commit 5f9f096e46c5bcf208fc75a861b109d215bc9142 Date: Sun Jul 27 19:12:40 2014 -0400 Updating PyRosetta dependency calculation algorithm commit 3fd8de37b01ac891c5668a3f0ae65127d73f1045 Date: Sun Jul 27 15:06:06 2014 -0700 adding -sampler_silent_file option to create movies for Rosetta developers stepwise talk. Also adding some copy/clone functions to options. I think those might not be necessary, but best to be safe. commit 0250ef6ffc882740ffd6b229f14dee434e85415f Date: Sun Jul 27 00:38:41 2014 -0400 Fixing Windows build commit 2f887c7a9d8244c80f5057bec94c309b4366786d Date: Sun Jul 27 00:34:24 2014 -0400 Fixing Mac PyRosetta build commit 28cd7d9ad8510ba6b86e063d58a858e998126760 Merge: aa8bac6 8a17ac1 Date: Sun Jul 27 04:37:24 2014 +0200 Contribute myriad bug fixes and additional unit testing to Broker 2.0 framework. commit 8a17ac1d360c69b09a8a6b5209cb8c073dd7db49 Date: Sun Jul 27 04:36:28 2014 +0200 Re-fix issues surrounding core namespace stuff in unit tests. commit aa8bac6640d404de390e2210096146e9c700eae9 Date: Sat Jul 26 20:40:16 2014 -0400 Membrane Framework Updates: Part 2 in a series of membrane framework commits =============================================================================== Author: Rebecca Alford Conformation: = Moved coordinate derived membrane info down into the membrane info object Renaming: = Renamed InitialMembranePositionMover => MembranePositionFromTopologyMover = Renamed MembranePositionRTMover => Set Membrane Position mover (with appropriate tests) commit 520eda7ae506a8e7377e1ec9cd36104cc486f4a0 Merge: 13f8d2b ab68c54 Date: Sat Jul 26 19:50:46 2014 -0400 Merging in recent master addition from kale commit ab68c54bef43ce17e8768408a9ec3f725b3dac76 Date: Sat Jul 26 13:35:36 2014 -0700 Add setters to ExtraRotamersGeneric. I found the ExtraRotamersGeneric task operation in the RosettaScripts documentation, and I wanted to use it from c++. Unfortunately, it only had parse_my_tag() implemented and no setter methods. This commit adds those methods. commit 13f8d2b8e7ea47897dd4982e6b5259a56cdc30dc Merge: 99b761f b44ff2d Date: Sat Jul 26 14:35:37 2014 -0400 Merging in updates to conformation commit 99b761ff146693aa843b26ab9a35422cff203f30 Merge: fe9d649 6fcf74f Date: Sat Jul 26 14:35:23 2014 -0400 Merging in renamed unit tests commit cb9b80126ab4987e188a572378ff440e5a439538 Merge: fe9d649 190b726 Date: Sat Jul 26 19:17:43 2014 +0200 Merge branch 'justinrporter/env_devel' into justinrporter/env_release Conflicts: source/test/protocols/environment/ProtectedConf.cxxtest.hh source/test/protocols/environment/claims/ClaimTests.cxxtest.hh commit fe9d649737b69f397a6735c7de653cb997fe731e Merge: 96ab30c ba9714e Date: Fri Jul 25 21:32:28 2014 -0500 Fixed bugs with ChiralMover and TryRotamers optimal connection point ChiralMover now updates backbone oxygens on upper terminus. Also, properly handles orienting functional group for residues that do not have three side chain residues to orient. Added case of D-Proline in NtermTruncation patch Updated atom connection points in optimal_connection_point function. This is used by TryRotamers for automatic fold tree creation and was failing to create properly aligned rotamers for HIS, LEU and ILE. Updated optimal atom based on a fixed atom in the terminal chi angle. Unit tests: pass Integration tests: ld_converter has minor coordinate changes due to the update to ChiralMover and cosmetic output changes. commit b44ff2d5d5cf7e1d47a07578b53e6a79ccdf92e7 Date: Fri Jul 25 21:11:40 2014 -0400 Updating unit tests to match new conformation setup - all tests pass commit 60210b27ec3be977ee7818f9a618475e0c392584 Date: Fri Jul 25 20:54:25 2014 -0400 Fixing unit tests to include new namespacing commit dbc08421145a342b2d6eddd2d7dc0b4212475863 Date: Fri Jul 25 20:11:13 2014 -0400 Combining membrane info and membrane conformation unit tests commit ba9714e8d8c9ec9132911e10759dbdc57e47b396 Date: Fri Jul 25 19:58:32 2014 -0400 Fixing Windows build commit 08fac696c65ddf7757d1d452d355e1361703b7e2 Date: Fri Jul 25 19:41:34 2014 -0400 Ran a basic test that the new conformation updates are working - will now go adjust the unit tests commit 1696313a970bed9307a7037c83826c8133c80be6 Date: Fri Jul 25 17:03:16 2014 -0400 More renaming to fix executable and unit test builds commit 22bae7e63a491e3ae717a29d27694aa4cc685c2e Date: Fri Jul 25 15:50:43 2014 -0400 Fixing more incomplete type definitions from the mem info extension. Will do things later on this to optimize the build speed (ideally pass through methods) commit a651f94de66d58571cfd09420c11610065d5dd0f Date: Fri Jul 25 12:44:31 2014 -0700 adding xcode ide project dir to .gitignore commit 1e9e97753fc85cb1f1ad7498b764316c29c56c81 Date: Fri Jul 25 15:41:45 2014 -0400 Fixing build errors due to incomplete type definitons - this is mostly due to things moving around in membrane info commit b13164ae1144cb0bcbaf1f5196e47c868ac903f9 Date: Fri Jul 25 15:40:32 2014 -0400 Fixing build on Windows platform commit ecdac6a61b06710296749bed71ddd8d9d0f09f3c Date: Fri Jul 25 15:30:13 2014 -0400 Updating add membrane mover to pass along a conformation reference at the top level commit 75d24429c8f906d5850425dea83937981d4fde0b Date: Fri Jul 25 14:56:46 2014 -0400 Doing a ton of renaming - renamed membrane() to membrane_info() such that it extends directly from conformation and contains an owning pointer to that object. Also moved membrane_center(), membrane_normal(), residue_z_position() and atom_z_position() down into membrane info commit a6943392a5055f42f725900187cc9621904abcbe Date: Fri Jul 25 14:52:07 2014 -0400 Global find and replace membrane() with membrane_info() commit fb20293063e918f2e29b69943cf930dcdb92cd72 Date: Fri Jul 25 14:41:13 2014 -0400 Cool - it looks like this scheme passes - going to moe other methods and a conf pointer down commit ffb3be1ff067667f5e65771c7f5702034d3628c7 Date: Fri Jul 25 14:01:41 2014 -0400 Updating my setting mechanism in membrane info - going to check this out commit 2baa5692f26ca5f89b71c18d4dc76eef619135c2 Date: Fri Jul 25 13:49:21 2014 -0400 Updating conformation object so it can just set a membrane info OP there commit 4acdd8676e0f44961216a96ad7f17fb76655b421 Date: Fri Jul 25 13:41:44 2014 -0400 Updating membrane info consturctors to take a nonconst conformation OP commit 6fcf74fef7b2df37acdb10198f5d5144919f50a1 Date: Fri Jul 25 13:06:47 2014 -0400 Fixing rosetta scripts build commit a3790a03ac5d776109bc3d094a5afa14d2d8d1cc Date: Fri Jul 25 13:05:15 2014 -0400 Fixing a bug in mpi_msd with the POSE_ENERGY and POSE_ENERGY_VECTOR commands. Thanks, David Nannemann for finding it! commit 96ab30c2ec69f024ecf6b819051d7faf8c919057 Merge: d599116 e34d2f5 Date: Fri Jul 25 11:42:56 2014 -0500 # [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 matcher_fixes # Changes to be committed: # (use "git reset HEAD ..." to unstage) # # modified: .gitignore # modified: database/chemical/carbohydrates/sugar_properties.list # modified: database/chemical/mm_atom_type_sets/fa_standard/mm_torsion_params.txt # modified: database/chemical/residue_type_sets/centroid/residue_types/membrane/EMB.params # 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modified: source/test/protocols/motif_grafting/MotifGraftMover.cxxtest.hh # modified: source/test/protocols/moves/MoverContainer.cxxtest.hh # modified: source/test/protocols/rigid/UniformRigidBody.cxxtest.hh # new file: source/test/protocols/simple_moves/UniformPositionMover.cxxtest.hh # modified: source/test/protocols/toolbox/task_operations/RestrictToCDRH3Loop.cxxtest.hh # new file: source/test/protocols/toolbox/task_operations/RestrictToLoopsTests.cxxtest.hh # new file: source/test/protocols/toolbox/task_operations/loops.txt # new file: source/test/protocols/toolbox/task_operations/utilities.hh # new file: source/update_residue_properties.sh # new file: source/xcode/input_from_cmd.cc # modified: source/xcode/make_project.py # new file: source/xcode/membrane/1afo.xml # new file: source/xcode/membrane/1afo_test.xml # new file: source/xcode/membrane/geometry/3DIN.A.pdb # new file: source/xcode/membrane/geometry/3DIN.B.pdb # new file: source/xcode/membrane/geometry/3DIN.C.pdb # new file: source/xcode/membrane/geometry/3DIN.D.pdb # new file: source/xcode/membrane/geometry/3DIN.E.pdb # new file: source/xcode/membrane/geometry/3DIN.F.pdb # new file: source/xcode/membrane/geometry/3DIN.G.pdb # new file: source/xcode/membrane/geometry/3DIN.H.pdb # new file: source/xcode/membrane/geometry/3DIN.pdb # new file: source/xcode/membrane/geometry/default.embed # new file: source/xcode/mp_parameters.cc # modified: tests/integration/tests/Werror_check/command # modified: tests/integration/tests/cyclization/command # new file: tests/integration/tests/load_mpframework/command # new file: tests/integration/tests/load_mpframework/flags # new file: tests/integration/tests/load_mpframework/inputs/1C3W_A.span # new file: tests/integration/tests/load_mpframework/inputs/1C3W_TR_A.pdb # new file: tests/integration/tests/membrane_ddG/command # new file: tests/integration/tests/membrane_ddG/flags # new file: tests/integration/tests/membrane_ddG/inputs/1QD6_C.span # new file: tests/integration/tests/membrane_ddG/inputs/1QD6_TR_C.pdb # new file: tests/integration/tests/membrane_relax2/command # new file: tests/integration/tests/membrane_relax2/flags # new file: tests/integration/tests/membrane_relax2/inputs/1C3W_A.span # new file: tests/integration/tests/membrane_relax2/inputs/1C3W_TR_A.pdb # modified: tests/integration/tests/rna_screen_phosphates/command # new file: tests/integration/tests/splice_in_generic/1emv_2_3u43_hlh.db # new file: tests/integration/tests/splice_in_generic/3u43_aligned_ImB.pdb # new file: tests/integration/tests/splice_in_generic/command # new file: tests/integration/tests/splice_in_generic/flags # new file: tests/integration/tests/splice_in_generic/observers # new file: tests/integration/tests/splice_in_generic/splice_in_generic.xml # new file: tests/integration/tests/splice_out_generic/1emv_aligned_ImB.pdb # new file: tests/integration/tests/splice_out_generic/3u43_aligned_ImB.pdb # new file: tests/integration/tests/splice_out_generic/command # new file: tests/integration/tests/splice_out_generic/flags # new file: tests/integration/tests/splice_out_generic/observers # new file: tests/integration/tests/splice_out_generic/splice_out_generic.xml # modified: tests/integration/tests/swa_rna_gagu_17_append_floating_base/command.sh # modified: tests/integration/tests/swm_protein_CCDmove/command # modified: tests/integration/tests/swm_protein_from_scratch/command # modified: tests/integration/tests/swm_protein_loop_sampler/command # modified: tests/integration/tests/swm_protein_move_inside_coiledcoil_by_bond/command # modified: tests/integration/tests/swm_protein_move_inside_helix_by_bond/command # modified: tests/integration/tests/swm_protein_preminimize/command # modified: tests/integration/tests/swm_rna_fourwayjunction/command # modified: tests/integration/tests/swm_rna_loop_design/command # modified: tests/integration/tests/swm_rna_move_inside_helix_by_bond/command # modified: tests/integration/tests/swm_rna_move_inside_helix_by_jump/command # modified: tests/integration/tests/swm_rna_move_two_strands/command # modified: tests/integration/tests/swm_rna_nickedhelix/command # modified: tests/integration/tests/swm_rna_singleloop/command # new file: tests/sfxn_fingerprint/scores/membrane_cen_scorefxn/1AFO_A.embed # new file: tests/sfxn_fingerprint/scores/membrane_cen_scorefxn/1AFO_A.pdb # new file: tests/sfxn_fingerprint/scores/membrane_cen_scorefxn/1AFO_A.span # new file: tests/sfxn_fingerprint/scores/membrane_cen_scorefxn/1afo.xml # new file: tests/sfxn_fingerprint/scores/membrane_cen_scorefxn/chains.txt # new file: tests/sfxn_fingerprint/scores/membrane_cen_scorefxn/command # new file: tests/sfxn_fingerprint/scores/membrane_cen_scorefxn/flags # new file: tests/sfxn_fingerprint/scores/membrane_fa_scorefxn/1AFO_A.embed # new file: tests/sfxn_fingerprint/scores/membrane_fa_scorefxn/1AFO_A.pdb # new file: tests/sfxn_fingerprint/scores/membrane_fa_scorefxn/1AFO_A.span # new file: tests/sfxn_fingerprint/scores/membrane_fa_scorefxn/1afo.xml # new file: tests/sfxn_fingerprint/scores/membrane_fa_scorefxn/chains.txt # new file: tests/sfxn_fingerprint/scores/membrane_fa_scorefxn/command # new file: tests/sfxn_fingerprint/scores/membrane_fa_scorefxn/flags # new file: tests/sfxn_fingerprint/scores/menv_smooth_sfxn/1AFO_A.embed # new file: tests/sfxn_fingerprint/scores/menv_smooth_sfxn/1AFO_A.pdb # new file: tests/sfxn_fingerprint/scores/menv_smooth_sfxn/1AFO_A.span # new file: tests/sfxn_fingerprint/scores/menv_smooth_sfxn/1afo.xml # new file: tests/sfxn_fingerprint/scores/menv_smooth_sfxn/chains.txt # new file: tests/sfxn_fingerprint/scores/menv_smooth_sfxn/command # new file: tests/sfxn_fingerprint/scores/menv_smooth_sfxn/flags # # Untracked files: # (use "git add ..." to include in what will be committed) # # source/src/apps/pilot/kdrew/InverseRotamers_autoAtomTree.xml # source/src/apps/pilot/kdrew/disembody_residue.sh # source/src/apps/pilot/kdrew/make_stubs_from_pdb.sh # tests/integration/test_run_20131224/ commit d59911649b81613466aa68bc6746852004ac0330 Date: Fri Jul 25 10:53:56 2014 -0500 Fixing bug in optimal_connection_point Updated several residue atom connection point to more appropriate atoms. For example, HIS was defaulting to CB which was causing weird behavior in inverse rotamer creation. Updating HIS to CG fixes this by setting up the fold tree in a way to keep the ring fixed. Also, updated LEU, ILE, VAL, CYS, SER, THR and PRO. commit 074e45c39aea92132302dd42b6cb360a5bdbe33e Date: Fri Jul 25 11:48:34 2014 -0400 Removing some crazy extra files from the xcode directory that were added accidentally commit 7f36bc9db614a0ba08dd78dbf0d8d2feab087e43 Date: Fri Jul 25 11:47:28 2014 -0400 Renamign unit test and source files according to the new mover names commit b3d9811dfe684e2655aaf1b4f4de5bcec7d68679 Date: Fri Jul 25 11:44:32 2014 -0400 Renaming files according to their new mover names commit 052bb47431fd0c7a0da4170b63efec954a2f8b52 Date: Fri Jul 25 11:42:56 2014 -0400 Renaming initial membrane position mover filenames' commit ce7f900cca843557eef8025e4ba04b0b07aaf96d Date: Fri Jul 25 11:40:02 2014 -0400 Global find and replace initial membrane position mover with membrane position from topology mover commit e6f32969d398705b01e75f5ed76043a330933a64 Date: Fri Jul 25 11:32:30 2014 -0400 Renaming all instances of membrane position translation mover to set membrane center mover commit d5c29b7c9e18f84d7760e20c1dfb62e2aec44cff Date: Fri Jul 25 11:29:35 2014 -0400 Performing a global find and replace for membrane rotation position mover to set membrane normal mover commit c04c42dbc440b23569d8e902c5618caf940404e4 Date: Fri Jul 25 11:27:37 2014 -0400 Performing a global find and replace for memrbane position rt mvoer to set memrbane position mover commit 078d45a78906a6f7f1356dde339789ca8b67a847 Date: Fri Jul 25 11:20:57 2014 -0400 Fixing #endif statement in julia's span object commit e34d2f529b1cad365f30b83b482503b5b8b46918 Date: Fri Jul 25 08:20:14 2014 -0400 Rosetta Membrane Protein Framework ==================================== Authors: Rebecca Faye Alford (rfalford12@gmail.com) Julia Koehler Leman (julia.koehler1982@gmail.com) Jeffrey J. Gray (jgray@jhu.edu) Thanks to: - Brian Weitzner, Justin Porter, Andrew Leaver-Fay and the Gray Lab for great code feedback - Evan Baugh for assistance with the PyMol Viewer - Sergey Lyskov for providing support & testing for the membrane framework project on benchmark2 This is the first in a series of commits for the membrane framework. Database: ------------------------------ = MEM.params - Membrane position residue with default position normal=(0, 0, 1), center=(0, 0, 0) = EMB.params - Embedding position residue with default position normal=(0, 0, 1), center=(0, 0, 0) MEM and EMB params have the residue type property MEMBRANE and are described in the fullatom and centroid residue type sets. Core Library: ------------------------------ core/conformation/membrane: = Membrane Exception Hierarchy - JD2 exceptions for when things go wrong. Shoud be used in the core layer, and are particularly useful for designing testable IO code. = Span: Describe a single transmembrane spanning region in the pose = SpanningTopology: Describe the total spanning topology of the protein (stored as a colleciton of Spans) = LipidAccInfo: Describe per-residue lipid exposed and buried surface areas (predicted by run_lips.pl server) = MembraneParams: Enum for cleaning up code related to membrane position coordinate access = MembranePlanes: Store the position of the membrane planes as a series of virtual residues. Will display as points - later used by the PyMol viewer for drawing CGO planes in visualization = MembraneInfo: Top Level container for membrane data (non-coordinate derived). core/membrane/geometry: = EmbeddingDef: Define the embedding of a part of the pose - can be a single span, chain or whole pose. Described by an embedding normal/center parameter = Embedding: Class for computing the embedding parameter. Can be from topology, sequence, or structure. = util: Some useful methods for working with/visualizing membrane proteins and fold trees Edits to Conformation: = Methods for setting up a MembraneInfo object in conformation = Mehtods for accessing membrane positon parameters = Methods for dealing with coordinate derived membrane information Protocols Library: ----------------------------- protocols/membrane: = AddMembraneMover: Initialize the membrane protein framework. This mover adds a membrane position residue, spanning topology, and optionally a lipophilicity object to the pose. Can be accessed via the command line, rosetta scripts or custom constructors (PyRosetta) = MembranePositionFromTopology: Move the membrane position to one based on the spanning topology and CA coordinates in the pose. = SetMembranePositionMover: Set the membrane normal/center position in the pose as custom positions = RandomMembranePositionMover: Randomnly rotate/translate the membrane position (first step to sampling) PyMOL Mover Updates: ----------------------------- = ShowMembranePlanesMover (in protocols/membrane/visualize) - Will add residues defining a top and bottom plane to represent the membrane planes. This feature is designed specifically for visualization, but should not affect simulation results = PyMOLMover: Added flags to send membrane center, normal and plane points over to the PyMolPyRosetta server = PyMolPyRosettaServer: Recieves membrane message, will draw planes representing the membrane for real-time visualization This feature can be turned on using the flag -membrane_new:view_in_pymol when an application is supported by the framework (see AddmembraneMover). Testing: ----------------------------- Unit tests associated with the membrane framework: * SpanTest * SpanningTopologyTest * MembraneInfoTest * MembraneConformationTest * AddMembraneMoverTest * InitialMembranePositionMoverTest * MembranePositionRTTest Status - All Tests Pass Integration test associated with the membrane framework: * load_mpframework * membrane_relax2 * membrane_ddG Current Test Changes - All added tests - Adding mphbond option print statement - Julia's MC print statement (56 test changes expected - centroid dslf and torsion change also currently broken) Status - no current changes Score Function Fingerprint Tests (Added): * membrane_cen_sfxn - Membrane low resolution energy function supported by the framework (terms adapted from those described in Yarov-Yaravoy et al. 2006) = membrane_fa_sfxn - Membrane high resolution energy function supported by the framework (terms adapted from those described in Barth, 2007) = menv_smooth - Smoothed membrane high resolution energy function supported by the framework (terms adapted from Vladmir's 2010 additions) Status - These tests will initially change from no diff - should then be stable but will observe the test server where appropriate. Build Checks = mac clang release/debug - pass = linux gcc release/debug - pass = PyRosetta - Merging into master is a test. Will fix Note: This commit is currently made being weary of integration test changes. Will watch for these where appropriate and follow up with comments. In the words of a great wizard, Mischief Managed! commit f301adef651c90b6cad85780dce95751b0a0a267 Date: Fri Jul 25 08:03:57 2014 -0400 Fixing a typo that would break the linux build commit 37cc5b5244ef77cc3fb670c5bd697b3037d6a186 Merge: ceee6e4 5e22e4c Date: Fri Jul 25 02:08:14 2014 -0400 Merging sergey's pyrosetta fix commit ceee6e48ce313bad5cc250399b59dc60dd68a917 Date: Fri Jul 25 02:06:47 2014 -0400 Fixing namespacing errors in unit tests and pdb info renaming issues in julia's pilot apps from rhiju's rename commit 56edfbf22484739de2cff53c33ce66f57cf85865 Date: Fri Jul 25 01:32:26 2014 -0400 Fixing a bunch of namespacing errors in sandwich features commit 5e22e4c0c5aac53dd363ba0729987425ae9dd270 Date: Fri Jul 25 01:05:02 2014 -0400 PyRosetta. Fixing dependency calculations on Windows platform. commit c597db8b84b6c3eca1c2f7cd64ba3c3c5a73f5c4 Date: Fri Jul 25 00:47:20 2014 -0400 Fixing a bunch more ambiguous namespacing errors commit 51def48f2196a65a0559143c3be942e3fea4a802 Date: Fri Jul 25 00:36:01 2014 -0400 Accounting for rhiju's renaming of the PDB_info object in julia's commit commit 8895aa5105099cc35e91a40de8d60d49f3ca5c8d Date: Fri Jul 25 00:14:21 2014 -0400 Fixing namespacing errors in Rhiju's stuff commit ceb7b428d86152927b65ee2bd2845b75a9bb1473 Date: Fri Jul 25 00:12:42 2014 -0400 Removing un-needed #include guard for embedding commit cfce42853d1f0bca2fa5c7599f107b6eb0902e5f Date: Fri Jul 25 00:03:10 2014 -0400 Fixing typo in residue type properties file commit 34c7d0e94dc3d5c1f7e6745880309710bdf92dd3 Merge: f3b6287 48b6ac0 Date: Thu Jul 24 23:41:44 2014 -0400 Merging master into our devel branch commit f3b62879d942e729ee4f3b20fafbaa829a9116b0 Merge: 6b51048 e9a0051 Date: Thu Jul 24 23:39:33 2014 -0400 Merging in remote mpframework devel from ninja into a devel finalized branch with some more master updates commit 6b510480c62d502d6fc6927bda99fad3aefbd368 Date: Thu Jul 24 23:39:13 2014 -0400 Updating the new residue properties stuff that Jason so awesomely updated - membranes should work now commit a78813ee21a2fd1fc27d9243a121770756e0bd9b Date: Thu Jul 24 23:32:53 2014 -0400 Resolving merge conflicts from Andrew's additions to the membrane potential class commit 9dcc39e4e07fc3d0661814792eee50f07a55645b Date: Thu Jul 24 23:31:43 2014 -0400 Removing julia's addiitonal comments to the docking protocol - shoudl be saved in an alternate experimental branch or in commit history commit 8b3f17d79d96f7a2ebecd70b881894f47560b504 Merge: 0b3c7bb 6404f96 Date: Thu Jul 24 23:30:11 2014 -0400 Merging pdb file data object with method for writing membrane data into the PDB info object. Julia's contribution :) commit e9a0051cdb9cf5671a58af7c9026d9cb6d4feff1 Date: Thu Jul 24 23:25:22 2014 -0400 Letting my perfectionism loose in the core layer commit f7a3fa5a29286dfc4b7416d536cbb2ca7c39e965 Date: Thu Jul 24 23:21:25 2014 -0400 Letting my perfectionism loose on the doxygen commit ba18118b59694a42a5433628c25bc36c04d0a273 Date: Thu Jul 24 23:15:43 2014 -0400 Adding some comments commit 5d17e1c7d04562961f7a9c531ff756ed82acc7a0 Date: Thu Jul 24 23:08:42 2014 -0400 Removing mp unit test files commit 68399ef51bf2e21dc0498ef02ffd55368ef4344d Date: Thu Jul 24 23:06:12 2014 -0400 Updating fixes to pymol viewer test in Rebecca's pilot apps commit 9f9966143c6b026f687a48182cbd015bd66f9cb4 Date: Thu Jul 24 18:18:06 2014 -0700 bugfix of previous merge error commit 6fe0ad033893b28fbbb69fed151ab90b944e2010 Merge: c9e965c 0c923ea Date: Thu Jul 24 14:34:15 2014 -0700 resolving merge conflicts commit 1e0df6409d8f49e404400fdc41b1ce4836214ef4 Date: Thu Jul 24 17:15:17 2014 -0400 adding a to-do note to RotamerSampleBase.hh about including a RotamerSamplerDOF_Type for easier addressing, fast-forwarding, and other i/o to RotamerSampler in the future. commit 5c9d734ebeb01dab5c8ff38bc86b01d99f0dc07a Date: Thu Jul 24 17:11:49 2014 -0400 adding nice output from RotamerSampler class, including nested description of each loop and its size and, in some cases, the DOF that is sampled. commit 5be19feb64c37650316f23dadec326967f14a1e0 Date: Thu Jul 24 14:35:59 2014 -0400 get rid of verbose output commit 81d0e7f36ac9a95e7b7b8f24be61c6600b642470 Date: Thu Jul 24 12:34:39 2014 -0400 setup align pose and native pose default to first inputted starting pose -- trying to keep SWM output models with reasonable alignments. commit 6a09aeb1616f3d9325db9e993069a13193c44c36 Date: Thu Jul 24 12:00:15 2014 -0400 fixed up namespaces and tracer names in stepwise/ after util reorganization/ commit 883e0b2dc807cfbe7010fbbcc8f4181ff154858c Merge: 026f09b 6fdbcd5 Date: Thu Jul 24 11:08:13 2014 -0400 merge from master into rhiju/swm_cleanup branch. commit 0bb688136989855a60fe5fd5972668aa17ab2bfa Date: Thu Jul 24 00:32:51 2014 -0400 Adjusting for dsbB commit c5c1ce38ecc1fd58c9e2291027d9e85af08abd8e Date: Wed Jul 23 23:38:55 2014 -0400 Updating basic version of membrane fastrelax protocol - possibly some bugs since global rmsd align = 0 in pymol commit 4d64e5c85d5446a83cbe2dbaaa5049a45aa0f8d2 Date: Wed Jul 23 23:08:19 2014 -0400 Adding minimal refine membrane relax application - going to test it in a large scale setting commit 026f09bdd57a3acf6b85b5ad2590a399689135db Date: Wed Jul 23 17:47:29 2014 -0400 splitting/refactoring stepwise/modeler/rna/util.hh into a separate legacy util.hh commit c9e965c12ef0833bdb339aa307671ca4005a5fb3 Date: Wed Jul 23 13:52:03 2014 -0700 changing name output of LegacyKIC_Sampler to fix Kale's unit tests commit 09134edbb13e18ad0ddff7e70584e1cbdafc366b Merge: 9a025a4 2aadce9 Date: Wed Jul 23 12:17:06 2014 -0700 Merge remote-tracking branch 'origin/master' into rpache/KIC_with_fragments commit 850f1bef29df28b776a0798276937cae1bf7f0cb Date: Wed Jul 23 14:18:12 2014 -0400 trying to align to pose1 by default, if no native is specified. Might eventually be better to keep all poses from -s inside align_pose, and choose to align based on whichever fixed domain is available in the root. commit 3a81be627224f3e6d6f170865c1582cb248c3c97 Date: Wed Jul 23 11:46:05 2014 -0400 Pre-merge, current state of the branch. Not so worried if things break here commit faa5fe4296d06821a6b9cb8a63bf11154e8022b9 Date: Wed Jul 23 11:36:55 2014 -0400 Updating doxygen in core/conformation/membrane objects commit 55211af835e81d399095c2dbea8a2c016d920248 Date: Tue Jul 22 23:51:09 2014 -0400 massive reorganization of stepwise/modeler/util.hh into mostly separate utils. commit 9a025a441ef9ab1ab831e7283d3dcaa4fc1f7a99 Merge: a0641b5 afcf7f1 Date: Tue Jul 22 20:15:22 2014 -0700 Merge remote-tracking branch 'origin/master' into rpache/KIC_with_fragments Conflicts: source/src/protocols.3.src.settings source/src/protocols/comparative_modeling/LoopRelaxMover.cc source/src/protocols/loop_modeling/samplers/LegacyKIC_Sampler.cc commit a0641b5e25109fb7958838c87b970fef6c775bc4 Merge: 5dccbe3 840a017 Date: Tue Jul 22 19:27:33 2014 -0700 Merge branch 'rpache/KIC_with_fragments' of github.com:RosettaCommons/main into rpache/KIC_with_fragments commit 5dccbe3148ccee1171f076cd304e42af76881555 Date: Tue Jul 22 19:17:33 2014 -0700 adding KIC_with_fragments integration test commit 4689fac6ffa35e82902ce6208ca85390a8dbce26 Merge: e881ac0 86c3b46 Date: Tue Jul 22 22:14:51 2014 -0400 Merging in membrane relax code commit e881ac04b0b5adea683d2b99a662a3f3a7643226 Date: Tue Jul 22 22:14:16 2014 -0400 Temporarily changing chain usage in pymol pyrosetta server - will be adding flags for this shortly commit 1e795b7f031a181688c6787cf686ad1fc31e3485 Date: Tue Jul 22 21:56:56 2014 -0400 further refactoring of util.hh throughout stepwise/ code. took this opportunity to put pdbslice into pose/util.hh and also to change names of getPoseExtraScores & setPoseExtraScores to getPoseExtraScore and setPoseExtraScore, since they only get/set one score at a time. commit b5df04bc7127e3168be6f7a95c324f305dcb1cf2 Date: Tue Jul 22 20:19:07 2014 -0400 cleanup of util.hh functions in stepwise/ directories. About halfway through. commit ee05304bd526a238591473a5cd3c338032c99729 Date: Tue Jul 22 18:03:22 2014 -0400 simplification of FoldTree delete_extra_vertices() to not take desired_root; this was needed to fix a bug in slide_jump(), which is now instead fixed internally to that function. Had to create a prepend_edge() function, which is like add_edge() but inserts the desired root-containing edge at the beginning of edge_list. commit 9cc470200d13baa600534ee43eb3629f56809243 Date: Tue Jul 22 13:08:21 2014 -0700 fixes to linux gcc build commit 20fc4a759cb613dbab2be9e8351a7495ead31ac9 Date: Tue Jul 22 16:07:41 2014 -0400 argh yet another fix to alignment, in case where a root atom triad is used to do superposition commit 90c4f29b11bd088bb62041ad470c4bb8b7d8498f Date: Tue Jul 22 12:37:42 2014 -0700 Revert PDBInfo rename in remaining src and test files, part deux. commit b5d3e90931efef9c686488290ab9941854300f0c Date: Tue Jul 22 12:00:16 2014 -0700 Revert PDBInfo and PDBPoseMap rename in remaining src and test files. commit c230d7be9ea248c9dbe39976721bb7b66bb63f42 Date: Tue Jul 22 14:56:53 2014 -0400 for builds from scratch, when outputting movie or final pose, align over all atoms commit 8f829a0219e3d99c7ff08a259315dddcf97f333c Date: Tue Jul 22 11:56:34 2014 -0700 Revert "Fixing the unit test build following Rhiju's renaming" This reverts commit b1fa4fe6eccfcae8e90a481ff51c93679807f469. Conflicts: source/src/core/conformation/Conformation.cc source/src/core/conformation/symmetry/SymmetricConformation.cc source/src/core/conformation/util.cc commit 6e7bacf1f3de7d09ee05c69d9b6d61526e4fc133 Date: Tue Jul 22 14:56:33 2014 -0400 bug fix to alignment when there are multiple domains... commit 8f199f02ea517c35a02dd4f1ae68e686ec11e529 Date: Tue Jul 22 14:56:16 2014 -0400 remove redundant line commit 9f423ddeb88e022aa63aa41e87fa26fa408d3308 Date: Tue Jul 22 11:47:20 2014 -0700 Revert "fixing PDBInfo --> PDB_Info, PDBPoseMap --> PDB_PoseMap, as I think this is Rosetta convention (underscores separating acronyms, for readability)" This reverts commit 020f84b2e5ad0627cf406fbcb73512faab34d448. Conflicts: source/src/protocols/environment/Environment.cc source/src/protocols/features/strand_assembly/SandwichFeatures.cc commit d3dc11011b3103f077fa427b0e0126684a632237 Date: Tue Jul 22 11:39:26 2014 -0500 Added case for D-proline in NtermTruncation patch commit fc18bb36251f2aa867e70ee1a75b0f65f5622a71 Date: Tue Jul 22 00:31:14 2014 -0400 fix to pose aligner in protein terminus case commit 251c86f3f80e97abd3c93fee0cacfdf29204b8a5 Date: Tue Jul 22 00:03:43 2014 -0400 fix to virtual_sugar checks with proteins. commit 6bbd8e2a9e11b5f12dced530a0075245b0828089 Date: Mon Jul 21 23:23:06 2014 -0400 fixing uninitialized variable in ConformationViewer which led to graphics sometimes going off screen. commit 2553ca6934bbf3e5739949ae00e322cc44a12d6e Date: Mon Jul 21 23:22:36 2014 -0400 fixing root choice error -- should always place root in a fixed domain if possible! commit 62d5033399f1c595b3c64b76173292cef4f11fdb Date: Mon Jul 21 22:41:18 2014 -0400 changing namespace stepwise/sampling to stepwise/modeler, which makes more sense now that most of sampling is held in rotamer_sampler commit 2a9daee42682d3d047a52913ecf3f52e44edf2bc Date: Mon Jul 21 22:09:41 2014 -0400 moving StepWiseMonteCarloOptions into options/ subdirectory for consistency with rest of protocols/stepwise directory hiererarchy. commit df0a462911446f5d36df5956def57079a6341c8b Date: Mon Jul 21 21:40:09 2014 -0400 fixing modeler_options/ directory to options/, less verbose commit cdb4b00b111f02d8dfca652215eaa230eacb3c36 Date: Mon Jul 21 21:26:33 2014 -0400 refactoring StepWise options to inherit from a unified options -- removes more copied code, yay. commit 86c3b4658381441ddc3645ec14aabe36d39d4852 Date: Mon Jul 21 21:22:41 2014 -0400 Temporary updates to membrane_ddG application commit cb7204c52a9080c97c1d09555e1594169629ebfd Date: Mon Jul 21 16:13:11 2014 -0400 for final superposition in stepwise monte-carlo/assembly, do alignment over all fixed domains seen in pose, not just the first one. commit ff7ca63793acf041c449e95d4c155d757fbad777 Date: Mon Jul 21 15:11:41 2014 -0400 Updating membrane relax protocol - sending over to louis commit 5594804a07ac14bd6de2209b15161fd6ef0dfc00 Date: Mon Jul 21 14:36:51 2014 -0400 major bug fix in cutpoint setup in full_model. oops. commit c651c47827a6f305bb86b217070ee4ecfff36f9b Date: Mon Jul 21 14:36:20 2014 -0400 do not read in DMS potential stats form disk unless we actually end up computing DMS potential -- speed up scoring. commit 3a34bd9e3dc11e18525bb260a6b142e913aea8f2 Date: Mon Jul 21 09:48:13 2014 -0400 Updating relax executable for membranes commit 22922e2997f943eb50387043f0405c965095d2f3 Date: Mon Jul 21 09:04:03 2014 -0400 trying to prevent a silly phosphate addition error in SWM RNA. commit da759ea09dddfefacbf9deac1b2a381912e0135a Date: Mon Jul 21 07:29:49 2014 -0400 Commenting the other mover out of the build settings again - going to start out with a plug in play - will just tweak movemap/min settings first then build up. Does not want to write cycles from scratch quite yet due to uncertainty here commit 3a0bd4353f6664bb39ae9760e7d5919c3eeec84a Date: Mon Jul 21 00:21:09 2014 -0400 Adding relax mover to build settings commit 26cd4f1243958d8fa7b2f12eb1319278878c3a8c Date: Mon Jul 21 00:11:27 2014 -0400 Adding membrane fast relax movers down in protocols/membrane, should move later but will keep present for now as a framework app. Not part of the build yet commit 0b3c7bb0c7295cda2b53b98135d6990a9046a71f Date: Sun Jul 20 23:36:23 2014 -0400 Fixing signed vs. unsigned integer comparison issue introduced in membrane ddG mover - will hopefully resolve build issues commit fd072cbcb43147b38b175f988dda95ffd6ef7e94 Date: Sun Jul 20 21:53:29 2014 -0400 Oops - thought I had resolved that merge conflict commit 5935f7e6407e77521e4280744572129efe739160 Date: Sun Jul 20 21:51:47 2014 -0400 Oops - thought I had resolved that merge conflict commit 264ee92a65e9ea2f003b8530005020a5d1c0bc2f Date: Sun Jul 20 21:46:04 2014 -0400 Membrane Framework Updates: 7/20/14 (Part 2 :)) ddG/Design: = Mutation Object: Store a position and residue to mutate to. Not so great - currently bypasses the resfile reading interface, but makes it easy to do a ddG monomer style run where I can load in multiple mutationa at once = MembraneDDG Mover: Compute the ddG score given a pack radius and a Mutation (position, residue to mutate to). Turns on the membrane framework, initializes the membrane position, computes native, repack & mutate and then compute the ddG. This code is possibly some duplication from Liz Kellogg's ddG_monomer application, but becasue that does not use the mover interface, nor is supported by JD2, it is much more difficult to plug the membrane in using a generalizable/extensible approach. = membrane_ddG: Application for running the membrane ddG mover (compute ddG with some refinement). Currently includes methods for our 3 test cases - ompA, ompLA and brd7 - these will eventually be refactored out but are present for convenience PyMol Viewer: = Bug fix: cast normal vector to a triple of floats (previously a triple of ints) = Fixed cgo set transparency - setting an alpha value in the object will set transparency of only the planes = Use triangle fan instead of triangle strip - cleaner rectangular planes = Method present for drawing a normal cgo vector - still in progress, will need to parse additional info SpanningTopology Object: = Added additional comments, reformated, fixed potential bugs due to returning of raw objects = Made documentation parseable by doxygen Linux GCC Build: = Removing unused variable warnings in spanfile_from_pdb Sfxn Fingerprint Tests: = These still may or may not run - I have no idea why...working on it? Test Changes = All unit tests should pass (unless there is dark magic on the test server) = membrane_ddG integration test should change because it does something real now commit 03eac2c6cdb3a8317f1e8877fb345b383933c085 Date: Sun Jul 20 21:25:19 2014 -0400 Adding some extra comments to pymol server, spanning topology commit e348dd3af7928b94030017156cabd6ddcd60d77f Merge: 51d0a0a 14873d0 Date: Sun Jul 20 21:15:19 2014 -0400 Removing another unused variable in the spanfile_from_pdb pilot app commit 51d0a0a6287f4884223c651f4ab9a36c0e0c6654 Date: Sun Jul 20 20:52:21 2014 -0400 Membrane Framework Updates: 7/20/14 = Fixing broken unit test - SpanningTopology = Integration test changes from the previous commit were expected and ok = Fixing score function fingerprint tests to use spanfile flags = Fixing integration tests to use updated spanfile flags TODO: Remove core/conformation/membrane/util.xx class. Methods should go in their respective objects commit e5db2eda710b1b89d0992cf3edcfa2acaf259432 Date: Sun Jul 20 20:39:23 2014 -0400 Fixing misplaced method in the library levels build commit e5a9f8a12886f258644b3e37e0c61f7ad6b5653b Date: Sun Jul 20 20:34:41 2014 -0400 Removing un-needed integration test due to recent code chanes ams smart ortho check xyz commit e3a1ccdec3d384a16cace3609e4b8a5734a77636 Date: Sun Jul 20 20:16:49 2014 -0400 Updating spanning topology unit test - typo in input file commit e030f4e4e14bbd10f14d8dd3f21a2ba77032cb41 Date: Sun Jul 20 18:34:40 2014 -0400 Fixing sfxn fingerprint tests to include the correct flags commit 14873d08e673ac58a751083f1ecf78e238c84425 Date: Sun Jul 20 16:48:25 2014 -0400 Quick fixes to spanning topology test commit e273586a858c50001a6dddcbef1324061f8a9323 Date: Sun Jul 20 15:31:50 2014 -0400 Doing a global find and replace for misnamed methods commit 05ad0c0f313ffef26ed0a2a590854bf8c2a3414e Date: Sun Jul 20 12:38:30 2014 -0400 Fixing formatting & doxygen and some potential bugs due to returning of raw objects in spanning topology objects. ALso renaming to convention commit 68c448f407c891d7605befe3d1270f69af6d7bb7 Date: Sun Jul 20 11:43:44 2014 -0400 Adding quick fixes - will go back later for additions commit 79d62c2fdf298cb2e923630521840c30d35bf400 Date: Sun Jul 20 10:25:25 2014 -0400 Added membrane ddG applicaiton commit 6aba651d4d2305aa3974951b678c34191845a0f2 Date: Sun Jul 20 10:21:58 2014 -0400 Beautiful - fixing repack within radius commit 91e34844da16846d8a11101345a713718c33b060 Date: Sun Jul 20 00:32:51 2014 -0400 Fixed ddG code - will do upper and lower neighbors. Now just needs to put things together, clean up the interface, and we should be good on this front commit e08ca8113264c5b8c2d5a3229732f02cd51ee93f Date: Sun Jul 20 00:05:59 2014 -0400 Still fixing something wrong with this point graph code commit 9dca2d019d5069db2b0d4c104478973245952bff Date: Sat Jul 19 20:49:57 2014 -0700 fix for chain_connections where one set of docking residues is not contiguous and happens to have some residues before and some after the residues in the other side. commit e1c5888290a998534a4eee5fc7ba9070158871dd Date: Sat Jul 19 23:30:50 2014 -0400 Adding code to ideally print the neighbors list - possibly inefficient commit 930887b2d1fd031a053f62b272a7fd0205c48ad2 Date: Sat Jul 19 10:15:30 2014 -0400 Fixing neighbor graph code for ddG to not just get the upper neighbors...urgh so annoying commit 9c7b3eb78cb16ef4d6042be6c8fd01fa0e8a04bb Date: Sat Jul 19 09:57:01 2014 -0400 Implemented pg neighbor count - going to check in pymol before I implement the rest of it commit 6b492ec5df079c991b9b401aebf7a32f0551f9c7 Date: Fri Jul 18 23:49:48 2014 -0400 Membrane ddG application compiles with design tasks commit c227ac3d3fc26be019ee93929d4b9f3fd414489f Date: Fri Jul 18 23:40:29 2014 -0400 Adding a missing #include for core chemical AA in membrane ddG app commit de06b4b38121d5a68351c4c58fb5c780b2cc404e Date: Fri Jul 18 23:37:24 2014 -0400 Adding bacteriorhodopsin mutation task to pilot app - shoud now have three methods for returning this information (though I would prefer some much better comments commit e4f223d0641a3fee1b5821db00d60548bd6e0685 Date: Fri Jul 18 23:20:28 2014 -0400 Customizing my membrane ddG application to use specific mutations - these should NOT get committed to master... commit e6d5e0b663678330bc1baa08f9b5997c666016a3 Date: Fri Jul 18 23:07:02 2014 -0400 Version of the ddG code using the mutation object inteface compiles commit 4ef6f03de3ccb5373808bb8994a7630bc07c3de0 Date: Fri Jul 18 22:57:03 2014 -0400 Updating internal interface to use mutation objects that I can setup by task in my pilot app for rapid generation of the data plots commit 090439fc7a36443778f5bd6c5e46696a82a07b5a Date: Fri Jul 18 22:55:49 2014 -0400 Reworking the ddG code to take in a generic list of mutations - this will enable me to build a flexible pilot app for running mutation tasks commit 560ae0bb55d1f82f91fd7f4ea2e7d98375c25395 Date: Fri Jul 18 22:36:06 2014 -0400 Adding mutations object to ddG code to improve generality commit 840a017b3fe85594872846b111a1d345e054a1f9 Merge: b326bfa c6e4ce1 Date: Fri Jul 18 17:16:13 2014 -0700 Merge commit 'c5e4ce1e050ea86c2bce46609a409a9e2a7d1143' into rpache/KIC_with_fragments commit b326bfa4bfd36dbdce87261b60b16a27c930ea87 Date: Fri Jul 18 16:02:59 2014 -0700 Update LoopModeler unit tests. commit 7158e664d27d7e2c9c7b48c3defabfc425fa3f93 Date: Fri Jul 18 17:51:12 2014 -0400 Adding mutation class to build settings commit 92a5f5b59a95534df08717ee0925c74228b5d381 Date: Fri Jul 18 17:47:52 2014 -0400 Adding mutation class - udpating ddg mover to do repacking. Will add teh ability to do this repacking soon commit 183cbe257fdde8e3d35ba44c89cc89f8f89b2c35 Merge: 58f672e 0f55db2 Date: Fri Jul 18 13:15:40 2014 -0700 Merge remote-tracking branch 'origin/master' into loops-xml commit 58f672e04d67e6ce117ce65c02260d42a39d9fd3 Merge: 6c3f004 a65064f Date: Fri Jul 18 13:15:13 2014 -0700 Merge remote-tracking branch 'origin/rpache/KIC_with_fragments' into loops-xml Conflicts: source/src/protocols/comparative_modeling/LoopRelaxMover.cc source/src/protocols/kinematic_closure/ClosureProblem.cc source/src/protocols/kinematic_closure/KicMover.cc source/src/protocols/loop_modeling/LoopBuilder.cc source/src/protocols/loop_modeling/LoopBuilder.hh source/src/protocols/loop_modeling/refiners/LocalMinimizationRefiner.cc source/src/protocols/loop_modeling/utilities/LoopMoverGroup.cc source/src/protocols/loop_modeling/utilities/LoopMoverGroup.hh source/src/protocols/loops/loop_closure/kinematic_closure/KinematicPerturber.cc commit 6c3f004d54dd892ddf551c56e2c479e921dee9ff Merge: c16f650 81518f5 Date: Fri Jul 18 09:55:15 2014 -0700 Merge branch 'master' of github.com:RosettaCommons/main commit c16f650b9abd56b44db3d6b651968d1a2d5c47de Date: Fri Jul 18 09:49:37 2014 -0700 Add LoopModeler (with a RosettaScripts interface). The LoopModeler class is meant to supersede the loopmodel application. I had to transcribe the code that reattaches the sidechains between centroid and fullatom mode into the new framework, so I can't be sure that my code works until I benchmark it. The RosettaScripts interface is largely in place, but there are still a few tweaks I need to make. commit 190b726eee8b7440d24a2affafd3ef5b36c02e3d Date: Fri Jul 18 18:38:56 2014 +0200 Updates for unit test compile. commit 842c6fcc22088fc7aee883e93c5fe5b78c780407 Date: Fri Jul 18 11:28:45 2014 -0400 Adding weights file for turning on pH mode with fullaton menv energy function commit f29b86aa07ac6bd3528fe84176e2f2734d70fc93 Date: Fri Jul 18 11:09:02 2014 -0400 Also adding some code for turning on ph variant types (protonated D and E) though not quite sure how to turn on the energy function to the pH I would need and see those changes. Flags for full repacking would also be nice commit 15603b9b3be0813e9bcc33f04b35a7574e642e2b Date: Fri Jul 18 11:04:37 2014 -0400 Going to try a full repack, also leaving the show method for quick assurance commit 1f93a3f4582be0ee501167d5700dea4f68cb134e Date: Fri Jul 18 09:49:18 2014 -0500 Update TorsionClaim::yield_elements for DOFelements' error messages. commit 5ee687a28a9be8e3c36697a4183709f8de4f99a4 Date: Fri Jul 18 07:54:15 2014 -0400 Updating ddG code to be more general - will now print a parseable file for quick data io and also iterate through a list of designed positions commit ebae420bcc5042e7fbf22d5268f946ec8c3c95c4 Date: Fri Jul 18 07:30:49 2014 -0400 Adjusting the ddG code to do per residue design as done in PyRosetta - much better scheme for this commit d0473ab69b36cced7dd53977f0efc5a778b37a4c Date: Fri Jul 18 06:57:28 2014 -0400 Switching some calls to pose into copy_pose so the ddG score output should now be nonzero commit 8e9d68caefb45ec133487260c2c95994d080311e Date: Fri Jul 18 06:56:04 2014 -0400 Yes - I think I finally got this code to do some design ' commit d3727fee835ffc8ea5849e8b59e60b31fece9679 Date: Fri Jul 18 06:43:00 2014 -0400 Going to try this code using a modified resfile - this should let me see if I can do design and restrict repacking in essence by hand commit c5da49c4cff279bd01b12aab4657d817418a61b2 Date: Thu Jul 17 22:28:53 2014 -0400 Adding additional updates to ddG membrane code commit 64b2be62a1815b534d86da6d69c6d469781f4b95 Date: Thu Jul 17 15:30:34 2014 -0500 ChiralMover orients on backbone atoms when not enough sidechain atoms 3 atoms are necessary for orienting a residue by the side chain but ALA for example does not have 3 side chain atoms so added functionality to use backbone atoms when necessary commit 12885b78ac2a25c5bd5bd2cae32954ad6a0b275d Date: Thu Jul 17 12:19:05 2014 -0500 Add residue selector annotation queue behavior to CutBiasClaim. commit 2dffb695fad044653556cc72370aefb57c899b3a Date: Thu Jul 17 10:36:03 2014 -0400 Trying to enable repack within radii for ddG plots commit bc4665ef621d5eda36f00853379eef529fda588a Date: Wed Jul 16 18:08:04 2014 -0500 Update backbone oxygen placement when chiral switch of upper_terminus ChiralMover will update phi and psi to be -1.0 * original phi/psi. For upper_terminus residues, psi is not defined and defaults to 0.0. This was producing weird placement of backbone oxygens. This commit updates the chiral residue N-CA-C-O torsion with -1.0 * original torsion. Not sure if necessary to fix hydrogens for lower terminus but probably should. commit 57c00d1cf158f09920aaba4659a056931c6f5c35 Date: Wed Jul 16 18:04:46 2014 -0400 updating pyrosetta server settings, running ddG app but the design will most likely chain commit 1d488da641aeff9452274cc43de151e3c9bf76b8 Date: Wed Jul 16 16:12:25 2014 -0500 Messing with RosettaScripts parse behaviors. commit 0b2b4ab6cfdd47d1ce20f6f30a381ee0843dcb25 Date: Wed Jul 16 16:05:16 2014 -0500 Create a 'NO_POSITION' definition for code readability. commit b29c50a6fa02ed0fbacddb32bed875fd8de50535 Date: Wed Jul 16 15:45:49 2014 -0500 Implement XYZClaim and VirtResClaim rosetta scripts parse methods. commit 8481aef8b38e298228346bb0bcd411efae64370a Date: Wed Jul 16 15:36:43 2014 -0400 updating mmebrane ddg app, and adding ddG mover to compile in the new branch commit ede176eba38177096f9740693fa19035500b948d Date: Wed Jul 16 15:26:49 2014 -0400 Adding some ddG mover code I wrote a wile ago into a newly merged branch commit 2543c04cb52c6c22742f54eacd9dd67c193343b4 Date: Wed Jul 16 14:21:46 2014 -0500 Now EnvironmentJump::test_autocut_placment uses TestClaimingMover. commit e2d95f9ce387b069b03cd8fd18bc0b1faa6a49d4 Date: Wed Jul 16 14:21:10 2014 -0500 Add Jump::operator== and Jump::operator!=. commit c50a1651a6e6490f27946f184f2c9a4600c2edfd Date: Wed Jul 16 21:26:15 2014 +0200 Updates for unit test compilation. commit 0a5776fdb705d439d24b0dc01e7574671b87aa64 Merge: 18526c4 d5ecedd Date: Wed Jul 16 14:37:31 2014 -0400 updates to MPframework Span: = added shift method = added not_valid methods SpanningTopology: = added add_span method = added reorder_spans method = added write_spanfile method = added nres_topo as check AddMembraneMover: = changed jump to MEM in apply function: setup_membrane core/conformation/membrane/util: = get name of spanfile(s) from options = normalized length of normal vector to 15 MPDocking: = fixed namespace errors DockingProtocol: = added comments and reorganized it for better readability = added comments about lowres/highres logic which is counterintuitive other = added show method to xyzMatrix commit 18526c4fa1acff45c9d6df8ee5590b02cefe3f0d Date: Wed Jul 16 14:36:14 2014 -0400 fixed flags in integration tests, added function to util to normalize normal vector commit fc62dc5bf89bfe67b2311e86d1c2209cfb478cc3 Date: Wed Jul 16 14:35:17 2014 -0400 fixed SpanningTopology unit test using try/catch block and exception in is_valid() function commit 0c86d3ed68a515d8e100a3b6580b7ccdaa5dc77e Date: Wed Jul 16 13:07:51 2014 -0500 Cleaning up EnvironmentJump to have a few more functions use Tester framework. commit d93058c987a750438b1cec50698d061fb36c922d Date: Wed Jul 16 12:49:01 2014 -0500 Swap out EnvironmentJump::test_jump_moves using Tester framework. commit 47f5c802cba6138fc6d8f5839126e49f4e0a3448 Date: Wed Jul 16 20:07:00 2014 +0200 Fix compilation issues with ProtectedPose. commit b274be169d50df9e916c44e6d1b7fe99ac81dcb6 Date: Wed Jul 16 12:04:51 2014 -0400 InitialMembranePositionMover: normalized length of normal to 15 for better visualization commit ca3a2c39b251d1f43913c8d933d58438bcdd502b Date: Wed Jul 16 09:44:39 2014 -0500 Fix a namespace inclusion issue in EnvironmentJump. commit 1c641022efb7ba5c06416bf349cd3ba2b1f0836b Date: Wed Jul 16 09:41:41 2014 -0500 Add new JumpClaim rosetta-scripts parsing test to EnvironmentJump unit test. commit bfd5cc5699dec5bb6169de9c675f9bd5131e991a Date: Wed Jul 16 09:34:15 2014 -0500 Remove duplicate TestClaimingMover code from ProtectedConf unit test. commit 94cef6211ad4a11747a68ebbee657f24d99dca5c Date: Wed Jul 16 16:46:53 2014 +0200 Fix several compilation issues with beginning of switch to new testing mover. commit d5ecedd7f4176d2558bf2b5caf6780a527c9a375 Date: Wed Jul 16 10:44:15 2014 -0400 Framework Update (7/16/14): = Added MEMBRANE to list of properties recognized by residue type. Called by is_membrane() = Added membrane property to MEM params files in centroid and fullatom residue typesets = Fixes annoying MEM CA bug that was occuring when additional membrane residues were added for representing the membrane planes commit c498b9880e36c201cf736150d394625924596eb9 Date: Wed Jul 16 10:42:00 2014 -0400 Fixed membrane CA Bug with residue type update commit 9da7edff874c158665da40edcdb8b15423b74c80 Date: Wed Jul 16 10:26:31 2014 -0400 Adding a temporary residue type check in atom index commit 2b7a89224937e38f9e8e2b86de0240e6cd5081a0 Date: Wed Jul 16 10:25:29 2014 -0400 Adding membrane property to both MEM params files as per new residue type updates commit 4bd349632aa3226e1273da126da262e3682d0016 Date: Wed Jul 16 09:21:14 2014 -0500 Add TestClaimingMover objects to share across environment-related tests. commit 1dfb68739482447f3b5a6aa68c44d6ae69311ec9 Date: Wed Jul 16 09:50:25 2014 -0400 Adding property 'membrane' to residue type commit d34afd43736c2b14baa65a985af8844a2999c767 Date: Tue Jul 15 21:41:18 2014 -0500 Fix a bug where JumpClaim would always claim its init strength to be the same as its control strength. Similar bug in XYZClaim and TorsionClaim. commit 4bc42fe45b130cec7b376f888d4401827899b707 Date: Tue Jul 15 20:33:53 2014 -0400 Fixing linux gcc builds commit 23135abca3b400b7940c4019931279bc637eac6a Date: Tue Jul 15 20:15:10 2014 -0400 Fixing a const-ness issue of the direction argument in a private method. The primart reason for this commit is the close_loop_in_single_direction has now had two virtual methods extracted from it. The more important of the two is actually responsible for updating all of the torsions of a particular residue based on some CCD math stuff. In this flavor of the mover, it iterates over the torsions in the residue and solves for them one by one (i.e. phi then psi). This was done in anticipation of some work being in the Dunbrack lab that might lead to phi and psi being solved for simulataneously. The other method sets the value of the max_per_move and max_total torsion deltas. The reasoning behind making this a virtual method is to provide a mechanism other than the residue's current secondary strucutre assignment to get these values. For example, one could imagine using a vector1< Real > of length loop_,size() where each element specifies the max per move torsion delat for that residue. I hope that this adds to the flexibility of this mover. commit 64e355acc03b937f45d5f44ba950708ea1222eb8 Merge: 77e82b9 c7499e1 Date: Tue Jul 15 18:55:57 2014 -0400 resolved merge conflicts commit 60fb8643105bdee0d72b57d9d9c789309624f319 Date: Tue Jul 15 17:43:09 2014 -0500 Add annotation calls to EnvClaimBroker. commit 282d368a0258bcc07da158d3a694ea47f6f6a56a Date: Tue Jul 15 17:38:04 2014 -0500 Develop system in EnvClaim that allows RsidueSelectors to make annotations for JumpClaims for use in claiming. commit 46a235643a05ee2fdb8e80ea9065d3cec8f1297a Date: Tue Jul 15 17:45:40 2014 -0400 Changing the order of the methods in the header (and in the cc to match). Adding a note about how to properly copy a RamaCheck instance if the derived type is unknown. commit 77e82b9b78fb9b27f0b628f3068915d63ae7cf19 Date: Tue Jul 15 17:45:32 2014 -0400 working on mpdocking and mpfolding pilot apps commit 89d0ced35e9b404f6aae89f4159859ec0fd35f97 Date: Tue Jul 15 17:44:49 2014 -0400 moved spanfile_name into util = gets name from options commit 5fb31799e33c3e9626ce01325f56af1c5292f4cd Date: Tue Jul 15 17:37:25 2014 -0400 Adding a clone method to RamaCheck, removing the rama() method in the derived classes. Also adjsuting some spacing because I want to. commit a2cad4f5044494231c6192d3a7ddac23bc61c9db Date: Tue Jul 15 16:15:54 2014 -0500 Add more sophisticated duplicate-checking in SequenceAnnotation (now checks if members are the same before failing. commit dfc7e6cb3c33b351f9929deaa6cea1cc1ada5c40 Date: Tue Jul 15 09:13:33 2014 -0400 Comitting my working version of Jason's pilot app thing. commit c7499e16b8d4cb316181e9f70c99993ef4061a54 Date: Tue Jul 15 07:53:35 2014 -0400 Membrane Framework Update: 7/15/14 Updates: = Movers no longer depend on an anchored foldtree = Default foldtree setup is a 'simple' foldtree = Unit tests updated to reflect this behavior Builds = Fixed a bug in UniformPositionMover - should correct the linux gcc build Unit Tests: All Membrane Framework Unit Tests Pass = Span = SpanningTopology = MembranePositionRT = MembraneInfo = MembraneConformation = AddMembraneMover = InitialMembranePosition Unit tests can be run using the script run_membrane_utests.py in the Rosetta/main/source directory but should be stripped out prior to master merge Integration Tests: Running = load_mpframework = membrane_ddG = membrane_relax Integration tests can be run using the script run_membrane_itests.py in the Rosetta/tests/integration directory but should be stripped out prior to master merge. commit 6fbffef93036a37b09c9f25b4490035d03121615 Date: Tue Jul 15 07:49:37 2014 -0400 Adding script for running membrane framework integration tests commit b9f631b0f9ce348dd23e681306660661e6a1fbb4 Merge: 060e00c 2050f91 Date: Tue Jul 15 07:22:32 2014 -0400 Merging in removed fold tree dependencies and additional mover checks commit 060e00c2ac8920c7c3ef6347c746c6bc769242b9 Date: Tue Jul 15 07:22:13 2014 -0400 Adding run membrane unit tests script to membrane source directory (should be removed prior to merging in master) - all membrane info unit tests pass (n=7) commit c62764835fe45810a8d966b9cf315c824cae069d Date: Tue Jul 15 07:17:07 2014 -0400 Fixing indentation and namespacing error in uniform position mover that broke the linux gcc build commit 2050f9128a30cf7b39da6613b07bc98f00b7a101 Date: Tue Jul 15 07:14:11 2014 -0400 Fixing jump number (defaults) in MmebraneInfo unit test. All tests should pass commit 9b1c31df4f606c1efba76cd951d5592cc2a2ad0b Date: Tue Jul 15 07:11:00 2014 -0400 Updating membrane conformaiton unit test to use position equal within delta method for normal approximation due to coordinate coorect in initial stub. Unit test passes commit c4c56e2ea6e6109b2207501c28d1f44266d7b769 Date: Tue Jul 15 06:46:04 2014 -0400 Updating default behavior to use a simple foldtree - add membrane mover unit test passes commit 3456a0792743397cf1dbd319230160e3837518f1 Date: Mon Jul 14 23:04:19 2014 -0400 Adding unit tests without fold tree anchor" commit c9cd4d9af3af68d54a857f9e8d8ded9067fa7299 Date: Mon Jul 14 22:40:12 2014 -0400 Fixing membrane rt and initial membrane position mover commit ca04bd1a105d6f90e00d71d89b6ae0a4e41ba474 Date: Mon Jul 14 22:13:21 2014 -0400 Fixing the RT movers to be independent of the foldtree - skips some steps and uses a straight set with ortho check commit c65d0936120002691de031840658c62c901edb4a Date: Mon Jul 14 21:47:38 2014 -0400 Getting rid of old membrane position perturb and transform movers commit a65064fa527a0e93e4ad772ec07bd8fb3f05e5ef Merge: 03a6e96 c9199ff Date: Mon Jul 14 18:31:56 2014 -0700 Merge branch 'rpache/KIC_with_fragments' of github.com:RosettaCommons/main into rpache/KIC_with_fragments commit 03a6e969b426bfb000667e6aa091e8ef63086d1c Date: Mon Jul 14 18:29:45 2014 -0700 changing LoopBuilder to respect the max_kic_build_attempts flag commit 08b746014e06bd2273593eee39559bcece074719 Date: Mon Jul 14 18:28:38 2014 -0700 changing KICMover to respect the max_kic_perturber_samples flag commit 26078dd43ff457bfe4fc15ba955d839a4208499d Date: Mon Jul 14 20:15:34 2014 -0400 Forgot to git add the pilot app membrane sampling - should fix the builds commit b278726e6d5cc306336597ed58a8429a66928a12 Date: Mon Jul 14 19:22:22 2014 -0400 Updating Rama check to work better with CcdLoopClosureMover. Writing lots of doxygen, it compiles and runs. commit 9826a4c3153cf8ba4ee95b21c322b4736b9b0f55 Date: Mon Jul 14 19:20:07 2014 -0400 More updates to CcdLoopClosureMover to account for RamaCheck being a thing. commit ed62478d4d936f3fc31f2dd25cc6d076519a5463 Date: Mon Jul 14 19:08:06 2014 -0400 Fixing membrane position RT - finally makes the correct determinstic rotation by changing the normal vector outside of the stub commit b66d90422a816863e233de8a31c8bbd03ddf9629 Date: Mon Jul 14 19:05:24 2014 -0400 All tests pass computing the rotation outside of the code commit 2590c849225089271aeedb047d38149e4d565104 Date: Mon Jul 14 18:51:19 2014 -0400 updating membrane position rt mover to make exact rotation/translation moves commit c17523312904eb01b269a7c1c36f081a207c42e4 Date: Mon Jul 14 18:43:24 2014 -0400 Membrane Framework Update: 7/14/14 = Updating Conformation udpate_membrane_position method - will do a stub ortho check during folding to ensure the coordinate frame was not invalidated = Adds update_membrane_position method back, but relies on a relative coordinate frame (be careful) commit 334427ffde295e0ac0d168e49796be367457fb02 Date: Mon Jul 14 18:37:22 2014 -0400 Updating initial membrane position mover to contain the correct expected values commit fc454f9402f9825995e9b1e9e5bb8fe25e0decf3 Date: Mon Jul 14 18:23:14 2014 -0400 Jeff's suggestion + my updates seme to work really well together - going to push this commit b66058f500520454666a35d858495400a01a3ad4 Date: Mon Jul 14 18:18:03 2014 -0400 Orthogonal coordinate frame checking works - going to adjust this in initial membrane position mover commit bb198c355cb7d3529c595faa10a10a51e9b811da Date: Mon Jul 14 17:49:50 2014 -0400 Adding a method to conformation that validates the membrane xyz coordinates as a valid orthogonal coordinate frame commit 34f9eacb669719ae0d447833a84b49e7a90a378b Date: Mon Jul 14 17:29:53 2014 -0400 Membrane Framework Updates: 7/13/14 Determinstic Moves for the Membrane Position = Params File: I used the xyz->spherical methods to compute a desired default set of internal coordinates to give the xyz coords we want. Now, when you load in a membrane params file by default, the center is at (0, 0, 0), normal is at (0, 0, 1). = Params File: Thickness is currently along the x axis - Unfortunately placing it along the z axis will create an invalid stub. This coordinate is never used in simulations, only sometimes for visualization so I am not so concerned for the moment - its not going to stop any science and we have some pretty good tools to visualize in the meantime before we can think about a different solution. = UniformPositionMover - Lives in protocols/simple_moves and will make a deterministic rotation or translation (separate movers). Unit test passes. Not specific to membranes - can be used n the general case. = MembranePositionRTMover - uses uniform position mover and will translate/rotate a membrane position from an old to new membrane position. Has a passing unit test = InitialMembranePositionMover - uses membrane position rt mover to move the membrane to a structure based starting position. Has a passing unit test. Currently fails on one case due to a weird negative zero thing I have been taking to Brian about - safe to use, but use with caution. Test Changes: = Should fix the unit test build, all unit tests associated with the framework should pass = All membrane framework integration tests will most likely change becuase the default stub has changed. commit 6fc3780392a56b77a2413c3de175af02b5f27eed Merge: 29735da 39c3d7e Date: Mon Jul 14 17:24:35 2014 -0400 Resolving merge conflicts between crumb and ninja mpframework_devel commit be09b9866b3e0f801caeb59f1a311f968b8a54f0 Date: Mon Jul 14 17:17:24 2014 -0400 Implementing regiser_options() in RamaCheckBase and calling it from CcdLoopClosureMover. commit 399ff19d43e9c635e904f1bd40b8522dabb2f5f3 Date: Mon Jul 14 17:09:48 2014 -0400 Fixing some silly mistakes that prevented compilation commit 29735da715f49dc1b5e3374e7f18ddd69e392b05 Date: Mon Jul 14 17:02:53 2014 -0400 updating centroid residue typeset file commit 77b3a24f3e400f80abf7809a42cad5a872205142 Date: Mon Jul 14 17:01:08 2014 -0400 Updating membrane params file which updates the default thickness setting to be 15A along the x axis commit c9199ffaec7f98b24668fd37df7158b75943c9ce Date: Mon Jul 14 11:38:07 2014 -0700 Consolidate the MinimizationRefiner hierarchy. commit 563bccf4d09162d13dae1cfa598a2ab3f0e1f2af Date: Mon Jul 14 14:25:50 2014 -0400 Removing the compute_rama_score method from CcdLoopClosureMover commit 9e59de510816c792986629992581758c135911f5 Date: Mon Jul 14 14:19:42 2014 -0400 Making CcdLoopClosureMover use the RamaCheck classes where possible. Removing now useless member variables, methods and options. commit 22b1389935c47216ee890352900e4e54a2c406a6 Date: Mon Jul 14 14:18:51 2014 -0400 Initial commit of RamaCheck classes. These will be helpful for encapsulating all of the RamaCheck stuff that we want to do with CCD. commit ebd860fca0a086ea62b103b4ecad6d034b56ff3a Date: Mon Jul 14 14:17:34 2014 -0400 Adding random membrane position mover commit cffbf1fff559f48035d95bb492468d410ed75148 Date: Mon Jul 14 14:07:27 2014 -0400 Playing around with a bunch of things - fixing cross product in membrane position rt mover commit 0fc63bab9b048b1681b20616a22fc33f037dd81f Date: Mon Jul 14 10:43:46 2014 -0400 Adding coordinate correct method - trying this out after a discussion about the weird negative 0 occurences commit c696bdb2f9e9336bdee1f4ee327bf6dbf3b84a76 Date: Sun Jul 13 23:21:07 2014 -0400 updating membrane params file in centroid residue typeset to take new params file updates" commit 58102415b5ae6ab4f865c6da343bf8bb7c946aad Date: Sun Jul 13 23:19:29 2014 -0400 Reverting back to use the anchored fold tree - this would take you some more time to debug commit 5811784cd3a4f128c4a8b50dc2da71ec91fd7094 Date: Sun Jul 13 23:14:30 2014 -0400 Fixing membrane position rotation mover test to depend on a simple fold tree commit 8681a45837a0cdc6494f0ce0766a11ae32d4bf0c Date: Sun Jul 13 23:00:11 2014 -0400 Adding correct version of initial position RT mover - the only issue I have right now is with the negative almost 0 rotation. Will ask someone in the lab tomorrow commit 2a1ae30c9854209bfbcc5e0b698997c551925518 Date: Sun Jul 13 22:44:44 2014 -0400 Fixing expected values to be correct in uniform position rotation mover commit 40e02416d1cc2fcf0862bf7d44bafaffce2a0f83 Date: Sun Jul 13 22:39:44 2014 -0400 Fixing spacing in membrane position rt mover in this branch commit 924f512b66b40caeefa0c0da4e7065b0f9f986fb Date: Sun Jul 13 22:37:24 2014 -0400 Membrane position RT test updated and passes - yay :) commit 5f65e8085f24f877db042709b4c4c4cbf97bc645 Date: Sun Jul 13 22:24:19 2014 -0400 Adding uniform posiiton mover test to settings commit 4b0ad17a59e4b30a400ccb0a4a8338790ede1a9b Date: Sun Jul 13 20:33:11 2014 -0400 Updating membrane params enum to respect the new structure of the params file commit 87c3caf5ac2a33ceffa0243672425ac1966c03e6 Date: Sun Jul 13 20:17:12 2014 -0400 Updating membrane params file to load in the correct normal parameter by default commit 988b780409998638aeac5e7a9e6b188f8287c895 Date: Sat Jul 12 16:27:55 2014 -0400 Initial commit of unit tests for CcdLoopClosureMover. Right now it just closes a loop and makes sure it is closed and that it happened within the allowed number of cycles. commit 393c392cd24a83d99a2fc6071b031ac49f046eef Date: Sat Jul 12 14:05:56 2014 -0400 Moving a comment to a more sensible place commit 39c3d7ebe8bef08cf6cc40a184d14467c3d6fb7f Date: Sat Jul 12 13:59:47 2014 -0400 Framework Update: Fixing Linux gcc and unit tests builds. Also - the menv smooth integration test change was due to the fact that it had never been run before and is therefore a false negative commit 541b049057ca83fb38a0686f512171df04a8fd47 Date: Sat Jul 12 13:54:46 2014 -0400 Updating a few comments commit 4c50ce8da8c3b894e941408477f2bca1f16a4d8d Date: Sat Jul 12 13:44:01 2014 -0400 Getting the Rama2B stuff to compile. I thought I was being so clever, but then there was const-ness parade of horribles. For now I've added a second i_var for the rama_2B map, and made both rama maps mutable so they can be initialized lazily in a const method. If this getting to be a bit much in terms of the amount of code dedicated to evaluating Rama, we should spin it off into its own class. Oh, right. This builds and runs and all of that good stuff. commit 5d28a0c0f96fc66dbf7d857b9d07b7266a8f3bf0 Date: Sat Jul 12 12:42:59 2014 -0400 Uncommenting compute_closure_metrics. It was mistakenly commented commit 50984235523d2e91486ec429b1b8c9946c56a25b Date: Sat Jul 12 12:37:43 2014 -0400 Commenting lips acc file io out of the unit test build as it is unused in the current iteration of the code commit 919b2872c7318271151e9ab0060c304705bf1896 Date: Sat Jul 12 12:34:03 2014 -0400 Fixing a typo in a comment. commit 732edfd61a8f0689e85d67f4bf539ed38f402d40 Date: Sat Jul 12 12:27:13 2014 -0400 Adding a new option to the options system: rama_2b. There is a new member variable in CcdLoopClosureMover that corresponds to this, accessor/mutator, options reading, initialization and copying. I also changed rama_ to a ReferenceCountCOP and made it mutable. There is a new private method called 'compute_rama_score' that handles all the rama_ stuff, including lazy initialization. All calculations of rama scores are routed through this method. Depending on the value of rama_2b, this method will initialize the 2B Rama maps, static_cast the RefCountOP to the appropriate class (either RamachandranCOP or Ramachandran2BCOP), compute the score and return. Rama2B is false by defualt becasue I haven't tested it. commit 266b68907e922bd8a0ed0851621dac527d35e65e Date: Sat Jul 12 12:21:06 2014 -0400 Missed a spot in transform into membrane mover commit d3cf812dc52bd1e0c8a0ef6db832e0bd87686f34 Date: Sat Jul 12 12:17:08 2014 -0400 Removing ambigious reference to Real in - conflict between platform, numeric and core in RT< perturb and transform movers commit e63cdbfb90e3157968db72559f39cf35b94c8763 Date: Sat Jul 12 11:53:35 2014 -0400 Removing unused variable chain from the build commit 6361438732ec749dfbe575c3b3a8fdc09b96ad45 Date: Sat Jul 12 10:47:30 2014 -0400 Changing the defaut CCD tolerance to 0.08 A to match the paper. commit 56ec2b43614d947a7a4958ef3fea9a0d131dacfb Date: Sat Jul 12 10:44:58 2014 -0400 Removing unnecessary headers from CcdLoopClosureMover.hh commit dae1a6d21e62ba8e2347b1652d75bd571bb5f269 Date: Sat Jul 12 10:36:01 2014 -0400 Removing 'Matrix' typedef. Fixinig const-ness and pass-by-value vs pass-by-reference issue in the private copy_data method. commit 121b598d6450c60e7fa7735c32e642812a1981d2 Date: Sat Jul 12 10:25:31 2014 -0400 Removing uneccessary inclusions from CcdLoopClosureMover, adjusting some spacing throughout. commit 5182be4d27e86876955c5f6d767df48969ae14d7 Date: Sat Jul 12 09:38:17 2014 -0400 Changing nearly all of the 'using namespace' calls to 'using' calls. I prefer this, but it makes very little difference. Re-enabling the computation of closure metrics, but now this happens in its own little privatge method that apply calls. Removing unecessary 'using namespace' calls. I think I'll try to figure out which headers can be removed next. commit 0113ce6ad53e2c07a646ae22182e0915d70dd15b Date: Fri Jul 11 23:34:31 2014 -0400 Moving ccd calculations to numeric code, lots of little cleaning things. This seems to work still. A good next step is to make the code in numeric use iterators instead of ints going from 1 to 3. commit b87a1f4663073be722d17e24724a42735f773913 Date: Fri Jul 11 23:28:42 2014 -0400 Whoops, forgot to commit this earlier. this makes it build. commit 8c712d660d9cb95e02518f6fd01c63e69198b4b4 Date: Fri Jul 11 23:27:53 2014 -0400 Adding a function to numeric that calculates the angle and resulting deviation for CCD moves. commit 6a47441d7d2be0e0256badc19a07e5507b54884b Date: Fri Jul 11 21:41:59 2014 -0400 fixed bugs from merging, added tracers for debugging commit a75dd2670a340c6ae379301eebbfa4b5b810f464 Date: Fri Jul 11 21:41:28 2014 -0400 added tracers to apply for debugging commit 3812926b7bf4429fbd9fd107005bb1fa574736b0 Date: Fri Jul 11 21:39:58 2014 -0400 fixed bug in AddMembraneMover and changed jump to MEM to 1 in setup function commit 2da0c4ac0ad9b8eee22772728ca2bfed785e7b5d Date: Fri Jul 11 21:34:56 2014 -0400 added mpfolding app, still working on pilot apps mpdocking_setup and testing rotations commit 3f6fd873d1b6c0607cbd3cec2d97f506ee487c12 Date: Fri Jul 11 21:32:44 2014 -0400 added show method to xyzMatrix commit 717111bad0320afdc0b0b9865c434c64b73336a9 Date: Fri Jul 11 18:42:07 2014 -0400 Making deviation a single real and not a vecotr, fixing the various calls to those functions that provide access to it and trying to flip theta_hat instead of alpha. Doens't buuild, have to go home. commit 81599fe418e9af143b13abc914eb5c9096ec109e Date: Fri Jul 11 18:38:50 2014 -0400 Cleaning up Jason's pilot app thing commit 34e8a6fc967303ec3aea3742dbd6227df95e67cc Date: Fri Jul 11 17:50:41 2014 -0400 Making some changes to get CCD to actually close loops. It closes loops! Huzzah! commit 98735f4459773002f0e52ef4d09db1c90a15f797 Date: Fri Jul 11 14:14:13 2014 -0400 CCD Refactor: deleting a crap ton of code; woo! Hopefully, the loop will close now. commit 0b1be2a2dea7fb658a8973138052b736fb98ee57 Date: Fri Jul 11 13:07:30 2014 -0400 fixed namespace errors in mpdocking, changed MEM in AddMembraneMover to jump to first residue, added comment to DockingProtocol about weird logic in running lowres/highres commit 41050b41024c003d582ad062aff8552a2ad94099 Date: Thu Jul 10 19:49:45 2014 -0400 fixed bug in SpanningTopology, spanfile_from_pdb only writes single spanfile if PDB contains single chain commit 8547408cd03291d3775cabaa5e8b9f54415f8c36 Date: Thu Jul 10 19:05:34 2014 -0400 Intermediate stage of testing out pose-based CCD moves. It's not looking great right now. commit 41758265c1b7fc99fc3dec9eb5641351831a1760 Date: Thu Jul 10 18:06:22 2014 -0400 fixed bugs, added comments commit b324d5d2c692859254b6c0e4ce94aba700be6925 Date: Thu Jul 10 17:12:17 2014 -0400 Eclipse, I hate you. commit 7d033df0976f0e8b5fc9fb061305603e6974b4cc Date: Thu Jul 10 16:55:43 2014 -0400 bug fixes; new M and F seem to work as planned; now we need to deal with 'refolding' commit 04008aac7dabc5f46b4adfd71020fbe481cad3c0 Merge: 8b84164 c281500 Date: Thu Jul 10 16:42:10 2014 -0400 merge /rfalford12/mpframework_devel into jkleman/refactor2, resolve conflicts commit 8b84164b3adbc06361bdc0659e3b4b539dab3ad5 Date: Thu Jul 10 16:24:45 2014 -0400 fixed bug in SpanningTopology, changed EXCN to utility_exits, added mpframework_test pilot app for easy testing, still debugging mpdocking_setup commit c2815005aa95b840fa99f7179cd3a4dcb30bd334 Date: Thu Jul 10 14:37:17 2014 -0400 Membrane Framework Updates (7/9/14) ============================================================ Movers = Deterministic/Uniform Rotation & Translation movers added to protocols/simple_moves = Membrane Position Rotation/Translation movers for moving the membrane residue = Randomized position movers based with deterministic movers Membrane Position Coordinates = Removal of #update_membrane_position() method in conformation and methods for setting xyz = Added correction in membrane_normal() to always pull a unit vector derived from the coordinate = Updated InitialPositionMover to use base rotation/translation mover described above Default FoldTree Settings = Added behavior for a non-default membrane fold tree anchored by an additional virtual residue. Can be turned on using the flag -membrane_new:anchored_foldtree Energy Terms = Updated #includes to remove incomplete conformation definition warnings = Fixed global namespacing errors Lipophilicity = Updated LipidAccInfo object to remove setters, meet coding conventions, clean ups, etc = Removal of LipsFileIO class - object initialized from file at construction = Modified MembraneInfo to take a single lipophilicity file (no more 'by chain') as well as corresponding options and input streams = Updated MPLipoEnergy to use the new object structure from MembraneInfo Smoothed Energy Function = Addition of MPEnvSmooth energy term (framework adapted) = Addition of a new fingerprint test, menv_smooth_sfxn containing smoothed fullatom energy function weights set Unit Testing: Updated the unit tests to include the following: = MembraneInfo = AddMembraneMover = MembraneConformation = MembranePositionRT In addition to pre-existing unit tests for the membrane code, which include MPDatabaseIO test and Julia's new unit tests for SpanningTopology and Span objects. Expected Integration Test Changes = All Framework integration tests will change due to io output errors. This will also diff against master merge which will also most likely produce a series of changes. commit 0b92325d8426f07a367b280bf07a93c67dabb323 Date: Thu Jul 10 14:35:47 2014 -0400 Adding flag to turn anchored fold tree on/off and also fixing method that was deleted temporarily in conformation - those changes will come later commit 48ee5b7fdf97267d5d04a5c5415a1d670c5ba703 Date: Thu Jul 10 14:23:41 2014 -0400 bug fixes commit cf19fc6d23b5bfb7fe9bfbf2ff93c36f2ad2b26b Merge: 6f362f9 1319064 Date: Thu Jul 10 11:30:05 2014 -0400 Resolving merge conflicts between mpframework devel and parallel devel branch commit 131906496f1c4942bc2b290a869eac74ac12c0ac Date: Thu Jul 10 10:33:34 2014 -0400 Membrane Framework Updates: Visualization in PyMol ==================================================== Added a feature to the PyMol mover/viewer for viewing the membrane planes as CGO planes derived from information in the membrane framework. = MembranePlanes Object - stores location of plane defining virtual residues = ShowMembranePlanesMover - mover for adding plane defining residues to the pose = AddMembraneMover will now automatically setup the pose for visualization in pymol if specified by the user upon initial add of the framework = PyMolMover contains a send_membrane_planes which sends over location of plane defining residues & other framework information = PyMolPyRosettaServer.py will parse a message containing plane residue locations, draw planes from these points and update in pymol during a PyMol viewer enabled simulation Updated: 7/10/14 commit fbdd192d32fa74da4349277add87c6a1f5fbcb80 Date: Wed Jul 9 22:54:55 2014 -0400 Updating documentation for the pymol viewer code" commit de6e89d3d463499f5a0f81294235b0aa7481bac1 Date: Wed Jul 9 22:28:43 2014 -0400 added add_span, reorder_spans, and write_spanfile methods to SpanningTopology commit cdd4c8201b630a4711c489928403273856961769 Date: Wed Jul 9 21:41:11 2014 -0400 added shift and not_valid methods to Span commit 64d843e51c49d5479f1ae95f2ca648161c8f6381 Date: Wed Jul 9 21:06:48 2014 -0400 Removing extra tracer statements from pymol membranes code commit 887364bad1312205d67808633dccf6c433cda1d0 Date: Wed Jul 9 21:05:34 2014 -0400 Working version of the pymol viewer for membranes - beautiful commit 2925f4f0a4756c92b2d6f7314e6f589a627b8bbd Date: Wed Jul 9 20:58:12 2014 -0400 forgot to add files commit 13f57192195843fe9e8e8cf3e2d4592a490ea510 Date: Wed Jul 9 20:55:43 2014 -0400 Added mpdocking_setup pilot app, still working on it added nres_topo as check in SpanningTopology small renames and comments commit a544db3766c72cb2b6e08e9840981d8667d5be1d Date: Wed Jul 9 20:34:36 2014 -0400 Has a full version of the pymol draw planes code - however pymol seems to freeze when it comes time to draw the cgo planes commit d796d552a4d6abd4c77bf9437364bbe435a10f19 Date: Wed Jul 9 18:22:17 2014 -0400 Updating server script and pymol viewer test pilot app commit 2c737403aa836b4cd2b311c29dcaa12b45848684 Date: Wed Jul 9 17:34:34 2014 -0400 Adding additional method to pose for grabbing total number of atoms up to a given residue commit 87e36983fb1a178129ec00b8cda504fe22d0ed4f Date: Wed Jul 9 15:37:03 2014 -0400 Enabling pymol mover on the C++ side to send message over to the Python side - no reciever implemented yet commit a447146b60ba6dac4093fb21677ed5d4cc05a399 Date: Wed Jul 9 15:29:40 2014 -0400 updating message formatting sent over by pymol to make it more like a splittable string" commit 835518bb689345892032d568dd188afd71df1604 Date: Wed Jul 9 15:24:31 2014 -0400 Fixing a bug in the view in pymol method that was allowing send plane info prior to initialization of plane points commit eded0cf8e0f528266bd4620e2a50a8fbd7bea6ed Date: Wed Jul 9 15:11:35 2014 -0400 CCD Refactor: adding get_anchor_matrix() method to replace get_overlap_positions and tons of other code commit dca2b00b25fe567b560fe787b79b018e153e0eb3 Date: Wed Jul 9 14:53:30 2014 -0400 Adding milestone 1: show planes viewer will add the membrane points on command commit d9ad13ca27b05e370a9c388bd4296dfbfe8aa7cf Date: Wed Jul 9 14:35:01 2014 -0400 Updating show membrane planes mover to support new options and remove support for a user provided radius (rg more reliable/practical commit 80fd2a12617c2186cd26e0822fc315d1d54463d1 Date: Wed Jul 9 14:29:44 2014 -0400 updating membrane planes to print the correct plane points, show membrane planes mover adds points to membrane info, adding options now commit 08b09f412ec27550268f226efceef8470f0d637b Date: Wed Jul 9 14:18:10 2014 -0400 Allowing show planes mover to directly add point info to membrane info object commit 0a83bb4eccf8b26098d2552ccd4a9175ed33aa2e Date: Wed Jul 9 14:16:41 2014 -0400 Adding pymol viewer testing pilot app commit 8a7e5139018c8f591957def9471e4d5037400c26 Date: Wed Jul 9 14:16:23 2014 -0400 Adding view in pymol option and plane info to read into membrane info commit b097728225776301a14d527bfc71c5bdb4c97fb3 Date: Wed Jul 9 14:03:53 2014 -0400 Adding updated version of show membrane planes viewer commit e363f388a8b5e891eca4ec157c3202995f2f91af Date: Wed Jul 9 13:46:04 2014 -0400 Adding membrane planes object to build settings commit 37cd92f7b6ed682603c0821c56549ab4ce915fb4 Date: Wed Jul 9 13:44:59 2014 -0400 Adding membrane planes classes commit c4b73ed51b3bf8ee7bb9a3ee87048862a6ae1e69 Date: Wed Jul 9 11:34:10 2014 -0400 deleted files of renamed energy terms commit 4965e0fe3fae0b0b14188525e0ac2cb4008a2d64 Date: Wed Jul 9 11:30:26 2014 -0400 Undoing commit where I renamed the membrane energy terms All energy terms should again start with MP, renaming them was a bad idea in the first place commit 11ab10e947b1089d71e8ad4530cb8a1f0cb628c6 Date: Wed Jul 9 11:13:50 2014 -0400 added comments to docking protocol commit 76d8d12d3bbd480fdeb43098a9f765f1f3d29c7b Date: Wed Jul 9 09:09:06 2014 -0400 Fixing build errors from global namespacing and andrew's get_score_function rename. Merging remote master up to Rocco's recent commit into ninja local master and into current mpframework devel. 7/9/14 commit 8297c165a18fb0bda8668fc28b991d81aad4a0a1 Date: Tue Jul 8 23:28:58 2014 -0400 Updating scoring manager due to merge conflict commit dca27af24b52bd269e02b57b4d623080d30454d1 Merge: 2e3d5a4 05685c8 Date: Tue Jul 8 22:47:21 2014 -0400 Merging recent master up to Rocco's commit (7/8/12) into current mpframework devel commit 05685c84f52abd1e7a9b90ab4f47971fc8bd50b6 Merge: 2884d93 15059e4 Date: Tue Jul 8 22:47:10 2014 -0400 Resolving merge conflicts in master commit 6f362f98d73cadb7bf525c469af5423e97d8c8eb Date: Tue Jul 8 22:41:29 2014 -0400 Quick changes in conf & rt mover commit 26c38d9112def80ee634c44c89247c7fcbdda196 Date: Tue Jul 8 19:44:42 2014 -0400 CCD Refactor: clarifying, i.e., trying to understand the math commit c2038dc13b868f32654bef2a38e44fc85049c5d7 Date: Tue Jul 8 18:13:42 2014 -0400 CCD Refactor: deleting what we think is a useless for loop commit 732bf70d8bee72d2034e895c10e18f5e88500f7f Date: Tue Jul 8 17:34:19 2014 -0400 updated mpdocking weights commit 923ed9e1eebe1c3a0193e4ad18b99c5624a0ffb3 Date: Tue Jul 8 17:19:37 2014 -0400 CCD Refactor: removed cutpoint as a parameter from all functions, since loop_ is a private datum commit 56cb0f67f3701961d09390035e45c3b769608f5b Date: Tue Jul 8 16:54:14 2014 -0400 CCD Refactor: removed n_mainchain_atoms/nbb as a parameter from all functions; now it is generated as needed for each use case and renamed to be more clear as to what it actually is in each case commit 7967d01180eac70fa8cff810e6f36c61dac552ce Date: Tue Jul 8 15:16:37 2014 -0400 updating rt mover test - includes deterministic translation via stub but should set translaiton via jump instead commit 3cf362593440298ecf93b12e6197aaa291f227aa Date: Tue Jul 8 14:36:06 2014 -0400 This is a fake all pass for rt position mover - translations are still inconsistent and should be done in a more generalizable way commit 633ebb7f4c69cf8f4f84d86e28e6d4eccd704614 Date: Tue Jul 8 14:31:11 2014 -0400 Going back to explicit translation, will need to fix this later on... commit b7cd0556e87740dc686370f4b00f851613fd84db Date: Tue Jul 8 14:01:56 2014 -0400 updating uniform rotation and translation in membrane position rt mover commit 0c99c80a8300d76ffd6c81048146ee48d9fa7b9f Date: Tue Jul 8 13:53:20 2014 -0400 Trying non absolute translation in membrane posiiton rt mover commit b904a96d786a6c417897817855972e5158ef9b09 Date: Tue Jul 8 13:39:39 2014 -0400 Updating membrane position mover unit test so the mover generalizes to any given jump - unit test still passes commit ac2d21d8ad0e2c89fcb99518f857af01c7be1ffe Date: Tue Jul 8 13:34:39 2014 -0400 Adding rotation & translation tests - all tests pass ' commit d334fa7fcf8214627cd300d825c576af2574e303 Date: Tue Jul 8 13:23:37 2014 -0400 renamed argvs in MembraneInfo commit 831c3af038c1bcea47aa5a621cd66a240ab121c3 Date: Tue Jul 8 13:22:47 2014 -0400 Adding check rotation pilot app - directly applying delta rot seems to fix the problems I was having - will change the rotation code to this and use flexible jump.set" commit b1d96e9d39ab890db11ad03571a8ae2f6c9f7606 Date: Tue Jul 8 12:33:05 2014 -0400 Adding renamed file to test settings commit caefcb75d05221e597e5e261d3f04aacffadc8e1 Date: Tue Jul 8 12:15:25 2014 -0400 Renamign membrane rt position mover test commit 985626f87b443eba3645f92df48efdae5ae07184 Date: Tue Jul 8 12:13:59 2014 -0400 Bug fixes in add membrane mover unit test commit 61578cf999eb1a91a6868c8023a9fa6e63088883 Date: Tue Jul 8 12:02:40 2014 -0400 added renamed MP energy files commit 1c9bae259d67dd6e84f0331e3ba065c5b5646d2b Date: Tue Jul 8 12:01:49 2014 -0400 renamed MP energy terms commit 825df0e27fc293c35213466d182fe5fb5959e91a Date: Tue Jul 8 12:01:19 2014 -0400 deleted mpdocking files commit 6c0a0d7ce928500427befe442f173d6b9da36650 Date: Tue Jul 8 12:01:03 2014 -0400 Updating doxygen on top of membrane conformation unit test. Also renaming add membrane mover unit test commit 6fe424afb7a73f0dbc9d378dc5336d866d95c2d6 Date: Tue Jul 8 11:57:24 2014 -0400 Removing old unit tests and accompanying unit test files commit aa652b9eb12df66703d16725a4b04dca58e56709 Date: Tue Jul 8 11:50:26 2014 -0400 Adding modified spanfile for post membrane add test" commit fa66188f9857fb0b77d7fa6759021cb9f91547b4 Date: Tue Jul 8 11:49:42 2014 -0400 Adding unit test for membrane conformation commit 224e7bb76b44cb3f5f60d72f15bed39bb9849d8d Date: Tue Jul 8 11:39:43 2014 -0400 Correcting spanning topology object for membrane residue counted in spanfile commit d365be6bff735110351f78725de5bac8a2061d9a Date: Tue Jul 8 11:34:24 2014 -0400 Fixing membrane info unit test - all tests pass ' commit 3e3b4861254d197629e7f5b84d4f7df50d194fe8 Date: Tue Jul 8 11:30:49 2014 -0400 Fixing build for both membrane info and membrane conformation unit tests commit a356dee071d6bc640374314e3ce0a19babbe1319 Date: Tue Jul 8 11:21:07 2014 -0400 Fixing global namespacing errors in Justin's unit tests that broke my build, adding back a new membrane info unit test commit 72f3025da638a236dfd97e933e9db1270a952ad7 Date: Tue Jul 8 11:02:38 2014 -0400 Adding new membrane info unit test to work with the updated version of the framework commit c4a8b8accd55d56c4eea523806fb5e9ad4fc21a5 Date: Mon Jul 7 19:16:27 2014 -0400 bug fix in a pilot app commit 2e3d5a4538d3673bfda1dd331114483dad9f4d27 Merge: 0581be1 bfe5732 Date: Mon Jul 7 18:14:31 2014 -0400 merge devel into jkleman/refactor2; resolved conflicts, compiles commit 0581be1f6c7cb6698407f9adc073271bd63c79e9 Date: Mon Jul 7 17:42:54 2014 -0400 fixed unit tests for SpanningTopology, tests for Span and SpanningTopology finally run correctly commit d502cdae3a0d077123b5cd2c68017a1d65d1e2f5 Date: Mon Jul 7 17:42:22 2014 -0400 added unit test for Span commit 054b7fe0c802033ae3fc47a7b9686e728b9b014e Date: Mon Jul 7 15:01:44 2014 -0400 CCD Refactor: removed an unused param from the debug_information_during_clousre() method commit 42b7bcd97ea747b922ebc9894529ed5e4ff2cab8 Date: Mon Jul 7 14:58:37 2014 -0400 CCD Refactor: fixed error in how backward deviation was calculated; this should fix all the tests that failed because the loop was claimed to have not been closed, even though the actual results were physically the same commit 029cdf853f8f2481b45952a0379457a5074e5006 Date: Mon Jul 7 14:19:20 2014 -0400 bug fixes commit d47ab918ebfdfd8dd765e3560f385cf822529400 Date: Mon Jul 7 11:08:38 2014 -0400 Fixing grabbing normal parameter from coordinates - seems correct and consistent now which is awesome commit 10dfff2981df0c8f775231db529da9b7be789352 Date: Mon Jul 7 11:03:28 2014 -0400 Updating add membrane mover to always fill the membrane residue with default initial coordinates prior to placement (doesn't want to deal with relative stub craziness) commit 36143425625c3657b32ba2ca67dc6e1330b6b7dc Date: Mon Jul 7 10:53:55 2014 -0400 Fixing the pilot apps build due to global namespacing errors - commenting out Julias mpdocking app for now until she can fix her namespacing issues commit 4691873f16fb66195ccb68d1061d903e8bb4e7fd Date: Mon Jul 7 10:28:46 2014 -0400 Updating computing membrane center/normal from the global frame in Conformation commit acb35ac42fd46299eaa8e0cf0566bf88f01d5a9d Date: Mon Jul 7 10:10:01 2014 -0400 Fixing more global namespacing errors caused by reducing namespace scope for lipid acc info data commit d1ba8f453f1b9bcdeba92261007431fd16c666f0 Date: Mon Jul 7 09:39:15 2014 -0400 Fixing a quick namespacing error enabled my my global namespacing mistake and fix in lips acc object down in core2 commit 88a7a1abc0962335af9d267d62482aa9bf5747d0 Date: Mon Jul 7 09:38:10 2014 -0400 Updating doxygen in lipid acc info objects commit 6c8523567e04aba0ef5efd85820ec9081ef12168 Date: Mon Jul 7 09:28:54 2014 -0400 Updating mlipo energy to match new interface in membrane info commit 16350ce4345f99124729257bbd3839779f772f40 Date: Mon Jul 7 09:25:47 2014 -0400 Updating defaults for membrane_new option to match input types commit b0d4105f3f940bb28e17b44531077a76e1903656 Date: Mon Jul 7 08:06:22 2014 -0400 Removing currently unused score types breaking the pyrosetta build from score type and socre types manager commit 996ae9d00cfbb4ba23128d76a66caf8ecb653247 Date: Mon Jul 7 08:03:12 2014 -0400 Fixing add membrane mover to use the correct option key commit f249194c48a95325adea2bd1d491b6e61c9a6718 Date: Mon Jul 7 08:02:07 2014 -0400 Updating option keys - changing lipsfiles to lipsfile commit f35900facd73131acba539bb5d0c8a08aaaa8160 Date: Mon Jul 7 07:59:06 2014 -0400 Adapting lips file object to only take one file - finished fixing this in add membrane mover commit f81b37676110f770ae03be6ee6f490b16b30eb72 Date: Mon Jul 7 07:57:10 2014 -0400 Fixing spanfile loader and things that were mistakenly commented out of the build commit 3d44aa75c768c89cd7ae70e698b0772e261d4981 Date: Mon Jul 7 07:55:20 2014 -0400 Removing spanfile and lipid file io classes disabling object mutability commit 031aa0c50e9a358d16208c0c60f4c773196d64d3 Date: Sun Jul 6 21:50:22 2014 -0400 Updating lipid accessibility info object - now reads independently commit 98f48015530e0e4e74d63703871b1deb91e04d2a Date: Sun Jul 6 19:22:24 2014 -0400 Updating conformation to take a single lips acc object instead of a list - no more by chain access commit 40bfc6c68ebbaebf54f7e5727434ddbb353c10f4 Date: Sun Jul 6 19:19:37 2014 -0400 Updating membrane info to take a single lipophilicity data object commit 0f905cbb720d0ee241d163984c6432e7cbeba4d8 Date: Sun Jul 6 19:08:06 2014 -0400 Adding new fingerprint test for fullatom high resolution energy function with smoothed env derivative commit 47bc8a7d2d8e484de994c3e2d2ee0f09350413d6 Date: Sun Jul 6 19:07:14 2014 -0400 Adding new high resolution weights set including the smooth menv term now adapted for mpframework commit 441d02fb093b92a73e5d88dfc09762f514a81f7e Date: Sun Jul 6 19:05:05 2014 -0400 Unhacking conformation and removing debugging tracers from old and new menv smooth energies commit 090503ce70d0346c8f8f208e509c7eda19b16f18 Date: Sun Jul 6 19:00:02 2014 -0400 Integration check for fullatom membrane environment smooth term complete :) commit ce01c9fa011523705abd1a566e1e837325f2a43d Date: Sun Jul 6 18:07:58 2014 -0400 Fixing database file path and starting tag in fa menv smooth energy commit eeef6f3c7babc1803f5d569ddc0d3a8eea436ca3 Date: Sun Jul 6 17:32:17 2014 -0400 updating fullaotm energy function app to score with menv smooth score types commit 6ee72550733e93766259b4ca465f90a0b9ba0c54 Date: Sun Jul 6 17:22:21 2014 -0400 Updating layer bounds in fullatom membrane environment term smoothed and using the framework residue depth. Otherwise, making no other changes for now commit 14509b7051525aed655de419b262e4e3d88f4ac0 Date: Sun Jul 6 17:03:16 2014 -0400 Adding membrane env smooth energy to build settings, note lipophilicity energy is there but untested for the time being commit 27f66ea587991d893c5a6687d534a88aa7715bc8 Date: Sun Jul 6 17:02:06 2014 -0400 Hooking fullatom env smooth energy into sfxn framework - adding score type FaMPEnvSmooth energy to ScoreType and score type manager commit 566d8ca5d849e875fdbbab7ed28a2dc71c8da7f0 Date: Sun Jul 6 15:57:10 2014 -0400 Replacing old depth incremented parameter with new z dependent parameter per-residue commit 12cddaec57e8d5fad7557644c58044e1da8389cc Date: Sun Jul 6 15:52:42 2014 -0400 Continued updates to fullatom smooth energy - has a derivative commit 1872cf67b66e68dc95065943ac350d835f50c15e Date: Sun Jul 6 15:46:34 2014 -0400 Starting to update implementation of smoothed environment energy. Also adding new scoretype FaMPEnvSmooth commit b1b2094b02776d9428fcb2927e333fdb6a2b60da Date: Sun Jul 6 15:34:29 2014 -0400 Adding header for menv smooth term commit 11a556415ac77543c62168acddf118fa879ec03d Date: Sun Jul 6 15:27:07 2014 -0400 Adding starting files for fullaotm membrane smoothed environment term - will be adapted for mpframework commit 5aaf00e8ed1d4e787637c04dabc8dd5bbaa4f627 Date: Sun Jul 6 15:22:25 2014 -0400 Temporarily removing secstruc and spanning penalties that were never implemented to clean up the directory and cleaning up lipophilicity energy (still needs work to break back down to not per-chain commit fa49eea85281de46cd451669d1c1006671204119 Date: Sun Jul 6 01:20:56 2014 -0400 Removing cc include guards from membrane info commit 47c09a431bd06c9c92041ce7ccc9818977db51b9 Merge: 0eeab62 637f9cf Date: Fri Jul 4 01:02:38 2014 -0400 merging with Brian's changes commit 0eeab6209a632f2e02c6f470cbb2ab786cf698b9 Date: Thu Jul 3 22:07:36 2014 -0400 CCD Refactor: changed all calls to ccd_moves() to use CcdLoopClosureMover; fixed renamed setter calls commit bfe5732116008effbe904f9cc184d56e0939f991 Date: Thu Jul 3 22:02:51 2014 -0400 Fixing linux gcc build commit 76feacd451561c18caadb509402b54de11b19447 Date: Thu Jul 3 21:33:01 2014 -0400 Removing unused varaible from the debug build in MPCBeta energy - also looked into integration test changes from the previous commit. These should be due to the deprecation of the use incorrect derivative option in hbonds energy which is reflected in the analagous commit in master commit 637f9cfed36dd5cebd75d2dbfef414f2b65dadde Date: Thu Jul 3 21:02:45 2014 -0400 Implementing parse_my_tag, using setters where possible in parse_my_tage and init_options. commit 63d0bd1a54c155417fad789dc4c458b97a49df7c Date: Thu Jul 3 20:39:51 2014 -0400 Requiring three inputs to the max_deviation ccd options, writing an init_options() method in CcdLoopClosureMover. commit 16ce1bfd75440b1679b90757683eec52ee1be96b Date: Thu Jul 3 19:48:01 2014 -0400 Adding a bunch of options to allow commandline customization to the CCD mover. commit ebf237dfb83a586bff935b24b4d318379d81d93f Merge: 30252be 763e97d Date: Thu Jul 3 19:26:36 2014 -0400 merging in changes from Brian commit 30252be217295d4664c6647ba379c41904716d17 Date: Thu Jul 3 19:25:47 2014 -0400 CCD Refactor: deleted the other CCD Mover altogether commit 763e97d24e88c65e170a85c01c1f7726be9b1e34 Date: Thu Jul 3 19:12:08 2014 -0400 Fixing a parenthesis-square bracket misfire. commit 84bdd396b9a988e680031b4da118214924beeefc Date: Thu Jul 3 19:06:36 2014 -0400 CCD Refactor: deleting almost every method from ccd_closure.hh and .cc commit 5623bf56204b23b413da2be1be18ed8967d9dc24 Merge: d0f1eed 86ccb30 Date: Thu Jul 3 19:02:19 2014 -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 weitzner/make-ccd-a-class # Your branch and 'origin/weitzner/make-ccd-a-class' have diverged, # and have 1 and 1 different commit each, respectively. # # Changes to be committed: # (use "git reset HEAD ..." to unstage) # # modified: source/src/protocols/loops/loop_closure/ccd/CcdLoopClosureMover.cc # modified: source/src/protocols/loops/loop_closure/ccd/CcdLoopClosureMover.hh # # Untracked files: # (use "git add ..." to include in what will be committed) # # .directory commit d0f1eedbdf4fd98f04d0c32e5f3ef120401ffedb Date: Thu Jul 3 19:02:12 2014 -0400 I have no idea what I modified on this check in. commit 86ccb305e30e97b67baf6bb808e13e423576d8a3 Date: Thu Jul 3 18:54:24 2014 -0400 const-correcting a bunch of stuff. making things nice, see. commit e90c8ba19cead26707fd6a67c2080cbd024c9eaa Date: Thu Jul 3 18:54:07 2014 -0400 CCD Refactor: moving all functions from ccd_closure to the Mover, Part 3 commit ca5eb9738bed3fbe51e8e132d0ee296315d7882a Merge: 46536ab d667f50 Date: Thu Jul 3 18:35:29 2014 -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 weitzner/make-ccd-a-class # Your branch and 'origin/weitzner/make-ccd-a-class' have diverged, # and have 1 and 1 different commit each, respectively. # # Changes to be committed: # (use "git reset HEAD ..." to unstage) # # modified: source/src/protocols/loops/loop_closure/ccd/CcdLoopClosureMover.cc # modified: source/src/protocols/loops/loop_closure/ccd/CcdLoopClosureMover.hh # # Untracked files: # (use "git add ..." to include in what will be committed) # # .directory commit 46536ab48945e52cedc9bc96026721633d94d5ec Date: Thu Jul 3 18:35:23 2014 -0400 CCD Refactor: moving all functions from ccd_closure to the Mover, Part 2 commit d667f5021303877fa54fb228933fc8a12ca28d1c Date: Thu Jul 3 18:32:19 2014 -0400 Const-correcting the shit out of 'debug_information_during_closure', which happens to have the ugliest signature ever. commit 32559d5f418ba6e077df671ad06414c4e6fb4b82 Merge: 98e9437 352527e Date: Thu Jul 3 18:24:53 2014 -0400 resolving merge conflicts commit 98e9437e19675bec196710f41deffe2335e6ba54 Date: Thu Jul 3 18:20:36 2014 -0400 CCD Refactor: moving all functions from ccd_closure to the Mover, Part 1 commit 352527ea35011aba1c2d0ee4187bec57a8120adc Date: Thu Jul 3 18:17:50 2014 -0400 Cleaning up the interface to CcdLoopClosureMover. Setters and getters no longer have a 'set' or 'get' prefix. Added a static map to go from chars to enums to represent secondary strucutre. Made a lot of things that should never be negative unsigned. commit 265ddc6fca7950a87061f9752bf5c5e889952c04 Date: Thu Jul 3 18:15:40 2014 -0400 Making some numbers that should never be negative unsigned. Added a check to prevent underflow. 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 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 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 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 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 a28950073d90146c9f5ae6f1aeff5d65cc536e28 Date: Thu Jul 3 14:39:56 2014 -0400 Alering CcdLoopClosureMover's show() to use the movemap data member directly to avoid copying a movemap as a part of printing... because that is absurd. commit 50b8bed05949809a251f4b0390d05e4ba6abd012 Date: Thu Jul 3 14:31:24 2014 -0400 Removing useless functions from CcdLoopClosureMover (loop_start() is unnecessary -- just get the loop and ask it whatever you want!) and updating show() to call Loop's show(). commit 53f6f7147af5dfd9ccf39569bacc9b48a71df018 Date: Thu Jul 3 14:24:21 2014 -0400 Adding a show() method to protocols::loops::Loop. Now the streaming operator (<<) calls this public method. I've added a little additional detail to the string representation of the loop (e.g. labeling what the various numbers represent), so this will change any integration tests that printed a Loop. The << operator is no longer friended (hooray!) because it can simply call the public method show(). commit 5da1a765726cbcfc3bf961062c082126f5aed03a Date: Thu Jul 3 14:09:20 2014 -0400 All of the shell code for perturb movers should be present commit 85dc07993cffbe1c2391ed93fb411ce40364b005 Date: Thu Jul 3 14:04:43 2014 -0400 fixed MoveMap bug in StepWiseProteinCCD_Closer 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 fa64d7a86857a906fcab75acd44ba3657be44e3b Date: Thu Jul 3 13:48:05 2014 -0400 Updating implementation of small gaussian perturbation movers for membrane position commit 761476c5e579eeb60a52e197677e577abf1c28c2 Date: Thu Jul 3 11:44:57 2014 -0400 Finished implementing membrane normal perturb mover 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 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 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 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 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 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 6678fc299dd1101deae4d68d7738bc327272b288 Date: Wed Jul 2 14:20:20 2014 -0400 Updating initial mover to make transformation instead of a position rt transform 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 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 6b41774e3e321a4a15c1b8a08535a41b4bdf30ca Merge: a9312e5 5ae4a79 Date: Tue Jul 1 22:38:23 2014 -0400 Merging in branch master from remote into ninja local 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 f48a9c78d4cb95630197fae09db3c8eb81c79890 Date: Tue Jul 1 18:00:20 2014 -0400 pointer bug fixes 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 91fafdf63679e2add15c22776b48edca69dbb2e4 Date: Tue Jul 1 13:45:02 2014 -0400 Adding a few more useful TODOs and making the copy constructor deep copy data to which we are pointing. commit fa3453015296c6d8517102e5f7377a5631831e44 Date: Tue Jul 1 10:34:14 2014 -0400 More comments. It took me a while to understand why the atom number was called “torsion” but I get it now… I get it now. commit 9e4a159076b2718972d6ba4615322fb88e9f06ce Date: Tue Jul 1 09:33:03 2014 -0400 Adding a couple of comments to note some functions that could be moved to core. 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 25c2c469cc6d005c8e4867ed412ba00adc54dc62 Date: Mon Jun 30 18:16:36 2014 -0400 Making comment about old vs new rama scores a FIXME so we can find it more easily. commit 362b416eab571a09c8f3d21c0cd53fad9c6b91ad Date: Mon Jun 30 18:08:41 2014 -0400 Tagged some functions to be moved to numeric, comments about simplifying the interface to CcdLoopClosureMover commit feb4db8e3bdeecdc1a67db3fe296a1645519c87b Date: Mon Jun 30 17:56:27 2014 -0400 Tiny spacing cleanups, using Loop::size() instead of computing it when needed and adding some TODOs commit 7bcca9a2fc6c6d3fcb559e58cb1db64766d2f1c8 Date: Mon Jun 30 16:18:04 2014 -0400 added SpanningTopology test, compiles, doesn't run; fixed bug in geometryUtil test 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 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 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 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 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 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 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 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 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 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 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 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 bf74a569b1edb33ed913894fdeffb6b49f242e52 Date: Fri Jun 27 22:37:58 2014 -0400 CCD Refactor: replaced call to fast_ccd_loop_closure() with CcdLoopClosureMover.apply() in StepWiseProteinCCD_Closer commit 5683cafcfdcedb523ce29222287b818326b122c9 Date: Fri Jun 27 22:24:25 2014 -0400 CCD Refactor: replaced call to fast_ccd_loop_closure() with CcdLoopClosureMover.apply() in WobbleMover commit 9c4252a7cf40211bdcfe9d947751c8f11b6a4f50 Date: Fri Jun 27 22:16:52 2014 -0400 CCD Refactor: replaced call to fast_ccd_loop_closure() with CcdLoopClosureMover.apply() in LoopMover_QuickCCD 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 02bbfaa5d9eef6e098f742c5135bcae8816bd863 Date: Fri Jun 27 22:09:45 2014 -0400 CCD Refactor: replaced call to fast_ccd_loop_closure() with CcdLoopClosureMover.apply() in Phil's test1 pilot app 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 029fff16f4d332877579f8a17023843e14d6d268 Date: Fri Jun 27 21:58:42 2014 -0400 CCD Refactor: replaced call to fast_ccd_loop_closure() with CcdLoopClosureMover.apply() in LoopRebuild commit 6566abea7803b5f3c500a48e5a21bfb00671e8df Date: Fri Jun 27 21:40:29 2014 -0400 CCD Refactor: replaced call to fast_ccd_loop_closure() with CcdLoopClosureMover.apply() in loops/loops_main.cc commit 9be31668805aa50cf4e56cc060a25b543a82962c Date: Fri Jun 27 21:16:46 2014 -0400 CCD Refactor: replaced further calls to fast_ccd_loop_closure() with CcdLoopClosureMover.apply() in devel/inv_kin_lig_loop_design/Protocol.cc commit ca4be2a0c362b7ad71a398a46329a13881761cbd Date: Fri Jun 27 20:49:33 2014 -0400 bug fix commit bf2e8254fcca5d97d8939b0d482a9a507a7d3d41 Date: Fri Jun 27 20:40:26 2014 -0400 accidental commit of nothing commit 5c8982ca0797aa94be3953a2b11e1c64a1e56ea5 Date: Fri Jun 27 20:37:47 2014 -0400 CCD Refactor: replaced call to fast_ccd_loop_closure() with CcdLoopClosureMover.apply() in devel/inv_kin_lig_loop_design/Protocol.cc commit be4022534d559081461141e0b5243622f6342d9f Date: Fri Jun 27 20:08:36 2014 -0400 CCD Refactor: replaced call to fast_ccd_loop_closure() with CcdLoopClosureMover.apply() in CCDLoopCloser commit b32969fc44b99efa616f852064908ffb2a1e81f9 Date: Fri Jun 27 19:50:08 2014 -0400 CCD Refactor: deleted fast_ccd_loop_closure() from ccd_closure.cc; now I will changed all calls to it to use CcdLoopClosureMover 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 ab291dba0a78404483c7ce17ea5555243f42a437 Date: Fri Jun 27 16:10:44 2014 -0400 bug fix commit e5767124836b2d0ed8d7d3e59507b1eb341373c2 Date: Fri Jun 27 14:49:14 2014 -0400 bug fix commit 3fc3b1937aa8af4f483e993fb8df5b49318b4adc Date: Fri Jun 27 14:06:19 2014 -0400 CCD Refactor: clarified confusing variable names; cleaned up code more commit 5fee5f90201056e508bce2c12148cbe584bc09bf Date: Fri Jun 27 10:30:22 2014 -0400 CCD Refactor: more private data added; new enum to simplify things; added const STEP_SIZE indexed by ChainDirection 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 e67d76e68c7c4322c14cad473ae383a63863c0b8 Date: Fri Jun 27 09:03:16 2014 -0400 fixed linker error commit 8aa7067d9315d9cb59d90c41df6cea8fdc71f04d Date: Thu Jun 26 23:30:29 2014 -0400 CCD Refactor: removed fast_ccd_loop_closure() method, having moved everything into apply() commit 281455e7881d3f676712736c2362a78e777e006d Date: Thu Jun 26 19:05:03 2014 -0400 CCD Refactor: copied over fast_ccd_loop_closure() to CcdLoopClosureMover 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 91a53e6fe670e4b46d987db85ddf76401b179b8c Merge: 556b9ba a90e2a7 Date: Thu Jun 26 18:03:09 2014 -0400 resolving merge conflict commit 556b9ba1cd9287cb8c56fc458403a440f0683c0d Date: Thu Jun 26 18:01:04 2014 -0400 bug fix commit 2926c542f7bd003e199cfd6470c0d130c6dcb419 Date: Thu Jun 26 16:00:54 2014 -0400 CCD Refactor: moved code from .hh into .cc commit a90e2a7d90d4a5377a2635910c486950c5e5e145 Date: Thu Jun 26 16:00:54 2014 -0400 CCD Refactor: moved code from .hh into .cc so we can #include a fwd.hh 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 04b7e7d91b4d7bad463a23dbb8991f4269f067e1 Date: Thu Jun 26 14:51:30 2014 -0400 CCD Refactor: finished reformatting CcdLoopClosureMover.cc, including adding new accessors commit 39a24d8d8a3159d967a2085a9e864a485991101d Date: Thu Jun 26 14:44:57 2014 -0400 added pilot app spanfile_from_pdb commit a790a63464897ebcacbdf9ccde383ccd6dd71151 Date: Thu Jun 26 11:02:19 2014 -0400 Adjusting spacing. commit 3b35620096233b54857c0beae4cbdbec2b193119 Date: Thu Jun 26 11:01:52 2014 -0400 bug fixes 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 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 5d88106ee718c5b0aab6e049fc65bcc84e8e71d3 Date: Wed Jun 25 22:10:01 2014 -0400 fixed thickness in params files, both for centroid and FA commit 6c97d3633c47f8ff5a0e2611ceefe7b1b685876b Date: Wed Jun 25 21:58:59 2014 -0400 CCD Refactor: updated/cleaned/fixed 'boiler plate' code in CcdLoopClosureMover.cc commit 7c9d51ce1b5b67cf5fe9eadc66a6a837a403ec0b Merge: 9266d88 2f42fb8 Date: Wed Jun 25 21:27:58 2014 -0400 Updated SpanningTopology Also added MPDocking, runs, but needs fixing commit 99cd24037ee37904973ceb8696eeb17935eee093 Date: Wed Jun 25 21:10:03 2014 -0400 CCD Refactor: updated/cleaned/fixed CcdLoopClosureMover.hh commit 2f42fb8efe5fe01a4bd8cae04db4b238f386c908 Date: Wed Jun 25 21:05:27 2014 -0400 MPDocking runs, but needs fixes commit 29ef5534ebbcc0f3f148addbc0137badc6387b04 Date: Wed Jun 25 20:26:08 2014 -0400 CCD Refactor: updated/cleaned/fixed CcdLoopClosureMover.fwd.hh commit cf710800ad70b3b647278616f4ed96f29a7f4899 Date: Wed Jun 25 17:27:36 2014 -0400 CCD Refactor: fixed tests commit 3cb8ebb6e24787c21a059319a97886537b6afb63 Date: Wed Jun 25 07:48:43 2014 -0400 minor tweaks commit 43773b422633e6b603d3970b5dae1c80d8ea0ffc Date: Tue Jun 24 20:48:26 2014 -0400 removing warnings: who the @%!* turned off Werror? commit 5721dec742b9268b5acabaf01dcd1e54f39a48b9 Date: Tue Jun 24 20:09:33 2014 -0400 bug fix commit aafee8a3881ef177778ecf12b0e49d87cb9f649e Date: Tue Jun 24 20:07:20 2014 -0400 bug fix commit d85d67bbce0f62ecb2c342c4422db62538fc4910 Date: Tue Jun 24 20:05:11 2014 -0400 bug fix commit fce3c66c94f2e7a9c77bdfebb5949a8bce69f69b Date: Tue Jun 24 19:31:01 2014 -0400 CCD Refactor: before swapping out a for loop with a cleaner one commit 7ada20ef7086b7dcd3a203f9c39d4246a556c2b1 Date: Tue Jun 24 19:13:36 2014 -0400 CCD Refactor: cleaned up copy_torsions_to_pose() method commit 4949deccb656a6a2827719704a52eb49f6038cef Date: Tue Jun 24 19:01:10 2014 -0400 CCD Refactor: cleaned up load_coords_and_torsions() method commit bf019a3f7c96be0bec699bec2d72b630f07cda7a Date: Tue Jun 24 18:22:56 2014 -0400 CCD Refactor: cleaning up cc file; moved enum def to hh file commit 8340b8d6a33b660351142c8893787b71d6426303 Date: Tue Jun 24 17:38:30 2014 -0400 CCD Refactor: cleaned rest of hh file and changed all types to better typedefs commit 472a6e6d7e2eec5fe3459fe1f9fa6e8fb5796060 Date: Tue Jun 24 17:27:49 2014 -0400 CCD Refactor: cleaned up #inclusion commit bb99c838d616c6ac22ad4ce3a83ab269590d661c Date: Tue Jun 24 17:21:25 2014 -0400 CCD Refactor: fixed file header Doxygen lines 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 3ca7572a5099d69e32c4b559a34e103a8c0b1617 Date: Tue Jun 24 14:56:53 2014 -0400 Changing "direction" to be an enum instead of an int. Changing a few types to be more detailed -- i.e. Real -> Angle when appropriate. Creating another small function to reduce nearly duplicated code in the get_deviation funciton. This code really isn't all that complicated -- a couple of days of work in earnest and we'll be all set! commit 01c97092352bb7408dc21056d55113d250aec5fe Merge: 8047629 5a3bcf7 Date: Tue Jun 24 13:55:29 2014 -0400 fixed merge conflict 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 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 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 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 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 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 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 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 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 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 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 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 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 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 ab636e1fb28731e39265f38cdc6d8e58980fe1a0 Date: Thu Jun 19 16:02:22 2014 -0400 fixed constructor in Span.cc 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 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 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 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 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 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 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 4f810f0d55a91f56de42499953bcd13881f41e81 Date: Wed Jun 18 18:07:53 2014 -0400 Implementing visualize membrane mover, hope it works 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 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 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 5b50902e286d694c56e5fe0f49269dd00fc787ed Date: Wed Jun 18 15:30:43 2014 -0400 Implementing center translate move in transform into membrane mover 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 a497b9a22e340149126fa5c57dde7fc5c0e3eff4 Date: Tue Jun 17 17:13:14 2014 -0400 resolving conflicts, 2 remaining 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 28abab5113bee4b214b8238bac9f29f295af352b Date: Tue Jun 17 15:21:26 2014 -0400 added core/conformation/membrane/Span.*, compiles, fingerprint tests pass 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 6d00d1d63a631150ab4e08e254dd94f22b30260d Date: Tue Jun 17 09:28:53 2014 -0400 Getting rid of non-relevant unit tests and fixing header only build commit 796791a16cf4f24a7cf6df755ab30adc9d884be3 Date: Tue Jun 17 07:41:07 2014 -0400 Fixing gcc build commit 40a6eb7978367b1183cb6e6937ab6601fe1379a4 Date: Mon Jun 16 23:14:51 2014 -0400 FINGERPRINT TESTS RUN :) 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 dc69ec5b8f495c99c3fd435fe6aa8cb772673446 Date: Mon Jun 16 21:26:40 2014 -0400 Updating local minimize app - will minimize after structure based embedding update 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 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 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 169d009415443f5ab22ccbfc3bf046fa8e6c29ec Date: Mon Jun 16 15:36:24 2014 -0400 Filling in optimize membrane mover - but ran into a scorefunction bug 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 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 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 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 08bed203a2981fb375c5ed3b2226577537d2e423 Date: Sun Jun 15 22:21:28 2014 -0400 Removing extra debugging tracers commit 486574abed882008893af0ddf389824d908b1f51 Date: Sun Jun 15 21:45:12 2014 -0400 Starting to update fingerprint apps based on the new refactor 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 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 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 e3aa16647ddf00f103630313be5b7702b82af4b7 Date: Fri Jun 13 21:03:45 2014 -0400 Updating pilot apps 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 b739ef41f73bff20a44db49cb19029360506823f Date: Fri Jun 13 12:56:18 2014 -0400 updating sfxn fingerprint tests for membrane centroid and fullatom energy functions commit 2e3ecdaa6954daeb95d82137af115480cd6bf6ce Date: Fri Jun 13 11:35:24 2014 -0400 Adding membrane unit test fixes 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 1eedcea0140327b1001d8ba930d1c3e372df0223 Merge: a541608 d9a7f83 Date: Thu Jun 12 21:47:00 2014 -0400 continuing to merge remote master into ninja local master 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 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 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 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 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 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 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 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 99e6f89112cc21ada2eebefe155eec3957a99e24 Date: Sun Jun 8 12:20:04 2014 -0400 Adding a ridiculously naive version of a membrane protein-protein docking application commit 6a00b07c11d04ad92c7d94b53add6da85f231c6a Date: Sun Jun 8 10:42:56 2014 -0400 Adding warning boxes for deprecated old membrane scoring code commit 859829d44047db089afcd9600cc691b69c61c652 Date: Sat Jun 7 18:31:20 2014 -0400 Adding dissulfide fix commit 2b15e4c7a0cbae2c5fd71d3f132078a5494490ac Date: Sat Jun 7 00:23:48 2014 -0400 Updating membrane fullatom weights file 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 53541aecd8ee0d69214c1f05f7259473256aaa93 Date: Fri Jun 6 16:29:43 2014 -0400 Membrane relax plus JD2 - up and running. Now to just make structures work 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 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 77bfd958d3bc466e12d95d06db52e202ece9efcc Date: Thu Jun 5 22:47:10 2014 -0400 Updating membrane relax app with some quick debugging changes commit f557261cfee4e8791f32652b4d7dcd69502ecc6b Date: Thu Jun 5 18:05:40 2014 -0400 Starting to debug crazy twobody energy bug 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 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 db2e4863477d8664c5b90b3b59958e4c9609c58e Date: Wed Jun 4 17:58:58 2014 -0700 changing max KIC perturber samples default value back to 2000 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 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 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 d2dd53e39bff1ea26cccd1ca49888ac5090f9b71 Date: Mon Jun 2 16:27:59 2014 -0400 Adding relax:membrane scorefunction modifications for mpframework relax mode commit 063af324d3aa8d3eff6c0dd8f3b961841f6f4d7c Merge: 0a5903b cc89ba4 Date: Fri May 30 10:09:11 2014 -0400 Merging branch remote master with lcoal ninja master commit ff2106eb3416a24fcb6bcfbe8455164f43e2001b Date: Wed May 28 10:45:31 2014 -0400 Updating most recent outline updates 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 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 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 7ed7873cf02506fb4aa377df365becb607482072 Merge: e3eb632 7f998ef Date: Thu May 15 16:39:03 2014 -0400 resolve merge conflict commit e3eb6326330a0150c7acc3cc7fe06e8c6c5194f0 Date: Thu May 15 16:25:57 2014 -0400 fix errors, compiles 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 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 ca5bfc89c2554d8cdb648b3983fbb4165f77095a Date: Thu May 15 13:13:07 2014 -0400 fixed documentation for input options 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 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 350b262fcff2970c91f1bc087306478c129598bf Date: Thu May 15 09:10:13 2014 -0400 Cleaned up and adapted membrane info object to do setup with fullatom information commit 3d54737520366cb6c56625ed81d6ed79a83065a9 Date: Thu May 15 08:55:38 2014 -0400 Cleaning up the header for membrane info - should make it more comprehensible 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 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 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 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 39de8304ddbfd37a16de088b8a8a45a10b506f7d Merge: e2321a9 ce2af8c Date: Tue May 13 17:33:39 2014 -0400 pull from remote commit 5fa019ad69ccf44c7902738ce6e25580484a04a8 Date: Tue May 13 11:42:55 2014 -0400 Removing hundreds of lines of dead code in the membrane etable code 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 0dc9e645a5c3ddc70a73426806491d8090aacdd1 Date: Mon May 5 13:51:37 2014 -0500 resolved merge conflicts in MEM and EMB params files 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 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 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 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 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 ba7f2ad279ace08331cfb8599f3a86e63a2d03f7 Date: Fri Apr 25 13:53:15 2014 -0400 Removing non helix penalty debugging tracers - this is a bogus term for now 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 30a8b20aa3155402bac8aafacf9207e8ad65fd35 Date: Fri Apr 25 00:27:49 2014 -0400 Debugged issue in membrane cbeta term - removing debugging tracers 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 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 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 fe71316a412273695a0284432ccab995b5032774 Merge: 191b217 3d1edb0 Date: Thu Apr 17 15:57:00 2014 -0400 merging crumb pyrosetta-friendly version with ninja local 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 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 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 ed2b6dd992dddadeb1849677694be8f9f309967e Date: Thu Apr 3 16:38:49 2014 -0400 Carbohydrates & Lipids: updating centroid database files 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 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 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 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 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 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 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 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 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 c2423b1a01a623a69b4e1452b6615e7b04673257 Date: Tue Nov 19 18:05:50 2013 -0800 add clone() method to UpdateEnzdesHeaderMover commit 0a8e899de7bcceb4ff2cbd498a778c6232df0c4e Date: Tue Nov 19 17:34:47 2013 -0800 fix typo in new updateEnzdesHeaderMover commit b2d858dfe4d66693c8e27291ae153ac7cb8cf0fe Date: Tue Nov 19 17:06:26 2013 -0800 Add mover to update the enzdes header block in case the enzdes residues change