Rosetta Membrane Framework Updates: - Added parse_my_tag function for RosettaScripts to CreateMembranePoseMover - Create Membrane Pose Mover will now **overwrite** the pose passed by JD2, so JD2 can handle a membrane pose - Added mover creator and full rosetta scripts hooks Unit Test Status: All Pass (linux tested, clang build broken) Integration Test Status: No Expected Changes Change Date: 3/15/14. Authors: Rebecca Alford, Julia Koehler Leman

• Summary

Warnings Removal: fixing cmake to match Scons

• Summary

WARNINGS WAR Z: Turing on Werror for all builds. List of warning types removed in this round: * Wheader-guard -- This occurs when one has a typo in his or her header guards. For example: #ifndef INCLUDED_core_scoring_MyEnergy_HH #define INCLUDED_core_scoring_myEnergy_HH * Wself-assign-field -- This occurs when you write code like this: foo = foo; * Wliteral-conversion -- This occurs when you are using raw values -- which you never should be doing -- and those raw values are then cast with a loss of precision. For example: void my_function(int bar) { // do stuff } my_function(1.23456); * Wstring-plus-int -- These occur in three varieties and in EVERY case they occured within utility_exit_with_message(). (Fixing these should greatly improve the error helpfulness of Rosetta.) This occurs when you try to append an int to a string with +. utility_exit_with_message() takes a string, not a stream, so you can't do this. The three varieties are when folks try to append ints, chars, or enums, which the compiler will treat the same. To append a char to a string use: + std::string(1, my_char) To append am int or an enum, I like to use boost:: lexical_cast, but there are other methods also. (A plug for Clang -- all of these were only caught by Clang 3.4, which the test server uses.) * Wunitialized -- This occurs usually when your code makes assumptions that may well be correct, but the compiler cannot figure that out. If I could figure them out, I fixed them, but in a few cases I could not, so I have shut this warning OFF until I can find those of you who can fix this one. This also occurs if you try to instantiate an object from within its own constructor! Also, I have cleaned, sorted, and organized basic.settings. Hopefully, it will be easier to find where settings are located now. ---------------------------------------- Unit test status: Pass Integration test status: 6 tests changed, all of which are the result of my fixing what I believe to have been a bug do to a cast of raw float values to a boolean [Wliteral-conversion] antibody_designer antibody_H3 antibody_H3_legacy pepspec hotspot_graft dock_with_hotspot

• Summary

Fixing MySQL build. Adjusting linking path to include somewhat-standard mysql lib path. Adding mysql prefix to MySQL includes. This should allow MySQL build to work out-of-the-box for mosts Linux distributions when MySQL-devel package installed.

• Summary

Merging vmullig/metals into master. This updates the handling of metalloproteins in a number of important ways: --Adds option of automatic detection of covalent bonds to metals on PDB load. --Adds option of automatic setup of atom_pair and angle constraints between metals and metal-binding residues on PDB load. --Adds METALBINDING property to residue types. --Adds METAL property to residue types. --Adds METAL_BINDING_ATOMS line to params files. --Adds automatic removal of protons that overlap with metal ions. --Adds flags controlling behaviour of automatic metal setup. --Adds Cu and Co (residue types and atom types). --Allows automatic identification of metals: " ZN", "ZN ", "ZN1", and "ZN2" are all interpreted as ZN. --Alters unit and integration tests that used a ZN1.params file; these now use ZNx.params. All of these changes are documented on the Gollum wiki ("Metals" section of "Rosetta Basics"). Unit test status: Pass (with some unit tests' ZN1.params files changed to ZNx.params). Integration test status: Many changed tests, but all for expected reasons: 1. Trivial output changes due to addition of Cu2p and Co2p atom types. 2. Trivial output changes due to addition of CU.params and CO.params (on by default -- adds 2 new residue types). 3. Specific integration tests now use ZNx.params instead of ZN1.params; their output now says "ZNx" wherever it used to say "ZN1". 4. The usual numerical instabilities. modified: database/chemical/atom_type_sets/fa_standard/atom_properties.txt modified: database/chemical/atom_type_sets/fa_standard/extras/NACCESS_sasa_radii.txt modified: database/chemical/atom_type_sets/fa_standard/extras/atom_orbital_hybridization.txt modified: database/chemical/atom_type_sets/fa_standard/extras/facts_born_params.epm1.txt modified: database/chemical/atom_type_sets/fa_standard/extras/gen_born_params.txt modified: database/chemical/atom_type_sets/fa_standard/extras/memb_fa_params.txt modified: database/chemical/atom_type_sets/fa_standard/extras/reduce_sasa_radii.txt modified: database/chemical/atom_type_sets/fa_standard/extras/sasa_radii_legacy.txt modified: database/chemical/atom_type_sets/fa_standard/extras/soft_rep_params.txt modified: database/chemical/atom_type_sets/fa_standard/extras/std_charges.txt modified: database/chemical/mm_atom_type_sets/fa_standard/mm_atom_properties.txt modified: database/chemical/residue_type_sets/fa_standard/residue_types.txt modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/ASP.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/CYS.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/CYV.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/CYZ.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/GLU.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/HIS.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/l-caa/HIS_D.params new file: database/chemical/residue_type_sets/fa_standard/residue_types/metal_binding_ncaa/BPY.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/CA.params new file: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/CO.params new file: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/CU.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/FE.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/FE2.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/K.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/MG.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/MN.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/NA.params modified: database/chemical/residue_type_sets/fa_standard/residue_types/metal_ions/ZN.params new file: source/src/apps/pilot/vmullig/MetalNotes.txt new file: source/src/apps/pilot/vmullig/metals_notes.txt new file: source/src/apps/pilot/vmullig/test_metalloproteins.cc modified: source/src/basic/options/keys/OptionKeys.cc.gen0.hh modified: source/src/basic/options/keys/in.OptionKeys.gen.hh modified: source/src/basic/options/keys/inout.OptionKeys.gen.hh modified: source/src/basic/options/option.cc.gen.hh modified: source/src/basic/options/options_rosetta.py modified: source/src/core.3.src.settings modified: source/src/core/chemical/ResidueType.cc modified: source/src/core/chemical/ResidueType.hh modified: source/src/core/chemical/residue_io.cc modified: source/src/core/conformation/Residue.hh modified: source/src/core/import_pose/import_pose.cc modified: source/src/core/import_pose/import_pose_options.cc modified: source/src/core/import_pose/import_pose_options.hh modified: source/src/core/io/pdb/file_data.cc modified: source/src/core/io/pdb/file_data_fixup.cc modified: source/src/core/io/pdb/pose_io.cc modified: source/src/core/pose/Pose.cc new file: source/src/core/pose/metalloproteins/util.cc new file: source/src/core/pose/metalloproteins/util.hh modified: source/src/core/pose/util.cc modified: source/src/core/pose/util.hh modified: source/src/core/scoring/ScoreFunctionFactory.cc modified: source/test/apps.test.settings modified: source/test/apps/public/ligand_docking/7cpa_7cpa_input.pdb modified: source/test/apps/public/ligand_docking/7cpa_7cpa_native.pdb renamed: source/test/apps/public/ligand_docking/ZN1.params -> source/test/apps/public/ligand_docking/ZNx.params modified: source/test/apps/public/ligand_docking/ligand_dock.cxxtest.hh modified: source/test/apps/public/ligand_docking/silent.out.ref modified: source/test/protocols.test.settings modified: source/test/protocols/ligand_docking/7cpa_7cpa_native.pdb modified: source/test/protocols/ligand_docking/ResidueTorsionRestraints.cxxtest.hh renamed: source/test/protocols/ligand_docking/ZN1.params -> source/test/protocols/ligand_docking/ZNx.params renamed: tests/integration/tests/contactMap/input/ZN1.params -> tests/integration/tests/contactMap/input/ZNx.params modified: tests/integration/tests/database_jd2_compact_io/7cpa_7cpa_input.pdb.gz renamed: tests/integration/tests/database_jd2_compact_io/ZN1.params -> tests/integration/tests/database_jd2_compact_io/ZNx.params modified: tests/integration/tests/database_jd2_compact_io/test_input.flags modified: tests/integration/tests/database_jd2_compact_io/test_output.flags modified: tests/integration/tests/grid_scores_features/flags modified: tests/integration/tests/grid_scores_features/inputs/7cpa_7cpa_input.pdb.gz modified: tests/integration/tests/grid_scores_features/inputs/7cpa_7cpa_native.pdb.gz modified: tests/integration/tests/grid_scores_features/inputs/7cpa_confs.pdb.gz deleted: tests/integration/tests/grid_scores_features/inputs/ZN1.params new file: tests/integration/tests/grid_scores_features/inputs/ZNx.params modified: tests/integration/tests/kinemage_grid_output/flags modified: tests/integration/tests/kinemage_grid_output/inputs/7cpa_7cpa_input.pdb.gz modified: tests/integration/tests/kinemage_grid_output/inputs/7cpa_7cpa_native.pdb.gz modified: tests/integration/tests/kinemage_grid_output/inputs/7cpa_confs.pdb.gz deleted: tests/integration/tests/kinemage_grid_output/inputs/ZN1.params new file: tests/integration/tests/kinemage_grid_output/inputs/ZNx.params modified: tests/integration/tests/ligand_database_io/flags_param_output modified: tests/integration/tests/ligand_database_io/inputs/7cpa_confs.pdb.gz modified: tests/integration/tests/ligand_database_io/inputs/7cpa_input.pdb.gz modified: tests/integration/tests/ligand_database_io/inputs/7cpa_native.pdb.gz deleted: tests/integration/tests/ligand_database_io/inputs/ZN1.params new file: tests/integration/tests/ligand_database_io/inputs/ZNx.params modified: tests/integration/tests/ligand_dock_7cpa/flags modified: tests/integration/tests/ligand_dock_7cpa/inputs/7cpa_7cpa_input.pdb.gz modified: tests/integration/tests/ligand_dock_7cpa/inputs/7cpa_7cpa_native.pdb.gz modified: tests/integration/tests/ligand_dock_7cpa/inputs/7cpa_confs.pdb.gz deleted: tests/integration/tests/ligand_dock_7cpa/inputs/ZN1.params new file: tests/integration/tests/ligand_dock_7cpa/inputs/ZNx.params modified: tests/integration/tests/ligand_dock_grid/flags modified: tests/integration/tests/ligand_dock_grid/inputs/7cpa_7cpa_input.pdb.gz modified: tests/integration/tests/ligand_dock_grid/inputs/7cpa_7cpa_native.pdb.gz modified: tests/integration/tests/ligand_dock_grid/inputs/7cpa_confs.pdb.gz deleted: tests/integration/tests/ligand_dock_grid/inputs/ZN1.params new file: tests/integration/tests/ligand_dock_grid/inputs/ZNx.params modified: tests/integration/tests/ligand_dock_script/flags modified: tests/integration/tests/ligand_dock_script/inputs/7cpa_confs.pdb.gz modified: tests/integration/tests/ligand_dock_script/inputs/7cpa_input.pdb.gz modified: tests/integration/tests/ligand_dock_script/inputs/7cpa_native.pdb.gz deleted: tests/integration/tests/ligand_dock_script/inputs/ZN1.params new file: tests/integration/tests/ligand_dock_script/inputs/ZNx.params modified: tests/integration/tests/startfrom_file/inputs/7cpa_7cpa_input.pdb.gz modified: tests/integration/tests/startfrom_file/inputs/7cpa_7cpa_native.pdb.gz modified: tests/integration/tests/startfrom_file/inputs/7cpa_confs.pdb.gz deleted: tests/integration/tests/startfrom_file/inputs/ZN1.params new file: tests/integration/tests/startfrom_file/inputs/ZNx.params modified: tests/integration/tests/startfrom_file/mover_flags modified: tests/integration/tests/startfrom_file/startfrom_flags modified: tests/integration/tests/write_mol_file/flags modified: tests/integration/tests/write_mol_file/inputs/7cpa_confs.pdb.gz modified: tests/integration/tests/write_mol_file/inputs/7cpa_input.pdb.gz deleted: tests/integration/tests/write_mol_file/inputs/ZN1.params new file: tests/integration/tests/write_mol_file/inputs/ZNx.params

• Summary

Ring Conformers: fixing major degrees-to-radians bug in my previous push 118 degrees != 118 radians Carbohydrate ring conformers now look good, even in strained cases. I also edited cyclohexylglycine params so that AtomTree does not flip out on ring conformation changes. (I was too quick to celebrate on my previous push; it is more complicated to make a ring system work with the RingConformationMover. One needs to ensure the AtomTree behaves properly by defining a CUT_BOND and at least one virtual atom. I'll document this all later once I refine things more.) Only the rings integration test changes, as expected.

• Summary

Fix hybridize integration test to prevent warning message

• Summary

Fixing PyRosetta build

• Summary

Adding PyRosetta build test script

• Summary

On his behalf, revert Kala's commits. Revert test server commits 56493 and 56494 This reverts commit 12a020b263aaafa9240b00a71767d95dec49046b, reversing changes made to c4ba068409eef69b385f04b04b8b5ab322aada8c. It also reverts commit 199441208b2b2f2, which effectively duplicates 12a020b263aaafa9240b00a71 (1994412 is a merge commit of two merge commits, each of which merge the same two commits).

• Summary

Removing dependencies on core in RingDetection so that the library build will be fixed

• Summary

Ring Conformers: Two large improvements to the ring conformer system NEWS: This push introduces 2 major changes: 1st, RingConformerSet and related code has been moved out of carbohydrate namespaces into more general ones. 2nd, tau angles are now stored in RingConformers. Now, if anyone wishes to use the RingConformationMover, they only need to define 2 less than the number of atoms in the ring nu angles and add the property CYCLIC to the .params file for a ResidueType. I have added an NCAA, cyclohexylglycine, to the rings integration test to demonstrate this. The addition of tau angles (internal bond angles) is because more highly strained rings have bond angle distortions. Now, when a ring is set to a strained conformer, the bond angles are also set to ideal values so that the ring "stays together". Currently, I only have the system fully working for 6-membered rings, but 5-membered rings should follow shortly, once I calculate/figure out ideal taus for them. ---------------------------------------- Unit test status: Pass Integration test status: ~150 This is because I introduced one more ResidueType into the Set. carbohydrates and rings will also change

• Summary

Add checks and warnings for non-ideal minimization. If you use non-ideal minimization (Cartesian minimization, or flexible bondlengths and angles), you need to have a scorefunction which is appropriately set up for it (e.g. cart_bonded on), otherwise your protocol will collapse your structure. This adds checks to the minimizers to validate that things are set up appropriately. (Similar checks have already been added to rtmin and the min_packer). While such checks result in errors for rtmin, the min_packer, and the CartesianMinimizer, for the (Sym)AtomTreeMinimizer they're only warnings. The reason for this is that several protocols being integration tested are currently using settings which trigger the state checks. As a bonus, more extensive output of the MoveMap settings via the show() function were added. Integration test changes expected due to warnings added for the following protocols: hybridization rna_denovo erraser_minimize The following integration test changes due to the extra information addeed to MoveMap::show() rings

• Summary

Remove warnings from pilot app

• Summary

Adding an integration test for motif extraction. Also, changing default behavior of VIP application to use 'thorough' relax instead of 'fast' relax, and to do a quick pre-relax in the app. This will cause changes in the vip test.

• Summary

Comment out unused variable to fix linux clang unit build

• Summary

Legend: