Fixed Cterm_amidation hydrogen naming Many residues have hydrogens named e.g. 1HE2/2HE2, which rendered the atom names in Cterm_amidation problematic sometimes. C-terminal glutamine with this patch applied would see protons flying all over the place, potentially affecting pose scoring, for reasons incomprehensible. Additional advantage: the new names, 1HN and 2HN, are the Correct Names according to PDB style and don't conflict with anything but mutually incompatible patches like Cterm methylamidation.

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Addeed if conditional to handle case where Splice.cc deals with one pose.

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Add information to 'option not found' error in utility::tag::Tag.

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merge of SWM phosphate-pack fix to master. Checked integration tests of this fix - changes to swm tests and apparent floating point changes in inverse_rotamer_remodel and match_1n9l

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Temporarily removing some pilot apps from pilot_apps.src.settings.all which are causing the debug compilation to fail due to errors-as-warnings. Kevin, please check these: several have unused variables, and sasa_buns.cc has a typo. These also seem to be causing the app_exception_handling integration test to fail.

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Change pose->set_new_conformation() to take a ConformationCOP rather than a ConformationOP since it clones it anyway.

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bugfix to finally allow SnugDock to work on antibodies with any antibody numbering scheme and cdr definition

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Modifying the Symmetric rotamer set functions to enable symmetric pose that contain peptoids Peptoids use a different orient_on_to_residue function to properly align the first side chain atom. This commit updates the symmetry code to call the alternate function when the targe tresidue is a peptoid backbone. Unit test status: All pass except the two DdgFilter test Integration test status: All pass except app_exception_handling and buried_unsat_kinemage

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Removing ORNX.params from the database. This was a residue type that I started to add but never got around to testing; I hadn't meant for it to make its way into master quite yet. No integration or unit test changes expected.

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Reenable warnings-as-errors in scons. Also fix warnings-as-errors issues with gcc and clang under linux. Hopefully the test server doesn't pick up any additional ones.

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Merging vmullig/cycpep into master. This tweaks GeneralizedKIC a bit, as well as fixing a problem in setting the position of atoms dependent on non-polymer connections on PDB import. (This might fix the problem with the UBQ_E2_thioester_extra_bodies and UBQ_E2_thioester_two_ubiquitins integration tests on the test server -- I'm not sure. I haven't been able to reproduce that failure.) Unit test status: All pass except the two that have been failing (protocols:DdgFilter:test_filter_parsing and protocols:DdgFilter:test_use_filter) Integration test status: No changed tests; two were already failing (app_exception_handling and buried_unsat_kinemage). As mentioned, the UBQ tests that fail on the test server don't fail when I run the integration tests. Changes to be committed: (use "git reset HEAD <file>..." to unstage) modified: source/src/core/chemical/AtomICoor.cc modified: source/src/core/chemical/AtomICoor.hh modified: source/src/core/conformation/Conformation.cc modified: source/src/protocols/generalized_kinematic_closure/GeneralizedKIC.cc modified: source/src/protocols/generalized_kinematic_closure/util.cc

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Add atom mapping facility to PDB file loading. -- Gemetric Remapping. The core of this commit is to allow Rosetta to remap atom names when loading PDB files, specifically in the case where you may have renamed the atoms. (Main use case was for sdf file loading, which don't have atom names.) For example, if you have a ligand params file with one set of atom names, but want to use it to load a PDB with different atom names for that residue, you can do that in one of three ways: * Call ResidueType::remap_pdb_atom_names( true ) in the code * Add the line "REMAP_PDB_ATOM_NAMES" to your params file. * Add the commandline flag "-remap_pdb_atom_names_for LG1 LG2", specifying one or more three letter names of the residues you wish to remap Then when that ResidueType is used in PDB loading, remapping will happen based on the percieved geometry of the input residue, matching up the elements and bonding as best as it can between what's in the ResidueType and the percieved geometry in the PDB residue. Each input residue of the same name3 can get different name mappings, although the name remapping occurs after the detection of the best ResidueType, so geometric remapping will not help with distinguishing between two residues with the same name3. -- Atom Aliases As part of the name remapping, it was simple to add atom aliases. That is, params file can now have an ATOM_ALIAS line, which tells Rosetta about alternative names for atoms. (Again, this happens post ResidueType decision.) For example, we could now add the line: ATOM_ALIAS 1HH1 HH11 To the ARG.params file to tell Rosetta that HH11 is a valid alternative name for the hydrogen it normally calls 1HH1, allowing direct coordinate loading for that atom from PDB NMR structures. Note that while I've added the facility to Rosetta, I haven't yet added any ATOM_ALIAS lines to the database, as I was seeing conflicting information about how to map PDB-typical atom names to Rosetta atom names. Specifically, depending on source I saw different chiralities for atoms. (e.g. do the ALA methyl protons HB1->HB2->HB3 go clockwise or counter-clockwise when viewed along the CA->CB vector?). -- Bug Fixes In PDB file loading there were issues with atom recognition. Specifically, coordinate assignment went via whitespace-stripped name, whereas missing atom detection went by whitespace-preserved name. This causes Rosetta to rebuild things like "OXT " atoms, which occur in a number of integration tests (the expected name is " OXT"). This commit now attempts to use the whitespace stripped version for coordinate assigment, and then bases the missing atom detection on which atoms had coordinates assigned. (This difference accounts for the bulk of the test changes.) Also, there was a chain-termini adjustment finalization which updated the residue type with the new terminius variants, but didn't attempt to assign coordinates to new atoms if there were (otherwise) ignored atoms with the appropriate names (e.g. " OXT"). This resulted in atoms that didn't get coordinates assigned, but that weren't necessarily annotated as missing atoms. This commit attempts to detect that somewhat, and assign coordinates if the atom is present. (But not as well as if the termini is detected originally.) -- Integration test changes expected: Extra Trace-level output ---------------- FAIL fold_and_dock Whitespace stripping issues on atom name loading -------------- FAIL contactMap FAIL database_jd2_compact_io FAIL grid_scores_features FAIL kinemage_grid_output FAIL ligand_database_io FAIL ligand_dock_7cpa FAIL ligand_dock_grid FAIL ligand_dock_script FAIL ligand_water_docking FAIL residue_data_resource FAIL sdf_reader FAIL startfrom_file FAIL write_mol_file Termini fixup coordinate related changes ---------------- FAIL zinc_homodimer_design Also silently affects: AnchorFinder motif_extraction rs_flexbbmoves zinc_heterodimer Cosmetic tracer changes ----------------------- FAIL AnchorFinder FAIL gen_lig_grids FAIL jd2test

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Removing debug output from DeclareBond.cc.

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Merging vmullig/ncaas into master. This changes some core functionality in a way that should reproduce the old functionality exactly, except in cases where terminal residues have backbone-backbone or backbone-sidechain connections (e.g. cyclic peptides). I'm trying to take out some of the instances of Rosetta assuming that each residue is connected to the i+1 and i-1 residues, so that terminal residues with connections will score properly. Unit tests: All pass Integration tests: 2 are failing to run in the master branch already (app_exception_handling, buried_unsat_kinemage) 2 expected changes; 13 others that seem to be random, small changes: UBQ_Gp_LYX-Cterm and UBQ_EZ_thioester: expected changes since the C-terminal glycine that's bonded to a sidechain should now score properly with p_aa_pp and omega. Small random changes: remodel_disulfides inverse_rotamer_remodel antibody_H3 relax_w_allatom_cst antibody_H3_legacy antibody_legacy -- NOTE: This one is producing bizarre output, both before and after this change (see the output PDB file). KIC_vicinity hotspot_graft rs_flexbbmoves antibody_designer antibody_graft jrelax Additional notes: --This change updates the way that residue backbone torsions are computed in Conformation.cc. Instead of assuming that each residue is connected to the i-1 residue at its lower connection, and the i+1 residue at its upper connection, Rosetta now checks what the residue is actually connected to and uses that for calculation of mainchain torsions. --This should not change torsion calculation or scoring in any usually-encountered case. --This should not affect the CTERM_CONNECT or NTERM_CONNECT types that were added when the peptoids branch was merged into master, recently. Those are still handled as special cases. --If anyone notices any aberrant functionality as a result of this change, please e-mail me (vmullig@uw.edu). I've tried to be as thorough in my testing as possible, but with a deep core change, it's always possible that something was broken.

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Fix raw pointer use in core::util::add_cutpoint_variants() Meilerlab Powercoding with Alyssa Lokits This addresses the core of bug 0000336 - removing the raw pointer use in core::util::add_cutpoint_variants() and remove_cutpoint_variants(). It also starts in on the comments made by Justin Porter, replacing core::util::add_cutpoint_variants() use with core::util::pose::correctly_add_cutpoint_variants() Attempts to fold in some of the other add_cutpoints/add_chainbreaks were made, but we ran out of time prior to debugging them. No test changes (aside from currently failing ones) expected.

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