date: Wed May 28 17:51:26 2014 +0200 2d weights commit 50e1d7211f8470b6e3474c63a424ab0f6bc5d5a4 Date: Wed May 28 17:47:29 2014 +0200 2d weights commit 0eccd76f2604902f8c0dd2b964afded23ae30b4c Date: Wed May 28 17:36:03 2014 +0200 sampling weights for 2dimensional grids commit 99463c3ebb97022346a458aa6e0c3d7aa10fd62e Date: Wed May 28 08:30:57 2014 -0700 creating ResidueChainVector option, which generalizes IntegerVectorOption to handle command line input like "A:1-4 B:1-3" to figure out residue numbers and chains. commit ff2106eb3416a24fcb6bcfbe8455164f43e2001b Date: Wed May 28 10:45:31 2014 -0400 Updating most recent outline updates commit 31d2b135389329124bf782b7f523f25d6137595d Date: Wed May 28 17:43:31 2014 +0300 Added bb-min function to splice commit 0b87c596110b900ccf6e4ae58dc2fd3e9ce52ded Date: Wed May 28 15:20:33 2014 +0200 debuging commit aa52fade3ea9883eb6a84b6b2757d7b482b7ee0a Date: Wed May 28 14:52:53 2014 +0200 fixed a bug for fnonnat calculation in docking/metrics.cc added 2-dimensional temperature based interpolation weights for thermodynamic movers commit 3253108ab3bd883c581a811643205e616c02de68 Merge: 8a0c5be a99a1e5 Date: Tue May 27 22:55:26 2014 -0700 run_i and run_j options added commit 8a0c5be48608cf2dbff31ce42bc23485a9e964dd Date: Tue May 27 22:53:58 2014 -0700 run_i and run_j options to split the rotation search into run_j number of jobs commit a99a1e5b89375f78cbe265d6a3e5bab60654d96f Date: Tue May 27 22:48:48 2014 -0700 run_i and run_j options to split the rotation search into run_j number of jobs commit a178b634108021e1644c28207772fb8d4f5bebf2 Date: Tue May 27 18:02:57 2014 -0700 allowing resnum and chain to be read in from FASTA file; and keeping track of conventional_chains in full_model_info. commit 9799c8939f0ef5a81875190596e9ffa90489b1ef Date: Tue May 27 16:55:14 2014 -0700 Bugfix: derivitives for RG (centroid minimization) are now correct for symmetric poses. Hybrid integration test changes expected. commit e170c85ea00ab13df7d80f018c0e92caf0eac21c Date: Tue May 27 16:50:53 2014 -0400 Refactoring PyRosetta versioning code commit 936d02e00de834ec0eed4583c25af38022bf534d Date: Tue May 27 13:38:51 2014 -0700 Fixed bug in LayerDesign bug altered layer cutoffs if use_sidechain_neighbors was set to False commit cf91804134916af9ee1b9d3523539c056f87885e Date: Tue May 27 15:50:21 2014 -0400 Fixing Windows build commit d915166b205a4855fd8554badbd9cf7ff64cd4b0 Date: Tue May 27 10:44:35 2014 -0400 Adding additional outline for header in new mpf class design commit 61a2a24939ef4a335dea1d46ebe47c020d350f1a Date: Tue May 27 10:35:11 2014 -0400 Adding membrane protein creator class outline to top of cc file, probably needs a header outline as well commit 3f521472aeb6bfbdef515de9c491e90c2d0f53a9 Date: Tue May 27 09:26:59 2014 -0400 Updating changes to membrane score function fingerprint tests commit 29c040d0bc17455c9f70383978c2485c6a308fa3 Date: Tue May 27 00:57:08 2014 -0400 Fixing Windows build commit 802764a8b9e548d6aedd0b3a8881683d69dfc154 Date: Mon May 26 18:36:46 2014 -0400 PyRosetta. Fixing compilation options for external C files. commit 9e86d399faad044b09478453c8ba6c092dad88a9 Date: Mon May 26 19:45:37 2014 +0300 Changes to Splice mover. Now treats protein tail segments different then loop segments. Integration test for splice_in and splice_out will fail commit 94498eedb2f534c6017d62418770ec26a8524cc2 Date: Mon May 26 02:02:10 2014 -0700 Tweaking an error message in Residue.cc. commit 1cba81ba419254b61a125a27df6326aa5f99de06 Date: Mon May 26 01:20:05 2014 -0700 Adding TYR as the parent type in BoronateLDopa.params. commit cd200f7c0594b71960b3d86d49e735e6310c3741 Date: Sun May 25 19:36:38 2014 -0700 Tweaking BoronateLDopa params file. All atom types should be right, now, and all chi angles should now be in there. commit bdbfe15259b1f03f701f687f0d1236bd1bed5859 Date: Sat May 24 03:34:26 2014 -0700 Updating comments at the head of design_cycpeptide_MPI.cc commit 33a43ea9a72e703a0705fb43a3f8224bafd56377 Date: Sat May 24 03:29:05 2014 -0700 Adding support for silent file input to design_cycpeptide_MPI.cc. --Negative states can now be supplied with any combination of -in:file:s, in:file:l, and -in:file:silent. --There must be as many PCA files as there are negative design states. --Currently, the postive state must still be a PDB file provided with -in:file:native. I will change this soon. (TODO: add a new option for specifying the state number of an entry in the negative states list.) --I haven't tested any of this yet, but it does compile. commit 7584aa63ec772163242f64a6cc1997e9bb7d3578 Merge: 94896fe 7e1eaa7 Date: Sat May 24 00:21:44 2014 -0700 Merging master into vmullig/cycpep. commit 94896fe03b1e80fbc7f4cbe5529e2b7730e13a90 Date: Fri May 23 17:40:02 2014 -0700 Fixing small mistake made in last merge with master. commit ad04366f1f6154090108729fab7e94b48d807245 Merge: c9bef64 42bf385 Date: Fri May 23 16:26:12 2014 -0700 # [ONE LINE DESCRIPTION OF CHANGE] # NEWS: [DETAILED DESCRIPTION OF CHANGE] # ---------------------------------------- # Unit test status: [Pass/Fail/Not Run] # Integration test status: [Number of changed tests / Not Run] # [NAME_OF_CHANGED_TEST_1]: explanation of change explanation of change ... # explanation of change, cont'd. # [NAME_OF_CHANGED_TEST_2]: explanation of change #+BugFix [BUG_NUMBER] [LINK_TO_BUG] # Uncomment and fill in the line above to indicate this commit # fixes a known bug. #+TEST # Uncomment the line above if you would like your commit to be tested by the testing server. # NOTE: Some commits (e.g. merges-to-master and current HEAD) will be automatically tested. commit c9bef642ce14c2d1567ece2306a517cd507d629f Merge: 51c5224 193ce68 Date: Fri May 23 01:42:13 2014 -0700 Merging master into vmullig/cycpep commit 51c5224295dad00f739f21f449fa8cc171bfbe9f Date: Thu May 22 23:47:31 2014 -0700 Tweaking certain functions that sometimes break the MPI build, depending on the compiler. I think I see what Doo Nam was trying to do, now. On certain MPI compilers, MPIBPool_RSD::create_comm() is creating problems because the variable "returnval" is created and set by an MPI function call, but only used for an assert() statement. I think the compiler optimizations are completely bypassing the assert() in release mode, which means that the compiler thinks that the variable's value is set but never used -- a warning that trips us up due to the warnings-as-errors. I'm switching these assert() checks to runtime_assert_string_msg() checks. The hit in performance will be negligible, and this stops the compiler from tripping. Plus, it's an assert worth making at runtime. commit 180db3bd8c2f6643c2f4ebb703eaa142036e23bd Date: Thu May 22 22:18:27 2014 -0700 Updating comments in bettercluster.cc to reflect changes. commit aa6877337be42479e130dbda542f21ad1d3f8874 Date: Thu May 22 22:13:39 2014 -0700 The bettercluster.cc app should now be able to take, as input, a user-specified list of additional atoms to use in the RMSD calculation. commit 420875021068deaef8c87a34b534d62e1322a092 Date: Thu May 22 21:53:21 2014 -0700 Adding support for extra atoms in RMSD calculation in bettercluster.cc commit 7c4c41064df9cf4137bc7d11b9d26bc65be6b0d1 Date: Thu May 22 21:42:36 2014 -0700 Adding support to bettercluster.cc for a user-specified list of additional atoms to use in the RMSD calculation. commit b046e585280b71128fb54e0b8f07de7c0aafd323 Date: Thu May 22 21:09:40 2014 -0700 Adding support for constraints files (for scoring and/or relaxing) to bettercluster.cc. commit 652ae1d3d2d6a8a4e8257b4b3ab3c01ac6865f43 Date: Thu May 22 17:12:32 2014 -0700 Fixed a bug in the Boltzmann GeneralizedKICselector. commit a0ee017d9a7a174d4a6e005cbb64985b7f3d8f11 Date: Thu May 22 15:33:23 2014 -0700 Added a lowest RMSD selector to GeneralizedKIC. commit 34073b1335bb094027df663c142ea913e2ede847 Date: Thu May 22 14:20:15 2014 -0700 Added a Boltzmann-weighted random selector to GeneralizedKIC. commit 49b85ef5b2d9f61876b26a362d22ff1897831e6e Date: Thu May 22 17:27:43 2014 +0200 Begin updating topo_driver to test two-CoM perturbed docking completely. StructPerturber is misbehaving. commit 69cbe4bd6ef58cbdd3e67bfd079def74a6d63f61 Date: Thu May 22 16:53:30 2014 +0200 XYZClaim and VRT claim yield_claim modifications (only claim real appropriate DoFs and claim all jumps respectively). commit b0e72711696097599a01c86ec5b8e5c189bb1d5d Date: Thu May 22 16:52:47 2014 +0200 Spacing and header housekeeping. commit 0ad4b8bcbd81e27269719777d02f51d4ec923caa Date: Thu May 22 16:26:39 2014 +0200 Housekeeping from InitStr refactor. commit cef1ec7921c09a5494e5d2251d2e946f8cfb3f7f Date: Thu May 22 16:06:28 2014 +0200 Refactor initialization to have the same behavior and control levels as sampling. commit a936a4e34d2d2577610a6a816697f4ac8af8ec58 Date: Thu May 22 01:59:54 2014 -0700 Use tag in score file with silent files. commit 3c9c28e57e2a134c7d14008da0871fb8209cc49e Date: Thu May 22 01:39:51 2014 -0700 Trying to get binary silent structure output in bettercluster.cc commit d4791e177c2b7eca1b45d459af60d3c6edb06060 Date: Thu May 22 00:55:46 2014 -0700 Adding silent file output to bettercluster.cc. Two silent files should be written, now. commit 27bdd2ad5a7b375f339161401e3f15475f22325d Date: Thu May 22 00:36:37 2014 -0700 Removing some unused lines of code from bettercluster.cc. commit fc279e6805e3b9e1a5c1888206012236babd73ad Date: Thu May 22 00:22:19 2014 -0700 Adding support to bettercluster.cc for silent file output. commit 6d56d929cc11aaf72ab96eeed719d832f3b0f3df Date: Wed May 21 21:11:40 2014 -0700 Trying to add support for silent file output to bettercluster.cc. commit 9febae934218c3750825baabba8b1c577fd02197 Date: Wed May 21 20:44:21 2014 -0700 Adding option for silent structure output to bettercluster.cc. commit b79842ce7b38eebb900dacb48d04aafd69b5a268 Date: Wed May 21 06:31:31 2014 -0700 fixing check to skip over already finished models commit 9964e8c46b8684ded4c7b52b436030fc5ab00e8f Date: Tue May 20 10:42:25 2014 -0400 Fix ScriptCM broken build. Integration tests produce only differing logs based on printed pointer address. commit 89bc7dd50deaa7be15acb78802b6130ad111e397 Date: Tue May 20 15:56:46 2014 -0700 Updating virtual atoms in ASX and LYX params files. commit 358b509c4eccd3679f7e366dc7ef9b794bd82046 Date: Tue May 20 15:52:23 2014 -0700 Updating ICOOR information for some virtual atoms in crosslinker params files so that virtual atoms are rebuilt automatically in the right place. commit ca6ad81b189d9495472254600343213c4fe04a00 Date: Tue May 20 14:33:18 2014 -0700 Tweaking lengths of connections in the bis(bromomethyl)benzene linker params files. commit a47ed2ef95a5bb072200b62d1d377648fefbb4fd Date: Tue May 20 09:45:10 2014 -0700 adding updated weights file for RNA SWM that increases hbond strength and lowers rna_torsion -- developed during structure prediction tests over last year. commit 8aeebec6bb013afe988121e0147af550d019a9a3 Merge: 70f64da ad4fff7 Date: Tue May 20 10:38:41 2014 -0400 Merge branch 'justinrporter/env_devel' into justinrporter/env_release commit 70f64da68790c55e34a9618db5976f3599fea64b Merge: 103cf72 24f749a Date: Tue May 20 09:45:39 2014 -0400 Merge env_devel into release branch. commit 103cf721b8adccda24014a3a782b612e97353925 Date: Tue May 20 09:34:35 2014 -0400 Remove unused varaiable. commit 688fc1bd0fe31f441f5dc5933642a6c73435b4af Merge: 7295620 f1f7a64 Date: Tue May 20 07:48:42 2014 -0400 Merge pp_modify into env_release top make an up-to-date release branch. commit ad4fff759cda417e5f56c2bdb5f5a5e882b023b5 Date: Tue May 20 13:43:57 2014 +0200 Fix topo_driver bug; add assert to CoMTracker. commit 0c3d70a6372e5b7db200b6c2d9091607d8ad1d51 Date: Tue May 20 00:53:04 2014 -0700 Adding AROMATIC property to 1.2_bisbromomethylbenzene.params commit a14a1a683da1a0637523038d25a4fa546c58f373 Date: Tue May 20 00:39:44 2014 -0700 Tweaking an error message that gives a bogus warning in some situtations. commit 9c2a49681902caf08e8fae024f71690998c095ab Date: Mon May 19 23:43:09 2014 -0700 Tweaking 1.2_bisbromomethylbenzene.params and 1.3_bisbromomethylbenzene.params. commit 6992bc05fe17232c6a6d2d0746d976e06d4e3e5f Date: Mon May 19 23:40:39 2014 -0700 Finally got 1.4_bisbromomethylbenzene.params working. commit cf8f3ce0247967f1e67c349d69c71b23c4543612 Date: Mon May 19 23:39:09 2014 -0700 Commenting out some debug output in GeneralizedKIC.cc. commit f94ac543c8eceff42ac360d3ae815eebf65b6b3c Date: Mon May 19 23:38:23 2014 -0700 Adding some debug output to GeneralizedKIC.cc. commit 2c851312f33f18b1acf0171dc62e76000e582115 Date: Mon May 19 23:06:02 2014 -0700 Tweaking bromomenthylbenzene crosslinker params files. commit 5a66bae9bb84015eb68d322d2a078bbaaf1d96cb Date: Mon May 19 21:43:53 2014 -0700 Trying to get 1.4_bisbromomethylbenzene.params to work... Still not working. commit 02dd3fa9b77642dbffef90a258272f88a8e27b72 Date: Mon May 19 21:30:25 2014 -0700 restoring o2prime_legacy_mode flag. trying to see why a 2prime hydroxyl in a GNRA tetraloop is not getting instantiated. commit 808b51e24d12882a5b945435ee1348fbbeacb761 Date: Mon May 19 21:13:44 2014 -0700 Fixing 1.4_bisbromomethylbenzene.params commit 654ea13e9d17d117aac6925ce8a652c95ba41156 Date: Mon May 19 20:53:04 2014 -0700 Changing atom order in bromomethylbenzene linker params files. commit 84d86bb86068d99277ad22a9ab98a317743fc6e7 Date: Mon May 19 20:49:23 2014 -0700 Remaking 1.4_bisbromomethylbenzene.params -- initial commit commit e7a013823e62f434d5b80ed4cd7d1e967ebf1533 Date: Mon May 19 20:48:18 2014 -0700 Tweaking 1.2_bisbromomethylbenzene.params commit dccd8b21d20f8c805608750c7c55cc95a119abb5 Date: Mon May 19 20:42:34 2014 -0700 Tweaking 1.2_bisbromomethylbenzene.params commit c97bec918bce201b321cf0111e881a8da8b61227 Date: Mon May 19 20:25:04 2014 -0700 Tweaking 1.3_bisbromomethylbenzene.params commit fa8593ed916507f0f359889d7f713b0308aefe17 Date: Mon May 19 20:10:19 2014 -0700 Fixed 1.3_bisbromomethylbenzene.params commit 13d7accdacb494ac3edf2251c81fb2115dd25576 Date: Mon May 19 20:05:20 2014 -0700 Fixed 1.2_bisbromomethylbenzene.params file. commit db137166ba7ea7773883137b21292e587d3d0d4e Date: Mon May 19 19:42:26 2014 -0700 Tweaking 1.2_bisbromomethylbenzene.params commit 5bc709ace212a9602653887014d6852224472c1c Date: Mon May 19 18:25:47 2014 -0700 Turning off some residue types in residue_types.txt. commit 56d7be82a5bb31b88f8b033bb352968242b0dbe1 Date: Mon May 19 18:20:42 2014 -0700 Tweaking 1.4_bisbromomethylbenzene.params commit fa230f4b92eedb23abb6899d522871f128a6b920 Date: Mon May 19 18:18:49 2014 -0700 Initial commit of 1.4_bisbromomethylbenzene.params commit 8fb791da2c2caea8390d047e4ca458683cf7e359 Date: Mon May 19 18:18:23 2014 -0700 Adding 1,4-bis(bromomethyl)benzene to residue_types.txt. Currently set to ON; will turn OFF. commit ebd688caf08355369166fd75f80ead0ed1562331 Date: Mon May 19 17:56:49 2014 -0700 Tweaking 1.2_bisbromomethylbenzene.params commit cb294f450a925495b88290155a9a7a2c2e66039b Date: Mon May 19 17:54:28 2014 -0700 Temporarily turning on CYX.params in residue_types.txt. commit bea217bb673e6093e4caef639c5363659bd280c1 Date: Mon May 19 17:17:57 2014 -0700 Tweaking 1.2_bisbromomethylbenzene.params commit 1e59518c74b457b3a0d6758fbe755ed0a4da617e Merge: 8f2d64a aa19456 Date: Mon May 19 17:04:06 2014 -0700 Pulling remote vmullig/cycpep and merging with local vmullig/cycpep commit 8f2d64ab271da74bd31c82a732d1b2ce467f8cc6 Date: Mon May 19 17:00:10 2014 -0700 --Added 1,2-bis(bromomethyl)benzene crosslinker --Tweaked 1,3-bis(bromomethyl)benzene crosslinker params file --Added these to residue_types.txt (currently turned ON; will turn OFF before committing). commit bfa141aa464b920cc0984839c87b443609ce5068 Date: Mon May 19 14:32:17 2014 -0700 fixing one more boundary case in superposition, discovered by check statement. commit eddd248a3f5e289d5fe906eb9d2521b18b2b3896 Date: Mon May 19 11:15:59 2014 -0700 fixing StepWisePoseAligner to properly calculate superimpose rmsd res. Turned back on consistency check in clusterer. commit 10f123c77591d673c1bcf45ae3140e188715cf33 Merge: 5e5c163 d17caa3 Date: Mon May 19 10:12:49 2014 -0700 auto merge. commit d17caa3560838d4f9a662a45f3c3ffc93cc175bf Date: Mon May 19 10:12:28 2014 -0700 seeing lots of early exits in stepwise monte carlo tetraloop runs because of assert in superimpose_res, temporarily turn off that check. commit 5e5c163a57af7341b9b0c4a299483085f74b0150 Merge: 14039f0 e9c4567 Date: Mon May 19 08:51:03 2014 -0700 merge from latest master commit e9c45677c8edff9a3d70512a626d98dba29613bc Merge: f974946 fd2f1cc Date: Mon May 19 07:54:20 2014 -0700 merge with master commit f974946e6a16b50c0b0af0a916a3dab8ac012264 Date: Mon May 19 07:52:56 2014 -0700 fixing virtual_bb cmdline selector commit 06b5d0fced2a135d1e6197d8345f9447059dd629 Date: Mon May 19 06:15:25 2014 -0700 Adding scorefile.py, utility to parse and extract data from score files in JSON format. commit 95f06d4c458a3723194c9a122280769774963b12 Date: Mon May 19 00:23:45 2014 -0700 Cleanup. commit c0fa2e701f248b2c5960931520b2228c9e41d7ee Merge: 2b65ca4 e64aa70 Date: Sun May 18 19:06:53 2014 +0200 Synchronizing local and github env_devels. commit f1f7a643ea9f20861f6b179fa1a76c754460c15b Merge: d0ae31f 4d5b1eb Date: Sun May 18 17:25:44 2014 +0200 Updating pp_modify with newest master state. commit d0ae31fba68ca7078a63e75c6dab0fa1c43a6e95 Date: Sun May 18 17:19:56 2014 +0200 Allow 'mover' and 'name' in EnvMover. commit b844d3596c54ea54baa1cdeb19b633e6880b4f56 Date: Sun May 18 17:08:53 2014 +0200 Fix issue with EnvMover using unprotected pose to end environment. commit cbff0ed6a655a0d92c300f404b1af663344b9bc5 Date: Sun May 18 17:03:18 2014 +0200 Fix bug in on-the-fly mover instantiation by cleaning up mover parsing in ParsedProtocol a bit. commit 7fa159618fe0a001ccf567a192666008cff58092 Date: Sat May 17 13:57:35 2014 -0400 Fixing order of arg initialization in membrane info - caused a bug in GCC commit d9807dace4d3481625e33d960b58b117b7b8e22a Date: Sat May 17 11:29:02 2014 -0400 Oops! Forgot to add spanfiles in sfxn fingerprint tests ' ' commit c416d6c68d6166ff2d3883115758e5699f4d6682 Date: Sat May 17 11:15:32 2014 -0400 Removing +30 on layer bounds and method for computing z position commit 745589ac7e4bee1f650ac66f80a7d06c251b8ab1 Date: Sat May 17 10:37:11 2014 -0400 Updating non +30 layer bounds in membrane environment term commit b5e2e936adb4007f3d5fb24ce6a68ee93b8cb5f8 Merge: 7ed7873 4d1e665 Date: Fri May 16 22:49:25 2014 -0400 Merging branch mpframework_devel and new fullatom energy function with sfxn fingerprint tests commit 4d1e665e1eb9e9dbbab03e3d9ebc0574cce38ee6 Date: Fri May 16 21:21:36 2014 -0400 Fixing command files for sfxn fingerprint tests commit 656d209c9625929c241f5b09967f48dd6e5224dd Date: Fri May 16 21:08:20 2014 -0400 Adding new centroid and fullatom membrane sfxn integration tests for new terms commit 413ddeaaca3260ea5b63081f6773000d3543977d Date: Fri May 16 21:07:43 2014 -0400 Removing old centroid integration test commit ee2e702656fb57e9b9093afa8b9a6585def97104 Date: Fri May 16 20:24:35 2014 -0400 Fixing membrnae fullatom scoring terms - scoring terms pass integration tests commit cd47d33ab3d53217f3b726e395ea968855491227 Date: Fri May 16 09:56:09 2014 -0700 Rename format name from Legacy to Text. commit 27b6547462981daf4c84c0082cafe644661692de Date: Fri May 16 09:24:50 2014 -0700 Fix score file output format with silent file output. commit aa19456cc8f132cd5413ac979837d44812bc8766 Merge: d3fc410 d26320a Date: Fri May 16 03:42:56 2014 -0700 # [ONE LINE DESCRIPTION OF CHANGE] # NEWS: [DETAILED DESCRIPTION OF CHANGE] # ---------------------------------------- # Unit test status: [Pass/Fail/Not Run] # Integration test status: [Number of changed tests / Not Run] # [NAME_OF_CHANGED_TEST_1]: explanation of change explanation of change ... # explanation of change, cont'd. # [NAME_OF_CHANGED_TEST_2]: explanation of change #+BugFix [BUG_NUMBER] [LINK_TO_BUG] # Uncomment and fill in the line above to indicate this commit # fixes a known bug. #+TEST # Uncomment the line above if you would like your commit to be tested by the testing server. # NOTE: Some commits (e.g. merges-to-master and current HEAD) will be automatically tested. commit f2a3dc5b3b7a08670a25ab82aac55a97f631aecb Date: Fri May 16 03:11:49 2014 -0700 Scorefile format generally works, but in silent mode output score file is in plain format because it is output by SilentStruct::print_score_header(). Probably the whole silent file / score file outputting needs to be refactored. Postponed temporarily. commit d3fc4101e6b3b3693af061b125fc4020a8ac79dc Date: Fri May 16 02:52:29 2014 -0700 Tweaking output of design_cycpeptide_MPI.cc so that P(Designstate) is meaningful. commit ca2d5d148935a5b8c7782b0ccc876989fffd8021 Date: Fri May 16 02:47:02 2014 -0700 Adding support for constraints files to design_cycpeptide_MPI.cc. Might need some debugging. commit 7dfcf2f7ea3d0a1aa49c559f4316e4f6a5e56069 Date: Fri May 16 01:05:08 2014 -0700 Fixed probability function output in design_cycpeptide_MPI.cc commit 454227491e5a441ab2103abe0d6a9b93fc7f3ffb Date: Fri May 16 00:34:41 2014 -0700 Tweaking output of design_cycpeptide_MPI.cc commit b41cddbb27c21539aef4f2fa59f688b9789405fe Date: Thu May 15 21:32:46 2014 -0700 Dealing with more bugs in design_cycpeptide_MPI.cc. commit 28452dd442de5fffeee5e09b302adc64de5c8bed Date: Thu May 15 21:26:12 2014 -0700 Adding some debug output to design_cycpeptide_MPI.cc commit 76b03d4e8ae031c005557824992a28d303ce6692 Date: Thu May 15 21:11:15 2014 -0700 SOOOOOO many bugs. commit 706e4abe3d17335d1767fad2b4de9f58d8a2b4c3 Date: Thu May 15 21:06:57 2014 -0700 Fixing more bugs in design_cycpeptide_MPI.cc commit ac9ffa2600cf225ae1032ba850e031149d2c2c18 Date: Thu May 15 20:59:03 2014 -0700 Fixing bugs in design_cycpeptide_MPI.cc commit 9a67eff02e1c3b57c7b17ddb16df60b3dae45c42 Date: Thu May 15 20:50:18 2014 -0700 Adding support to design_cycpep_MPI.cc for a user-specified list of covalent bonds between atoms in a pose. This is needed for noncanonical linkers. commit 0a5903b84f7fa5d063f0b5b61004e418ac835214 Merge: 9e8f7ff d26320a Date: Thu May 15 20:53:59 2014 -0400 Merging local and ninja master commit e5b630bc665613c2709b756e8c15c8014dd9e26c Date: Thu May 15 20:46:46 2014 -0400 Adding bug fixes and updates to membrane info and fa mbenv energy commit e50f750f02c4d86026b3287507626b3a4cf876a8 Date: Thu May 15 17:27:13 2014 -0700 The design_cycpeptide_MPI.cc app no longer crashes with noncanonical linkers. Now to add support for covalent linkages and for constraints files. commit 7ed7873cf02506fb4aa377df365becb607482072 Merge: e3eb632 7f998ef Date: Thu May 15 16:39:03 2014 -0400 resolve merge conflict commit 3ca81b4035bc390466d826435651395a81e65985 Date: Thu May 15 13:26:10 2014 -0700 Commenting out unused variable in Conformation.cc commit e3eb6326330a0150c7acc3cc7fe06e8c6c5194f0 Date: Thu May 15 16:25:57 2014 -0400 fix errors, compiles commit 460bbcb12f3e0870b4c5b787aaed0407e5e3a22b Date: Thu May 15 13:20:41 2014 -0700 Commenting out unused variable in FoldTree.cc commit c417e0cc62394793f8abcc28210743d0bda7612b Merge: 7d0bc12 fa06be4 Date: Thu May 15 15:58:06 2014 -0400 merged mpframework_devel into here, resolved conflicts commit 5d9e166bab7447f69f60fb35809af697390e4437 Date: Thu May 15 15:57:41 2014 -0400 updating membrane fa sfxn fingerprint executable and addint to pilot/membrane build settings commit adb05cf613ca9e9a2f451856172b51c80176129e Date: Thu May 15 15:50:20 2014 -0400 Adding fa mp env and fa mp solv energy method registrators to init.cc commit 67e3a7d8563946684498a001edebeb12f2a11e14 Date: Thu May 15 15:47:56 2014 -0400 Bug fixes to compile FaMPEnvEnergy term commit 61db198b741f12b326ac64be983a6094b1383520 Date: Thu May 15 12:41:51 2014 -0700 Fix to build: order of variable initialization in ResidueType fixed. commit 7d0bc120af78c7262688eea0a6213ab2116f0204 Date: Thu May 15 15:39:38 2014 -0400 trying to fix the silent file stuff commit eb10885862baeb19ca798215c1bd26b22caa8295 Date: Thu May 15 15:27:39 2014 -0400 Started a pilot app that will eventually execute the fa sfxn fingerprint tests commit 4ab2fae433fe10c8dd2c16455396ad25e573f69d Date: Thu May 15 15:27:05 2014 -0400 Adding fa accessors to membrane info and bug fixes to get compilation in FaMPSolvEnergy commit 1fe4f7676f2457afe5bd038edeb3b342b70b9f74 Date: Thu May 15 13:57:22 2014 -0400 Fixing typos in hbond options class with new mphbond option commit 41d225c97968e9132e13d551ec7b378ac2197240 Date: Thu May 15 13:55:28 2014 -0400 added comments commit 114bbea640f29a481c3b63fa286fb8a23642ea8c Date: Thu May 15 13:55:14 2014 -0400 Adding membrane framework supported hbond correction commit 7880ed30cebcb2332f33a521fd9a5f2263b6260e Date: Thu May 15 13:54:34 2014 -0400 Adding membrane framework supported hbond correction commit f246478732919016db2fd129d1a2b5f837dc86ca Date: Thu May 15 13:51:58 2014 -0400 removing methods I thought I needed but dont from hbonds.cc commit a8d4e79f3d8d3d7fcc980d655b9669cc5ac3af47 Date: Thu May 15 13:51:41 2014 -0400 removing methods I thought I needed but dont from hbonds.cc commit fa06be4cbfa25db9d287852ef5c780e5848731e0 Merge: ca5bfc8 c22033c Date: Thu May 15 13:46:14 2014 -0400 pulling from remote commit 057e7b20b2bc75636099489c3d17b5c68cbd253f Date: Thu May 15 13:41:27 2014 -0400 Adding steepness getter to membrane info for use in hbonding code commit e87400f3820c3cf5c8e178d1342d75cdf040f3ac Date: Thu May 15 13:40:38 2014 -0400 Adding steepness getter to membrane info for use in hbonding code commit ed99cd5eb4522a7ad6cd4cb3ebfbdf3a5cf480df Date: Thu May 15 13:33:54 2014 -0400 Adding mphbond to hbond options object commit 09e4aaba8283153f832804ba7f34bea84fc80012 Date: Thu May 15 13:25:01 2014 -0400 Adding membrane_new:scoring:hbond option for turning on framework supported hydrogen bodning correction in code commit 01042dff16b8cbee23f75c45331373cb1dae249d Date: Thu May 15 10:20:12 2014 -0700 Adding missing ScoreStructJSON files. commit ca5bfc89c2554d8cdb648b3983fbb4165f77095a Date: Thu May 15 13:13:07 2014 -0400 fixed documentation for input options commit bdb0abd8754091477161ac813b5108c3fa54bf51 Date: Thu May 15 09:51:06 2014 -0700 Adding JSON scorefile format; untested. commit 7af79562fb280179eb2b4e2c0e070f04a15d5c9c Date: Thu May 15 11:53:21 2014 -0400 Adding missing score types to ScoreType.hh files commit 85ad9f7d356a8328a28b605b93c7df3d641755f8 Date: Thu May 15 10:45:22 2014 -0400 Initial big fixes to fix the build of FaMPSolv and FaMPEnv + score type fixes commit e64aa70b5e043832eaaa27992eba8cee40de08ed Date: Thu May 15 16:29:13 2014 +0200 Add com-testing topo_driver code. commit 580fa91431e3e2a9c39d1bcea4c8ac285b792966 Date: Thu May 15 16:28:24 2014 +0200 Add assert for zero-size CoM computation vector. commit ae2a2a11c7f66dcf05b261e0d09b194043fd311d Date: Thu May 15 16:17:28 2014 +0200 Various fixes to VirtResClaims and EnvClaimBroker to accommodate new system. commit f377c037cc91ce95417812362c53d429ebe4ab35 Date: Thu May 15 10:17:06 2014 -0400 Oops - made all of the membrane info methods private by accident ' commit 80515b7c57a78389275eb2328b7093ac073c451e Date: Thu May 15 10:14:35 2014 -0400 Finishing clean ups in membrane info class for new fullatom code commit 59ae5d091d6212c419784cc48bb47d31c58b26b6 Date: Thu May 15 15:11:34 2014 +0200 Modify FragmentJumpCM to do intra-residue stubs more specifically. commit 350b262fcff2970c91f1bc087306478c129598bf Date: Thu May 15 09:10:13 2014 -0400 Cleaned up and adapted membrane info object to do setup with fullatom information commit f175decb50e50db15543992a70e0f5d4cd698306 Date: Thu May 15 15:08:12 2014 +0200 Fix a bugs associated with set_jump_stubs_intra_residue. commit 4ed5da2cb69a3d762c627d680224037273997d47 Date: Thu May 15 14:58:16 2014 +0200 Remove atom1/atom2 setters/getters from JumpClaim because the FT doesn't allow it. commit fb62930dba1fc3316a217d04b89d7ceecfbb8484 Date: Thu May 15 14:57:18 2014 +0200 Output beautification. commit 3d54737520366cb6c56625ed81d6ed79a83065a9 Date: Thu May 15 08:55:38 2014 -0400 Cleaning up the header for membrane info - should make it more comprehensible commit 3f3fb720bfa877d36ae2527419053608fd0ace43 Date: Thu May 15 14:41:34 2014 +0200 Refactor jump claiming to allow explicit intra-stub-residue setting, as well as better management of data calculated by the broker about JumpElements. commit 50a9dd6dbb3a05ccaacc37ffcaa20e98861fcdc6 Merge: e6b3da5 cd4b049 Date: Wed May 14 19:29:42 2014 -0700 merge changes in yfsong/cycpep commit cd4b049f24fa31f7c5cb8df15f0a1e0a875ebb4f Date: Wed May 14 19:24:53 2014 -0700 fixing a small bug with accessing pdb_info in peptide stub mover commit e6b3da535fbb9b0ccc2a7ebac31ed33ed7dd0568 Merge: 968b999 e4a62b5 Date: Wed May 14 18:53:22 2014 -0700 Merging remote vmullig/cycpep into local vmullig/cycpep. commit 968b999093bf3d00a2aa6bda6af38807c50e64a0 Date: Wed May 14 18:50:58 2014 -0700 Adding clone() function to BBGaussianMover. commit 9a0f9b8e9ca84144150aea6500d7b30dbd5385d0 Merge: 71860a8 405d69a Date: Wed May 14 18:43:54 2014 -0700 Merge remote-tracking branch 'origin/cycpep/collab' into yfsong/cycpep commit e4a62b53aab4bdb36821789cb223884a65e79462 Merge: 348a3e7 58bc818 Date: Wed May 14 18:07:40 2014 -0700 Merging master into vmullig/cycpep commit 0cb5358aa1a59bd93a70cd80e7a6698c06288eb9 Date: Wed May 14 20:31:37 2014 -0400 Implementing env and solv energy creator methods commit b1e5c41ebf5c7c9532aa193a03ecc0f4503aa878 Date: Wed May 14 20:12:36 2014 -0400 Implementing the rest of fullatom solvation energies commit 348a3e7b42a5ab2c6fec1f49f13e157267aef727 Date: Wed May 14 17:08:52 2014 -0700 Trying to get design_cycpeptide_MPI.cc working with noncanonical linkers. commit e95ba9bcd918a008a9a291d1639374abc0f9e9f2 Date: Wed May 14 16:32:41 2014 -0700 Adds filters to be used with rosetta scripts for epigraft and others: SimpleRMSD, Fragments, SSamount commit 18e24603bfcc3aea7c45e39857ea25c9cd2b238b Date: Wed May 14 17:51:11 2014 -0400 Implementing more of the solvation energy term" commit b0e51077e4669dfba8abcfa7a976ccd69dfe2d1c Date: Wed May 14 17:11:29 2014 -0400 Starting to implement the solvation energy term commit ce08454301fd397c756706ca39e04872f9db0fd7 Date: Wed May 14 15:50:28 2014 -0400 Implemented rough version of fullatom membrane environemnt energy commit aed653521043a161a070f84b2f38dbb88d8439a1 Date: Wed May 14 15:34:15 2014 -0400 Moving stuff back into membrane info commit 80e652a5871ebddf574f57e3d2bc10f1f096c2ba Date: Wed May 14 13:20:52 2014 -0400 Adding fullatom score types to score type manager commit fa00ed8d9897fa5c0a2d2b735de8092b5cbdd875 Date: Wed May 14 13:18:17 2014 -0400 Adding new utility class for fa calculations, starting to implement these in derivative setup in env term, also adapting membrnae info to hold this new data. Maybe I can make it so this is not typeset dependent whatsoever?? commit 908e9d0c3712d385eedc4f74e13be8aa11aa7248 Date: Wed May 14 17:43:28 2014 +0200 Fix an issue with the iteration through the movers in sequence mode. commit a42e21d82a074be3550fa0e38ef62501a3525d1d Date: Wed May 14 16:42:02 2014 +0200 Fix a bug where the parsed protocol sometimes attempted to apply movers in empty iterators. commit 8e69e177061afb902e7026f7202e9687ff88721a Date: Wed May 14 15:00:20 2014 +0200 Clean up compiler errors from copying Oliver's refactor. commit 98d973dbb298b62c48b84a1b0098bf5eb36e6565 Date: Wed May 14 14:53:17 2014 +0200 Recreate Oliver's refactor of ParsedProtocol to not require that all filters be re-invoked at the end of the protocol. commit 5efc1b1ad3b4635253e849d2085438d7d7d0bf9f Date: Wed May 14 14:30:18 2014 +0200 Add on-the-fly mover instantiation (i.e. unnamed movers in PROTOCOLS). commit 405d69a375bcad90e98ed08ad806fb888a7f03b4 Date: Wed May 14 02:43:31 2014 -0700 Fixing debug-mode compile by commenting out unused variables. commit a67d06e49c55b980be3e8edda7f9ba9e7fd1fd03 Date: Wed May 14 11:14:05 2014 +0200 Begin work on ScriptCM, without interface for ScriptableCM yet. commit 0d726272b8d3274a7c06dd45d1f14ac33252c19c Date: Wed May 14 11:13:35 2014 +0200 Begin development of EnvLabelSelector as the cached selection selector. commit d7d7e5eed3f30630d406f22dada9bbb60e841fb6 Date: Wed May 14 01:39:04 2014 -0700 Fixing debug-mode compile. commit 8cdc6d59b7a293af6dbeafc844e2f9ad15c0b324 Merge: 691b84d db3958a Date: Wed May 14 01:10:45 2014 -0700 Merging master into vmullig/cycpep to get fixes to MPI debug-mode build. commit 691b84d0bc718f679d1d96bea546de68c525162d Date: Tue May 13 23:24:58 2014 -0700 Moving design_cycpeptide_MPI.cc from vmullig/vikbranch to vmullig/cycpep. commit 74f4e50c168460eb019ea38c6a2db2c8e62c4386 Merge: 2015fb0 93d7e3a Date: Tue May 13 22:59:25 2014 -0700 Merging master into vmullig/cycpep to get fixes to MPI build. commit 71860a852c3bec30a9d96fc74e515d4c16eb9c8f Date: Tue May 13 20:55:33 2014 -0700 Add insert residue by bond function commit 2015fb0675f778bca13c0b13d18723bbf42d79d1 Merge: 91559cf befc6f6 Date: Tue May 13 19:47:39 2014 -0700 Merging vmullig/metals into vmullig/cycpep to get tweaks that make metalloproteins work with RosettaScripts. commit 7eaedd8b8cdc3cc9a310af394742f8717ef6425e Date: Tue May 13 22:37:33 2014 -0400 Adding header, fwd header and starter cc code for new fa env and solv terms commit ba7bac5e06d5cf68e3ea9b6b0e7a6e74e9c81049 Date: Tue May 13 22:14:11 2014 -0400 Implementing pieces of the fa env term commit 9e1ad1c0e6d7848ae57d21e6a198d275d07c6538 Date: Tue May 13 22:03:12 2014 -0400 Adding templates for new fa solv and env energy terms which will be framework adapted commit c22033c9492bfdb76b5703bab7c54113950fdb8c Date: Tue May 13 19:04:02 2014 -0400 Quick bug fixes - membrane etable with new annotations compiles commit adc9babea0f8c1569cce200f343a5eae41a00057 Date: Tue May 13 18:55:43 2014 -0400 Adding finished header to forward file and staging hh file for commit" commit 4629ead2f04d91af93d405772b762cf1fc5410bc Date: Tue May 13 18:54:42 2014 -0400 Adding more comments and updates to annotated sfxn commit 09a9d1b3f9af39525e7496a6b7ff62dc0e0796c6 Date: Tue May 13 18:46:17 2014 -0400 Removing a ton more dead code in membrane etable commit 91559cf416dade00fcafd10f3f3d9aeb8d894833 Merge: 9a0810a 4770aa9 Date: Tue May 13 15:15:41 2014 -0700 Merging yuan/bbg into cycpep/collab to get Yuan's BBG mover for peptide work. (Thanks, Yuan!) commit 9f0fa9ba66523eedf523bce7fd598ce0ca0c4c93 Date: Tue May 13 18:10:42 2014 -0400 Cleaning up membrane etable hh file, adding comments and formatting fixes. Also started updating base memb etable but then realized its no longer used commit c5743752b26e21de3b52e657d2107d1631995492 Date: Tue May 13 17:57:18 2014 -0400 ResidueType: added VIRTUAL_RESIDUE property commit 39de8304ddbfd37a16de088b8a8a45a10b506f7d Merge: e2321a9 ce2af8c Date: Tue May 13 17:33:39 2014 -0400 pull from remote commit 42e7ede9fbdc1fdc4fcac4381dc3176d89c17901 Date: Tue May 13 12:26:51 2014 -0700 fixes to more unit tests. commit 5fa019ad69ccf44c7902738ce6e25580484a04a8 Date: Tue May 13 11:42:55 2014 -0400 Removing hundreds of lines of dead code in the membrane etable code commit dc2d572d608ee7b4ac3c6569ad17fc918e965840 Date: Tue May 13 17:39:51 2014 +0200 Removal of depricated internal_only_ in XYZClaim. commit d0500ca97fd394c06460f61102760e41a6f4303d Date: Tue May 13 17:39:10 2014 +0200 Implementation of RosettaScripts parsing of Claims through a static method call in EnvClaim. commit ce2af8c1a1931174f34fc6e56c76f2ee11f224e1 Date: Tue May 13 09:59:54 2014 -0400 I prematurely merged in msater into this branch. Wasn't ready, so I reset the branch to remote. It looks like everything is ok here - the branch builds. So I am goign to go ahead and push, but if we find issues we can always revert the work commit ca52b2cd2fb3dbb30a392bf29bf9740173c7a4ed Date: Tue May 13 09:57:28 2014 -0400 Fixing spacing in membrane data class so it reads much more nicely... commit 2b65ca4ee94536e8558c6e34461be9d415631dc0 Date: Mon May 12 21:17:33 2014 +0200 Early development on ScriptCM commit 9a53ccb20f203b56a63adfbd1a3a1f80062c336a Date: Mon May 12 14:59:12 2014 +0200 Add ScriptCM draft implementation. commit 9a0810aa82d70e0a1d6c7516eb54cf2af5191477 Date: Mon May 12 18:18:55 2014 -0700 GeneralizedKIC now works with start and end pivots that are not alpha carbons. commit 5dfd6e721c7ed364d846fd2cdf10401d58c5fb4e Date: Mon May 12 17:27:46 2014 -0700 Trying to get GeneralizedKIC working when the first and last pivots are not the 5th or 5th-last atoms, respectively. commit 24f749ab926f85348155dbf1f09002dd4b4bbda6 Date: Mon May 12 20:01:02 2014 +0200 Change CoM naming to mirror mover name, fix indexing of residue selector vector. commit 460e9296e11679df30766c955968fd96f969c27c Date: Mon May 12 19:58:24 2014 +0200 fix build issues with CoMTrack unit test. commit 1590146456527fe361622c356d8ba3e7f4e74e14 Date: Mon May 12 19:57:52 2014 +0200 Fix build issues with UniformRigidBody.cxxtest.hh commit 1795fc2b14165369a8f431567114cb3cbec2dacc Date: Mon May 12 19:39:46 2014 +0200 update UniformRigidBody unit test. commit 608331ce6d3e8681d95a26a85fba1941a69dfe99 Date: Mon May 12 19:36:35 2014 +0200 Fix a bug where unprotected conformations for which an unlock is created fail on relocking. commit 1dcb42e341ab05a86ddb3c3bdae13931678c321b Date: Mon May 12 18:28:51 2014 +0200 Fix an issue with EnvClaimBroker where labels for degenerate jumps weren't being added. commit ae9810658454be640d474cadce8202dfb425990b Date: Mon May 12 11:31:04 2014 +0200 Fix a scoping issue so that now test-wide pose is correclty constructed. commit 722d455f6bea6af775c546518aaded191199e409 Date: Mon May 12 17:41:08 2014 +0200 Create UniformRigidBody unit test. commit 37f91daccf6fca3f487d4552ffa38ffc204216cc Date: Mon May 12 17:37:58 2014 +0200 Improve output from Broker failure and fold tree brokering procedure. Fix a bug where inherited cuts would sometimes be mistake for a failed brokering. commit f04fdfcb0539ba043135a96b022d650465fb1507 Date: Mon May 12 17:15:04 2014 +0200 Stop URBCM from creating new virtual residues. commit cb2c31b13b3bf38e612dc11841ecd80803536fbb Date: Mon May 12 17:09:35 2014 +0200 Build UniformRigidBodyCM to only run the docking jump. commit 771eba24ec61d61503a112724f3d367585439f2d Date: Mon May 12 16:11:56 2014 +0200 Add a boost::lexical_cast string-parsing constructor to LocalPosition. commit f4bd35d5999a2bd2c7cd305feac67fe6933b3fd9 Date: Mon May 12 15:29:04 2014 +0200 Make DofPassport output more professional, modify error message condition to account for both 'interpretations' of virtual residue (i.e. the ResidueType is full of nonsense). commit 0b69aa0d3bf45e1568f3eaff2ce0a0e33b567b1e Date: Mon May 12 15:25:58 2014 +0200 Add a CoM-recalculation on ::apply check to CoMTrack unit test. commit 1c474030661e974f21c02c4ab35be19c99e93674 Date: Mon May 12 15:22:04 2014 +0200 Fix a bug in DofPassport::const_iterator where it would give the 'empty DOF_ID' (i.e. atom 0, rsd 0) as an accessible dof. commit aaadab511bca89566f8458d6cd263954b2f9e50b Date: Mon May 12 14:46:53 2014 +0200 Modify StructPerturberCM to rely of DofPassport rather than computing DOF_IDs itself when possible. commit c3b5bd232a3903999502a782912b2450584784f8 Date: Mon May 12 14:45:39 2014 +0200 Add DofPassport iterator. commit a8e97647cce3e5968f0bb69bcb0c649d7ec9a6c5 Date: Mon May 12 14:30:30 2014 +0200 Remove useless typedef in ClaimingMover. commit 0efd6c3bff8f5decf6c2247f9e34fef145331dcc Date: Mon May 12 14:35:46 2014 +0200 Add @author tags, remove useless includes and commented code from UniformRigidBodyCM. commit ff044037121ef4d311e49aed9d5dc15e9385e11f Date: Mon May 12 14:33:05 2014 +0200 Remove outdated method and add @author tags in UniformRigidBodyCM commit 23ac7a87fa9225b0d6fdcdb9ea1726990662a075 Date: Mon May 12 14:21:34 2014 +0200 Add check in TorsionClaim to make sure that it only makes calls to Conformation::dof_id_from_torsion_id when that id is valid (to avoid asserts). commit 510d0a9c18c6bb7c135eb0531ef99e5ba9500c85 Date: Mon May 12 13:56:42 2014 +0200 Fix a bug where virtual residues couldn't be rendered into the movemap. commit 3d989164619d1bb7fe6b3f9a2a5ad8b3aa4f1e13 Date: Mon May 12 13:15:15 2014 +0200 Remove std::cout from CoMTrack.cxxtest.hh commit 49a6623f3193b109398891233742323cd7cb59ba Date: Mon May 12 13:12:03 2014 +0200 Add label/magnitude constructor for StructPerturberCM. commit 5a7c8374a0cde261f1a8c7d0661b6004f966e59e Date: Mon May 12 12:59:36 2014 +0200 Fix an issue where sometimes automatic cuts could be placed outside the cycle region. commit 56d9b0e3dc545477cd123985e060b9bb26fa0bcd Date: Mon May 12 11:28:14 2014 +0200 Fix unit test build. commit 0b549fef898008aaf9ad6506992114ef5eca3dd6 Date: Mon May 12 11:07:21 2014 +0200 Add CoMTrack unit test. commit 845925a2860b13da5a0332c0599a468faef659a1 Date: Mon May 12 10:13:07 2014 +0200 Separate out CoM tracking CM into a separate file. commit 14039f0d03234e113d3dc4c93ce6f9feab784f9e Merge: ea61a2a d975c62 Date: Sun May 11 18:50:37 2014 -0700 merge from master after recent big merge. commit ea61a2abad875b3187a18e604b648653f2d231b9 Merge: a10c6af 2f7831a Date: Sun May 11 18:44:08 2014 -0700 Final merge from master before merge of rhiju/swm_general into master. commit fccac23b0080ab63022d3c2213c51be6938749e0 Date: Sun May 11 17:47:39 2014 +0200 Fix a build error. commit 6d5ccf54cf5885d19cc1eccc5f71de35f9339883 Date: Sun May 11 17:40:28 2014 +0200 Fix a bug in the EnvironmentJump unit test where annotated sequence string comparison was used to find cuts. This was clearly dumb. commit 2b277a6304ee96bc391c3063252b911884580487 Date: Sun May 11 17:31:24 2014 +0200 Fix a bug in FoldTreeSketch::insert_cut( vector1< Real > ) in which it always summed the biases to 0. commit fabf452b79d579594f89420c529ac00750d6581a Date: Sun May 11 17:24:58 2014 +0200 Fix a bug where auto_cuts would go into an infinite loop if cuts are also inherited. And a bug where masked_bias was incorrectly constructed. commit 6c210e494b526ef2b7fe29f5cb40507a749f5fc8 Date: Sun May 11 15:55:25 2014 +0200 Fix an issue where Environment::end return an empty conformation. commit 6aefeeaf35a750343cbac44ecf65cf5c19ce910e Date: Sun May 11 15:54:48 2014 +0200 Fix an issue where vrt-less fold trees would make invalid delete_residue calls. commit f53b90715b931c4021baba9233ac2d2b24fd9bc0 Date: Sat May 10 18:14:43 2014 +0200 Removing the assert(false) I was using to stop execution after the update_com call. commit 898166271b27ee09c8fe2df53062835cd5aa7bd6 Date: Sat May 10 18:12:57 2014 +0200 Adding an additional TODO tag for Justin. commit 5171e5dc2f14842e646c319980481c70838fb724 Date: Sat May 10 18:06:34 2014 +0200 Huzzah! Adding new private method to UniformRigidBodyCM: update_tracking_residue. This allows you to reposition a virtual residue to some specified position without moving any of the other atoms. Simple tests with asserts show this is working. It is surprisingly easy to understand. Woo! commit 217c3a6a85d23417e8c7e33d1637ab2baa5bc7da Date: Sat May 10 17:51:51 2014 +0200 Add cxxtest emulating #define statements to topo_driver commit f85ea4094610aaf5b396cdbfabeda0ae2efa8129 Date: Sat May 10 17:44:28 2014 +0200 Add comment explaining vrt delete code. commit 561b189f73e009de76370a327106d4443dd08fc2 Date: Sat May 10 17:37:14 2014 +0200 Add vrt-stripping behavior to Environment. commit b18a5dcd212140971ed9d62567f22ce2df6b9a01 Merge: 29655b8 aa54fc7 Date: Sat May 10 13:40:49 2014 +0200 Merging UniformRigidBodyCM changes with unit test development. commit 29655b8e35a0fdadfa9b3a0496bf5acabea6288c Date: Sat May 10 13:39:35 2014 +0200 Write test_cut_inheritance test. commit f61fdf1607b645b0525eaff4a705ef9baa022e95 Date: Sat May 10 13:37:47 2014 +0200 Modify FoldTreeSketch interface to perform cycle cutting using a cut-bias mask; remove physical fold tree from EnvClaimBroker. commit 42c9f3d0fcb5bd64a4e6a3b60721867b6532d310 Date: Sat May 10 10:30:25 2014 +0200 Add debug output to EnvClaimBroker cut inheritance. commit ee63e16fa25eb87178b40832f210f3ae4ce2669d Date: Fri May 9 19:52:33 2014 -0700 Tweaking PeptideStubMover to update PDBInfo as residues are added or deleted. commit aa54fc7442268b8c7dbe010e6efa4ca1a28e8b3b Merge: 30dd069 baefaff Date: Fri May 9 23:19:09 2014 +0200 Merge Oliver/Brian CoM pow-wow with Justin Env-fixing. commit 30dd069dcf0947bf507a325a9d66d6dd9b09b441 Date: Fri May 9 23:17:43 2014 +0200 Modify UniformRigidBodyCM to properly calculate the CoM when the CoM VRT anchor point isn't at the origin. commit 2f7aa6747e0101557fd96090004a75dded677304 Date: Fri May 9 23:06:50 2014 +0200 Add autocut testing unit test to EnvironmentJump. commit 611e942fb04a6342dbf47849d6748fbec2023df5 Date: Fri May 9 23:06:02 2014 +0200 Improve error message for double-cutting. commit 9b8268cb1d5d7e69816b6619c01d41066e49368e Date: Fri May 9 22:38:25 2014 +0200 it works now commit ae18384391bbccbed7faab072427389de03c34a5 Date: Fri May 9 22:16:23 2014 +0200 Remove lazy movemap construction; replace with observer pattern. commit ad13fc3b6b5c231ea51690a7f763fee82f922592 Date: Fri May 9 22:08:00 2014 +0200 Remove tracer output from failed ProtectedConformation accesses. commit baefaff266a97693d8d7fe1ec1162cd07a8fcf4f Date: Fri May 9 22:04:45 2014 +0200 Fix a few bugs in the EnvironmentJump unit test; create JumpClaims such that their cut can be modified after creation. commit e69464b75aefee37326bb559601a54a62b926cdd Date: Fri May 9 20:33:01 2014 +0200 Fix Environment* unit test compile errors. commit 55a3716a50441bd578cd73915e8904bd64032e90 Date: Fri May 9 20:21:53 2014 +0200 Fix an issue where ClaimingMover was checking double-passport issuance incorrectly. commit 99f4c70bf30cb59b78e83af30b6709dd95e4ac7f Date: Fri May 9 20:17:19 2014 +0200 Fix a bug where ClaimingMover was doing a check incorrectly. commit 4994a9cf649aa70022ec6d34374e24f9caad9028 Date: Fri May 9 19:20:48 2014 +0200 Remove wierd #IFNDEBUG directives in ProtectedConformation. commit e0e69b347c326b94d46fa83512a4d0e624f70191 Date: Fri May 9 19:17:51 2014 +0200 Small bug fixes in EnvMover. commit 1c9922c4960f9650143f013b868de4b583611c9d Date: Fri May 9 19:04:27 2014 +0200 Implementation of UniformRigidBodyCM that is ACTUALLY ABLE to put the CoM in the middle. commit 5dbcedf9e30027f24be0039f821baca7376f077a Date: Fri May 9 18:49:06 2014 +0200 Fix UniformRigidBodyMover unused parameter warnings. commit 0548a5bc16fe5c23937499ceecdbbaea4b368519 Merge: e9c7091 78c1bde Date: Fri May 9 18:44:32 2014 +0200 Merging remote Environment interface changes and unit test changes with updates on shark. commit 78c1bde2ba6f4a48214002f86a3f039b03eeef7d Date: Fri May 9 18:42:44 2014 +0200 Split Environment unit test into two files. commit cd1c65bc4689eea38da394e4b0792261a8922c04 Date: Fri May 9 18:16:16 2014 +0200 Add auto_cut and inherit_cuts options to Environment. commit e9c70916dab198ead6750768cb9b3663df18c9fd Date: Fri May 9 17:47:22 2014 +0200 Update Environment unit test to changed claim strength interfaces. commit f4dd0d7a0ced6d2bac5d2271b286593e9a7fbce1 Merge: 6376ab0 f104159 Date: Fri May 9 17:32:22 2014 +0200 Updating env_devel with hotfixes from master. commit 6376ab05ee44be45418d6c2d1f7d513682eff882 Merge: 2aab03b bf3190b Date: Fri May 9 17:01:46 2014 +0200 Adding in a few bug fixes from env_fix. commit 2aab03bda316be25c40625958d3a3a585eafae22 Date: Fri May 9 16:59:11 2014 +0200 Debugging of JumpClaim and VrtClaim production. commit bf3190b3e55c01ba7b11b5b9c268f9c3f132e948 Date: Fri May 9 16:23:11 2014 +0200 Update ProtectedConformation new push_passport interface. commit 21ef5654cc2e9e344e8e534ed2c1ace60c02f67b Merge: 86f15d1 f104159 Date: Fri May 9 10:14:05 2014 -0400 Merging master in to peptoid branch commit 3ac71934d5bec79ed8c0fc62e73da9791a2b3b6c Date: Fri May 9 15:55:11 2014 +0200 Modify the DofUnlock popping step to run a check to be sure that the correct pass is being popped. commit 9185b933ae96c08cb8b6a1af5db9a2bff9627393 Date: Fri May 9 01:57:18 2014 -0700 Mistake in some warning messages now fixed. commit 771e3ee54df23b1abff4873ba839274a86ad7cd2 Date: Fri May 9 01:56:54 2014 -0700 Forgot to uncomment something. The atom_pair_distance GeneralizedKICfilter now works. commit 61ddf15113da70b61cf69c7a2a568e9f92c50e47 Date: Thu May 8 23:52:46 2014 -0700 Tweaking ASX and LYX params files. commit 6f6e9353652191238a63cca12af0a6615e13a7cb Date: Thu May 8 19:39:36 2014 -0700 Tweaking N_acetylated.txt patch for DPRO. commit 72956208a6411d207bd99eefae132c1d2cf5ec9b Date: Thu May 8 23:16:48 2014 +0200 Update ParsedProtocol to allow on-the-fly mover instantiation. commit 86f15d161000b2b6753910b07a76b62c3b2e8739 Merge: b475e0e 23007e6 Date: Thu May 8 11:42:51 2014 -0400 Merge master commit b475e0ea2a4954f4951020b38a1a70312acf45be Merge: 3c93a60 a5705a9 Date: Thu May 8 10:59:50 2014 -0400 Merge master in to pptoid branch commit 386db9faa55c925275cf26bb0c82d166b8d9d6f7 Merge: 9e56890 ee7a051 Date: Thu May 8 14:39:27 2014 +0200 Merging env_release (with master updates) to env_devel and Brian-broker updates. commit 9e56890f1039c55cc2185c6a14909c1121795513 Date: Thu May 8 14:20:55 2014 +0200 Modify UniformRigidBodyCM to take a ResidueSelector for the mobile region. commit 900102f8ddf9d8732f501c729b8eeff65948e79b Date: Thu May 8 14:20:20 2014 +0200 Add vector1_bool::index and ::operator\!. commit d642a200df1ff3d3495e8b37856ea6f3457623b8 Date: Thu May 8 11:44:07 2014 +0200 Remove multiple inheritance from UniformRigidBodyCM. commit 4b854625fddbb69bcb8981dd8e18ceb05bffe063 Date: Thu May 8 09:58:11 2014 +0200 Modify set strength command to require setting both values simultaneously. commit b4fe9ef4df9d4a9a37f6aa5e1c87c9eec9b14400 Date: Wed May 7 15:59:03 2014 -0700 Adding support for GeneralizedKICfilter parameters and a shorthand for the atom_pair_distance filter to GeneralizedKIC class. commit 4bb79a4ca38c88bb913fb16dd7cc98d0d0373bdc Date: Wed May 7 15:04:39 2014 -0700 Added apply function for atom_pair_distance filter in GeneralizedKICfilter.cc. commit 005260063c2f8111d5e7d8f63e15e33e3616a0f1 Date: Wed May 7 14:26:36 2014 -0700 Adding 'get' functions for GeneralizedKICfilter params. commit 3c93a60d3b0251a630ae7b5e96d3ed7c1e4b2621 Merge: f209c06 a6d86d6 Date: Wed May 7 16:52:33 2014 -0400 Merge from master commit 90e130775a8bc74a950a3d2e4d8af998ac0089d0 Date: Wed May 7 13:21:46 2014 -0700 Adding filter parameters to GeneralizedKICfilter class. commit 8dae9bf89727278e812537bfcb6ca162de0722f2 Date: Wed May 7 20:46:46 2014 +0200 UniformRigidBodyCM/Mover in draft iteration complete. commit f209c06530a3c2cf9ed68b03f9cacd06e109f629 Date: Wed May 7 14:22:04 2014 -0400 Fix compilation errors in peptoid design app commit 77fa4d671e190e39c80369869fe987172192e437 Date: Wed May 7 16:49:46 2014 +0200 Modify the JumpClaim to allow independant setting of the two positions' add-vrt-if-it's-not-there behavior. commit 26e501efbf96cec756beb8d6bf393269759805ac Date: Wed May 7 16:48:02 2014 +0200 Add SequenceAnnotation::resolve_seq for whole labels. commit db91fccf93ee5d169b5e9c08bb47567bd1acdd53 Date: Wed May 7 16:14:06 2014 +0200 Add active environment accessor to ClaimingMover, change passport stack to hold an AP to the Environment. commit 37771d6375bea4b28fb92669792822ab0641b9aa Date: Wed May 7 15:41:06 2014 +0200 Add a lazy create-virtual-residue-jump-targets functionality to JumpClaim, support it in the ResidueElement framework. commit bbf0929b8d93ec1a83e54aa217715cbaecd10596 Date: Wed May 7 13:18:04 2014 +0200 Add reference conformation access to DofPassport. commit 5393fb46411702d2f7f5bc3daeea3f7ec4de72db Date: Wed May 7 11:02:03 2014 +0200 Add UniformRigidBodyCM for producing standard rigid body moves in an unbiased way in the broker system. commit 31fd3296a244108ff365fc1a0820bf6c9486472b Date: Wed May 7 10:57:43 2014 +0200 Modify DofPassport to hold on to a pointer to a Conformation for reference and movemap conversion. commit 913100ac81e2af48519090152c0e18c08d8cc1fc Date: Wed May 7 10:55:41 2014 +0200 Add random.functions.hh for computing more complex random values (e.g. unbiased unit vector in 3 dimensions). commit 9b4a9d09d56d4549c1aa8a766f8167726283ed33 Date: Wed May 7 01:07:38 2014 -0700 Fixing a compile problem with GeneralizedKICperturber. commit 6459fecbc228170df178f7351d5c50a7ae36ecb9 Date: Wed May 7 00:46:01 2014 -0700 Fixing compile problems with GeneralizedKICperturber. commit 9f0481f57da9553d84bf56ba7d456fee18cdea5f Date: Wed May 7 00:31:00 2014 -0700 Addng a perturb_dihedral perturber to GeneralizedKIC. commit 9cd0955536133a11ca93f2f01d10acb20ea24d29 Merge: 53fddf1 a88cfb8 Date: Tue May 6 19:12:57 2014 -0700 Merge remote-tracking branch 'origin/cycpep/collab' into yfsong/cycpep commit a88cfb85506cbe671e6739e786889ccaecfa5690 Date: Tue May 6 18:04:24 2014 -0700 Tweaked 1,3-bis(bromomethyl)benzene params file. commit cf2cb7f8a8dab774713227658876dad3ee0e69ce Date: Tue May 6 17:47:30 2014 -0700 Adding jump rebuilding to bettercluster.cc. I THINK bettercluster.cc is now in a position where it can be used for Yifan's nonstandard linker. commit 3f338a89a99fd249791c8594fecf2f3512edc971 Date: Tue May 6 17:07:36 2014 -0700 PCA_visualizer now works with nonstandard linkers. commit 1615c7303735e9d400736711bcb45ab075d5f338 Date: Tue May 6 15:30:03 2014 -0700 I think I've got bettercluster.cc working with nonstandard linkers, now... Still need to add support for declaring bonds. commit 32f719f159cf365ee7d74a9e2b0a5bfd958bf7f6 Date: Tue May 6 15:26:25 2014 -0700 Added PCA_visualizer.cc to vmullig's pilot apps. commit b03c992bdde5e2fb968183a341b92120d2ca15af Merge: d300dab 263a9a4 Date: Tue May 6 15:37:43 2014 -0400 Merge commit d300dab593bedd1d6720088088db77c77df127ba Merge: 76d35ba ece74ce Date: Tue May 6 14:59:54 2014 -0400 Merging master in to peptoids commit 259f3e08ef801b423787a693e39d814964acc05c Date: Mon May 5 22:16:23 2014 -0700 Tweaking alglib to make it compile in debug mode with all the warnings-as-errors stuff turned on. commit 499e4b6af856eaae81ef5367ac7b8b8c5ac6c1b1 Date: Mon May 5 22:13:21 2014 -0700 Trying to get bettercluster.cc working with Yifan's linker. commit 53fddf130b1e13e4da2dc5bbec6e43e0ac1dc9cf Merge: 9d5d794 7761f2f Date: Mon May 5 13:38:16 2014 -0700 merge from collab commit f798847ea8585186be23ea155ea9dc58d2aa01b9 Date: Mon May 5 13:38:07 2014 -0700 Trying to get bettercluster.cc working with nonstandard linkers. commit 0dc9e645a5c3ddc70a73426806491d8090aacdd1 Date: Mon May 5 13:51:37 2014 -0500 resolved merge conflicts in MEM and EMB params files commit a6d0470648ca12aa4fc36964988c2045f498801a Date: Mon May 5 13:11:05 2014 +0200 adding pdb numbering output to respair energies reporting in ScoreCutoffFilter. no test changes expected commit 9d5d794d27aeb686baf734e2b0b9234f25a6b76d Date: Sun May 4 22:00:25 2014 -0700 add changes to bettercluster commit 7761f2fd4a4da063475f8a94e2cd5e44f5b859f3 Date: Sun May 4 21:30:41 2014 -0700 Adding bettercluster.cc to vmullig/cycpep branch. commit 4770aa9e142b215e564b139e8cd69d7b8128a984 Date: Sun May 4 17:22:15 2014 -0700 Fixing compiling issue commit c802d5452a0bfc96a42a9b76183c2dc32eeb9d18 Date: Sun May 4 14:31:43 2014 -0700 add bettercluster from vmullig branch commit 382f68d544093de5971a5f17c51e48e061dc4ba0 Date: Sun May 4 00:37:12 2014 -0400 Chaing fonts to sans serif in tau_angles script commit f59cd1a92b1385a0b50bf0b064b07cb1970ef04f Merge: e3fa230 9e8f7ff Date: Sat May 3 23:00:30 2014 -0400 Merging branch master 5/3/14 with mpframework devel into a merge testing branch. The only unresovled merge conflicts are in the membrane residue params files which needs to be corrected by julia commit 9e8f7ffc4720825fedc7e138c48e4727a21d5eae Merge: c968d61 fe5d0b7 Date: Sat May 3 22:55:33 2014 -0400 Merge of ninja local master with mpframework devel merge testing branch commit e3fa23021a4211b3f19bf8e0b06e87c361e88c33 Merge: 4ff8b62 a67748c Date: Sat May 3 21:53:07 2014 -0400 Merging of branch mpframework_devel and mpframework_sfxn commit a67748c5cee9b511e11b394e464508afb848c6a2 Date: Sat May 3 21:49:13 2014 -0400 Fixing indentation issues that don't respect coding conventions commit 9da7eebf4a6f3c773136a695feaf2579202b1f0e Date: Sat May 3 21:44:03 2014 -0400 Removing old unit tests for membrane scoring - this functionality is covered more appropriately in an integration test commit 263a9a4002bbda889524c1e3172cd1848c88354d Date: Sat May 3 20:49:34 2014 -0400 Removing more undefined functions commit 7cafca54f4e2831a7f632e4c66660d8757469cf0 Date: Sat May 3 20:32:05 2014 -0400 PyRosetta. Removing undefined function. This should fix runtime error. commit a4044f6a89cb3999f52812670bd0d50a90eeb988 Date: Sat May 3 19:45:21 2014 -0400 Adding passing membrane centroid scorefunciton integration test for new socres commit 10101f3f4da99710a0703f00f5a2d6c51811b156 Date: Sat May 3 19:44:55 2014 -0400 updating membrane scorefunction app commit e37ee222f6a673cddf0c181d60c2cff1eb41bac1 Merge: a7d6f6f fe5d0b7 Date: Sat May 3 15:48:22 2014 -0700 Merge remote-tracking branch 'origin/master' into yfsong/cycpep commit f78c16516236effcc5472664f8f86e645e0b58c4 Date: Sat May 3 01:03:30 2014 -0400 Fixing PyRosetta build commit 84dcecab54078220923ff7baeef80935711d5a0f Date: Fri May 2 23:02:29 2014 -0400 Modifying resource definition file to take files from the current working directory commit 30c7bcf90da20fedca9eea3544524b94a356586a Date: Fri May 2 23:01:54 2014 -0400 Adding required input files for integration test commit 785343f0fde130e27d884e7e9a1f6dc2c6cfb892 Date: Fri May 2 22:59:42 2014 -0400 Adding integration test dir for membrane sfxn commit 7213ea392c19dfe29f72e030b67a3e50142599a9 Date: Fri May 2 22:59:24 2014 -0400 Adding integration test for membrane centroid score function commit 76d35ba2522aab329e6bf10be02e9c8cb2bf578f Date: Fri May 2 15:38:05 2014 -0400 Fixing PyRosetta build. Adding missing header. commit b12c9d166ac69f515e97ff425a94e234763e882b Date: Mon Apr 21 12:25:02 2014 -0400 Cherry pick PackerTask bug fixes from master commit a7d6f6f60895929181aa9cc68ba8091ddd9b79f1 Merge: a591080 98f2885 Date: Wed Apr 30 19:03:17 2014 -0700 Merge remote-tracking branch 'origin/master' into yfsong/cycpep Conflicts: source/src/protocols/cyclic_peptide/CreateAngleConstraint.cc source/src/protocols/cyclic_peptide/CreateDistanceConstraint.cc source/src/protocols/cyclic_peptide/CreateTorsionConstraint.cc commit 3ce43050fdef8c3e2006e1db6277f2fc5fe4bdc5 Date: Wed Apr 30 17:25:56 2014 -0700 Auto adjust factorA based on last_proposal_density_ratio fixing a virtual function bug commit aa5695889807a186cedcbece17192868ceea94f0 Date: Wed Apr 30 18:23:30 2014 -0400 Fix iteration commit a2f59a4d207d706e3f583441dfa71d0d49edb40c Date: Wed Apr 30 14:39:15 2014 -0700 Adding new logic for fix_tail, use_all and for multiple segment commit 120ffaed621477d564869ee1ec4d652d9962275a Date: Wed Apr 30 13:39:37 2014 -0400 outlined test for pair term, still unsure about some issues though commit 856e7e0ce5a9ca80b23430c728f0d036eb616148 Date: Wed Apr 30 13:32:40 2014 -0400 Updating Menv energy cases commit 9fba307df9cbf72adc7d316fbbb1708992d75949 Date: Wed Apr 30 13:30:35 2014 -0400 Outlining tests in MPEnv energy unit test commit 8a2ed5e5f10a1b8cfd5448c40ab3bf4fc9d9635e Date: Wed Apr 30 13:21:04 2014 -0400 Updating MPEnvEnergy test and adding template for mp cbeta energy commit 4fa1473b52910af48dbd763d54360416d9a092d3 Date: Wed Apr 30 10:56:38 2014 -0400 updating Menv energy unit test template commit d2466784b73078e65b04f710cafdeeeb14ff5b48 Date: Wed Apr 30 08:24:36 2014 -0400 Adding some new files to test directory that got deleted earlier plus normal and x pos debugging tracers in membrane info commit b14ec210a0ed6c05283cb87b28637ad3efe19a1e Date: Tue Apr 29 22:55:34 2014 -0400 Still working on unit tests commit 43a5b89f269309103ad3c9b59606500d442733e6 Date: Tue Apr 29 20:46:39 2014 -0400 Adding cytB test data and updating full menv energy unit test commit d3022497efb9c448efe111be710124333300df94 Date: Tue Apr 29 20:08:42 2014 -0400 Adding structure of 1afo for scoring test data commit c304a39965b273e30cfe2d1c08db0336c2201c80 Merge: 48b245d 5f9fb99 Date: Tue Apr 29 16:55:45 2014 -0700 Merging master into vmullig/cycpep to fix PyRosetta build. commit 83ced04e65ced03da75d0bb0405bdd996b41413f Date: Tue Apr 29 15:24:46 2014 -0700 Making bbgmover parsable by RosettaScripts commit 4fa31ae1735bb40ca4f28e0da68e5fa4c77f53e5 Date: Tue Apr 29 16:58:42 2014 -0400 Adding bug fixes in MP env energy commit f17adf51b55a0c8ad36328d568baa81829d6ef66 Date: Tue Apr 29 16:54:53 2014 -0400 Fixing membrane info unit test with z position changes and updating mp environment energy unit test commit 4ff8b624cd9ae6170461f62be3799ae25a7a04f7 Date: Tue Apr 29 13:51:29 2014 -0400 Fixing more merge conflicts and resolving reversed coding convention updates commit 6aef0547579581fdaa53d8297153c019e58b2bd2 Date: Tue Apr 29 13:08:06 2014 -0400 Fixing spacing in core settings commit a84066e54a96361d2af506bbc41909d00a61cc7a Merge: 46305274 1e1999d Date: Tue Apr 29 13:00:52 2014 -0400 Resolving merge conflicts in spanfile io and merging mpframework devel into julia's branch first commit c968d614535389cddb723e9e071f9073eacf9705 Merge: 7b359f1 55e4f83 Date: Tue Apr 29 12:54:17 2014 -0400 updating ninja local master with remote master commit 80ccad48733d1a43ef0b9c32450cfaa06b98d59c Date: Tue Apr 29 12:53:23 2014 -0400 Working on local updates for unit tests commit 4baaf1b010f8eaf902cc808c959575f1e3bed464 Date: Mon Apr 28 17:26:48 2014 -0700 Only apply small move on tail short segment commit 48b245d1d3ea280c167fe6a17b37e3b71806ce20 Merge: 5e7fd6f 8828281 Date: Mon Apr 28 16:49:46 2014 -0700 Pulling from origin. commit 5e7fd6f1e9dc352351fcafa24e9dee68c9021d87 Merge: a474181 fc9b792 Date: Mon Apr 28 16:48:07 2014 -0700 Merging master into vmullig/cycpep to get fixes (?) to PyRosetta build. commit 8828281a3240c376d83aef05463d16b78884b090 Date: Mon Apr 28 16:34:55 2014 -0700 Fixing order of initialization of variables in ResidueType.cc. commit a30bfeac32cf891a5b55077cf0cd3ab364b3ce88 Date: Mon Apr 28 14:24:43 2014 -0700 NEW logic: BBG mover default movemap is empty, need to be init by parse_my_tag or outside commit 624e77d8c0fda0c8ff6c34ff5282d0a4212ded68 Date: Mon Apr 28 17:04:58 2014 -0400 fixing list iterator erasing typo commit a5910807f454a8184b05e3c9836805587ea38184 Date: Mon Apr 28 01:17:14 2014 -0700 fixing a compiling issue commit a4741811849a11563f7124920f9c046a0a0361b3 Merge: df6e6d4 f0fcf83 Date: Mon Apr 28 00:01:44 2014 -0700 Merging master into cycpep/collab. commit 1cb331352ddb364b408fae829e45173f2989c030 Date: Sun Apr 27 17:48:28 2014 -0700 Refactoring, move get* func up into base class commit df6e6d46d63c9778a6fa4dd8979d189cde96c06a Date: Sun Apr 27 14:55:16 2014 -0700 implement constraint movers commit 5cda8663d89bdc51b1aa3532badad722abe9feb4 Date: Sun Apr 27 02:05:10 2014 -0700 Refactor get_VdRdPhi() and get_L_move() commit 02b27549cbcd5e662f6f3dc15f9e889ca1987b72 Date: Sat Apr 26 23:59:14 2014 -0700 MathMatrix index at 0 which cause segfalt, roll back to Vec of Vec again commit 769c817fb2ef58e970193d808559f36ce7c78a32 Date: Sat Apr 26 21:38:17 2014 -0700 Rename Vector->xyzVector, vector1 -> Vector, v> -> MathMatrix commit 58ecf29a76169e319a20893ab2879184f88d6954 Merge: 2b40003 d2ea0c7 Date: Fri Apr 25 15:51:11 2014 -0700 Merge remote-tracking branch 'origin/cycpep/collab' into yfsong/cycpep commit 2b40003523500e4a102943ca96cc035ac6f6c856 Date: Fri Apr 25 15:50:03 2014 -0700 add improper dihedral in residue type commit daad6578f5428b93319ac15557f2dfc9e81f3c4d Date: Fri Apr 25 16:38:02 2014 -0400 Allowing peptoid to CAA design commit ba7f2ad279ace08331cfb8599f3a86e63a2d03f7 Date: Fri Apr 25 13:53:15 2014 -0400 Removing non helix penalty debugging tracers - this is a bogus term for now commit d28b4c8b78777a3ed107f56399a56affd5ec0259 Date: Fri Apr 25 13:16:52 2014 -0400 Fix two bugs with NCAAs and the PackerTask, change behavior of EMPTY Adds a new Resfile action called RESET and changes behavior of EMPTY. Previously, once a position became a NCAA, it could not be mutated back to a CAA. Also, once a NCAA was enable at a position, it could not be disabled. The RESET action enables all CAAs at a position like the default state when a ResidueLevelTask is created. This allows the PIKAA action to behave properly. The RESET action also disables any NCAAs that have been enabled, allowing you to reenable any you want turn on. The behavior of EMPTY has been changed to also disables any NCAAs that have been enabled, allowing you to reenable any you want turn on. To design both CAAs and NCAAs at the same position use RESET, for example... 5 A RESET NC HLU PIKAA AVL To design just NCAAs use EMPTY, for example... 5 A EMPTY NC HLU commit 7798d888c781206040c2db2f6c6055741f99f7a7 Date: Fri Apr 25 12:58:55 2014 -0400 Fixing score type full names so they fit on the score file commit c740335003e64e98389ac5b3c3d00e80d6079b4a Date: Fri Apr 25 12:50:53 2014 -0400 Updating penalties to incldue corrections for virtual residues - all of the scors are correct except for non helix socres. commit 38fc2850e54d9fccb87693febe75803c1cd6536c Date: Fri Apr 25 09:13:49 2014 -0400 Adding new residue energies breakdown class from Rocco's pilot app so it can be used in Unit tests commit f33b4122351b1c5b9e1ed03d677690e5c35aef32 Date: Fri Apr 25 08:25:13 2014 -0400 Remvoing the bug in mp cbeta energy and m pair energy - three working energy terms :D commit 37b9cd4f940a44eec32a7b9589b1533de6075368 Date: Fri Apr 25 03:09:43 2014 -0700 Added a simple RMSD filter that is not static New RmsdSimpleFilter, that can be used to measure between a reference pose saved by SavePose and the current pose object. It is not static, so the objects are created and evaluated at the execution point. The previous RmsdFilter is static so it can't work for comparing chain B of the designs. commit 30a8b20aa3155402bac8aafacf9207e8ad65fd35 Date: Fri Apr 25 00:27:49 2014 -0400 Debugged issue in membrane cbeta term - removing debugging tracers commit c277e0ff0ad96f146c8b5e490f105cd654ade071 Date: Wed Apr 23 20:31:36 2014 -0700 Merge Fragments to Motifgraft and Fix JD2 This commit merges asford-silva fragments filter and Fix Luki's changes to rosettascripts and JD2 that break motifgraft. commit 85a60cb22610a0422829e222e8934f0292d1e46e Date: Wed Apr 23 15:30:33 2014 -0700 fragment libraries are now passed to the FragmentPerturber as const reference commit f90ce13b764237e64b618df84767249010ade7af Date: Wed Apr 23 16:39:06 2014 -0400 Debugging of apps after merge commit d20ca1b6758dd7938e3c4644397e5bbfcb59681d Date: Wed Apr 23 14:59:26 2014 -0400 Reverting to old z_position containing membrane info files commit c99213f3e32bc7b51e5d20ba5b8ef8677308e1eb Date: Wed Apr 23 14:17:31 2014 -0400 Adding new app for analyzing new mp energy terms commit 50b3e81e87f865975cbd17fc30c0506bba821910 Merge: 3097032 1e1999d Date: Wed Apr 23 13:40:14 2014 -0400 Resolving merge conflicts from mpframework devel into mpframework scoring function commit 30970328e2a493a6a93597484c14b70742fe918e Date: Wed Apr 23 13:30:38 2014 -0400 Adding new weights files for new membrane scoring terms commit 61444971e2834f11848125950a0a61365bf5664c Date: Wed Apr 23 13:30:20 2014 -0400 Adding quick fix to non helix penalty commit 56de40a242db9bcf90b3f3f8d15043270b397972 Merge: ed077ac 90e112d Date: Wed Apr 23 01:14:35 2014 -0700 Merge Master to Fragments commit 536998ebe44f9b864fa883479ed66f25ed9ea8fb Date: Tue Apr 22 14:11:20 2014 -0700 implementation of the FragmentPerturber class; this finally enables sampling using KIC with fragments commit 1c022533998d7fd1d4bb5dac5d23724de635c4ce Date: Tue Apr 22 14:07:50 2014 -0700 throwing a BadInput exception if KIC with fragments is enabled, but no fragment libraries are provided; also fixes a bug where the refine stage would still use standard KIC even if KIC with fragments is set commit 5fb929d2f111aceb1c922a8bf399a5c6b8a5f8df Date: Tue Apr 22 16:37:41 2014 -0400 Pushing some debugging changes..haven't pushed in a while commit 1d46784a864bd45dfda7318ae2f714223c3aeb13 Date: Mon Apr 21 12:25:02 2014 -0400 Have packer tack compare interchange ability group rather than AA type to determine if we are designing at a position commit c8de331b0b6be14424a58157cb3d50333927b8d2 Date: Sun Apr 20 22:55:02 2014 -0400 Fixing the scoring feature reporter so neighbor computation is more efficient and can actually finish on larger cases commit cca14de1a1ef5cdd21fdb6e1b71f05449e1925e6 Date: Sat Apr 19 23:31:27 2014 -0400 Adding centroid membrane weights all weighted at 1.0 for generating of unit test reference scores commit e13e26e06897899d7902fcafae5e7538a9305baa Date: Fri Apr 18 11:35:50 2014 -0400 added file commit 711960f9824ce7f5db8fd3f6b6341b762484a980 Date: Fri Apr 18 11:35:25 2014 -0400 change to mp_apps commit 678f256884ebbb34f2176e4624f4a08bc68ac950 Date: Thu Apr 17 19:11:04 2014 -0700 fixed packaged_bindings build. commit fe71316a412273695a0284432ccab995b5032774 Merge: 191b217 3d1edb0 Date: Thu Apr 17 15:57:00 2014 -0400 merging crumb pyrosetta-friendly version with ninja local commit 9d03eb76e6b41352eef884e9643466e20aa5fee1 Merge: 2c53ef8 99e9ced Date: Wed Apr 16 22:19:50 2014 -0700 Merge remote-tracking branch 'origin' into javierbq/pyrosetta_egg commit 6b448e257801d9401feb9483bb0ae52791cb3982 Date: Wed Apr 16 17:05:16 2014 -0700 adding the function overlapping_with_region, which returns the number and list of all fragment alignment frames that somehow overlap with the given region (also allows those frames that start before the region and reach into it); currently only implemented for ConstantLengthFragSet (the FragSet parent class simply calls the region method by default) commit 191b217d1bf8cadd5772b7e2f203a216041fb726 Date: Wed Apr 16 15:07:58 2014 -0400 Finished C++ version of scoring features reporter commit 73f022492e744b10a08b4984683b5314b841b70e Date: Wed Apr 16 14:23:15 2014 -0400 adding overwrite flag to flags file commit 04db17cf2e7d3d596127185fe22561fce2329bbe Date: Wed Apr 16 11:10:36 2014 -0400 changing itest to test for more cases, does not run correctly commit 03adc6c9822ef0b9574050a27ee51ab4ed4c7fca Date: Tue Apr 15 23:49:18 2014 -0400 Adding a features reporting app - shouldn't build because I amde some chnages after I first ran it. Work in progress commit 521d913b7fbb79a427840754c8d241df089a2d3c Date: Tue Apr 15 14:45:42 2014 -0700 including Frame.hh (instead of Frame.fwd.hh) in FrameList.hh to fix compilation; this is needed due to FrameList inheriting from vector1 commit 606f429c9168df05d662d859e8d3f2da11278d53 Date: Tue Apr 15 13:35:54 2014 -0400 Ediding pilot apps settings for rosetta bin build commit ccdde94f00f857c52adee63af1176fc0de62c256 Date: Mon Apr 14 13:55:31 2014 -0400 adding noahs interface ddg calculator commit 1749f18b9fa9b5e7a30656ec40d1e2c894b140d1 Date: Thu Apr 10 00:40:05 2014 -0400 remove all all.hh files except for FArray and options system commit 9e5f4e2f50d3ff7e8019a728d334f718795fb925 Merge: 48a76c0 7f238cc Date: Thu Apr 10 00:23:57 2014 -0400 merge master into branch commit 48a76c06b9f5f125c05625695ddf3cb58e140691 Date: Thu Apr 10 00:05:32 2014 -0400 Remove version comments from fa_standard residue_types commit 3d1edb0bdbbb6bd05178f86e744957ef9c942e98 Date: Wed Apr 9 17:09:17 2014 -0400 Reversing bug fixes I made that were fixed for real in master commit 76e1af72eed9c28b17a7d1bdc7fd80d4b7da43a0 Merge: 247619e 83f5c18 Date: Wed Apr 9 16:42:19 2014 -0400 Merge branch 'master' into rfalford12/mpframework_sfxn commit 247619eb233e31285f7caccbb60fdb51e0544808 Merge: f95b08d ac9be95 Date: Wed Apr 9 16:03:53 2014 -0400 Merge of mpframework_sfxn branch with remote master commit f95b08dce534b2989f6213d99caf3ae366e028e8 Date: Wed Apr 9 10:09:27 2014 -0400 Fixing case sensitive typos in mp score terms that broke the gcc build commit 7160ba19db710933171ab0bb70f977e5cf241a29 Date: Wed Apr 9 09:58:09 2014 -0400 Renaming MPCbeta energy classes to have consistent file names - case typos broke build commit bd538d85e5f78c2d78a9991d988757ef02fa8b32 Merge: c97a34d 836ac40 Date: Wed Apr 9 09:21:43 2014 -0400 Merge branch 'rfalford12/mpframework_sfxn' of github.com:RosettaCommons/main into rfalford12/mpframework_sfxn commit 1e1999d37ec9bbd252929b5528887c9bdac84e01 Date: Tue Apr 8 10:56:29 2014 -0400 Fixed linking error for clang 5.1 unit tests commit 756a6789e83ef93c0dd010bd90b2660b1cf622a6 Date: Tue Apr 8 10:34:34 2014 -0400 Editing resource loader creators such as to not include old code commit 680daee49586793c6fa6bf0b2fe7a6bcbefa338b Merge: d405b32 fe404b2 Date: Tue Apr 8 00:51:47 2014 -0400 Merging in coding conventions...agaIN commit d405b324d035f57fb2b0ef285c10781f188b45b4 Date: Tue Apr 8 00:43:48 2014 -0400 Temp local changes commit 714fd3e73bc8ad2177e412aa7aa5b0823b54ee09 Date: Tue Apr 8 00:04:14 2014 -0400 Making quick changes to tests - everything should compile commit bd21b22f6a50762c0bd9daa7212e0293614877ba Date: Mon Apr 7 23:23:06 2014 -0400 Merge of mpframework devel and coding convention updates commit fe404b25645537b11a4637ed46a8c210b2f3ec5c Date: Mon Apr 7 22:55:26 2014 -0400 Updating unit tests to sync with new coding convention changes commit 8e5984b01803d0578cc889f475f371d712eaae29 Date: Mon Apr 7 22:31:54 2014 -0400 Some bug fixes to coding convention updates commit 8a398b541c5d430fbe0c9a8befc0bcb602f9c552 Date: Mon Apr 7 22:14:38 2014 -0400 updating spanning topology for coding conventiosn commit e34907616a6616c65c144729e36724fc0d52c22b Date: Mon Apr 7 22:12:40 2014 -0400 Updating lipid acc info and membrane info for the coding conventions commit b504457f2b7a9c17ef4a9de4cbb39492bf57535a Date: Mon Apr 7 21:51:52 2014 -0400 More coding convention updates commit 107693b7baa23faa0a6670a8db2a0fcc351f7da0 Date: Mon Apr 7 21:47:45 2014 -0400 Removing embed search params fallback confguration (old code) from file system commit 1cfcf818ae4574ddf4f31c9750f8d19038388851 Date: Mon Apr 7 21:43:57 2014 -0400 Updating IO code to obey the coding conventions and getting rid of old resource manager code commit d1964793c3548e95b91887028725c1c695d78cee Date: Mon Apr 7 21:35:50 2014 -0400 More coding convention updates in membrane protein factory commit 9e1164af1ed7bfd2f95f366ca5380b66985db21d Date: Mon Apr 7 21:34:11 2014 -0400 Updating geometry util and membrane protein factory to accommodate coding conventions commit 8b52a654be6810d525b83b218d7e3f5864f89ffe Date: Mon Apr 7 19:01:21 2014 -0400 Quick coding convention updates in EmbeddingFactory - much of this code will get changed anyways commit baf7cd231866df6fc41115541a788cc1c2fa91e7 Date: Mon Apr 7 18:59:39 2014 -0400 Getting rid of the random awkward header in MembraneProteinFactory commit 20a7f9f02b3cb830deb315b2c570a8a97a70d30d Date: Mon Apr 7 18:56:37 2014 -0400 Adding coding convention updates in core/membrane/geometry/MembraneResidueFactory commit 8408e77d462eaeaa33947b16ad09941cfdad47f0 Date: Mon Apr 7 18:46:12 2014 -0400 Updating coding convention issues in geometry/util. in the framework code commit 63f795d152275dc6bb2a14dc8c6c41cb34a5108e Date: Mon Apr 7 11:49:32 2014 -0400 added pose.total_atoms, compiles, runs as expected commit b8995c6df6d60f06dc9dde82740a4184b65fc3fa Date: Sun Apr 6 14:38:00 2014 -0400 added files that I forgot to add in last commit commit 8472b8d057ebd3559356e459c59cc0b8ec9a34d1 Date: Sun Apr 6 14:36:59 2014 -0400 added functionality in dump_pdb for writing out membrane, compiles, runs as expected commit 8d902a1ccef5e710ac693e3508c7155f2655230b Merge: e72d240 6be1270 Date: Sat Apr 5 01:30:56 2014 -0400 need input options in this branch commit e72d2406a29d0bdde35b498989688cb4ad560114 Date: Sat Apr 5 01:30:48 2014 -0400 added file commit 01d8a3778cf78e4f8c040d0b29bbe34ee5fc957a Date: Sat Apr 5 01:30:18 2014 -0400 added function in file_data commit 5506b3d0747b2e50f4f3d13c99d92ecd25d63d04 Date: Sat Apr 5 01:26:57 2014 -0400 Commenting out unfinished membrane app from the build commit 6be1270a1dbce2d127b2c0f23b77e6446b406720 Date: Fri Apr 4 16:17:39 2014 -0400 updated position of MEM and EMB, compiles, runs correctly commit e26fb5a131f4805424b1137eb9e64d004343522b Date: Fri Apr 4 14:29:56 2014 -0400 fixed indents commit b50539f8ab3c76db2cd972bbabd280be05b2818b Date: Fri Apr 4 14:26:38 2014 -0400 Updating embedding MCM search commit 836ac4042497a3eac638664955677cda58b0621f Date: Fri Apr 4 01:31:04 2014 -0400 Added embedding mcm search and a couple of quick changes commit ac62d454001f8ab6562bb6bf6a603cd0647d7463 Date: Fri Apr 4 01:17:40 2014 -0400 Initial add of developmental embedding mcm search method commit f19e6e9cf57eaf187fb0693aca3bc33d673ddf9d Date: Thu Apr 3 20:01:02 2014 -0700 fixing compilation of LoopRelaxMover commit c97a34dc1791016c475bdaa02bcd1d4ecc086382 Date: Thu Apr 3 22:37:17 2014 -0400 Resolivng issue with some warnings turned errors commit 266e2bdcc73a2933d5a0977a50478050d0baaa97 Date: Thu Apr 3 22:31:55 2014 -0400 Correcting typo created in a merge conflict resolution in MmebraneInfo commit e82bf4129b02e4f2310a96af2f10c0e0d1a05db0 Merge: c94b8a0 8e63058 Date: Thu Apr 3 22:04:54 2014 -0400 Resolving merge conflicts between ninja master and crumb commit ece27a314a01c4b132ecf33e88d2b08c20f01fbb Date: Thu Apr 3 18:57:18 2014 -0700 adding FragmentPerturber class and registering it in protocols.3.src.settings; still requires implementation commit 46b10661476e12e30a113295b615a1a134fb5d9d Date: Thu Apr 3 18:44:24 2014 -0700 adapting the LoopRelaxMover to execute KIC with fragments when the given flags are set (currently in debug mode for testing purposes) commit 8e6305896977e966ebbd073b8d2aebd2afe2987e Date: Thu Apr 3 18:56:35 2014 -0400 Membrane lips compiles commit 618cb33dd41f61f4352292fd9320004c2d8d4409 Date: Thu Apr 3 18:45:00 2014 -0400 Adding residue zpos method in tm proj penalty commit 46305274eb1daeeb61f25a1238071d1dd30966e5 Date: Thu Apr 3 18:29:07 2014 -0400 changed exceptions, moved MPfactory to protocols, updated mp_apps commit 99a4c89717bc297a9bb514b2719ca4be2671095b Date: Thu Apr 3 18:28:36 2014 -0400 Updating design of tm proj penalty to split up computation and checks commit 5c44c52d936d7594aab4e38d4dbc5a6a49a21eee Date: Thu Apr 3 15:56:05 2014 -0400 Just kidding on that last one - tm proj is a whole structure penalty - changed it by mistake commit 8882d4683c014cf7614fb2ff448a517eff6015c6 Date: Thu Apr 3 15:55:06 2014 -0400 Fixing documentation issue from copying in mp nonhelix pen and working on implementing onebody interface in tm proj penalty commit fbf7a534b6607261f3fccb871a753990dd803049 Date: Thu Apr 3 15:51:49 2014 -0400 Fixing indentation and documentation in MP tm proj penalty method commit 9ad408ab0c395f9018f71f935b78123f52f02656 Date: Thu Apr 3 15:47:36 2014 -0400 Fixing compilation errors in mp non helix penalty commit 568728c016b565cb72656fe0837a445a5a6a8864 Date: Thu Apr 3 15:29:47 2014 -0400 fixing bug commit 51a29dca011b71cedced79439198d74e7f7b415c Date: Thu Apr 3 15:15:06 2014 -0400 updating non helix penalty to separate evaluation from edge case handling - also cleaned up and made a one body energy commit 7bee135bec5656ba02be4de457a8005aaf4b003e Date: Thu Apr 3 15:05:46 2014 -0400 Also removing symmetry from NonHelix - will put it back, I promise :) commit 6b1b12e85e1065ea67fe9ceacbced17dd6b3e806 Date: Thu Apr 3 15:04:04 2014 -0400 Temporarily removing symmetry from the energy terms as it simplifies use of the framework commit c80b7164a84c361686dd0936e8cba928994a50c6 Date: Thu Apr 3 14:56:14 2014 -0400 Just made an awesome framework update - framework gets z_pos in one line of code vs 4 on the old frmwk commit 4a2e67aa7e8a93841fb28cec8fede2f7dd78aae6 Date: Thu Apr 3 14:45:50 2014 -0400 Fixing indentation in MPNonHelix penalty commit 868bd686d77570af0c01f5413b042b09ec1a7fdc Date: Thu Apr 3 14:44:30 2014 -0400 Fixing compilation errors in the new MP termini penalty - everything in that class compiles commit 4f0c5fca7d9b22aaa84e30a04d842031288adf49 Date: Thu Apr 3 14:39:08 2014 -0400 Reimplemented MPTermini penalty as a one body context dependent energy commit 48998cf3444a476ee0809ef1bb2fb1c4cb4a9049 Date: Thu Apr 3 14:34:26 2014 -0400 moved MPfactory to protocols.a.4 commit 5b8bcdc7e51a830df37e32a335f6f0dfce3c1e8d Date: Thu Apr 3 14:22:24 2014 -0400 Updating energy term documentation in MPPairEnergy commit 393db99fa62e5137801d838f96db16909dc69fd4 Date: Thu Apr 3 14:16:24 2014 -0400 Updating energy term documentation in MPEnv energy commit ab8205579f985491f7662ad51a6d24a1b5c55649 Date: Thu Apr 3 14:08:14 2014 -0400 Updating Energy term documentation in MPCbeta Energy commit b4b0db11227c40af86a557849b3f2761677fc70b Date: Thu Apr 3 02:38:52 2014 -0400 Adding notes for mp sec struc penalty commit 1672f6a3e95dca645a030310a02ecf24377c0b57 Date: Thu Apr 3 02:03:17 2014 -0400 Starting to implement secstruc as a residue onebody penalty. Also adding new score types for secstruc and span to the enum commit 959ce604c9fe0e6e0666053a9bffbce92bf89f1f Date: Thu Apr 3 01:51:19 2014 -0400 Updating fwd header and creator header for secstruct penalty and adding header info in cc and hh commit 445686325b5bc198f6966536b294e5e97324ca0c Date: Thu Apr 3 01:13:31 2014 -0400 Renaming MP sec struct penalty from SS penalty commit 931eaeea8a0276655c3a49623f7834f950dabe78 Date: Thu Apr 3 01:07:59 2014 -0400 Much more compiles - but still has a way to go commit 50588fac39001897bd0f9519225100ae66e744a7 Date: Thu Apr 3 00:47:58 2014 -0400 Also finished resdesign of non helix and tm proj penalty commit 946eefc43e60eab2785e7fc6513bd90a35722a62 Date: Thu Apr 3 00:32:59 2014 -0400 Depth be gone in core/conformation/membrnae commit bd3fea4585ffa3b33ff791d2fdacd223bf2b9501 Date: Thu Apr 3 00:27:48 2014 -0400 Depth be gone from scoring :D commit f96b3367adb78524daacaf02224e37028357a23e Date: Thu Apr 3 00:22:02 2014 -0400 Renaming MPBasePotential => MembraneData in core/scoring/membrane commit a3c403d9f31f4a17be9aca8e77e80d5ef91371b2 Date: Thu Apr 3 00:10:35 2014 -0400 Adding new method for temrini to header commit d830f16bd3765375f17471ee472bb0b593211ac3 Date: Thu Apr 3 00:09:35 2014 -0400 Updating mplipo energy without spit and temrini penalty with redesign for funciton commit 862581ad9c7dfa070758bc7dcc28c71e0e362323 Date: Wed Apr 2 22:36:17 2014 -0400 temp change commit e2321a91e2b2b7ba58f3eab72b12f4bdca110e80 Merge: dfa28ff 3f24752 Date: Wed Apr 2 21:32:49 2014 -0400 getting mp scripts commit 3f24752a34f7b002ec950819e4ce695566c8c2df Date: Wed Apr 2 19:46:08 2014 -0400 Adding python equivalents for shared mp scripts commit 8a630d48ba7d03ec3a87b3d896e0decda855e48b Date: Wed Apr 2 19:43:04 2014 -0400 Adding shared scripts directory including coloring scripts, python scripts for computing topo, etc commit 765a2b326e75bc1cbd65fcf5e748c1ec20d236e8 Merge: 049109d e8ddf4d Date: Wed Apr 2 19:42:19 2014 -0400 merge of jkleman updates commit 8d4b6cc8fa91ee3f973a4b1245820d2f8e659000 Date: Wed Apr 2 19:42:04 2014 -0400 QUick updates commit df42d05a10327dd936ffa5632582439dfa35881b Date: Wed Apr 2 15:58:23 2014 -0400 Implementing MPLipo energy creator and fwd header commit 91bafac1e401fc9b60ae5e861ffae1415d31a142 Date: Wed Apr 2 15:42:24 2014 -0400 Started to fix termini penalty - and then I realized these should possibly be per residue - will stop for now and ask about it today commit 12fc2c9e66a51131303e75f20e7ab97ecf03bec2 Date: Wed Apr 2 15:28:56 2014 -0400 Fixing indentation of classes in MPPair, MPCbeta, and MPEnv terms commit adae9c50a9df42c18c5d8ffcffa48fa3c9691ce7 Date: Wed Apr 2 15:26:19 2014 -0400 Fixing indentation in mpair term commit 8ed84ab28b17bf7d56bdb126880a76ca85e9e4c9 Date: Wed Apr 2 15:25:50 2014 -0400 Some additional clean ups to the mpair term commit ed6989a0854c3d542327cb9ee02f6c1f44d03ab2 Date: Wed Apr 2 15:20:22 2014 -0400 updating pair term to split computation of score with rsd and pose inputs commit e8fd9bc2babd7ae5c17956a62eb676feef6090d7 Date: Wed Apr 2 14:25:32 2014 -0400 Updating comput env score to work with function inputs commit 69de7d0a6131e0dafaf2713d4d717a1a6537aeaa Date: Wed Apr 2 13:57:52 2014 -0400 Compute mp cbeta score commit 22be2aa1f9cae9065a6901aec7869ebd78026899 Date: Wed Apr 2 13:29:12 2014 -0400 Updating energy method MPCBetaEnergy - redesigned for testing - separated the actual computaiton of score from rosetta objects commit e118a4f1df7aa0565eace3c123e53394b06bb38d Date: Wed Apr 2 11:21:48 2014 -0400 Updating MPBasePotential to be called MembraneData - somewhat more appropriately named thanks brian commit 76bb2e04bd7b0045d0324c7469cea573743b8558 Date: Tue Apr 1 23:32:55 2014 -0400 Reversing constness - turns out the log tables do need to somewhat change internally. Can either reformat this or change later commit 1af58048e8ccfea875634e4eefb21dec5524d74b Date: Tue Apr 1 23:23:08 2014 -0400 Hopefully updating const correctness in mp potential class commit 2d79ff4dcdddf27f88f5359dd7543b82da71d7c7 Date: Tue Apr 1 23:21:51 2014 -0400 Updating indentation in MPBaePotential commit 72e0844d855f846a90ffe8a2087940f90beef9cd Date: Tue Apr 1 23:18:52 2014 -0400 changed pose_from_pdb to fxn in core3.io.pdb, compiles, runs commit b37dae522d75cf0ad5b6f8f127381d06413bb937 Date: Tue Apr 1 22:23:07 2014 -0400 Quick notes in this app commit e645fbf4b9836ebe6a28b62f5904eeedfc94a7ff Date: Tue Apr 1 22:21:46 2014 -0400 Adding pilot apps for testing new membrane energy terms commit ad4d9480428fb8d0ed3f864927146a209a2824c0 Date: Tue Apr 1 20:26:48 2014 -0400 debugged, doesn't compile commit 7b359f191854de8e306a29507a29913f57dd69e1 Merge: f2557e3 3bdade7 Date: Tue Apr 1 17:40:30 2014 -0400 Resolving merge conflicts with membrane FA potential commit 587028ad198510514c7bcc8e9abac0a52392e8f1 Date: Tue Apr 1 14:32:26 2014 -0700 refactoring LoopBuild main function to load fragment data whenever fragment files are given on the command line; this implicitly enables fragment loading for KIC with fragments commit 1ae1eba72a2d4d278cbf4599856c17258bfff8cf Date: Tue Apr 1 01:54:46 2014 -0400 added files to mp_apps commit 9dce53db4ef8d56de738ceef301fa28927de61de Date: Tue Apr 1 01:49:22 2014 -0400 added functions for reading inputs, doesn't compile commit 9369e1b020a3a8c1951a1a1cc694ff33cd0aaf18 Date: Mon Mar 31 23:18:28 2014 -0400 Restoring embedding factory to initial stage - wants to do this change in a separate branch commit 18d0aba6ba13b8a463bba1616b4cb2137b18e1a2 Date: Mon Mar 31 23:10:51 2014 -0400 Updating the Embedding factory interface to work with some cleaner internal behaviors - this will temporarily break the build until I correct the implementations commit 0451f4d76a5e6369d64f853b41d619537f5f0518 Date: Mon Mar 31 18:19:09 2014 -0700 fixing compilation of LoopBuilder with custom perturber constructor; the given custom perturber can overwrite bond lengths, angles and omega torsions after idealization if so desired commit dfa28ff01f73fe22a6ee36053c0f6f25263d8d66 Merge: 5bdddd7 cce2f56 Date: Mon Mar 31 21:12:22 2014 -0400 Resolving merge conflicts in merge of jkleman branch recent updates commit 5bdddd7d4df2639b255a64d785779fd4836caa1c Date: Mon Mar 31 21:05:52 2014 -0400 Patching MPFramework Namespacing bug fixes into branch from mpframework_devel post 3/27 commit cce2f56071a2e08d84d6e06c56f3a6b9424fb094 Date: Mon Mar 31 19:58:25 2014 -0400 fixed namespacing in tests EmbedSearchParamsLoader and SpanFileIO commit c94b8a0fb333afcbfbbac697bcae953f9e63f26e Merge: 6637cce 4159d25 Date: Mon Mar 31 19:54:57 2014 -0400 Merge branch 'rfalford12/mpframework_sfxn' of github.com:RosettaCommons/main into rfalford12/mpframework_sfxn commit 4159d2572b04156454eb77b0c9c4659e303c4f5c Date: Mon Mar 31 19:10:55 2014 -0400 Adding stub code for lipo, sspred, and mp spanning penalty commit 6637cceebe7fe447db9cdf84865b1ba7afb29397 Date: Mon Mar 31 18:24:41 2014 -0400 Removing unused variables in MembraneInfo commit 4057f09b8c08d13d7169dec53d00d04961460eeb Date: Mon Mar 31 16:55:33 2014 -0400 created pilot app to read spans from commandline and adjusting the MPfactory constructor, compiles commit c96f9b986c5299cd2f63ac5a19ec76bc525f5258 Date: Mon Mar 31 16:47:18 2014 -0400 Adding MPPair unit test - only does one total energy check commit 87f2de371bf3192e4eaffe7b07a2e29e764bbde4 Date: Mon Mar 31 16:37:41 2014 -0400 commit 6380d808d43644b9d88461e8f2838d64fea53bff Date: Mon Mar 31 16:28:48 2014 -0400 !! commit f621b6044eb383c9bf3d61195ddd8b52e7c918e6 Date: Mon Mar 31 15:19:41 2014 -0400 More work on the unit testing template - still figuring this out commit 384f86d85af42ad1f67af1a347191671d42b838a Date: Mon Mar 31 15:05:28 2014 -0400 Adding membrane penalties to energy method registrators commit 26db3f81acfca08f80e261aec26d3280f79ae5b8 Date: Mon Mar 31 15:01:09 2014 -0400 Adding mp scoring template unit test to build sttings commit 9eb16edc7bbef94749f7953f5cfdb7d642a62d9f Date: Mon Mar 31 14:53:18 2014 -0400 Added MP TM projection penalty to build settings commit 12df3cd0d3ec3548965ebdce9ea4bbe3996bd1d0 Date: Mon Mar 31 14:48:45 2014 -0400 Implemented full MP tm proj penalty commit 43af59bf7510c998ccf6b24bfe70cfeff97c155d Date: Mon Mar 31 14:46:27 2014 -0400 Implemented tm proj forward and creator headers commit 4c398d868ca991388c613830331eae84527bfcf3 Date: Mon Mar 31 14:42:12 2014 -0400 Quick documentation fix in MP non helix penalty creator header commit 067db8cd90ab3d2d9c03c7330764e6566532877c Date: Mon Mar 31 14:41:27 2014 -0400 Quick bug fixes - MPNonHelixPenalty compiles commit 27dd9fe2ebec77a8549a0a6f212015c4d03d4ab0 Date: Mon Mar 31 14:39:29 2014 -0400 Implemented MP non helix penalty score tmer commit 1d8baa62b5bc76d41358d865116dfe7268020433 Date: Mon Mar 31 14:34:19 2014 -0400 Added stub code for MP non helix penalty commit f8e4cb8d31919511dfac508f92fc10da8a93cac7 Date: Mon Mar 31 14:30:06 2014 -0400 Quick fixes in MPTermini penalty - term compiles commit b2d7a9acf5d099274a0a60436b6b865ed2179965 Date: Mon Mar 31 14:19:03 2014 -0400 Updating membrane penalties methods to include overhead methods for calls from energy terms commit a33397c5d4fa2893f1e770a028db2d79120b2c38 Date: Mon Mar 31 14:12:39 2014 -0400 Adding overloaded methods to penalties for use with scoring methods commit 9f0597488e3860c5b3d0f856bc41a80c87a4da2c Date: Mon Mar 31 12:48:41 2014 -0400 commit c20896fa3079ed0f10b6fb719f2b03c33636f842 Date: Mon Mar 31 00:53:40 2014 -0400 Started to implement termini penalty as a scoring method commit 7d87abdabc42bc9078889dc06f65b746f5d5c0f3 Date: Mon Mar 31 00:23:56 2014 -0400 Initial add of penalties energy terms - framework supported commit 3fd384427e6cc4c0b8e20217296b2e29a82c1ee3 Date: Sun Mar 30 21:21:22 2014 -0400 checking options done, compiles, runs as expected; only need to make sure that EMB and MEM do what they are supposed to commit 72def467ff4449e87245efc210fdc34ebefe0c69 Date: Sun Mar 30 13:07:06 2014 -0400 Setting up unit test template for new mp energy terms to score with one term and test with it commit 463c3f1f170ac001c572ee4e8cf56d57668bb2b3 Date: Sun Mar 30 12:45:28 2014 -0400 Adding shell code for mp energy term unit tests and fixing namespace icnludes in new energy method creators for mp terms commit 3bdc46e36159d94195b776124293dc93dea5e2a5 Date: Sun Mar 30 12:21:27 2014 -0400 Registering new MP energy methods in init.cc - I think commit 103e054267c228cd0659c5b7b9987f625bfcd550 Date: Sun Mar 30 12:15:11 2014 -0400 All three new mpframework energy terms compile - plugged into score tpes but not the methods yet commit df27bf72fea04a4f62ae7b6095fba5bd90483daf Date: Sun Mar 30 11:45:12 2014 -0400 MPEnv Energy method compiles commit 3d6e8ffbc623c65e91bbe14a343c3ae529871b1a Date: Sun Mar 30 11:31:16 2014 -0400 Quick fixes in MPCbeta energy so it compiles commit 89a1ea0b151f33cc76813b0af0f4d418fd89b01e Date: Sun Mar 30 11:21:36 2014 -0400 Adding new mpframework score types to ScoreType.cc and ScoreTypeManager.cc commit ab79423cc03ce63e3cb2bb90fe4ef673c6445a51 Date: Sun Mar 30 11:12:25 2014 -0400 Debugging MPCbeta energy term and adding const member acces into MembraneINfo in Conformation commit 373b8f4b0fa1093accf3a58dde1ac9d5181b1d5a Date: Sun Mar 30 10:36:05 2014 -0400 commented out unwanted options commit 7b6e1562ee7ee3492b4336fe5de5c7311fc21866 Date: Sun Mar 30 00:21:24 2014 -0400 Bug fixes in the scoring manager - should be all set commit 6a3dd957370e743892f563919b53f7be06d65137 Date: Sun Mar 30 00:17:47 2014 -0400 Adding MPBase potential hooks into the scoring manager - pray it compiles and I didn't just kill all of rosetta commit 1169455f017ba1a4e2ca951a03a14e22671e1b33 Date: Sun Mar 30 00:10:28 2014 -0400 Taking MP energies out of the build for now - needs to do a few other updates beforehand commit 2ef47acd0f48c1167d0f34295df772158cf4ae30 Date: Sun Mar 30 00:08:32 2014 -0400 Const correct :) new MembraneInfo with improved interface compiles commit de795111b519a5c5b0050c382b402bdddca01c28 Date: Sun Mar 30 00:05:12 2014 -0400 Correcting set xyz compiler error in membrane info commit e0eda40c1a6109abec518d8bafb2d1dd882e56a9 Date: Sun Mar 30 00:04:09 2014 -0400 Correcting set xyz compiler error in membrane info commit 5ecbdbb3302e089a79a8a84d9e17a493ad2f649f Date: Sat Mar 29 23:29:03 2014 -0400 Updating membrane info with recent refactoring updates - will need to fix compiler errors in setting xyz info commit eca2c87157ff66d4bd0476485edc0da6e7a62dc9 Date: Sat Mar 29 23:20:13 2014 -0400 Quick change in pair energy for now - also adding energy methods to build temporarily so they can be re-indexed by XCode commit fd5277e8be003a84cbb6233a45f4657691586525 Date: Sat Mar 29 23:17:19 2014 -0400 Implemented MPPair energies - rough estimate. We now have all three terms roughly implemented though are not yet compiled. everything has creators but currently relies on some important dependencies commit 3e527858d73766de5b8dd7a67d5a34640cf4ea56 Date: Sat Mar 29 22:41:36 2014 -0400 Adding MPEnv energy creator and MPenv energy methods commit 54d2df5567ac93a4452a064ce1ce780b2a6c59d7 Date: Fri Mar 28 22:18:06 2014 -0400 Updating CBeta and MPair energies commit 25689ffe1f64b0028775401db294c38a22f0a759 Date: Fri Mar 28 22:01:25 2014 -0400 Adding MPair energy creator header commit 73857f768e39c5c03feb2ca69d984735d5efdff0 Date: Fri Mar 28 21:58:57 2014 -0400 Adjusting new cbeta method to use internal base potential commit 0a7ffc131a0bb7d95790cea93aea4018894b2801 Date: Fri Mar 28 21:47:03 2014 -0400 Implemented MPCbeta energy method commit eeabbaad6e6c09f139019b61fd9f8454854873a3 Date: Fri Mar 28 21:30:05 2014 -0400 Adding creator class header for mp cbeta energy commit 2c53ef8705d1e2f507cc1eedea27e69960151136 Date: Fri Mar 28 17:09:36 2014 -0700 Update packaged_bindings README.md and default build flags. commit 6b26f7ac4cdf53825ee8b21d9a4c6fa54448b6be Date: Fri Mar 28 16:40:36 2014 -0700 Isolate packaged_bindings toolset and source files. Breaking packaged_bindings toolset into subdirectory to modification without compromising existing pyrosetta infrastructure. commit 46cbccf06d544683908e81a9dfe5afcc5fa476a0 Date: Fri Mar 28 18:51:07 2014 -0400 Implementing stub interface in MPCbeta method commit 58d3451dea92998888a549e559a0ab95fe370f59 Date: Fri Mar 28 18:47:25 2014 -0400 Implemented MCbeta header commit 86600ea342bbe85b169778629adccdaf6377f569 Date: Fri Mar 28 18:36:54 2014 -0400 Adding stub code in cc and hh files for MEnv term commit 8344084fa1d8b324e8b2dbebef7998d985613758 Date: Fri Mar 28 18:34:55 2014 -0400 Adding stub code in cc and hh files for MCbeta term commit 80105713c667df4b438d55d214850c3757cf4517 Date: Fri Mar 28 18:32:24 2014 -0400 Adding stub code in cc and hh files for MPair term commit e070fa7226029fc214bb664a130362dcf626d604 Date: Fri Mar 28 18:30:32 2014 -0400 Initial add of mp energy term files for Menv, MCbeta, and Mpair and implemented forward headers commit 7902d5aac0bbeb49a72efa4a65886976b557b3c1 Date: Fri Mar 28 14:21:47 2014 -0700 Move pyrosetta_egg_generator into 'packaged_bindings' subdir. commit d9b9a69839323413326c9c9834af2ca90d07b783 Merge: 1dd9654 e8ddf4d Date: Fri Mar 28 16:30:13 2014 -0400 need the binary apps for testing the corrected EMB & MEM residues commit f175d778e007fa728362e50c827f63a6a31a0590 Date: Fri Mar 28 16:25:42 2014 -0400 Yay - MPBasePotential compiles ' commit 6a1f54d20512b3ae911fd4f4b223442dcf1939e1 Date: Fri Mar 28 16:19:39 2014 -0400 Changing cenist private member naming to include the _ so compilation isn't ambiguous commit 0bf344a81f585b8d333c70fe4ad3647eeccfda4c Date: Fri Mar 28 16:10:58 2014 -0400 Updating core.3 settings to build the base potential - still has trouble with the referencing issues in io silent struct that are legacy on clang 5.1 Otherwise there shouldn't be issues with the penalties unit tests commit 21f33db946a9b54d651f8e55f83e3f840c87689c Date: Fri Mar 28 16:09:22 2014 -0400 MPBasePotential - Implemented database IO, initialization, and access methods, Should be good from here - will try to compile it commit 1dd9654ea80dbaba31a6de502e95dcb742f8d4d4 Date: Fri Mar 28 16:05:01 2014 -0400 corrected EMB and MEM residue types for fa_standard and centroid commit 68aebf05e853c31cceb42822fe2d9bfa9aaa5533 Date: Fri Mar 28 15:44:20 2014 -0400 MPBasePotential: Finished adding methods to the base class commit 49703cb71f3f737e7c8156ee276e68b85f284d29 Date: Fri Mar 28 15:36:49 2014 -0400 MPBasePotential: Adding class definition for the header commit 2e3ca126e818a1eece1df4402b14db9a968012dc Date: Fri Mar 28 15:27:11 2014 -0400 Implemented forward header - easiest part :) commit f4effec36e7bcd363b100d7da1eab97dc1eb7ea0 Date: Fri Mar 28 15:24:38 2014 -0400 Updating headers and include guards in mp base potential fwd.hh, hh. and cc commit cb065957cf7bdc95c3f8bee1af27afc645f574e3 Date: Fri Mar 28 15:20:45 2014 -0400 Crazy syntax error in core.3 build file prevented penalties from compiling - fixing now commit f666dec480c4d76e70d45cc41fbf5c3256e6459f Date: Fri Mar 28 15:19:17 2014 -0400 Adding membrane penalites test to version control commit d1442109c0a4bdb2f17028c6d06430c32939937c Date: Fri Mar 28 15:18:59 2014 -0400 I have added and built the membrane penalties code and test - but there seems to be a linking error in the unit tests. Might try rebuilding the libraries first from scratch commit de45af77d026e14af16c051d7444f3ed7e759c3e Date: Fri Mar 28 15:06:50 2014 -0400 Initial add of MP base potential files - going to write stub code commit a35b70c8008f4e360ddd14b71329494ba563bef9 Date: Fri Mar 28 11:24:32 2014 -0400 Adding membrane penalties to mp sfxn branch commit 7a67caba2593256ebeb5c17751a254e57623691f Date: Thu Mar 27 22:43:24 2014 -0400 split up read and check function, doesn't compile commit 049109d21442b08b06a044690002862a3eed1655 Date: Thu Mar 27 21:37:26 2014 -0400 updating local changes quick commit b378c781be4930eda8ec2df5dbcfbb94bb2e58a6 Date: Thu Mar 27 18:04:49 2014 -0400 checking parameters compiles and runs correctly commit e8ddf4d219ba9b61fc30d424ce976d525ca4d3cf Merge: 5586904 257f668 Date: Thu Mar 27 11:54:43 2014 -0400 Merge branch 'rfalford12/mpframework_devel' of github.com:RosettaCommons/main into rfalford12/mpframework_devel commit 55869043c862253fe3fe2c16e5eb78ff61ebcf68 Date: Thu Mar 27 11:54:07 2014 -0400 Adding renamed command files for mp apps commit 257f66880ae43e7a02b5d9f0f3d4f31c6db714a6 Merge: 2d62022 b58f599 Date: Thu Mar 27 10:04:35 2014 -0400 merge of local ninja mpframework devel with remote and crumb commit 2d6202289784777d52f6e699d743748b12145b36 Date: Thu Mar 27 10:04:00 2014 -0400 Removing unnecessary methods from the embedding factory and also updating read pose from seuqnece app that I am working on commit b58f5993fd946f619383227be7a744bd4ff0d659 Date: Thu Mar 27 09:19:39 2014 -0400 Adding mp apps inputs and outputs into Rosetta/main commit ef97e8309d1f8bba998dbc78fc34085d2aecbcb2 Date: Thu Mar 27 09:18:02 2014 -0400 Updating quick big dominik introduced into sequence profile commit 5466c05c0ab2920414260c9fb1f6fc9661fd9e9f Date: Thu Mar 27 09:07:07 2014 -0400 added to_string function in xyzVector commit d2d3a587beaf0417f79c5458698148d11fe6977e Date: Wed Mar 26 23:19:15 2014 -0400 Fixing some invalid tracers in the embed from topo app - woudl need to give it a subset of the pose for this or traverse the full embedding. being used out of its original context commit 03db5367e03ec5db2a76c0c7738888d7f3adf4e1 Date: Wed Mar 26 23:05:37 2014 -0400 Forgot to change private member to one used by the inputs - fixing now commit c9e4b50ca1aa317e11d0bc10c98be090c98c64bd Date: Wed Mar 26 22:52:16 2014 -0400 oops...forgot to init from cmd in cmp mover commit 592717265446328bce7ebfe0ccca4e2bfa6a886a Date: Wed Mar 26 21:51:55 2014 -0400 Updating bugs so the apps complie - pushing to louis commit 519296b4d636b8705180e619aa14a5083907fe3d Merge: d3a113c 5f747a3 Date: Wed Mar 26 18:41:39 2014 -0700 resolving conflict in options.settings when merging-in master (rev. 56584) commit d3a113ce5af8057b633f56828a3d880584680787 Date: Wed Mar 26 18:31:44 2014 -0700 making perturb_kic_refactor and perturb_kic_with_fragments report when initial kinematic closure failed commit f825821e85255ca7a441cb6f40aefa534db9e342 Date: Wed Mar 26 18:29:40 2014 -0700 added clang 5.1 to option settings commit 21c2e42f63facfea324dba0a4b14f66e6a47a318 Date: Wed Mar 26 21:11:28 2014 -0400 Commenting in embed from topo pilot app commit 2ebe91431af1e8fd7483782f4e89e71b1cbb6bdb Date: Wed Mar 26 20:43:39 2014 -0400 Fixing new embedding method to not use private members - accident sorry ' commit 4147bd84d9be74c09fde51dc2f466da4a8eb5cef Date: Wed Mar 26 20:30:55 2014 -0400 Forgot to add src apps pilot membrane to github commit fe5a9a7b9dc75777988e8173e63453ae54205af5 Date: Wed Mar 26 20:30:34 2014 -0400 Adding non initialization based embedding from topology method to the embedding factory, also adding some tester apps to src/pilot/apps/membrane commit 174b28a025de7702c46dcfe52da79290cd2a3b51 Date: Wed Mar 26 20:13:08 2014 -0400 added show() funtion to xyzVector. Doesn't compile. commit dad1ac1491b24cf8de47c50a272d1c61421af881 Date: Wed Mar 26 12:30:42 2014 -0400 added functions, compiles and runs commit 1918f45dc39bed2c86f9372dc3efae03738f91ab Date: Wed Mar 26 10:53:58 2014 -0400 added function commit 192abfdd214f02f7fde570a75a8809868daaaffb Date: Wed Mar 26 00:34:33 2014 -0400 Moving metrics into a more extensible location for sampling commit 67beb9308a64378d347ac651dfc80276be8d98e5 Date: Tue Mar 25 21:26:47 2014 -0700 updated pyrosetta_egg_generator/exclude.py commit 304eceee4d01b196bc56e65659dc5e8e93865327 Date: Tue Mar 25 18:54:22 2014 -0700 adding custom-perturber constructor to LoopBuilder; this allows to use a custom perturber for picking phi/psi torsions during the initial loop build; bond lengths and angles, as well as omega torsions are still idealized commit fbf745d4aa998034e85d936ac5c9153eac71d1f8 Date: Tue Mar 25 21:06:53 2014 -0400 read_membrane function in parameter checking. Doesn't compile commit b666a869075fad5f28f1ca74c0a25113e3c0d985 Merge: 6e173fd 1ccd1e0 Date: Tue Mar 25 15:24:44 2014 -0700 merge origin:master with local branch. commit 171605e09b227c5cc0cb5ee25a6f1588bc0c244b Date: Tue Mar 25 12:11:50 2014 -0400 comment out parameter checking to put that into a new branch commit 010263bd09f8ece48f52cc14331ed918ef8d5a91 Date: Tue Mar 25 11:40:19 2014 -0400 working on checking parameters commit 6e173fdee59b9928bc31c7ffb146cc631a87a0ec Merge: 980ba42 dfe26f3 Date: Mon Mar 24 18:22:29 2014 -0700 Merge branch 'master' of github.com:RosettaCommons/main commit 980ba42144e436d98f565540eb869f8298432826 Date: Mon Mar 24 17:32:57 2014 -0700 Rename src/python/attic to the pyrosetta_egg_generator. commit 6df4c0837ebf77fc24b962ae753ac95e28d11d73 Date: Mon Mar 24 17:01:57 2014 -0700 Change included filename to match the one in thee recently updated boost library. commit 1422d5f82e440f2a34f0fbe19e9f754dbea22254 Date: Mon Mar 24 16:49:02 2014 -0700 Fixed the compilation flags of BuildPackagedBindings. commit f2557e370867546b495f29cb00ec04d6c8e008a6 Date: Mon Mar 24 13:54:22 2014 -0400 updating fa potential with consistent include guards commit 52158add4a8aeff2fdda0503707d3bb06ce0adaa Merge: 8d4ace3 d544ed2 Date: Mon Mar 24 13:48:55 2014 -0400 Merge of ninja master with local master commit 8d4ace3d6d103219b513b1c8c3a4f4d3d342047a Date: Mon Mar 24 13:48:50 2014 -0400 Updating include guards in membrane potential to hopefully fix the pyRosetta build ' commit c299b31ed530ad6bae76e73bdb4f8dae6c205af5 Date: Mon Mar 24 11:52:35 2014 -0400 added parameter files for MPframework to database: membrane/, scoring/weights/membrane_parameters.patch, scoring/weights/membrane_penalties.patch, pilot app jkleman/mp_parameters.cc for reading in commit ed88671a0564091f1d1256067edc49d006775919 Merge: 1e57937 e08b130 Date: Mon Mar 24 10:35:22 2014 -0400 merge from master commit 1e5793705e628eb8a20959ce5e0a31f356173b47 Date: Mon Mar 24 10:29:05 2014 -0400 k commit b64af7504900b62ccf15d961d59d066f8dd5bf80 Date: Sun Mar 23 02:05:37 2014 -0400 Updating mac clang build to pass commit 90b207e4c175bc950baa88687517d3e5dfe6f3d8 Date: Sat Mar 22 23:14:48 2014 +0100 Applying fix to mac 5.1 clang build commit 0a8dd8eeb1b1191acd4eeb62a860cc1231a577a1 Date: Fri Mar 21 17:04:44 2014 -0700 adding perturb_kic_with_fragments and refine_kic_with_fragments options commit 34671a5cc851b32c0035e48a457446b7c31ef1f0 Date: Fri Mar 21 17:03:10 2014 -0700 adding user-specific xcode IDE files to .gitignore commit c8170c64bd9afeb23eac769735ec31e4d436612a Date: Mon Mar 17 18:04:40 2014 -0700 Updating my notes. commit 5b5901c7a39e416f9689e3480ca8e64d5ea09107 Merge: 6a8ccc6 c24aa6a Date: Mon Mar 17 17:59:15 2014 -0700 Merging master into vmullig/ncaas. commit 1db1903df29b4ca6ca8bdb8af78b791300fbba64 Date: Mon Mar 17 15:18:10 2014 -0400 for got the unfolded energies commit 6a8ccc6d7d38876eb6b8a3a95ab851634a1a59eb Date: Sun Mar 16 23:47:17 2014 -0700 A few more residue types that I forgot to turn off. commit 3ed38b3cab1867f493b83c64894453e3b3a0b6eb Date: Fri Mar 14 14:19:17 2014 -0400 It needs to design commit 3a10854cb731fbb81f0e6c6d493322b109779db8 Date: Wed Mar 12 16:21:21 2014 -0400 First pass at a ddg_monomer like protocol that works with interfaces and is compatible with NCAAs. commit c08531297474b26fc97482e89c2eeea6bc8bfc3f Merge: 43aeef6 799a524 Date: Wed Mar 12 11:22:07 2014 -0400 merge from master commit 43aeef6f01d0a4b0816892a7657ffa34e455a4f1 Date: Wed Mar 12 11:21:22 2014 -0400 wtf... commit 8e57260a3ba6af60c60c67fa60ceb743638fad64 Merge: 77e5f88 7f4e27d Date: Wed Mar 12 11:20:40 2014 -0400 conclude merge commit 77e5f8837527294eb89581ddc2332c994ecdb54d Date: Tue Mar 11 17:10:00 2014 -0400 kh commit 1614f1fffbe2f6a8022f862fc83be323bab4fad8 Date: Tue Mar 11 16:18:37 2014 -0400 wtf commit 8b2c26f69dbed22f80fcfe3103568b611a5a0b1b Date: Tue Mar 11 11:48:00 2014 -0400 i commit e9d0ce199c2bdea360cc1f8b3ca78a5f6a5c69c4 Date: Mon Mar 10 16:18:02 2014 -0400 a commit 4e6afe18ece9ebbfbce6c75612be38a0615c1c09 Merge: a8d8ad3 ad1f7c9 Date: Mon Mar 10 12:08:48 2014 -0400 Merge branch 'khouli/buns' of github.com:RosettaCommons/main into khouli/buns commit a8d8ad3426fb6c38f7dcd4a1da625353eaadfbf6 Date: Mon Mar 10 12:07:39 2014 -0400 a commit ad1f7c9bb5b4288ab91267b06f9d500fb3fe9e5a Date: Mon Mar 10 12:02:00 2014 -0400 a commit d6b87f40d14a92588bb402ad0de4539779826893 Date: Mon Mar 10 06:11:23 2014 -0400 wtf commit 0c2d589b618b6f58987b4cce444c3004cf9db15a Date: Mon Mar 10 03:09:11 2014 -0400 i commit 62a4c1c25e808b45c1ee52ef5a41c162e9db916a Date: Sun Mar 9 21:54:31 2014 -0400 a commit d6344d954d251c276509961a33c9ccaeff5e2e04 Date: Fri Mar 7 12:35:43 2014 -0500 k commit e37819fee492fdcbac8c557441219d0243911f40 Date: Thu Mar 6 11:45:20 2014 -0500 k commit fd17eab9bc107d5df661de1ebd586070f9efc3d9 Date: Wed Mar 5 17:25:16 2014 -0500 Options to be used for using three letter codes in ddg_monomer commit 7404c21214cad4075813f45e1d456d08f0502aa1 Merge: cb7a0e4 adcacd3 Date: Wed Mar 5 12:09:14 2014 -0800 Merge remote-tracking branch 'origin/master' into kylebarlow/general_dev commit fb0fca21683cb3167d090f991fb0ee2db8595df5 Date: Mon Mar 3 13:58:02 2014 -0500 k commit 2032770991ab8c755d410eb1a064ccaf67ec664d Date: Mon Mar 3 13:55:00 2014 -0500 ! commit 07ccb0c92da7c25e1efb3c0a9aa40cca003f62bc Date: Mon Mar 3 13:42:04 2014 -0500 some compilers think this reference to PathVectorOption is ambigious commit 1c3f1dd1ef9220d83183925de30bd9180cc6291d Date: Mon Mar 3 12:22:47 2014 -0500 vsasa_buns and sasa_buns commit 045a6e1871353a08d5a9b4fc2d80b2a2d451deb4 Date: Mon Mar 3 12:11:09 2014 -0500 remember to undo residue type stuff commit cd8e03e7104ecf4b9aca07d344634b3198b1df54 Date: Fri Feb 28 18:14:43 2014 -0500 Adding extra rotlib path option and using it for NCAA and peptoid rot libs commit 328a7f66844083a07cd981fbbd76cd6d9c87fc2c Merge: 41a4c3e 693ec8e Date: Fri Feb 28 17:24:56 2014 -0500 merge from master commit 41a4c3e1cc5330b5ebc1dc98a7087ca79ebb8bf5 Date: Fri Feb 28 17:24:30 2014 -0500 a commit d0857bc6ec3976b1d7428d66e0bd4702582fcbe2 Date: Fri Feb 28 14:57:38 2014 -0500 Add additional dependancy to library to avond undefined symbols commit 9fddbad60a0353ad1bce478e026cfbc3f2a34202 Date: Fri Feb 28 14:56:43 2014 -0500 Fix header ifdef logic commit 2dd4ecea3793f08b310401dbfebd90366b8a84f7 Date: Fri Feb 28 14:55:49 2014 -0500 Remove initialized but unused variable from MutateResidueMover commit b3a42b9d68990ec3526fda9282259d9969102b8d Date: Fri Feb 28 12:41:41 2014 -0500 Ensuring that multiple LAT matches from a single PDB file are handled properly when parsing the database. commit f5ef3b170f85b57d98934f69fa0e726b3e99b88e Merge: 29e7b69 9afa6b8 Date: Thu Feb 27 16:51:16 2014 -0500 merge from master commit 29e7b693ff25e2a6edaeda20d506fa7b9f471431 Merge: 8d348cc 813508d Date: Thu Feb 27 16:50:51 2014 -0500 a commit 8d348cca8138e7a080cb3106d62db4f614e4c3ec Date: Thu Feb 27 08:39:18 2014 -0500 kh commit 374fd6884159f5dbbf085b899ba774fde7e72464 Merge: 17ec7e4 bbadbb7 Date: Tue Feb 25 23:12:51 2014 -0500 merge from master commit 17ec7e4ee508cc5302f013bee896e2e88c42d89f Date: Tue Feb 25 23:12:26 2014 -0500 warnings war z commit 698179544aa3d6f8f7a4504a1007353ec93506b4 Date: Tue Feb 25 12:11:15 2014 -0600 Initial changes for better debugging. commit 9f4e88f149a55e2690bf4621b78da2a607cfee9f Date: Mon Feb 24 23:47:57 2014 -0500 compil commit 98c245100dd908b0e378f21438d78fabb3531f18 Merge: f2dbb00 0e9f8a7 Date: Mon Feb 24 22:41:51 2014 -0500 merge from master commit f2dbb00ed12a22f975861ff3afdd9257f9ab4146 Date: Mon Feb 24 22:23:36 2014 -0500 wat_dist commit 6b17f0ce7fd22470c679392fe115d1e44541c7fb Date: Wed Feb 19 18:18:35 2014 -0800 wat_distances pilot app commit 6bc88f4e8035a2bff3e6d2302fa85de8e46a3222 Date: Wed Feb 19 13:44:10 2014 -0500 VarSolDRotamerDots no longer have static member variables, responsibilities of vsasa settings moved to VarSolDistSasaCalculator commit 3e121400c2d9d818d593f1f3b239b7cdc952c430 Merge: ce4c720 b5b2e78 Date: Mon Feb 17 15:45:20 2014 -0500 Merge commit ce4c7205043e6270091f764aace9671ec4855297 Date: Mon Feb 17 15:44:32 2014 -0500 Adding rotamer library information to some peptoid side chains commit b5b2e7882bace408d400ed3cfcd1a43efad6f57a Date: Mon Feb 17 15:18:48 2014 -0500 Ignore reporting of MM info during integration tets commit 0b95ecd128a51486a72764a78899954849b08eda Date: Wed Feb 12 16:45:18 2014 -0500 Adding new peptoid side chains commit 690a323c5d1f9289fe8e06e9d68ab8954abee953 Date: Wed Feb 12 16:43:31 2014 -0500 Adding new lines to end of params files commit 8127351cd7ccee0e7fbb9c4529718cad53e2f23d Date: Sun Feb 9 21:07:46 2014 -0500 statistically derived vsasa radii commit cfe6095ad713a7ccee2916aa25664a6bd5e0cf1a Date: Fri Feb 7 00:39:42 2014 -0500 to contador commit 1d7e0e1ff7c186c11993c347e382e1c93b1c92a9 Date: Sat Jan 25 17:17:00 2014 -0500 copy-paste error commit 6979cd4edacbb906169aa2e2377004f14aa2201a Date: Sat Jan 25 16:49:44 2014 -0500 killdevil commit 651610b2ff6f6922ba7949a44322233e080f3857 Date: Thu Jan 23 02:11:39 2014 -0500 vsasa sweeps on killdevil commit 6f04e8bf1e6fd2e830e7acccefbb3e8847fe7bdd Date: Wed Jan 22 16:31:31 2014 -0500 Adding a cyclization ITest to test CyclizationMover commit 250b80ec45b9640352c984e6ac165fccea1a6039 Date: Wed Jan 22 13:45:51 2014 -0500 Updating the make_rot_lib ITest to include peptoids commit 98f01f1df6d8dd05ead7b5faf169ccbb8f68c3d3 Date: Wed Jan 22 11:26:58 2014 -0500 Updating ncaa_fixbb ITest to design with peptoids as well commit fa62b18ba4bcf58a60e72423bb43e197aa2f1eb2 Date: Tue Jan 21 17:09:18 2014 -0500 Updating USEC ITest to test using sequence match fragments and peptoids commit 024e8d426341c89b782be8fe5604f410e557acf4 Date: Tue Jan 21 15:38:07 2014 -0500 Despite doing esentially the same thing, using MutateResidue mover doesn't crash commit 142183a3baea26d4a06c87f870050a1677df953d Date: Mon Jan 20 11:21:40 2014 -0500 Commenting this out to cut down on residue types. Will be turned on by cyclization itest. commit dc86b9e990b87c74eb2bd6b26ec3ef9e718ca41b Date: Mon Jan 20 11:09:43 2014 -0500 Header shifting, indenting of app commit accbedd23dd8d8e38778471498a573cbe851d9e8 Date: Mon Jan 20 10:54:09 2014 -0500 Changing function definition and calls to remove unused variable warnings commit 7d4703e96d177565c3e3d6f3aee0f8a009e30c2a Date: Thu Jan 16 17:11:45 2014 -0500 to killdevil commit 3e9c420a7b22293924595e824754982700d72976 Date: Thu Jan 16 17:02:38 2014 -0500 waterFeatures commit 240d831ef9985a1976ea0da2aaefb26544189135 Date: Thu Jan 16 16:07:46 2014 -0500 typo commit d57c21a44e4ea1babc9fa6da95bc0491f0db5f41 Date: Thu Jan 16 13:59:36 2014 -0500 removed .kh files commit 1a9629e7b438e021ab39301e84c22a0c7efc4c55 Date: Thu Jan 16 13:58:54 2014 -0500 Trying to fix conflicting calcs in BuriedUnsats2 commit 38d34cf1f3c84326ef6ee2606ba8136f9a46394d Date: Thu Jan 16 11:28:55 2014 -0500 git test commit c5b44ee8cff97aa3f7378ff664cf055f04aa6312 Date: Thu Jan 16 01:21:52 2014 -0500 Buns2 calc creates unique calculator strings commit 35554e5ed7dd685f31f8c91a02251b201c611d89 Date: Tue Jan 14 11:11:58 2014 -0500 Changing make_rot_lib integration test use new MakeRotLib app, updating flags and inpuits commit b86d27b3228ca281765d7edbc3fb7b4af54b1e97 Date: Tue Jan 14 11:10:51 2014 -0500 Fixing Acetyl vs Acteyl typos in MakeRotLibJobInputer commit f2ee31c323595f75dd4410f1d2093022f11f5954 Date: Tue Jan 14 11:09:45 2014 -0500 Adding try/catch blocks to new MakeRotLib app commit 4027296e09c02dfd520b33c95980a41af715f573 Date: Fri Jan 10 15:47:04 2014 -0500 Bug fix in Ramachandran unit tests Ranchandran unit tests had a silent off-by-one error when comparing a zero-based array to a vector1 in the test_phipsi_in_allowed_rama function. There is infact no valine in the left-handed helix range that passes the rama threshold so the sequence was changed and one of the other tests had to be updatred since they use the same pose. commit e5e6f41abcc29cdef1a8bf56d470915c0b75d01b Date: Wed Jan 8 18:14:49 2014 -0500 Removing duplicated MM torsion params commit 2f26750e7ac177c7475d7344d3ae30fb879539b8 Date: Sun Jan 5 20:07:43 2014 -0500 WaterFeatures commit 6d21a99d85ff049b8c33290fe71d72ceae097838 Date: Sun Jan 5 16:34:32 2014 -0500 WaterFeatures commit 1dc5d8466a1233be4c20d34f77d981c18a6b5ed5 Merge: f621c9d b22878c Date: Sun Jan 5 08:06:35 2014 -0500 merge from master commit f621c9d08c9000c42247ee2732b44d2ded46b449 Date: Sun Jan 5 08:02:29 2014 -0500 WaterFeatures commit 4af9be720c6593cfad32cf7d54b4d81d86b77c81 Date: Sun Jan 5 05:33:02 2014 -0500 VarSolDRotamerDots tests now cover wobble and probe radius commit 5831418847d871db428136da56e75c59c3da2924 Date: Fri Jan 3 17:20:18 2014 -0500 Update MMAtomNames in pre-talaris metal ion params files to reflect names in MMAtomProperties.txt commit 0e47280873632213cba59d342692dbbbfe6dff0b Date: Fri Jan 3 15:41:11 2014 -0500 Forgot to add peptoid related data members of ResidueType to its copy-construcutor This resulted in everything being concidered a peptoid. commit ee2de24039144d54b0eb54ede2f306e3d21125bb Merge: a2b0434 0dc2c80 Date: Fri Jan 3 11:56:27 2014 -0500 huh? what happened? merge from remote commit a2b0434f293ece482e4e75b0bae26553315bc659 Date: Fri Jan 3 10:57:45 2014 -0500 WaterFeatures, kh xtal water app commit 8c9713a219d6313da74588ae9fbbc0394f6a9070 Date: Thu Jan 2 12:35:59 2014 -0500 Acetylated typos commit 2cd6366f2ff0f698257f60429c954423dee3c501 Merge: bd2700d 5d4b129 Date: Tue Dec 31 14:58:24 2013 -0500 Merged master into peptoid branch. Happy yew year me! commit 38e08dfb5d494b08a16d306995fdfb0cb5b22c40 Date: Sun Dec 22 18:10:29 2013 -0600 Updated VarSolDSasa unit tests. commit bd2700d80de41ac2dfd4a1158b09b6a9dd1d424a Date: Fri Dec 20 17:25:31 2013 -0500 patching tests commit 9db38a5a6c0a2f5be5e4ec424b293e860a001059 Date: Fri Dec 20 15:15:17 2013 -0500 patching database commit d481bd105e059042c4e61278613a3cdf3d0d856d Merge: 88ad072 396ed21 Date: Tue Dec 3 11:06:52 2013 -0500 merge from master commit 05fcabf4a16874028517062bd91489139fe69605 Date: Fri Dec 20 12:07:23 2013 -0500 removing empty gitignore files and resulting empty directories commit 11b4ebbc8c269b4df68e6b0170606546ce5648e3 Date: Thu Dec 19 17:40:11 2013 -0500 patching apps commit 88799903b0d93041353416509eb16f2563bfda6d Date: Thu Dec 19 17:07:33 2013 -0500 patching devel commit a262b2e1fe3be09696dd7705958f51a46a101303 Date: Thu Dec 19 16:49:49 2013 -0500 patching protocols commit 0fd07749342272725deece61e2bd23aef9355a70 Date: Thu Dec 19 11:36:30 2013 -0500 patching core again commit 4c61a49c5f69d8055e80e727f6714cd21dba0f57 Date: Thu Dec 19 11:15:55 2013 -0500 patching core commit 879b143b4d8ec37d997fa8734d08985efd67d097 Date: Wed Dec 18 17:11:02 2013 -0500 patching utility commit c0e67d300a0414eb7be87ceb20b723b7b1a16981 Date: Wed Dec 18 17:08:08 2013 -0500 patching basic commit b387a5443ee8fbbc93a65b0eb665f360451537ad Date: Wed Dec 18 17:00:01 2013 -0500 patching objexxfcl commit 62ab931822067751080f200b7ff9562dcc20451a Date: Wed Dec 18 16:55:54 2013 -0500 Adding new options commit b594030f73b3877fb392c2fa2011ceacf4a4f4ce Date: Wed Dec 18 16:45:22 2013 -0500 Deleting two empty files commit aaa6e4c445d116a0280e27dfcef8982d2b116e53 Date: Wed Dec 18 15:44:40 2013 -0500 update email address commit 0c9e35d5c3ca26c8c0bd3ff6155579e101531db1 Date: Wed Dec 18 15:05:57 2013 -0500 removing empty gitignore files and resulting empty directories commit 0dc2c805ad6640712f27cdbec5ac4f4d675a4608 Merge: 88ad072 396ed21 Date: Tue Dec 3 11:06:52 2013 -0500 merge from master commit 88ad072bcc96d3f33679fab622c2990c4cdaa466 Date: Mon Nov 11 22:34:29 2013 -0500 moar probes commit d86288beb55b39336c83483ed51d4064822feffe Merge: 44f8e6e 68e66e5 Date: Mon Nov 11 19:13:46 2013 -0500 merge from master commit 44f8e6e09ac296ebb40403fa96d97c9cbfb7d266 Date: Mon Nov 11 16:12:56 2013 -0500 Added more sasa probes commit ed077acbab8f1d78481b231b9ee90cb090f93245 Date: Thu Nov 7 19:02:09 2013 -0800 Updating FragmentLookup to support symmetry. Updating FragmentLookup to operate only on the asymmetric unit of symmetric poses. Lookup only returns results for the asymmetric unit of pose, does not denormalize results across dependent residues. Moving fragment residue span resolution logic into FragmentLookup.cc. commit 7370703874156de33d26f7780cde59f00e94b886 Date: Wed Nov 6 18:56:47 2013 -0800 Update FragmentLookup to support non-protein residues. Update FragmentLookup fragment generation to support non-protein residues. This provides compatibility for mixed-type poses and poses containing virtual residues. Fixes #37. commit 1b86d39dc306104aa2559266d5f800bf6bcd7efd Date: Fri Nov 1 16:08:46 2013 -0700 Adding FragmentLookupFilter documentation. commit 28a1bfd31165e446d1e5370a488144e47046a840 Date: Thu Oct 31 12:38:41 2013 -0700 Adding FragmentLookupResult::match_score parameter. Adding match_score value to FragmentLookupResult and FragmentLookupFilter reporting. Adding stub implementation in lookup, to be expanded later. commit 556031062768b0c6e9efbcd0661bc28aaa6fc8d5 Date: Wed Oct 30 19:51:23 2013 -0700 Adding first and closest fragment lookup modes to FragmentLookupFilter. Adding lookup mode control to fragment filter and adding additional result logging. commit daae07f56388eea77e58f2e1cbc70c39283c5fff Date: Wed Oct 30 11:36:16 2013 -0700 Adding FragmentLookupFilter reporting and cached result access. commit 4d34f01eaea89689f864d93968604d79897d1f9e Date: Mon Oct 28 19:57:39 2013 -0700 Add FragmentStore resolution via BinaryFragmentStoreBackend. Adding fragment store resolution via BinaryFragmentStoreBackend to StructureStoreManager class. Fixing error in BinaryFragmentStoreBackend binary file read. commit a82379f8e11f9360dc193b9f277aee3dba3de33a Date: Mon Oct 28 18:38:33 2013 -0700 Adding BinaryFragmentStoreBackend and tests. Adding BinaryFragmentStoreBackend, accessing read-only fragment stores without HDF5 support. Adding basic test coverage of fragment lookup and BinaryFragmentStore. commit 2893231941c58c63a6db2b4c578f7ba21db0007a Date: Mon Oct 28 17:58:49 2013 -0700 Updating test build to for test data subdirs and verbose test output. Updating unittest SConscript to correctly represent dependencies between test data file and test libraries. This implicitly inserts dependencies on test data directories, allowed test data subdirectories. Updating test run script to support control over tracer levels and provide list of available test suites. commit 61c1e09919fb5f0c953cf89059a819e6c77c76c8 Date: Fri Oct 25 14:31:01 2013 -0700 Registering FragmentLookupFilter and FragmentLookup tests. Adding filter registration for FragmentLookupFilter and adding basic FragmentLookup unit test coverage. Fixing errors in H5FragmentStoreBackend datatype declaration and attribute parsing. commit 1d83eb2373188c4c676c07071f27a8e97980b069 Date: Thu Oct 24 22:05:53 2013 -0700 Adding FragmentLookupFilter protocol component and backend options. Adding basic FragmentLookupFilter component, calling into core FragmentLookup. Adding pose-processing to FragmentLookup. Adding option to specify source fragment library. commit 328ff5b4930825190d66a74f68dc65499d02d1a4 Date: Thu Oct 24 13:56:51 2013 -0400 Adding a fourth Hbond to look for in tau_angles.R commit a28a33a5ad47b33fc489699ff01567cc9bdd9e10 Date: Thu Oct 24 01:08:52 2013 -0700 Initial FragmentLookup implemenation. commit 50b5d4af3bd9be83be62386acc6df017e597da4b Date: Wed Oct 23 23:24:07 2013 -0700 Adding H5FragmentStoreBackend. Adding initial HDF5 FragmentStore backend and integrating into StructureStoreManager. Implementation is guarded by USEHDF5 definition. commit 67a76c49427c06736c344a413d29e9ebf25a1c71 Date: Wed Oct 23 21:03:54 2013 -0700 Initial FragmentLookup type skeleton. Adding fragment lookup algorithrms to numeric namespace and initial fragment lookup, store, and manager types. commit dcdf236f49787a2cedd494d0569af01fffd11f90 Date: Wed Oct 23 14:24:06 2013 -0700 Initial hdf5 build support and stub IndexedStructureStore. Adding 'hdf5' build extra, which adds linking against HDF5 libraries. commit 2c0b8067600878c5fbe01c4ed31123e77ab8bcac Date: Fri Oct 11 19:04:08 2013 -0400 Fixing a bug in an R script that caused a resulting vector to be in the wrong order. The order was very important. commit 94d34c9ce8c28ddef7cf2e51d471b77fc3478795 Date: Thu Oct 10 16:06:08 2013 -0400 Updating the tau_angles features analysis script to include information on important Hbonds for H3 bulge stability. commit 074c600bcf33cf7db0b465fa40af1aa084d5e2e8 Merge: 39ae118 506ea9d Date: Thu Oct 10 02:22:27 2013 -0400 # [ONE LINE DESCRIPTION OF CHANGE] # NEWS: [DETAILED DESCRIPTION OF CHANGE] # ---------------------------------------- # Unit test status: [Pass/Fail/Not Run] # Integration test status: [Number of changed tests / Not Run] # [NAME_OF_CHANGED_TEST_1]: explanation of change explanation of change ... # explanation of change, cont'd. # [NAME_OF_CHANGED_TEST_2]: explanation of change #+BugFix [BUG_NUMBER] [LINK_TO_BUG] # Uncomment and fill in the line above to indicate this commit # fixes a known bug. # On branch khouli/buns # Your branch is ahead of 'origin/khouli/buns' by 29 commits. # (use "git push" to publish your local commits) # # Changes to be committed: # (use "git reset HEAD ..." to unstage) # # modified: source/src/devel/splice/FindEndpointsOperation.cc # modified: source/src/protocols/protein_interface_design/filters/DesignableResiduesFilter.cc # # Untracked files: # (use "git add ..." to include in what will be committed) # # source/cscope.files # source/cscope.in.out # source/cscope.out # source/cscope.po.out # source/cscope.sh # source/src/apps/pilot/kevin/bur_nodon_tyr.cc # source/src/apps/pilot/kevin/sandbox.cc # source/src/protocols/features/WaterFeatures.cc # source/src/protocols/features/WaterFeatures.fwd.hh # source/src/protocols/features/WaterFeatures.hh # source/src/protocols/features/WaterFeaturesCreator.cc # source/src/protocols/features/WaterFeaturesCreator.hh # source/src/protocols/features/_site_environment_ta # tests/features/Rplots.pdf # tests/features/_arguments.py # tests/features/acc_unsat_probabilities.txt # tests/features/condor_job_ids # tests/features/don_unsat_probabilities.txt # tests/features/sample_sources/.gitignore # tests/features/scripts/analysis/plots/hbonds/AHdist.R # tests/features/scripts/analysis/plots/hbonds/cosAHD.R # tests/features/submit.sh # tests/features/test.png # tests/scientific/biweekly_statistics/ commit 39ae118ca4c9146761a242f6edaf5be57c009d30 Merge: ff53dd1 a2cd384 Date: Wed Oct 9 14:34:56 2013 -0400 merge from master commit ff53dd133660c9d5ec8467eb8d9c547a4568c6e2 Merge: 79cc949 61d136b Date: Wed Oct 9 12:45:09 2013 -0400 merge from master commit 79cc949ca8e682d2a850552317458f90023991ca Merge: d572152 999e7a4 Date: Sat Oct 5 14:24:53 2013 -0400 merge from master commit d572152df47d33fbda3d717a41c057eb7bc2dcb3 Date: Mon Sep 30 18:00:14 2013 -0400 Correcting foreignkey constraints for heavy_id related HBondFeatures table entries commit 253c340a0d0f280d4e7f9904a62afa2de5daa503 Date: Wed Sep 25 18:57:28 2013 -0400 heavy id for acceptors was wonky commit 5bfa5a7d16d12e6adc96878ca02c7c87c44986a6 Date: Wed Sep 25 15:53:43 2013 -0400 debugged commit 33f06e865d9fd3530cd2042859d7e4e9fc3b6a21 Date: Fri Sep 20 15:02:15 2013 -0400 fixing ide weirdness... commit f0adf6cc7f17d0a17a71c2ba2ff35dedadbffa14 Merge: e2706d5 f66c42a Date: Thu Sep 19 23:33:49 2013 -0400 merge from master commit e2706d58538b66a6cefa9a9ff2b501f5ddbfe8d5 Merge: ed77f79 a425d63 Date: Thu Sep 19 08:31:51 2013 -0400 Merge branch 'khouli/buns' of github.com:RosettaCommons/main into khouli/buns commit df6ef8448edb372a68d71baf665c74609b11fc77 Date: Mon Sep 16 18:10:08 2013 -0400 Adding alpha101 density plot and a alpha v tau scatterplot to tau_angles.R commit 6d47105f7c00aeefe5c02cdc0c5b15d0a8253678 Date: Sun Sep 15 15:06:22 2013 -0400 Adding alpha_vm_estimates.R commit a425d63deb81b60b5bfbd867fc476770dfd44900 Date: Sat Sep 14 14:04:30 2013 -0400 boost includes and using statements in TaskOperationFeatures commit 6dadf3d4e234a3ef11b40e47e47d2afc07963d50 Date: Thu Sep 12 14:36:33 2013 -0400 fixed hbonds.cc commit ed77f7938d587a08aa2e237e19f36662bdac18ae Date: Tue Sep 10 14:33:04 2013 -0400 bleh commit c60e4ba563747bcd4f6c1dcdf9bf18a11622ce5a Merge: 867aa68 e5c34eb Date: Mon Sep 9 15:39:13 2013 -0400 merge from master commit 867aa6806a707177cd67ac6f4e8c86818109d78e Date: Mon Sep 9 15:38:55 2013 -0400 TaskOperationFeaturesReporter commit 2be5d1401360bafe6d5b71a9be129bc0c8d19f3a Date: Sat Sep 7 21:56:18 2013 -0400 Darkening color of first layer in plot, adjusting spacing between facet panels in scatterplot matrix script. commit a4ad8950a500c2d42ff81c011ee3be0b84d1dbe6 Date: Sat Sep 7 21:54:56 2013 -0400 Darkening color of first layer in plot and adding alpha back for single dof density estimates script. commit 0039574c7501420d61a4582a3315b69d32203477 Date: Sat Sep 7 19:02:14 2013 -0400 Making some plots look better in black and white. commit b35c15c760a990b9dd14fb8a077f486fa5d3bb4f Date: Thu Sep 5 10:58:28 2013 -0400 Making the signle_dof_density_estimate plots look better at small sizes. commit 59786b8ba827d3857ee2d765a488fa3138f122af Date: Thu Sep 5 00:00:21 2013 -0400 Adjusting appearance of anchor_transform_correlation to work better at smaller sizes. commit f4ecc197fc4327b0aa07760044df705ec50bc14a Date: Wed Sep 4 20:56:13 2013 -0400 Splitting save_plots into two calls - one uses cairo and one does not. This makes transparency work in both png and eps formats during the same run. commit ee39c5a3a1dfcad40a4d6981656a8fab898b02c0 Date: Wed Sep 4 20:19:21 2013 -0400 Updating location of some annotations after switching from radians to degrees. commit cbc5f413f8b6ffc8039ded84185be5bf9bcd74f8 Date: Wed Sep 4 19:26:24 2013 -0400 HBondFeatuers now reports chem_group_sasa commit f33ffc776efd6d61788ed2f655b0ca7618331280 Date: Wed Sep 4 19:02:26 2013 -0400 Updating tau queryin scripts to use the newly named db tables. commit 9789e403f0287f588627306060f9156dea779dde Date: Wed Sep 4 19:01:48 2013 -0400 Fixing the switched the labels for tau and alpha. commit c55ae9d607d140a101fca661b584b0e4f460d097 Date: Wed Sep 4 14:20:50 2013 -0400 Updating features.py to know about the directory renaming and switch to git. commit 0c3414719334c82cc052c7a16575308cd64098c5 Date: Wed Sep 4 14:21:54 2013 -0400 Fixing a return ref to stack var issue, bad insert stmt and ctor problem. commit 8141e3ce55f6bfb625de68d0307da7af09f2a610 Date: Wed Sep 4 12:51:36 2013 -0400 Reworking LoopAnchorFeatures ============================ After finding that a certain combination of the one-residue and three- residue approach worked well, I am removing the distinction and merging the relevant information into a single table. This should reduce the number of JOIN operations necessary to get useful information out of the database. * Improved const correctness * renamed "omega" column "tau101" (pseudo-bond angle of last three CAs) * removed "alpha" column (pseudo-bond angle of first three CAs) * added "alpha101" column (pseudo-dihedral from CA_end-2 -> CA_end+1) * value used by the Nakamura group The "tau101" and "alpha101" names are based on the names used by the phipsi program commit f4234fa91f2156a1f6bab6249133bd7bfa003cb6 Date: Wed Sep 4 10:51:22 2013 -0400 Updating Xcode project commit cc16c4bba9597927bf5f9879afa078a80aef809a Date: Tue Sep 3 15:35:53 2013 -0400 example buns commit ee83522a6675e3bcb08bccebc05f7e2e05a69041 Date: Tue Sep 3 02:33:44 2013 -0400 HBondFeatures for many sasa probe radii and variable radius commit ff2b86ff3e8fc2c3bf3f26755dccdb78e11f2005 Merge: 7ecf580 232ce6d Date: Sun Sep 1 20:43:33 2013 -0400 merge from master commit 7ecf5802e3108f3f746b7ee223ac2a32769275ae Date: Sun Sep 1 19:13:00 2013 -0400 BuriedUnsatCalc2 and BuriedUnsatFilt2 behavior has converged commit d6cbdb8c509c89c2abc739fa7f8dd4b0c9394622 Merge: 7351393 a6f0a1e Date: Wed Aug 28 23:26:49 2013 -0400 merge from master commit 73513933ff8a3e61b5622f133aa7eb224d1a2e15 Date: Wed Aug 28 17:25:48 2013 -0400 removed khouli/explicit_water remnants commit 3085dbdef131349d6d68040467f90843c6370991 Merge: 29c32ed 80e5737 Date: Wed Aug 28 11:01:56 2013 -0400 merge from master commit 29c32ed0fbc70ffe659b98f5e78772f778f7c163 Date: Wed Aug 28 10:45:56 2013 -0400 removed explicit water stuff, now in khouli/explicit_water commit e707ca0e63dfb537611a18226c4f0755c41842f3 Date: Wed Aug 28 10:21:45 2013 -0400 xcode commit bc035bed22ed593952204ca48c612428b908d921 Date: Wed Aug 28 10:19:11 2013 -0400 removed bur_nodon_tyr.cc from tracking commit d85795601625244bbc5f7855aa7ebf7bc2137b1b Date: Wed Aug 28 10:17:02 2013 -0400 move buns2 calc and filter to devel commit 0f95b3cfecb93ccb85cfc69beef32e2d74fdb424 Date: Tue Aug 27 18:21:27 2013 -0400 moved calculator and filter to devel, added rosetta_scripts tag options commit 7757a1605a42eb4405a1473e98e1ee242084d136 Merge: 581cc6f 7ae9e26 Date: Sun Aug 25 04:10:36 2013 -0400 merge from master commit 581cc6f31d6ff8d045faf2aa4e196bd8cd43bea9 Merge: d165eef c1463dd Date: Sun Aug 25 01:03:48 2013 -0400 merge from master commit d165eefe896a5ec72ae7be0e9c4cf5ac14a5acf7 Date: Thu Aug 15 09:50:24 2013 -0400 opt keys commit f346ccadd81529f4f7cabb974b1f22f186487c10 Merge: 30f03ce 9e46ba3 Date: Wed Aug 14 23:32:40 2013 -0400 merge from master, add bur_nodon_tyr commit 30f03ce38a84f30e2f56d72dbbc1811419c74cc3 Date: Wed Aug 14 23:29:53 2013 -0400 started bur nondonating tyr app commit f92bf1db9006c2a96f44ac306bfd7f9a8d3814a2 Date: Tue Aug 13 23:52:12 2013 -0400 small file comment header fixes commit 563e51992f09468bd9bc3e0a79e96f9037d14e21 Date: Tue Aug 13 23:28:51 2013 -0400 working BuriedUnsatisfiedPolarsCalculator2 commit c6a66a4d1e8c101b24ffdaa74b1625bf8ae26609 Merge: 480ae5a b628352 Date: Tue Aug 13 17:02:47 2013 -0400 Merging in master. commit 480ae5aee0cb4db512119770dc79566d6f07ebd4 Date: Tue Aug 13 12:27:40 2013 -0400 BuriedUnsatPolarsCalculator2 works, beginning work on filter2, files moved out of devel and into protocols/toolbox commit 3d73838c554955b97c68e9b184f6884d5d3561b1 Date: Thu Aug 8 11:53:45 2013 -0400 created files for buriedunsat2 filter commit 74fb21f965527c2b62e878bd26a0aaf43a103362 Date: Thu Aug 8 10:56:06 2013 -0400 working bunsat2 calculator in devel commit fced6a3c351b3d990331d26c560e649dad0677df Merge: 8bd33a8 943d19d Date: Wed Aug 7 09:58:01 2013 -0400 merge from master commit 8bd33a8eb4086662144b97ec7c0941cd00c1aea0 Date: Wed Aug 7 09:57:35 2013 -0400 preparing to merge from master commit 0d9b80abec71ee6f162431df13921118fdfce0f0 Merge: f15a6eb 06b47ca Date: Tue Jul 23 13:48:13 2013 -0400 merge from master commit f15a6eb258605609efcf3c1cdc8c2f0b4e512e6e Date: Fri Jul 12 18:00:08 2013 -0400 added app BuriedUnsatPolarsFinder3 to run and display output of new buried unsat calc; taking laptop to Apple store to get fixed commit 7b85bc2f6a30b453284c634565a8ab6a27f79ce1 Date: Thu Jul 11 23:32:02 2013 -0400 buriedunsatscalc2 commit 673d540e5d185501dc9788e628562e15f2b53a36 Date: Thu Jul 11 15:07:54 2013 -0400 small changes to BuriedUnsatCalc2 commit 5a86095e228cf4993a2b4308d16feb252f58a403 Date: Thu Jul 11 03:06:56 2013 -0400 calculator started in devel commit 1d6fc9c17e3abdce8d4ae3c44f42e79df6df83ce Date: Mon Jul 8 12:22:00 2013 -0400 change loop over bunsats to be on heavyatoms commit 7136486725903712a4f1aabec871d3bb06a8ef9a Date: Mon Jul 8 01:16:24 2013 -0400 working version of BuriedUnsatsFinder2 commit 5710a0a29034cf5f469e882deca715f2372e3695 Date: Wed Jul 3 03:56:59 2013 -0400 refactoring bder/BuriedUnsatPolarsFinder.cc into kevin/BuriedUnsatPolarsFinder2.cc refactoring bder/BuriedUnsatPolarsFinder.cc into kevin/BuriedUnsatPolarsFinder2.cc, not yet compilable copied salt bridge features reporter as template for buried unsat features reporter commit 679f43dceea0d22da1bb3f4b19bf00b2f98879a6 Merge: 3f5694a 36dc2e9 Date: Tue Jul 2 18:55:49 2013 -0400 Merging with Kevin's changes. commit 3f5694aacfed1532ac5ebaa6985725473c732dfb Date: Tue Jul 2 18:52:16 2013 -0400 when deleting waters, --i is needed in the for-loop commit 36dc2e99e407748732a671cf9bb43258bb8890e0 Date: Tue Jul 2 16:39:50 2013 -0400 water iteration --i bug in xtal_water_bunsat.cc commit 56ebb6b400fd41750a0c1eaa62cffb49c52ec9c2 Date: Tue Jul 2 15:02:21 2013 -0400 bug fix in BuriedUnsatPolarsFinder.cc commit 222ebaa4146042193879e45bbac51461f3da81ba Merge: 41a3632 4604080 Date: Tue Jul 2 13:48:25 2013 -0400 Merging master into my branch called bder/supercharge_test_change, which has xtal_water_bunsat.cc and BuriedUnsatPolarsFinder.cc in src/apps/pilot/bder/ commit 41a36329d60ac45ee3af6c4bdf6a63f4983c6fff Date: Tue Jul 2 13:43:04 2013 -0400 Adding xtal_water_bunsat application, updating BuriedUnsatPolarsFinder to use VarSolDist for SASA calculation and a supplemental distance + AHD angle check for hbond detection. commit d706ac9a0226a9f13690d504b0cf6b7494ea67b4 Date: Tue Jul 2 10:23:40 2013 -0400 BuriedUnsatPolarsFinder uses VarSolDist, Talaris2013, and a separate distance+AHD check for hbonds. Overall I am satisfied with the lists of buried unsat atoms from native structures. I want to improve the organization of the code. commit 59208df8680761b56ea35e6e422a9fce9a923274 Date: Thu Jun 27 14:32:46 2013 -0400 In VarSolDRotamerDots, extra shells were added for SASA calculations. Probe radius is set from the sasa_calculator_probe_radius option. commit e6f3cba0c3e575872bbe259428a75744cfea8b96 Date: Tue Jun 25 18:02:38 2013 -0400 Added more shells to Andrew's sasa calculator commit 21f81f58097a3facc71709cf0eb92a1366685e84 Date: Tue Jun 25 17:13:38 2013 -0400 including Andrew's sasa calculator in my_bunsat_finder commit 1d96f156a9498acee759ea0bde5345e99308e439 Date: Tue Jun 25 12:24:54 2013 -0400 in my_bunsat_finder, searching only dry_pose residues to avoid inconsistencies in atomid's commit e2e5171335d1a20a945eb2a62c6de6597658c97d Date: Tue Jun 25 09:55:43 2013 -0400 in my_bunsat_finder, printing PDB name in output line commit b303b6d98364aae82eaae0e891cac9b37937ee86 Date: Mon Jun 24 16:48:49 2013 -0400 adding pilot app, apps/pilot/bder/my_bunsat_finder.cc