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Revisions №61433

branch: master 「№61433」
Commited by: Sergey Lyskov
GitHub commit link: 「56c232a7e5b5cad7」 「№4999」
Difference from previous tested commit:  code diff
Commit date: 2020-09-24 23:00:53
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
PyRosetta4.notebook gcc-9.gcc.python37.PyRosetta4.unit linux.clang.cxx11thread.serialization.python37.PyRosetta4.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug alpine.gcc.build.debug clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug gcc-9.gcc.build.debug mysql postgres linux.clang.python36.build.debug linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL mac.clang.python36.build.debug build.header build.levels build.ninja_debug graphics static build.xcode beautification code_quality.clang_analysis code_quality.clang_tidy code_quality.cppcheck serialization code_quality.submodule_regression integration.mpi integration.release_debug integration.tensorflow integration.thread integration performance profile release.source scientific.ligand_scoring_ranking linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release gcc-9.gcc.unit util.apps

Merge pull request #4999 from RosettaCommons/revert-4714-roccomoretti/rdkit_submodule2 Revert "Add RDKit as a submodule to Rosetta."

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Failed sub-tests (click for more details):
src/apps/benchmark/performance/performance_benchmark.cc src/apps/benchmark/scientific/ddg_benchmark.cc src/apps/benchmark/scientific/design_contrast_and_statistic.cc src/apps/benchmark/scientific/rotamer_recovery.cc src/apps/public/DRRAFTER/drrafter_error_estimation.cc src/apps/public/DRRAFTER/fit_helix_in_map.cc src/apps/public/analysis/InterfaceAnalyzer.cc src/apps/public/analysis/ResidueDisorder.cc src/apps/public/analysis/batch_distances.cc src/apps/public/analysis/per_residue_solvent_exposure.cc src/apps/public/analysis/report_hbonds_for_plugin.cc src/apps/public/analysis/residue_energy_breakdown.cc src/apps/public/analysis/score.cc src/apps/public/analysis/shobuns.cc src/apps/public/antibody/antibody.cc src/apps/public/antibody/antibody_CR_paratope.cc src/apps/public/antibody/antibody_H3.cc src/apps/public/antibody/antibody_designer.cc src/apps/public/antibody/identify_cdr_clusters.cc src/apps/public/antibody/packing_angle.cc src/apps/public/calculate_sasa.cc src/apps/public/carbohydrates/dock_glycans.cc src/apps/public/carbohydrates/glycan_clash_check.cc src/apps/public/comparative_modeling/avrg_silent.cc src/apps/public/comparative_modeling/cluster_alns.cc src/apps/public/comparative_modeling/fix_alignment_to_match_pdb.cc src/apps/public/comparative_modeling/full_length_model.cc src/apps/public/comparative_modeling/iterhybrid_selector.cc src/apps/public/comparative_modeling/partial_thread.cc src/apps/public/comparative_modeling/score_aln.cc src/apps/public/comparative_modeling/score_aln2.cc src/apps/public/comparative_modeling/spheregrinder.cc src/apps/public/comparative_modeling/super_aln.cc src/apps/public/comparative_modeling/template_features.cc src/apps/public/constel.cc src/apps/public/coupled_moves/coupled_moves.cc src/apps/public/cyclic_peptide/simple_cycpep_predict.cc src/apps/public/darc/DARC.cc src/apps/public/darc/make_ray_files.cc src/apps/public/darc/theta_ligand.cc src/apps/public/ddg/cartesian_ddg.cc src/apps/public/ddg/ddg_monomer.cc src/apps/public/ddg/ensemble_generator_score12_sidechain_ver2.cc src/apps/public/ddg/minimize_with_cst.cc src/apps/public/design/beta_peptide_modeling.cc src/apps/public/design/create_clash-based_repack_shell.cc src/apps/public/design/fixbb.cc src/apps/public/design/mpi_msd.cc src/apps/public/design/sequence_recovery.cc src/apps/public/design/supercharge.cc src/apps/public/design/zinc2_homodimer_design.cc src/apps/public/design/zinc2_homodimer_setup.cc src/apps/public/design/zinc_heterodimer_design.cc src/apps/public/docking/docking_protocol.cc src/apps/public/dump_capped_residue.cc src/apps/public/electron_density/denovo_density.cc src/apps/public/electron_density/density_tools.cc src/apps/public/electron_density/grower_prep.cc src/apps/public/enzdes/CstfileToTheozymePDB.cc src/apps/public/extract_pdbs.cc src/apps/public/fiber_diffraction/FiberDiffractionFreeSet.cc src/apps/public/hydrate/hydrate.cc src/apps/public/interface_design/anchored_design/AnchorFinder.cc src/apps/public/legacy_sewing/sewing_hasher.cc src/apps/public/ligand_docking/ligand_rpkmin.cc src/apps/public/ligand_docking/select_best_unique_ligand_poses.cc src/apps/public/magnesium/mg_modeler.cc src/apps/public/match/gen_apo_grids.cc src/apps/public/match/gen_lig_grids.cc src/apps/public/match/match.cc src/apps/public/membrane/mp_domain_assembly.cc src/apps/public/membrane/mp_seqrecov.cc src/apps/public/membrane/mp_span_from_pdb.cc src/apps/public/membrane/mp_viewer.cc src/apps/public/minimize.cc src/apps/public/minimize_ppi.cc src/apps/public/motif_dock/make_motif_tables.cc src/apps/public/motif_tools/extract_motifs.cc src/apps/public/mutate.cc src/apps/public/ncaa_utilities/UnfoldedStateEnergyCalculator.cc src/apps/public/nmr/ligand_transform_with_pcs.cc src/apps/public/noncanonical_backbones/hbs_design.cc src/apps/public/noncanonical_backbones/oop_design.cc src/apps/public/noncanonical_backbones/peptoid_design.cc src/apps/public/pH_protocol.cc src/apps/public/pepspec/pepspec.cc src/apps/public/pepspec/pepspec_anchor_dock.cc src/apps/public/pocket/make_exemplar.cc src/apps/public/pocket/pocket_measure.cc src/apps/public/pocket/pocket_relax.cc src/apps/public/pocket/pocket_suggest_target_residues_by_ddg.cc src/apps/public/recces/legacy/recces_turner.cc src/apps/public/remodel.cc src/apps/public/restype_converter.cc src/apps/public/rna/erraser/erraser2.cc src/apps/public/rna/rna_denovo.cc src/apps/public/rna/rna_design.cc src/apps/public/rna/thread/rna_thread.cc src/apps/public/rna/thread/rna_thread_and_minimize.cc src/apps/public/rna/util/analyze_base_pairing.cc src/apps/public/rna/util/cs_rosetta_rna.cc src/apps/public/rna/util/nucleobase_sample_around.cc src/apps/public/rna/util/rna_cluster.cc src/apps/public/rna/util/rna_database.cc src/apps/public/rna/util/rna_extract.cc src/apps/public/rna/util/rna_features.cc src/apps/public/rna/util/rna_graft.cc src/apps/public/rna/util/rna_helix.cc src/apps/public/rna/util/rna_motif.cc src/apps/public/rna/util/rna_predict_chem_map.cc src/apps/public/rna/util/rna_score.cc src/apps/public/rna/util/rna_suitename.cc src/apps/public/rnp_ddg/rnp_ddg.cc src/apps/public/rosetta_scripts/revert_design_to_native.cc src/apps/public/scenarios/beta_strand_homodimer_design/exposed_strand_finder.cc src/apps/public/scenarios/beta_strand_homodimer_design/homodimer_design.cc src/apps/public/scenarios/beta_strand_homodimer_design/homodimer_maker.cc src/apps/public/scenarios/ca_to_allatom.cc src/apps/public/scenarios/chemically_conjugated_docking/UBQ_E2_thioester.cc src/apps/public/scenarios/chemically_conjugated_docking/UBQ_Gp_CYD-CYD.cc src/apps/public/scenarios/doug_dock_design_min_mod2_cal_cal.cc src/apps/public/sequence_tolerance.cc src/apps/public/sewing/ligand_sewing_tools/backside_hbond_finder.cc src/apps/public/sewing/ligand_sewing_tools/generate_starting_zinc_sites.cc src/apps/public/sewing/ligand_sewing_tools/metal_site_finder.cc src/apps/public/sewing/ligand_sewing_tools/zinc_statistic_generator.cc src/apps/public/sewing/segment_file_generator.cc src/apps/public/stepwise/build_full_model.cc src/apps/public/stepwise/legacy/swa_protein_main.cc src/apps/public/stepwise/legacy/swa_rna_main.cc src/apps/public/stepwise/legacy/swa_rna_util.cc src/apps/public/stepwise/resample_full_model.cc src/apps/public/stepwise/stepwise.cc src/apps/public/vip.cc src/apps/public/weight_optimization/torsional_potential_corrections.cc src/apps/tests/test_C-terminal_conjugation.cc src/apps/tests/test_CarbohydrateInfo.cc src/apps/tests/test_carbohydrate_scoring.cc src/apps/tests/test_coenzymes.cc src/apps/tests/test_explicit_membrane_input.cc src/apps/tests/test_non-canonical_connectivities.cc src/core/chemical/AtomICoor.cc src/core/chemical/ChemicalManager.cc src/core/chemical/GlobalResidueTypeSet.cc src/core/chemical/Metapatch.cc src/core/chemical/MutableChiRecord.cc src/core/chemical/MutableICoorRecord.cc src/core/chemical/MutableResidueType.cc src/core/chemical/Patch.cc src/core/chemical/PatchOperation.cc src/core/chemical/PoseResidueTypeSet.cc src/core/chemical/ResidueDatabaseIO.cc src/core/chemical/ResidueProperties.cc src/core/chemical/ResidueProperty_mappings.cc src/core/chemical/ResidueSubGraphTypes.cc src/core/chemical/ResidueType.cc src/core/chemical/ResidueTypeBase.cc src/core/chemical/ResidueTypeFinder.cc src/core/chemical/ResidueTypeKinWriter.cc src/core/chemical/ResidueTypeSelector.cc src/core/chemical/ResidueTypeSet.cc src/core/chemical/ResidueTypeSetCache.cc src/core/chemical/VariantType_mappings.cc src/core/chemical/adduct_util.cc src/core/chemical/atomtype_support.cc src/core/chemical/automorphism.cc src/core/chemical/bond_support.cc src/core/chemical/carbohydrates/CarbohydrateInfo.cc src/core/chemical/gasteiger/GasteigerAtomTyper.cc src/core/chemical/icoor_support.cc src/core/chemical/mainchain_potential/MainchainScoreTable.cc src/core/chemical/mmCIF/mmCIFParser.cc src/core/chemical/orbitals/AssignOrbitals.cc src/core/chemical/residue_io.cc src/core/chemical/residue_support.cc src/core/chemical/rna/RNA_Info.cc src/core/chemical/rna/util.cc src/core/chemical/rotamers/NCAARotamerLibrarySpecification.cc src/core/chemical/sdf/MolFileIOData.cc src/core/chemical/sdf/MolFileIOReader.cc src/core/chemical/sdf/mol_writer.cc src/core/chemical/util.cc src/core/conformation/AtomGraph.cc src/core/conformation/Conformation.cc src/core/conformation/PointGraph.cc src/core/conformation/Residue.cc src/core/conformation/Residue.functions.cc src/core/conformation/ResidueFactory.cc src/core/conformation/ResidueKinWriter.cc src/core/conformation/ResidueMatcher.cc src/core/conformation/UltraLightResidue.cc src/core/conformation/carbohydrates/GlycanNode.cc src/core/conformation/carbohydrates/GlycanTree.cc src/core/conformation/carbohydrates/GlycanTreeSet.cc src/core/conformation/carbohydrates/GlycanTreeSetObserver.cc src/core/conformation/carbohydrates/util.cc src/core/conformation/membrane/MembraneInfo.cc src/core/conformation/parametric/Parameters.cc src/core/conformation/parametric/ParametersSet.cc src/core/conformation/parametric/ParametrizationCalculator.cc src/core/conformation/parametric/RealValuedParameter.cc src/core/conformation/signals/LengthEvent.cc src/core/conformation/symmetry/MirrorSymmetricConformation.cc src/core/conformation/symmetry/SymmetricConformation.cc src/core/conformation/symmetry/SymmetryInfo.cc src/core/conformation/symmetry/SymmetryTransform.cc src/core/conformation/symmetry/util.cc src/core/conformation/util.cc src/core/energy_methods/AACompositionEnergy.cc src/core/energy_methods/AARepeatEnergy.cc src/core/energy_methods/AbegoEnergy.cc src/core/energy_methods/ArgCationPiEnergy.cc src/core/energy_methods/AromaticBackboneRestraintEnergy.cc src/core/energy_methods/AspartimidePenaltyEnergy.cc src/core/energy_methods/BranchEnergy.cc src/core/energy_methods/BurialEnergy.cc src/core/energy_methods/Burial_v2Energy.cc src/core/energy_methods/CartesianBondedEnergy.cc src/core/energy_methods/CenHBEnergy.cc src/core/energy_methods/CenPairEnergy.cc src/core/energy_methods/CenPairMotifDegreeEnergy.cc src/core/energy_methods/CenPairMotifEnergy.cc src/core/energy_methods/CenRotEnvEnergy.cc src/core/energy_methods/CenRotPairEnergy.cc src/core/energy_methods/CentroidDisulfideEnergy.cc src/core/energy_methods/ChainbreakEnergy.cc src/core/energy_methods/ChemicalShiftAnisotropyEnergy.cc src/core/energy_methods/ContactOrderEnergy.cc src/core/energy_methods/ContextDependentGeometricSolEnergy.cc src/core/energy_methods/ContextIndependentGeometricSolEnergy.cc src/core/energy_methods/CovalentLabelingEnergy.cc src/core/energy_methods/CovalentLabelingFAEnergy.cc src/core/energy_methods/CustomAtomPairEnergy.cc src/core/energy_methods/D2H_SA_Energy.cc src/core/energy_methods/DEEREnergy.cc src/core/energy_methods/DFIRE_Energy.cc src/core/energy_methods/DNAChiEnergy.cc src/core/energy_methods/DNATorsionEnergy.cc src/core/energy_methods/DNA_BaseEnergy.cc src/core/energy_methods/DNA_DihedralEnergy.cc src/core/energy_methods/DNA_EnvPairEnergy.cc src/core/energy_methods/DNA_ReferenceEnergy.cc src/core/energy_methods/DipolarCouplingEnergy.cc src/core/energy_methods/DirectReadoutEnergy.cc src/core/energy_methods/DistanceChainbreakEnergy.cc src/core/energy_methods/DisulfideMatchingEnergy.cc src/core/energy_methods/DumpTrajectoryEnergy.cc src/core/energy_methods/ElecDensAllAtomCenEnergy.cc src/core/energy_methods/ElecDensAtomwiseEnergy.cc src/core/energy_methods/ElecDensCenEnergy.cc src/core/energy_methods/ElecDensEnergy.cc src/core/energy_methods/EnvEnergy.cc src/core/energy_methods/EnvSmoothEnergy.cc src/core/energy_methods/ExactOccludedHbondSolEnergy.cc src/core/energy_methods/FACTSEnergy.cc src/core/energy_methods/FA_ElecEnergyAroAll.cc src/core/energy_methods/FA_ElecEnergyAroAro.cc src/core/energy_methods/FA_GrpElecEnergy.cc src/core/energy_methods/FaMPEnvEnergy.cc src/core/energy_methods/FaMPEnvSmoothEnergy.cc src/core/energy_methods/FaMPSolvEnergy.cc src/core/energy_methods/Fa_MbenvEnergy.cc src/core/energy_methods/Fa_MbsolvEnergy.cc src/core/energy_methods/FastDensEnergy.cc src/core/energy_methods/FastSAXSEnergy.cc src/core/energy_methods/FiberDiffractionEnergy.cc src/core/energy_methods/FiberDiffractionEnergyDens.cc src/core/energy_methods/FreeDOF_Energy.cc src/core/energy_methods/FullatomDisulfideEnergy.cc src/core/energy_methods/GaussianOverlapEnergy.cc src/core/energy_methods/GenBornEnergy.cc src/core/energy_methods/GenericBondedEnergy.cc src/core/energy_methods/GoapEnergy.cc src/core/energy_methods/HRFDynamicsEnergy.cc src/core/energy_methods/HRF_MSLabelingEnergy.cc src/core/energy_methods/HackAroEnergy.cc src/core/energy_methods/HolesEnergy.cc src/core/energy_methods/HybridVDW_Energy.cc src/core/energy_methods/HydroxylTorsionEnergy.cc src/core/energy_methods/LK_PolarNonPolarEnergy.cc src/core/energy_methods/LK_hack.cc src/core/energy_methods/LinearBranchEnergy.cc src/core/energy_methods/LinearChainbreakEnergy.cc src/core/energy_methods/LoopCloseEnergy.cc src/core/energy_methods/MHCEpitopeEnergy.cc src/core/energy_methods/MPCBetaEnergy.cc src/core/energy_methods/MPEnvEnergy.cc src/core/energy_methods/MPHelicalityEnergy.cc src/core/energy_methods/MPPairEnergy.cc src/core/energy_methods/MPResidueLipophilicityEnergy.cc src/core/energy_methods/MPSpanAngleEnergy.cc src/core/energy_methods/MPSpanInsertionEnergy.cc src/core/energy_methods/MembraneCbetaEnergy.cc src/core/energy_methods/MembraneCenPairEnergy.cc src/core/energy_methods/MembraneEnvEnergy.cc src/core/energy_methods/MembraneEnvPenalties.cc src/core/energy_methods/MembraneEnvSmoothEnergy.cc src/core/energy_methods/MembraneLipo.cc src/core/energy_methods/MgEnergy.cc src/core/energy_methods/MotifDockEnergy.cc src/core/energy_methods/MultipoleElecEnergy.cc src/core/energy_methods/NPDHBondEnergy.cc src/core/energy_methods/NetChargeEnergy.cc src/core/energy_methods/OccludedHbondSolEnergy.cc src/core/energy_methods/OccludedHbondSolEnergy_onebody.cc src/core/energy_methods/OmegaTetherEnergy.cc src/core/energy_methods/P_AA_Energy.cc src/core/energy_methods/P_AA_pp_Energy.cc src/core/energy_methods/P_AA_ss_Energy.cc src/core/energy_methods/PairEnergy.cc src/core/energy_methods/PeptideBondEnergy.cc src/core/energy_methods/PointWaterEnergy.cc src/core/energy_methods/PoissonBoltzmannEnergy.cc src/core/energy_methods/ProClosureEnergy.cc src/core/energy_methods/ProQ_Energy.cc src/core/energy_methods/RG_Energy_Fast.cc src/core/energy_methods/RG_Energy_RNA.cc src/core/energy_methods/RG_LocalEnergy.cc src/core/energy_methods/RNA_BulgeEnergy.cc src/core/energy_methods/RNA_ChemicalMappingEnergy.cc src/core/energy_methods/RNA_ChemicalShiftEnergy.cc src/core/energy_methods/RNA_DataBackboneEnergy.cc src/core/energy_methods/RNA_FA_ElecEnergy.cc src/core/energy_methods/RNA_FullAtomStackingEnergy.cc src/core/energy_methods/RNA_FullAtomVDW_BasePhosphate.cc src/core/energy_methods/RNA_JR_SuiteEnergy.cc src/core/energy_methods/RNA_LJ_BaseEnergy.cc src/core/energy_methods/RNA_MgPointEnergy.cc src/core/energy_methods/RNA_PairwiseLowResolutionEnergy.cc src/core/energy_methods/RNA_StubCoordinateEnergy.cc src/core/energy_methods/RNA_SugarCloseEnergy.cc src/core/energy_methods/RNA_SuiteEnergy.cc src/core/energy_methods/RNA_TorsionEnergy.cc src/core/energy_methods/RNA_VDW_Energy.cc src/core/energy_methods/RNP_LowResEnergy.cc src/core/energy_methods/RNP_LowResPairDistEnergy.cc src/core/energy_methods/RNP_LowResStackEnergy.cc src/core/energy_methods/RamaPreProEnergy.cc src/core/energy_methods/RamachandranEnergy.cc src/core/energy_methods/RamachandranEnergy2B.cc src/core/energy_methods/ReferenceEnergy.cc src/core/energy_methods/ReferenceEnergyNoncanonical.cc src/core/energy_methods/ResidualDipolarCouplingEnergy.cc src/core/energy_methods/ResidualDipolarCouplingEnergy_Rohl.cc src/core/energy_methods/RingClosureEnergy.cc src/core/energy_methods/SASAEnergy.cc src/core/energy_methods/SAXSEnergy.cc src/core/energy_methods/SSElementMotifContactEnergy.cc src/core/energy_methods/SecondaryStructureEnergy.cc src/core/energy_methods/SequenceDependentRefEnergy.cc src/core/energy_methods/SmoothCenPairEnergy.cc src/core/energy_methods/SmoothEnvEnergy.cc src/core/energy_methods/SplitUnfoldedTwoBodyEnergy.cc src/core/energy_methods/SplitUnfoldedTwoBodyEnergyCreator.cc src/core/energy_methods/StackElecEnergy.cc src/core/energy_methods/SuckerEnergy.cc src/core/energy_methods/SugarBackboneEnergy.cc src/core/energy_methods/SurfEnergy.cc src/core/energy_methods/SurfVolEnergy.cc src/core/energy_methods/SymmetricLigandEnergy.cc src/core/energy_methods/TNA_SuiteEnergy.cc src/core/energy_methods/UnfoldedStateEnergy.cc src/core/energy_methods/VdWTinkerEnergy.cc src/core/energy_methods/WaterAdductHBondEnergy.cc src/core/energy_methods/WaterAdductIntraEnergy.cc src/core/energy_methods/WaterSpecificEnergy.cc src/core/energy_methods/XtalMLEnergy.cc src/core/energy_methods/YHHPlanarityEnergy.cc src/core/energy_methods/non_scorefxn_exact_model.cc src/core/energy_methods/pHEnergy.cc src/core/environment/DofPassport.cc src/core/fragment/BBTorsionAndAnglesSRFD.cc src/core/fragment/FragData.cc src/core/fragment/FragmentSetLoader.cc src/core/fragment/Frame.cc src/core/fragment/IndependentBBTorsionSRFD.cc src/core/fragment/JumpSRFD.cc src/core/fragment/SingleResidueFragData.cc src/core/fragment/rna/FullAtomRNA_Fragments.cc src/core/fragment/rna/RNA_FragmentHomologyExclusion.cc src/core/fragment/util.cc src/core/import_pose/FullModelPoseBuilder.cc src/core/import_pose/PDBSilentStruct.cc src/core/import_pose/RNA_BasePairHandler.cc src/core/import_pose/RNA_DeNovoSetup.cc src/core/import_pose/RNA_HelixAssembler.cc src/core/import_pose/RNA_JumpMover.cc src/core/import_pose/atom_tree_diffs/atom_tree_diff.cc src/core/import_pose/import_pose.cc src/core/import_pose/libraries/ChunkSet.cc src/core/import_pose/libraries/RNA_ChunkLibrary.cc src/core/import_pose/libraries/RNA_JumpLibrary.cc src/core/import_pose/pose_stream/LazySilentFilePoseInputStream.cc src/core/import_pose/pose_stream/PoseInputStream.cc src/core/import_pose/pose_stream/SilentFilePoseInputStream.cc src/core/init/init.cc src/core/io/StructFileRepOptions.cc src/core/io/carbohydrates/pose_io.cc src/core/io/external/PsiPredInterface.cc src/core/io/mmcif/cif_reader.cc src/core/io/mmcif/cif_writer.cc src/core/io/mmtf/mmtf_reader.cc src/core/io/mmtf/mmtf_writer.cc src/core/io/pdb/build_pose_as_is.cc src/core/io/pdb/pdb_writer.cc src/core/io/pose_from_sfr/PoseFromSFRBuilder.cc src/core/io/pose_from_sfr/chirality_resolution.cc src/core/io/pose_to_sfr/PoseToStructFileRepConverter.cc src/core/io/raw_data/DecoyStruct.cc src/core/io/raw_data/DisulfideFile.cc src/core/io/rna/RDAT.cc src/core/io/sequence_comparation/DesignContrast.cc src/core/io/serialization/serialize_pose.cc src/core/io/silent/BasicSilentStructCreators.cc src/core/io/silent/BinarySilentStruct.cc src/core/io/silent/RNA_SilentStruct.cc src/core/io/silent/ScoreJumpFileSilentStruct.cc src/core/io/silent/SilentStruct.cc src/core/io/silent/SilentStructFactory.cc src/core/io/util.cc src/core/kinematics/jacobian/ModuleType1.cc src/core/kinematics/jacobian/SeriesJacobians.cc src/core/membrane/hull.cc src/core/optimization/AtomTreeMultifunc.cc src/core/optimization/CartesianMinimizerMap.cc src/core/optimization/CartesianMultifunc.cc src/core/optimization/MinimizerMap.cc src/core/optimization/cartesian_minimize.cc src/core/optimization/symmetry/SymAtomTreeMinimizer.cc src/core/optimization/symmetry/SymAtomTreeMultifunc.cc src/core/optimization/symmetry/SymMinimizerMap.cc src/core/optimization/symmetry/sym_atom_tree_minimize.cc src/core/pack/annealer/AnnealerFactory.cc src/core/pack/annealer/FixbbCoupledRotamerSimAnnealer.cc src/core/pack/annealer/FixbbLinkingRotamerSimAnnealer.cc src/core/pack/annealer/FixbbPwatSimAnnealer.cc src/core/pack/annealer/FixbbSimAnnealer.cc src/core/pack/annealer/MultiCoolAnnealer.cc src/core/pack/annealer/SequenceSymmetricAnnealer.cc src/core/pack/annealer/SmartFixbbSimAnnealer.cc src/core/pack/dunbrack/DunbrackEnergy.cc src/core/pack/dunbrack/DunbrackRotamer.cc src/core/pack/dunbrack/RotamerConstraint.cc src/core/pack/dunbrack/RotamerLibrary.cc src/core/pack/dunbrack/RotamericSingleResidueDunbrackLibraryParser.cc src/core/pack/dunbrack/SingleResidueDunbrackLibrary.cc src/core/pack/dunbrack/SingleResidueDunbrackLibraryCreator.cc src/core/pack/dunbrack/cenrot/CenRotDunEnergy.cc src/core/pack/dunbrack/cenrot/SingleResidueCenrotLibrary.cc src/core/pack/dunbrack/cenrot/SingleResidueCenrotLibraryCreator.cc src/core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/ApproximateBuriedUnsatPenalty.cc src/core/pack/guidance_scoreterms/approximate_buried_unsat_penalty/util.cc 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src/core/pack/rotamer_set/UnboundRotamersOperation.cc src/core/pack/rotamer_set/WaterAnchorInfo.cc src/core/pack/rotamer_set/bb_independent_rotamers.cc src/core/pack/rotamer_set/rna_rotamer_building_functions.cc src/core/pack/rotamer_set/rotamer_building_functions.cc src/core/pack/rotamer_set/symmetry/SymmetricRotamerSet_.cc src/core/pack/rotamer_set/symmetry/SymmetricRotamerSets.cc src/core/pack/rotamer_set/water_rotamer_building_functions.cc src/core/pack/rotamer_trials.cc src/core/pack/rotamers/SingleBasicRotamerLibrary.cc src/core/pack/rotamers/SingleLigandRotamerLibrary.cc src/core/pack/rotamers/SingleLigandRotamerLibraryCreator.cc src/core/pack/rotamers/SingleNCAARotamerLibraryCreator.cc src/core/pack/rotamers/SingleResidueRotamerLibrary.cc src/core/pack/rotamers/SingleResidueRotamerLibraryCreator.cc src/core/pack/rotamers/SingleResidueRotamerLibraryFactory.cc src/core/pack/rotamers/StoredRotamerLibraryCreator.cc src/core/pack/rtmin.cc src/core/pack/scmin/AtomTreeCollection.cc 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src/core/pose/metrics/simple_calculators/InterfaceDefinitionCalculatorBase.cc src/core/pose/metrics/simple_calculators/InterfaceSasaDefinitionCalculator.cc src/core/pose/motif/reference_frames.cc src/core/pose/ncbb/util.cc src/core/pose/ref_pose.cc src/core/pose/rna/RNA_BasePairClassifier.cc src/core/pose/rna/RNA_IdealCoord.cc src/core/pose/rna/RNA_SuiteName.cc src/core/pose/rna/util.cc src/core/pose/selection.cc src/core/pose/subpose_manipulation_util.cc src/core/pose/symmetry/util.cc src/core/pose/toolbox/AtomID_Mapper.cc src/core/pose/toolbox/AtomLevelDomainMap.cc src/core/pose/util.cc src/core/pose/variant_util.cc src/core/pose/xyzStripeHashPose.cc src/core/scoring/APBSWrapper.cc src/core/scoring/CenRotEnvPairPotential.cc src/core/scoring/ChemicalShiftAnisotropy.cc src/core/scoring/DipolarCoupling.cc src/core/scoring/DockingScoreFunction.cc src/core/scoring/Energies.cc src/core/scoring/EnvPairPotential.cc src/core/scoring/GenBornPotential.cc 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src/core/scoring/SecondaryStructurePotential.cc src/core/scoring/SmoothEnvPairPotential.cc src/core/scoring/SplitUnfoldedTwoBodyPotential.cc src/core/scoring/UnfoldedStatePotential.cc src/core/scoring/VdWTinkerPotential.cc src/core/scoring/WaterAdductHBondPotential.cc src/core/scoring/aa_composition_energy/AACompositionConstraint.cc src/core/scoring/aa_composition_energy/AACompositionEnergySetup.cc src/core/scoring/aa_composition_energy/SequenceConstraint.cc src/core/scoring/atomic_depth/AtomicDepth.cc src/core/scoring/atomic_depth/util.cc src/core/scoring/bin_transitions/BinTransitionCalculator.cc src/core/scoring/bin_transitions/BinTransitionData.cc src/core/scoring/carbohydrates/util.cc src/core/scoring/carbon_hbonds/CarbonHBondEnergy.cc src/core/scoring/constraints/AmbiguousNMRDistanceConstraint.cc src/core/scoring/constraints/AngleConstraint.cc src/core/scoring/constraints/AtomPairConstraint.cc src/core/scoring/constraints/BackboneStubConstraint.cc 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src/core/scoring/constraints/NonResidueTypeConstraint.cc src/core/scoring/constraints/RTConstraint.cc src/core/scoring/constraints/ResidueCouplingConstraint.cc src/core/scoring/constraints/ResidueTypeConstraint.cc src/core/scoring/constraints/ResidueTypeLinkingConstraint.cc src/core/scoring/constraints/SequenceProfileConstraint.cc src/core/scoring/constraints/SiteConstraint.cc src/core/scoring/constraints/SiteConstraintResidues.cc src/core/scoring/constraints/util.cc src/core/scoring/cryst/PhenixInterface.cc src/core/scoring/cryst/util.cc src/core/scoring/custom_pair_distance/FullatomCustomPairDistanceEnergy.cc src/core/scoring/disulfides/CentroidDisulfideEnergyContainer.cc src/core/scoring/disulfides/CentroidDisulfidePotential.cc src/core/scoring/disulfides/DisulfideAtomIndices.cc src/core/scoring/disulfides/DisulfideMatchingDatabase.cc src/core/scoring/disulfides/DisulfideMatchingEnergyContainer.cc src/core/scoring/disulfides/DisulfideMatchingPotential.cc 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src/core/scoring/methods/chainbreak_util.cc src/core/scoring/methods/dfire/DFIRE_Potential.cc src/core/scoring/methods/util.cc src/core/scoring/mhc_epitope_energy/MHCEpitopeConstraint.cc src/core/scoring/mhc_epitope_energy/MHCEpitopeEnergySetup.cc src/core/scoring/mhc_epitope_energy/MHCEpitopePredictorMatrix.cc src/core/scoring/mhc_epitope_energy/MHCEpitopePredictorPreLoaded.cc src/core/scoring/mm/MMBondAngleResidueTypeParam.cc src/core/scoring/mm/MMBondAngleResidueTypeParamSet.cc src/core/scoring/mm/MMBondAngleScore.cc src/core/scoring/mm/MMBondLengthScore.cc src/core/scoring/mm/MMLJScore.cc src/core/scoring/mm/MMTorsionScore.cc src/core/scoring/mm/mmtrie/MMEnergyTableAtom.cc src/core/scoring/motif/motif_hash_stuff.cc src/core/scoring/motif/util.cc src/core/scoring/motif/xfrags.cc src/core/scoring/netcharge_energy/NetChargeConstraint.cc src/core/scoring/netcharge_energy/NetChargeEnergySetup.cc src/core/scoring/nmer/NMerPSSMEnergy.cc src/core/scoring/nmer/NMerRefEnergy.cc src/core/scoring/nmer/NMerSVMEnergy.cc src/core/scoring/nmr/NMRDummySpinlabelEnsemble.cc src/core/scoring/nmr/NMRDummySpinlabelVoxelGrid.cc src/core/scoring/nmr/NMRGridSearch.cc src/core/scoring/nmr/NMRSpinlabel.cc src/core/scoring/nmr/pcs/PCSData.cc src/core/scoring/nmr/pcs/PCSMultiSet.cc src/core/scoring/nmr/pcs/PCSSingleSet.cc src/core/scoring/nmr/pre/PREData.cc src/core/scoring/nmr/pre/PREMultiSet.cc src/core/scoring/nmr/pre/PRESingleSet.cc src/core/scoring/nmr/rdc/RDCData.cc src/core/scoring/nmr/rdc/RDCMultiSet.cc src/core/scoring/nmr/rdc/RDCSingleSet.cc src/core/scoring/nmr/util.cc src/core/scoring/nv/NVscore.cc src/core/scoring/orbitals/OrbitalsScore.cc src/core/scoring/orbitals/OrbitalsStatistics.cc src/core/scoring/packing/HolesEnergyRes.cc src/core/scoring/packing/PoseBalls.cc src/core/scoring/packing/PoseBallsLite.cc src/core/scoring/packing/compute_holes_score.cc src/core/scoring/packing/compute_holes_score_res.cc src/core/scoring/packing/surf_vol.cc src/core/scoring/packstat/LeeRichards.cc src/core/scoring/packstat/compute_sasa.cc src/core/scoring/power_diagram/PowerDiagram.cc src/core/scoring/rms_util.cc src/core/scoring/rna/RNA_AtomVDW.cc src/core/scoring/rna/RNA_CentroidInfo.cc src/core/scoring/rna/RNA_LowResolutionPotential.cc src/core/scoring/rna/RNA_Motif.cc src/core/scoring/rna/RNA_SuitePotential.cc src/core/scoring/rna/RNA_TorsionPotential.cc src/core/scoring/rna/RNP_LowResPairDistPotential.cc src/core/scoring/rna/RNP_LowResPotential.cc src/core/scoring/rna/RNP_LowResStackData.cc src/core/scoring/rna/TNA_SuitePotential.cc src/core/scoring/rna/chemical_shift/RNA_CS_MagneticAnisotropy.cc src/core/scoring/rna/chemical_shift/RNA_CS_Parameters.cc src/core/scoring/rna/chemical_shift/RNA_CS_RingCurrent.cc src/core/scoring/rna/chemical_shift/RNA_CS_Util.cc src/core/scoring/rna/chemical_shift/RNA_ChemicalShiftPotential.cc src/core/scoring/rna/data/RNA_DMS_LowResolutionPotential.cc src/core/scoring/rna/data/RNA_DMS_Potential.cc 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src/core/select/residue_selector/ResidueSpanSelector.cc src/core/select/residue_selector/SSElementSelector.cc src/core/select/residue_selector/ScoreTermValueBasedSelector.cc src/core/select/residue_selector/SecondaryStructureSelector.cc src/core/select/residue_selector/SymmetricalResidueSelector.cc src/core/select/util.cc src/core/select/util/SelectResiduesByLayer.cc src/core/select/util/burial_utilities.cc src/core/select/util/interface_vector_calculate.cc src/core/sequence/ABEGOManager.cc src/core/sequence/DerivedSequenceMapping.cc src/core/sequence/SSManager.cc src/core/sequence/sequence_motif.cc src/core/sequence/util.cc src/core/simple_metrics/composite_metrics/CompositeEnergyMetric.cc src/core/simple_metrics/composite_metrics/ElectrostaticComplementarityMetric.cc src/core/simple_metrics/metrics/DihedralDistanceMetric.cc src/core/simple_metrics/metrics/RMSDMetric.cc src/core/simple_metrics/metrics/ResidueSummaryMetric.cc src/core/simple_metrics/metrics/SelectedResiduesPyMOLMetric.cc src/core/simple_metrics/metrics/SequenceMetric.cc src/core/simple_metrics/metrics/SequenceSimilarityMetric.cc src/core/simple_metrics/metrics/TotalEnergyMetric.cc src/core/simple_metrics/per_residue_metrics/HbondMetric.cc src/core/simple_metrics/per_residue_metrics/PerResidueClashMetric.cc src/core/simple_metrics/per_residue_metrics/PerResidueDensityFitMetric.cc src/core/simple_metrics/per_residue_metrics/PerResidueEnergyMetric.cc src/core/simple_metrics/per_residue_metrics/PerResidueGlycanLayerMetric.cc src/core/simple_metrics/per_residue_metrics/PerResidueRMSDMetric.cc src/core/simple_metrics/per_residue_metrics/WaterMediatedHbondMetric.cc src/core/util/ChainbreakUtil.cc src/core/util/SwitchResidueTypeSet.cc src/core/util/cryst_util.cc src/core/util/disulfide_util.cc src/core/util/kinematics_util.cc src/core/util/metalloproteins_util.cc src/protocols/RotamerDump/RotamerDumpMover.cc src/protocols/abinitio/AbrelaxApplication.cc src/protocols/abinitio/ClassicAbinitio.cc src/protocols/abinitio/DomainAssembly.cc src/protocols/abinitio/FoldConstraints.cc src/protocols/abinitio/FragmentSampler.cc src/protocols/abinitio/IterativeBase.cc src/protocols/abinitio/KinematicAbinitio.cc src/protocols/abinitio/KinematicControl.cc src/protocols/abinitio/MembraneAbinitio.cc src/protocols/abinitio/ResolutionSwitcher.cc src/protocols/abinitio/StrandConstraints.cc src/protocols/abinitio/Template.cc src/protocols/abinitio/Templates.cc src/protocols/abinitio/abscript/AbscriptLoopCloserCM.cc src/protocols/abinitio/abscript/AbscriptMover.cc src/protocols/abinitio/abscript/AbscriptStageMover.cc src/protocols/abinitio/abscript/ConstraintPreparer.cc src/protocols/abinitio/abscript/FragmentCM.cc src/protocols/abinitio/abscript/FragmentJumpCM.cc src/protocols/abinitio/abscript/RigidChunkCM.cc src/protocols/abinitio/abscript/StagePreparer.cc src/protocols/abinitio/abscript/StructPerturberCM.cc src/protocols/abinitio/vs_test.cc src/protocols/analysis/GlycanInfoMover.cc src/protocols/analysis/InterfaceAnalyzerMover.cc src/protocols/analysis/LoopAnalyzerMover.cc src/protocols/analysis/burial_metrics/PolarGroupBurialPyMolStringMetric.cc src/protocols/analysis/simple_metrics/SequenceRecoveryMetric.cc src/protocols/anchored_design/AnchorMovers.cc src/protocols/anchored_design/AnchorMoversData.cc src/protocols/antibody/AntibodyCDRGrafter.cc src/protocols/antibody/AntibodyFeatures.cc src/protocols/antibody/AntibodyFeaturesCreator.cc src/protocols/antibody/AntibodyInfo.cc src/protocols/antibody/AntibodyModelerProtocol.cc src/protocols/antibody/AntibodyNumberingConverterMover.cc src/protocols/antibody/CDRsMinPackMin.cc src/protocols/antibody/CloseOneCDRLoop.cc src/protocols/antibody/GraftCDRLoopsProtocol.cc src/protocols/antibody/GraftOneCDRLoop.cc src/protocols/antibody/GraftedStemOptimizer.cc src/protocols/antibody/H3CterInsert.cc src/protocols/antibody/H3PerturbCCD.cc src/protocols/antibody/H3RefineCCD.cc src/protocols/antibody/LHRepulsiveRamp.cc src/protocols/antibody/RefineBetaBarrel.cc src/protocols/antibody/clusters/CDRCluster.cc src/protocols/antibody/clusters/CDRClusterFeatures.cc src/protocols/antibody/clusters/CDRClusterMatcher.cc src/protocols/antibody/clusters/CDRClusterSet.cc src/protocols/antibody/clusters/util.cc src/protocols/antibody/constraints/CDRDihedralConstraintMover.cc src/protocols/antibody/constraints/ParatopeEpitopeSiteConstraintMover.cc src/protocols/antibody/constraints/ParatopeSiteConstraintMover.cc src/protocols/antibody/constraints/util.cc src/protocols/antibody/database/AntibodyDatabaseManager.cc src/protocols/antibody/design/AntibodyDesignMover.cc src/protocols/antibody/design/AntibodySeqDesignTFCreator.cc src/protocols/antibody/design/GeneralAntibodyModeler.cc src/protocols/antibody/design/MutateFrameworkForCluster.cc src/protocols/antibody/design/NativeAntibodySeq.cc src/protocols/antibody/design/util.cc src/protocols/antibody/grafting/grafter.cc src/protocols/antibody/metrics.cc src/protocols/antibody/residue_selector/AntibodyRegionSelector.cc src/protocols/antibody/residue_selector/CDRResidueSelector.cc src/protocols/antibody/snugdock/SnugDock.cc src/protocols/antibody/snugdock/SnugDockProtocol.cc src/protocols/antibody/task_operations/AddCDRProfileSetsOperation.cc src/protocols/antibody/task_operations/AddCDRProfilesOperation.cc src/protocols/antibody/task_operations/DisableAntibodyRegionOperation.cc src/protocols/antibody/task_operations/DisableCDRsOperation.cc src/protocols/antibody/task_operations/RestrictToCDRsAndNeighbors.cc src/protocols/antibody/util.cc src/protocols/antibody_legacy/AntibodyClass.cc src/protocols/antibody_legacy/AntibodyModeler.cc src/protocols/antibody_legacy/CDRH3Modeler.cc src/protocols/antibody_legacy/GraftMover.cc src/protocols/antibody_legacy/LHRepulsiveRampLegacy.cc src/protocols/antibody_legacy/LHSnugFitLegacy.cc src/protocols/antibody_legacy/Ubiquitin_E2C_Modeler.cc src/protocols/backbone_moves/RandomizeBBByRamaPrePro.cc src/protocols/backbone_moves/local_backbone_mover/FreePeptide.cc src/protocols/backrub/BackrubMover.cc src/protocols/backrub/BackrubProtocol.cc src/protocols/backrub/BackrubSidechainMover.cc src/protocols/backrub/util.cc src/protocols/boinc/util.cc src/protocols/branch_angle/BranchAngleOptimizer.cc src/protocols/calc_taskop_filters/ConservedPosMutationFilter.cc src/protocols/calc_taskop_filters/MultipleSigmoidsFilter.cc src/protocols/calc_taskop_filters/OperatorFilter.cc src/protocols/calc_taskop_filters/RelativePoseFilter.cc src/protocols/calc_taskop_filters/RotamerBoltzmannWeight.cc src/protocols/calc_taskop_filters/RotamerBoltzmannWeight2.cc src/protocols/calc_taskop_filters/SigmoidFilter.cc src/protocols/calc_taskop_movers/ConsensusDesignMover.cc src/protocols/calc_taskop_movers/CreateSequenceMotifMover.cc src/protocols/calc_taskop_movers/DesignRepackMover.cc src/protocols/calc_taskop_movers/ForceDisulfidesMover.cc src/protocols/canonical_sampling/AsyncMPITemperingBase.cc src/protocols/canonical_sampling/CanonicalSamplingApplication.cc src/protocols/canonical_sampling/CanonicalSamplingMover.cc src/protocols/canonical_sampling/HamiltonianExchange.cc src/protocols/canonical_sampling/MetricRecorder.cc src/protocols/canonical_sampling/MetropolisHastingsMover.cc src/protocols/canonical_sampling/ParallelTempering.cc src/protocols/canonical_sampling/SidechainMetropolisHastingsMover.cc src/protocols/canonical_sampling/SimulatedTempering.cc src/protocols/canonical_sampling/TemperatureController.cc src/protocols/canonical_sampling/TemperingBase.cc src/protocols/carbohydrates/GlycanSampler.cc src/protocols/carbohydrates/GlycanTreeMinMover.cc src/protocols/carbohydrates/GlycanTreeModeler.cc src/protocols/carbohydrates/IdealizeAnomericHydrogens.cc src/protocols/carbohydrates/LinkageConformerMover.cc src/protocols/carbohydrates/RingPlaneFlipMover.cc src/protocols/carbohydrates/SimpleGlycosylateMover.cc src/protocols/carbohydrates/TautomerizeAnomerMover.cc src/protocols/carbohydrates/util.cc src/protocols/cartesian/md.cc src/protocols/chemically_conjugated_docking/Gp_extra_bodies.cc src/protocols/chemically_conjugated_docking/Gp_quantification_metrics.cc src/protocols/chemically_conjugated_docking/UBQ_GTPaseMover.cc src/protocols/cluster/cluster.cc src/protocols/comparative_modeling/Align_RotamerEvaluator.cc src/protocols/comparative_modeling/AlignmentClustering.cc src/protocols/comparative_modeling/ExtraThreadingMover.cc src/protocols/comparative_modeling/IgnoreSubsetConstraintSet.cc src/protocols/comparative_modeling/LoopRelaxMover.cc src/protocols/comparative_modeling/LoopRelaxThreadingMover.cc src/protocols/comparative_modeling/MultiThreadingMover.cc src/protocols/comparative_modeling/PartialThreadingMover.cc src/protocols/comparative_modeling/StealSideChainsMover.cc src/protocols/comparative_modeling/ThreadingMover.cc src/protocols/comparative_modeling/coord_util.cc src/protocols/comparative_modeling/features/TorsionFeature.cc src/protocols/comparative_modeling/util.cc src/protocols/constel/AromaticFilter.cc src/protocols/constel/ChainTerm.cc src/protocols/constel/FilterByProxTerm.cc src/protocols/constel/FilterBySASA.cc src/protocols/constel/NeighTeller.cc src/protocols/constel/PairConstelFilters.cc src/protocols/constel/Primitives.cc src/protocols/constel/SearchOptions.cc src/protocols/constel/SingResCnlCrea.cc src/protocols/constel/cnl_info.cc src/protocols/constraint_filters/ConstraintScoreCutoffFilter.cc src/protocols/constraint_filters/ShowConstraintsFilter.cc src/protocols/constraint_generator/AtomPairConstraintGenerator.cc src/protocols/constraint_generator/CoordinateConstraintGenerator.cc src/protocols/constraint_generator/DihedralConstraintGenerator.cc src/protocols/constraint_generator/DistanceConstraintGenerator.cc src/protocols/constraint_generator/HydrogenBondConstraintGenerator.cc src/protocols/constraint_generator/MembraneSpanConstraintGenerator.cc src/protocols/constraint_generator/MetalContactsConstraintGenerator.cc src/protocols/constraint_generator/ResidueTypeConstraintGenerator.cc src/protocols/constraint_generator/TerminiConstraintGenerator.cc src/protocols/constraint_generator/util.cc src/protocols/constraint_movers/AddConstraintsToCurrentConformationMover.cc src/protocols/constraint_movers/CstInfoMover.cc src/protocols/constraints_additional/BindingSiteConstraint.cc src/protocols/constraints_additional/COMCoordinateConstraint.cc src/protocols/constraints_additional/MaxSeqSepConstraintSet.cc src/protocols/constraints_additional/SequenceCoupling1BDConstraint.cc src/protocols/constraints_additional/SequenceCouplingConstraint.cc src/protocols/contact_map/ContactMap.cc src/protocols/coupled_moves/CoupledMovesProtocol.cc src/protocols/cryst/TwoDLattice.cc src/protocols/cryst/cryst_movers.cc src/protocols/cryst/cryst_rms.cc src/protocols/cryst/refinable_lattice.cc src/protocols/cryst/spacegroup.cc src/protocols/cryst/wallpaper.cc src/protocols/cutoutdomain/CutOutDomain.cc src/protocols/cyclic_peptide/CreateAngleConstraint.cc src/protocols/cyclic_peptide/CreateDistanceConstraint.cc src/protocols/cyclic_peptide/CreateTorsionConstraint.cc src/protocols/cyclic_peptide/CrosslinkerMover.cc src/protocols/cyclic_peptide/CycpepSymmetryFilter.cc src/protocols/cyclic_peptide/DeclareBond.cc src/protocols/cyclic_peptide/FlipChiralityMover.cc src/protocols/cyclic_peptide/OversaturatedHbondAcceptorFilter.cc src/protocols/cyclic_peptide/PeptideCyclizeMover.cc src/protocols/cyclic_peptide/PeptideInternalHbondsMetric.cc src/protocols/cyclic_peptide/PeptideStubMover.cc src/protocols/cyclic_peptide/RamaMutationSelector.cc src/protocols/cyclic_peptide/SymmetricCycpepAlign.cc src/protocols/cyclic_peptide/TryDisulfPermutations.cc src/protocols/cyclic_peptide/crosslinker/CrosslinkerMoverHelper.cc src/protocols/cyclic_peptide/crosslinker/Metal_HelperBase.cc src/protocols/cyclic_peptide/crosslinker/OctahedralMetal_Helper.cc src/protocols/cyclic_peptide/crosslinker/SquarePlanarMetal_Helper.cc src/protocols/cyclic_peptide/crosslinker/SquarePyramidalMetal_Helper.cc src/protocols/cyclic_peptide/crosslinker/TBMB_Helper.cc src/protocols/cyclic_peptide/crosslinker/TMA_Helper.cc src/protocols/cyclic_peptide/crosslinker/TetrahedralMetal_Helper.cc src/protocols/cyclic_peptide/crosslinker/TrigonalPlanarMetal_Helper.cc src/protocols/cyclic_peptide/crosslinker/TrigonalPyramidalMetal_Helper.cc src/protocols/cyclic_peptide_predict/SimpleCycpepPredictApplication.cc src/protocols/ddg/CartesianddG.cc src/protocols/ddg/ddGMover.cc src/protocols/ddg/ddG_main.cc src/protocols/denovo_design/calculators/CavityCalculator.cc src/protocols/denovo_design/components/ExtendedPoseBuilder.cc src/protocols/denovo_design/components/FoldGraph.cc src/protocols/denovo_design/components/Picker.cc src/protocols/denovo_design/components/RandomTorsionPoseFolder.cc src/protocols/denovo_design/components/RemodelLoopMoverPoseFolder.cc src/protocols/denovo_design/components/Segment.cc src/protocols/denovo_design/components/SheetDB.cc src/protocols/denovo_design/components/StructureData.cc src/protocols/denovo_design/components/StructureDataFactory.cc src/protocols/denovo_design/components/StructureDataObserver.cc src/protocols/denovo_design/connection/ConnectionArchitect.cc src/protocols/denovo_design/filters/CavityVolumeFilter.cc src/protocols/denovo_design/filters/ExposedHydrophobicsFilter.cc src/protocols/denovo_design/filters/PreProlineFilter.cc src/protocols/denovo_design/filters/SSPredictionFilter.cc src/protocols/denovo_design/filters/SSShapeComplementarityFilter.cc src/protocols/denovo_design/movers/AlignResiduesMover.cc src/protocols/denovo_design/movers/BuildDeNovoBackboneMover.cc src/protocols/denovo_design/movers/DeclareStructureDataCovalentBondMover.cc src/protocols/denovo_design/movers/DisulfidizeMover.cc src/protocols/denovo_design/movers/ExtendChainMover.cc src/protocols/denovo_design/movers/FastDesign.cc src/protocols/denovo_design/movers/FoldTreeFromFoldGraphMover.cc src/protocols/denovo_design/movers/RotateSegmentMover.cc src/protocols/denovo_design/movers/SealFoldTreeMover.cc src/protocols/denovo_design/residue_selectors/NamedSegmentSelector.cc src/protocols/denovo_design/task_operations/ConsensusLoopDesignOperation.cc src/protocols/denovo_design/util.cc src/protocols/design_opt/GreedyOptMutationMover.cc src/protocols/design_opt/PointMutationCalculator.cc src/protocols/dna/DNAParameters.cc src/protocols/dna/DesignProteinBackboneAroundDNA.cc src/protocols/dna/DnaChains.cc src/protocols/dna/DnaInterfaceFinder.cc src/protocols/dna/DnaInterfaceMinMover.cc src/protocols/dna/DnaInterfaceMultiStateDesign.cc src/protocols/dna/DnaInterfacePacker.cc src/protocols/dna/PDBOutput.cc src/protocols/dna/RestrictDesignToProteinDNAInterface.cc src/protocols/dna/RotamerDNAHBondFilter.cc src/protocols/dna/SeparateDnaFromNonDna.cc src/protocols/dna/WatsonCrickRotamerCouplings.cc src/protocols/dna/util.cc src/protocols/dna_dock/DNAClashCheckFilter.cc src/protocols/dna_dock/PropagateClashCheckFilter.cc src/protocols/docking/ConformerSwitchMover.cc src/protocols/docking/DockMCMCycle.cc src/protocols/docking/DockMCMProtocol.cc src/protocols/docking/DockMinMover.cc src/protocols/docking/DockTaskFactory.cc src/protocols/docking/DockingEnsemble.cc src/protocols/docking/DockingEnsemblePrepackProtocol.cc src/protocols/docking/DockingHighRes.cc src/protocols/docking/DockingHighResLegacy.cc src/protocols/docking/DockingInitialPerturbation.cc src/protocols/docking/DockingPrepackProtocol.cc src/protocols/docking/DockingProtocol.cc src/protocols/docking/EllipsoidalRandomizationMover.cc src/protocols/docking/SidechainMinMover.cc src/protocols/docking/membrane/MPDockingMover.cc src/protocols/docking/membrane/MPDockingSetupMover.cc src/protocols/docking/membrane/MPFindInterfaceMover.cc src/protocols/docking/membrane/QuickRelaxPartnersSeparately.cc src/protocols/docking/metrics.cc src/protocols/docking/stateless/SaneDockingProtocol.cc src/protocols/docking/util.cc src/protocols/domain_assembly/AddAssemblyConstraints.cc src/protocols/domain_assembly/AssembleLinkerMover.cc src/protocols/domain_assembly/PostDockAssemblyScorer.cc src/protocols/electron_density/BfactorFittingMover.cc src/protocols/electron_density/DockIntoDensityMover.cc src/protocols/electron_density/ReportFSC.cc src/protocols/electron_density/ScaleMapIntensities.cc src/protocols/electron_density/SetupForDensityScoringMover.cc src/protocols/electron_density/VoxelSpacingRefinementMover.cc src/protocols/electron_density/util.cc src/protocols/energy_based_clustering/EnergyBasedClusteringProtocol.cc src/protocols/environment/ClientMover.cc src/protocols/environment/CoMTrackerCM.cc src/protocols/environment/DofUnlock.cc src/protocols/environment/EnvClaimBroker.cc src/protocols/environment/EnvExcn.cc src/protocols/environment/EnvMover.cc src/protocols/environment/Environment.cc src/protocols/environment/ProtectedConformation.cc src/protocols/environment/ScriptCM.cc src/protocols/environment/claims/CutBiasClaim.cc src/protocols/environment/claims/EnvClaim.cc src/protocols/environment/claims/EnvLabelSelector.cc src/protocols/environment/claims/JumpClaim.cc src/protocols/environment/claims/TorsionClaim.cc src/protocols/environment/claims/VirtResClaim.cc src/protocols/environment/claims/XYZClaim.cc src/protocols/enzdes/AddorRemoveCsts.cc src/protocols/enzdes/BackboneSampler.cc src/protocols/enzdes/EnzFilters.cc src/protocols/enzdes/EnzRepackMinimize.cc src/protocols/enzdes/EnzdesBaseProtocol.cc src/protocols/enzdes/EnzdesFixBBProtocol.cc src/protocols/enzdes/EnzdesFlexBBProtocol.cc src/protocols/enzdes/EnzdesMovers.cc src/protocols/enzdes/EnzdesTaskOperations.cc src/protocols/enzdes/ModifyStoredLigandRBConfsMovers.cc src/protocols/enzdes/PackRotamersMoverPartGreedy.cc src/protocols/enzdes/RemoveLigandFilter.cc src/protocols/enzdes/SecondaryMatchProtocol.cc src/protocols/enzdes/enzdes_util.cc src/protocols/enzymatic_movers/DNAMethyltransferaseMover.cc src/protocols/enzymatic_movers/EnzymaticMover.cc src/protocols/enzymatic_movers/KinaseMover.cc src/protocols/enzymatic_movers/NTerminalAcetyltransferaseMover.cc src/protocols/evaluation/AlignEvaluator.cc src/protocols/evaluation/PCA.cc src/protocols/evaluation/util.cc src/protocols/evolution/AASynthesisFitnessCostFilter.cc src/protocols/evolution/AlignmentAAFinderFilter.cc src/protocols/evolution/AlignmentCleanerTools.cc src/protocols/evolution/AlignmentGapInserterFilter.cc src/protocols/evolution/EvolutionaryDynamicsMover.cc src/protocols/evolution/NucleotideMutation.cc src/protocols/farnesyl/InstallFarnesylMover.cc src/protocols/farnesyl/SampleFarnesylMover.cc src/protocols/features/AtomAtomPairFeatures.cc src/protocols/features/AtomInResidueAtomInResiduePairFeatures.cc src/protocols/features/AtomTypesFeatures.cc src/protocols/features/BetaTurnDetection.cc src/protocols/features/ChargeChargeFeatures.cc src/protocols/features/DatabaseJobInputter.cc src/protocols/features/DdGFeatures.cc src/protocols/features/HBondFeatures.cc src/protocols/features/HBondParameterFeatures.cc src/protocols/features/HelixCapFeatures.cc src/protocols/features/InterfaceDdGMover.cc src/protocols/features/InterfaceFeatures.cc src/protocols/features/LoopAnchorFeatures.cc src/protocols/features/ModelFeatures.cc src/protocols/features/OrbitalsFeatures.cc src/protocols/features/OrbitalsFeaturesCreator.cc src/protocols/features/PairFeatures.cc src/protocols/features/PdbDataFeatures.cc src/protocols/features/PoseCommentsFeatures.cc src/protocols/features/PoseConformationFeatures.cc src/protocols/features/ProteinBackboneAtomAtomPairFeatures.cc src/protocols/features/ProteinBackboneTorsionAngleFeatures.cc src/protocols/features/ProteinBondGeometryFeatures.cc src/protocols/features/ProteinRMSDFeatures.cc src/protocols/features/ProteinRMSDNoSuperpositionFeatures.cc src/protocols/features/ProteinResidueConformationFeatures.cc src/protocols/features/ProteinSilentReport.cc src/protocols/features/ReportToDB.cc src/protocols/features/ResidueConformationFeatures.cc src/protocols/features/ResidueFeatures.cc src/protocols/features/ResidueGridScoresFeatures.cc src/protocols/features/ResidueScoresFeatures.cc src/protocols/features/ResidueSecondaryStructureFeatures.cc src/protocols/features/ResidueTotalScoresFeatures.cc src/protocols/features/ResidueTypesFeatures.cc src/protocols/features/RotamerFeatures.cc src/protocols/features/RotamerFeaturesCreator.cc src/protocols/features/RotamerRecoveryFeatures.cc src/protocols/features/RotamerRecoveryFeaturesCreator.cc src/protocols/features/SaltBridgeFeatures.cc src/protocols/features/ScreeningFeatures.cc src/protocols/features/SecondaryStructureSegmentFeatures.cc src/protocols/features/SimpleMetricFeatures.cc src/protocols/features/SmotifFeatures.cc src/protocols/features/StructureFeatures.cc src/protocols/features/StructureScoresFeatures.cc src/protocols/features/TaskOperationFeatures.cc src/protocols/features/TaskOperationFeaturesCreator.cc src/protocols/features/TrajectoryMapFeatures.cc src/protocols/features/UnrecognizedAtomFeatures.cc src/protocols/features/WaterFeatures.cc src/protocols/features/helixAssembly/ConcurrencyTest.cc src/protocols/features/helixAssembly/ConcurrencyTestCreator.cc src/protocols/features/helixAssembly/HelicalFragment.cc src/protocols/features/helixAssembly/HelixBundleFeatures.cc src/protocols/features/strand_assembly/CheckForSandwichFeatures.cc src/protocols/features/strand_assembly/SandwichFeatures.cc src/protocols/features/strand_assembly/SandwichFeaturesCreator.cc src/protocols/features/strand_assembly/SandwichFragment.cc src/protocols/features/strand_assembly/StrandBundleFeatures.cc src/protocols/features/strand_assembly/StrandFragment.cc src/protocols/features/strand_assembly/WriteToDBFromSandwichFeatures.cc src/protocols/features/strand_assembly/WriteToFileFromSandwichFeatures.cc src/protocols/features/util.cc src/protocols/fibril/fibril_util.cc src/protocols/filters/BasicFilters.cc src/protocols/filters/Filter.cc src/protocols/filters/ReplicateFilter.cc src/protocols/fldsgn/BluePrintBDR.cc src/protocols/fldsgn/CircularPermutation.cc src/protocols/fldsgn/MatchResidues.cc src/protocols/fldsgn/MatchResiduesMover.cc src/protocols/fldsgn/NcontactsCalculator.cc src/protocols/fldsgn/SheetConstraintGenerator.cc src/protocols/fldsgn/filters/CoreDunbrackFilter.cc src/protocols/fldsgn/filters/HelixBendFilter.cc src/protocols/fldsgn/filters/HelixKinkFilter.cc src/protocols/fldsgn/filters/InterlockingAromaFilter.cc src/protocols/fldsgn/filters/ParallelBetaPairingPreferenceFilter.cc src/protocols/fldsgn/filters/SecondaryStructureCountFilter.cc src/protocols/fldsgn/filters/SecondaryStructureFilter.cc src/protocols/fldsgn/filters/SecondaryStructureHasResidueFilter.cc src/protocols/fldsgn/filters/SheetTopologyFilter.cc src/protocols/fldsgn/filters/StrandCurvatureByLevels.cc src/protocols/fldsgn/potentials/AACompositionEnergy.cc src/protocols/fldsgn/potentials/SetSecStructEnergies.cc src/protocols/fldsgn/potentials/sspot/HSPairPotential.cc src/protocols/fldsgn/potentials/sspot/NatbiasSecondaryStructureEnergy.cc src/protocols/fldsgn/potentials/sspot/NatbiasStrandPairPotential.cc src/protocols/fldsgn/potentials/sspot/SSPairPotential.cc src/protocols/fldsgn/potentials/sspot/util.cc src/protocols/fldsgn/topology/BB_Pos.cc src/protocols/fldsgn/topology/SS_Info2.cc src/protocols/fldsgn/topology/Sheet.cc src/protocols/fldsgn/topology/util.cc src/protocols/flexpack/FlexPacker.cc src/protocols/flexpack/interaction_graph/FlexbbInteractionGraph.cc src/protocols/flexpack/interaction_graph/OTFFlexbbInteractionGraph.cc src/protocols/flexpack/rotamer_set/FlexbbRotamerSet.cc src/protocols/flexpack/rotamer_set/FlexbbRotamerSets.cc src/protocols/flexpep_docking/FlexPepDockingAbInitio.cc src/protocols/flexpep_docking/FlexPepDockingFlags.cc src/protocols/flexpep_docking/FlexPepDockingLowRes.cc src/protocols/flexpep_docking/FlexPepDockingPoseMetrics.cc src/protocols/flexpep_docking/FlexPepDockingProtocol.cc src/protocols/floppy_tail/FloppyTailMover.cc src/protocols/floppy_tail/FloppyTail_publication.cc src/protocols/flxbb/DesignTask.cc src/protocols/flxbb/FlxbbDesign.cc src/protocols/flxbb/FlxbbDesign_main.cc src/protocols/flxbb/InterlockAroma.cc src/protocols/flxbb/LayerDesignOperation.cc src/protocols/flxbb/utility.cc src/protocols/fold_from_loops/NubInitioMover.cc src/protocols/fold_from_loops/constraint_generator/AutomaticSheetConstraintGenerator.cc src/protocols/fold_from_loops/constraint_generator/SegmentedAtomPairConstraintGenerator.cc src/protocols/fold_from_loops/filters/RmsdFromResidueSelectorFilter.cc src/protocols/fold_from_loops/filters/ScorePoseSegmentFromResidueSelectorFilter.cc src/protocols/fold_from_loops/movers/AlignByResidueSelectorMover.cc src/protocols/fold_from_loops/movers/DisplayPoseLabelsMover.cc src/protocols/fold_from_loops/movers/LabelPoseFromResidueSelectorMover.cc src/protocols/fold_from_loops/movers/NubInitioLoopClosureMover.cc src/protocols/fold_from_loops/movers/SplitAndMixPoseMover.cc src/protocols/fold_from_loops/selectors/ConstraintResidueSelector.cc src/protocols/fold_from_loops/selectors/CutpointResidueSelector.cc src/protocols/fold_from_loops/selectors/ProteinResidueSelector.cc src/protocols/fold_from_loops/utils/Nub.cc src/protocols/fold_from_loops/utils/utils.cc src/protocols/forge/build/Bridge.cc src/protocols/forge/build/BuildInstruction.cc src/protocols/forge/build/BuildManager.cc src/protocols/forge/build/ConnectRight.cc src/protocols/forge/build/GrowLeft.cc src/protocols/forge/build/GrowRight.cc src/protocols/forge/build/SegmentInsert.cc src/protocols/forge/build/SegmentRebuild.cc src/protocols/forge/build/SegmentSwap.cc src/protocols/forge/components/BDR.cc src/protocols/forge/components/VarLengthBuild.cc src/protocols/forge/constraints/InverseRotamersRCG.cc src/protocols/forge/methods/chainbreak_eval.cc src/protocols/forge/methods/fold_tree_functions.cc src/protocols/forge/methods/pose_mod.cc src/protocols/forge/methods/util.cc src/protocols/forge/remodel/RemodelAccumulator.cc src/protocols/forge/remodel/RemodelData.cc src/protocols/forge/remodel/RemodelDesignMover.cc src/protocols/forge/remodel/RemodelEnzdesCstModule.cc src/protocols/forge/remodel/RemodelGlobalFrame.cc src/protocols/forge/remodel/RemodelLigandHandler.cc src/protocols/forge/remodel/RemodelLoopMover.cc src/protocols/forge/remodel/RemodelMover.cc src/protocols/forge/remodel/RemodelRotamerLinks.cc src/protocols/forge/remodel/RemodelWorkingSet.cc src/protocols/frag_picker/FragmentCandidate.cc src/protocols/frag_picker/FragmentPicker.cc src/protocols/frag_picker/FragmentScoreFilter.cc src/protocols/frag_picker/nonlocal/NonlocalFrags.cc src/protocols/frag_picker/scores/AtomBasedConstraintsScore.cc src/protocols/frag_picker/scores/FragmentAllAtomCrmsd.cc src/protocols/frag_picker/scores/FragmentChunkCrms.cc src/protocols/frag_picker/scores/FragmentCrmsd.cc src/protocols/frag_picker/scores/FragmentCrmsdResDepth.cc src/protocols/frag_picker/scores/FragmentDME.cc src/protocols/frag_picker/scores/GunnCost.cc src/protocols/frags/TorsionFragment.cc src/protocols/generalized_kinematic_closure/GeneralizedKIC.cc src/protocols/generalized_kinematic_closure/filter/GeneralizedKICfilter.cc src/protocols/generalized_kinematic_closure/perturber/GeneralizedKICperturber.cc src/protocols/generalized_kinematic_closure/selector/GeneralizedKICselector.cc src/protocols/generalized_kinematic_closure/util.cc src/protocols/grafting/AnchoredGraftMover.cc src/protocols/grafting/CCDEndsGraftMover.cc src/protocols/grafting/GraftMoverBase.cc src/protocols/grafting/simple_movers/DeleteRegionMover.cc src/protocols/grafting/simple_movers/KeepRegionMover.cc src/protocols/grafting/util.cc src/protocols/hbnet/HBNet.cc src/protocols/hbnet/HBNetStapleInterface.cc src/protocols/hbnet/HBNetTaskOperations.cc src/protocols/hbnet/HBNet_util.cc src/protocols/hbnet/NetworkState.cc src/protocols/hbnet/UnsatSelector.cc src/protocols/helical_bundle/BackboneGridSampler.cc src/protocols/helical_bundle/BackboneGridSamplerHelper.cc src/protocols/helical_bundle/BundleGridSampler.cc src/protocols/helical_bundle/BundleGridSamplerHelper.cc src/protocols/helical_bundle/BundleParametrizationCalculator.cc src/protocols/helical_bundle/BundleReporterFilter.cc src/protocols/helical_bundle/FitSimpleHelix.cc src/protocols/helical_bundle/FitSimpleHelixMultiFunc.cc src/protocols/helical_bundle/MakeBundle.cc src/protocols/helical_bundle/MakeBundleHelix.cc src/protocols/helical_bundle/PerturbBundle.cc src/protocols/helical_bundle/PerturbBundleHelix.cc src/protocols/helical_bundle/parameters/BundleParameters.cc src/protocols/helical_bundle/parameters/BundleParametersSet.cc src/protocols/helical_bundle/parameters/OmegaBundleParameter.cc src/protocols/helical_bundle/util.cc src/protocols/helical_bundle_predict/HBPHelixAssignments.cc src/protocols/helical_bundle_predict/HBP_HelixCoilMoveGenerator.cc src/protocols/helical_bundle_predict/HelicalBundlePredictApplication.cc src/protocols/helix_capper/HelixNCapperMover.cc src/protocols/hotspot_hashing/HotspotStub.cc src/protocols/hotspot_hashing/HotspotStubSet.cc src/protocols/hotspot_hashing/SICSearchPattern.cc src/protocols/hotspot_hashing/SearchPatternRotSetOp.cc src/protocols/hotspot_hashing/StubGenerator.cc src/protocols/hotspot_hashing/SurfaceSearchPattern.cc src/protocols/hotspot_hashing/movers/PlaceProbeMover.cc src/protocols/hotspot_hashing/movers/PlaceSurfaceProbe.cc src/protocols/hybridization/BackboneTorsionPerturbation.cc src/protocols/hybridization/BackboneTorsionSampler.cc src/protocols/hybridization/CartesianHybridize.cc src/protocols/hybridization/CartesianSampler.cc src/protocols/hybridization/ChunkTrialMover.cc src/protocols/hybridization/DDomainParse.cc src/protocols/hybridization/DomainAssembly.cc src/protocols/hybridization/FoldTreeHybridize.cc src/protocols/hybridization/FragmentBiasAssigner.cc src/protocols/hybridization/HybridizeFoldtreeDynamic.cc src/protocols/hybridization/HybridizeProtocol.cc src/protocols/hybridization/InsertChunkMover.cc src/protocols/hybridization/MRMover.cc src/protocols/hybridization/TMalign.cc src/protocols/hybridization/util.cc src/protocols/hydrate/Hydrate.cc src/protocols/hydrate/hydrate_functions.cc src/protocols/idealize/IdealizeMover.cc src/protocols/idealize/idealize.cc src/protocols/indel/IndelOptimizationMover.cc src/protocols/indexed_structure_store/DirectSegmentLookup.cc src/protocols/indexed_structure_store/FragmentLookup.cc src/protocols/indexed_structure_store/FragmentStore.cc src/protocols/indexed_structure_store/FragmentStoreManager.cc src/protocols/indexed_structure_store/SSHashedFragmentStore.cc src/protocols/indexed_structure_store/SegmentSequenceProfile.cc src/protocols/indexed_structure_store/filters/FragmentLookupFilter.cc src/protocols/indexed_structure_store/movers/DirectSegmentLookupMover.cc src/protocols/indexed_structure_store/movers/SegmentSequenceProfileMover.cc src/protocols/indexed_structure_store/pose_utility.cc src/protocols/indexed_structure_store/utility.cc src/protocols/init/register1.cc src/protocols/init/register4.cc src/protocols/interface/util.cc src/protocols/jd2/InnerJob.cc src/protocols/jd2/PoseInputStreamJobInputter.cc src/protocols/jd2/ScreeningJobInputter.cc src/protocols/jd2/VectorPoseJobDistributor.cc src/protocols/jd2/archive/ArchiveBase.cc src/protocols/jd3/full_model_inputters/SilentFileFullModelInputter.cc src/protocols/jd3/pose_inputters/SilentFilePoseInputter.cc src/protocols/jobdist/JobDistributors.cc src/protocols/jobdist/not_universal_main.cc src/protocols/jobdist/standard_mains.cc src/protocols/jumping/JumpSample.cc src/protocols/jumping/MembraneJump.cc src/protocols/jumping/PairingLibrary.cc src/protocols/jumping/ResiduePairJump.cc src/protocols/jumping/ResiduePairJumpSetup.cc src/protocols/jumping/util.cc src/protocols/kinematic_closure/ClosureProblem.cc src/protocols/kinematic_closure/ClosureSolution.cc src/protocols/kinematic_closure/perturbers/Rama2bPerturber.cc src/protocols/kinematic_closure/perturbers/RamaPerturber.cc src/protocols/kinmatch/FunGroupTK.cc src/protocols/legacy_sewing/conformation/Assembly.cc src/protocols/legacy_sewing/conformation/AssemblyFactory.cc src/protocols/legacy_sewing/conformation/ContinuousAssembly.cc src/protocols/legacy_sewing/conformation/DisembodiedAssembly.cc src/protocols/legacy_sewing/conformation/Model.cc src/protocols/legacy_sewing/sampling/LegacyAddStartnodeFragments.cc src/protocols/legacy_sewing/sampling/LegacyAppendAssemblyMover.cc src/protocols/legacy_sewing/sampling/LegacyAssemblyConstraintsMover.cc src/protocols/legacy_sewing/sampling/LegacyAssemblyMover.cc src/protocols/legacy_sewing/sampling/LegacyEnumerateAssemblyMover.cc src/protocols/legacy_sewing/sampling/LegacyGivenPathAssemblyMover.cc src/protocols/legacy_sewing/sampling/LegacyGreedyAssemblyMover.cc src/protocols/legacy_sewing/sampling/LegacyMonteCarloAssemblyMover.cc src/protocols/legacy_sewing/sampling/LegacyRepeatAssemblyMover.cc src/protocols/legacy_sewing/sampling/SewGraph.cc src/protocols/legacy_sewing/sampling/requirements/LegacyGlobalLengthRequirement.cc src/protocols/legacy_sewing/sampling/requirements/LegacyRequirementSet.cc src/protocols/legacy_sewing/sampling/requirements/LegacyResidueRetentionRequirement.cc src/protocols/legacy_sewing/scoring/LegacyBlosumScorer.cc src/protocols/legacy_sewing/scoring/LegacyCalciumMotifScorer.cc src/protocols/legacy_sewing/scoring/LegacyClashScorer.cc src/protocols/legacy_sewing/scoring/LegacyInterModelMotifScorer.cc src/protocols/legacy_sewing/scoring/LegacyMotifScorer.cc src/protocols/legacy_sewing/scoring/LegacyPartnerMotifScorer.cc src/protocols/legacy_sewing/util/io.cc src/protocols/legacy_sewing/util/util.cc src/protocols/ligand_docking/AddHydrogen.cc src/protocols/ligand_docking/AddHydrogens.cc src/protocols/ligand_docking/AtomCountFilter.cc src/protocols/ligand_docking/ChainExistsFilter.cc src/protocols/ligand_docking/CompleteConnectionsFilter.cc src/protocols/ligand_docking/CompoundTranslate.cc src/protocols/ligand_docking/ComputeLigandRDF.cc src/protocols/ligand_docking/FinalMinimizer.cc src/protocols/ligand_docking/GALigandDock/EntropyEstimator.cc src/protocols/ligand_docking/GALigandDock/GALigandDock.cc src/protocols/ligand_docking/GALigandDock/GAOptimizer.cc src/protocols/ligand_docking/GALigandDock/GridScorer.cc src/protocols/ligand_docking/GALigandDock/GriddedAtomTreeMultifunc.cc src/protocols/ligand_docking/GALigandDock/LigandAligner.cc src/protocols/ligand_docking/GALigandDock/LigandConformer.cc src/protocols/ligand_docking/GALigandDock/RotamerData.cc src/protocols/ligand_docking/GALigandDock/util.cc src/protocols/ligand_docking/GrowLigand.cc src/protocols/ligand_docking/HBondAcceptorFilter.cc src/protocols/ligand_docking/HBondDonorFilter.cc src/protocols/ligand_docking/HeavyAtomFilter.cc src/protocols/ligand_docking/HighResDocker.cc src/protocols/ligand_docking/HighResEnsemble.cc src/protocols/ligand_docking/InterfaceBuilder.cc src/protocols/ligand_docking/InterfaceScoreCalculator.cc src/protocols/ligand_docking/LigandBaseProtocol.cc src/protocols/ligand_docking/LigandDesign.cc src/protocols/ligand_docking/LigandDockProtocol.cc src/protocols/ligand_docking/MinimizeBackbone.cc src/protocols/ligand_docking/MinimizeLigand.cc src/protocols/ligand_docking/MolarMassFilter.cc src/protocols/ligand_docking/MolecularMassFilter.cc src/protocols/ligand_docking/MoveMapBuilder.cc src/protocols/ligand_docking/ProtLigEnsemble.cc src/protocols/ligand_docking/RandomConformerMover.cc src/protocols/ligand_docking/RandomConformers.cc src/protocols/ligand_docking/ResidueTorsionRestraints.cc src/protocols/ligand_docking/RigidSearchMover.cc src/protocols/ligand_docking/Rotate.cc src/protocols/ligand_docking/Rotates.cc src/protocols/ligand_docking/SlideTogether.cc src/protocols/ligand_docking/StartFrom.cc src/protocols/ligand_docking/TetherLigand.cc src/protocols/ligand_docking/Transform.cc src/protocols/ligand_docking/TransformEnsemble.cc src/protocols/ligand_docking/Translate.cc src/protocols/ligand_docking/WriteLigandMolFile.cc src/protocols/ligand_docking/grid_functions.cc src/protocols/ligand_docking/ligand_functions.cc src/protocols/ligand_docking/ligand_options/interface_distance_functions.cc src/protocols/ligand_docking/ligand_scores.cc src/protocols/ligand_docking/rdf/StandardRDFFunctions.cc src/protocols/ligand_docking/util.cc src/protocols/loop_build/LoopBuild.cc src/protocols/loop_build/LoopBuildMover.cc src/protocols/loop_build/LoopMover_SlidingWindow.cc src/protocols/loop_grower/FragmentExtension.cc src/protocols/loop_grower/LoopGrower.cc src/protocols/loop_grower/SheetSampler.cc src/protocols/loop_grower/util.cc src/protocols/loop_modeler/LoopModeler.cc src/protocols/loop_modeling/refiners/MinimizationRefiner.cc src/protocols/loop_modeling/refiners/RepackingRefiner.cc src/protocols/loop_modeling/refiners/RotamerTrialsRefiner.cc src/protocols/loop_modeling/utilities/AcceptanceCheck.cc src/protocols/loop_modeling/utilities/PrepareForFullatom.cc src/protocols/loop_modeling/utilities/TrajectoryLogger.cc src/protocols/loop_modeling/utilities/rosetta_scripts.cc src/protocols/loophash/BackboneDB.cc src/protocols/loophash/FastGapMover.cc src/protocols/loophash/LocalInserter.cc src/protocols/loophash/LoopHashDiversifier.cc src/protocols/loophash/LoopHashLibrary.cc src/protocols/loophash/LoopHashMap.cc src/protocols/loophash/LoopHashMoverWrapper.cc src/protocols/loophash/LoopHashRelaxProtocol.cc src/protocols/loophash/LoopHashSampler.cc src/protocols/loophash/MPI_LoopHashRefine.cc src/protocols/loophash/MPI_LoopHashRefine_Master.cc src/protocols/loophash/Mover_LoopHashRefine.cc src/protocols/loophash/WorkUnit_LoopHash.cc src/protocols/loops/Loop.cc src/protocols/loops/loop_closure/ccd/CCDLoopClosureMover.cc src/protocols/loops/loop_closure/ccd/RamaCheck.cc src/protocols/loops/loop_closure/ccd/SlidingWindowLoopClosure.cc src/protocols/loops/loop_closure/ccd/ccd_closure.cc src/protocols/loops/loop_closure/jacobi/JacobiLoopClosureMover.cc src/protocols/loops/loop_closure/kinematic_closure/KinematicMover.cc src/protocols/loops/loop_closure/kinematic_closure/KinematicPerturber.cc src/protocols/loops/loop_mover/LoopCM.cc src/protocols/loops/loop_mover/perturb/LoopMover_CCD.cc src/protocols/loops/loop_mover/perturb/LoopMover_KIC.cc src/protocols/loops/loop_mover/perturb/LoopMover_QuickCCD.cc src/protocols/loops/loop_mover/perturb/LoopMover_QuickCCD_Moves.cc src/protocols/loops/loop_mover/refine/LoopMover_Backrub.cc src/protocols/loops/loop_mover/refine/LoopMover_CCD.cc src/protocols/loops/loop_mover/refine/LoopMover_KIC.cc src/protocols/loops/loop_mover/refine/LoopRefineInnerCycle.cc src/protocols/loops/loop_mover/refine/LoopRefineInnerCycleContainer.cc src/protocols/loops/loop_mover/refine/LoopRefineInnerCycleFactory.cc src/protocols/loops/loop_mover/refine/RepackTrial.cc src/protocols/loops/loop_mover/refine/ShearMinCCDTrial.cc src/protocols/loops/loop_mover/refine/SmallMinCCDTrial.cc src/protocols/loops/loopfinder.cc src/protocols/loops/looprelax_protocols.cc src/protocols/loops/loops_definers/LoopsExplicitDefiner.cc src/protocols/loops/loops_main.cc src/protocols/loops/make_loops.cc src/protocols/loops/util.cc src/protocols/magnesium/MgHydrater.cc src/protocols/magnesium/MgMinimizer.cc src/protocols/magnesium/MgMonteCarlo.cc src/protocols/magnesium/MgOrbitalFrameFinder.cc src/protocols/magnesium/MgScanner.cc src/protocols/magnesium/MgWaterHydrogenPacker.cc src/protocols/magnesium/SampleGrid.cc src/protocols/magnesium/minimize_util.cc src/protocols/magnesium/util.cc src/protocols/mainchain_potential/GenerateMainchainPotential.cc src/protocols/make_rot_lib/MakeRotLibJobInputter.cc src/protocols/make_rot_lib/MakeRotLibMover.cc src/protocols/make_rot_lib/MakeRotLibOptionsData.cc src/protocols/match/BumpGrid.cc src/protocols/match/MatchPositionModifiers.cc src/protocols/match/Matcher.cc src/protocols/match/MatcherMover.cc src/protocols/match/MatcherTask.cc src/protocols/match/downstream/ActiveSiteGrid.cc src/protocols/match/downstream/ClassicMatchAlgorithm.cc src/protocols/match/downstream/DownstreamAlgorithm.cc src/protocols/match/downstream/GeometrySecMatchRPE.cc src/protocols/match/downstream/LigandConformerBuilder.cc src/protocols/match/downstream/RigidLigandBuilder.cc src/protocols/match/downstream/ScoringSecMatchRPE.cc src/protocols/match/downstream/SecondaryMatcherToDownstreamResidue.cc src/protocols/match/downstream/SecondaryMatcherToUpstreamResidue.cc src/protocols/match/output/DownstreamRMSEvaluator.cc src/protocols/match/output/MatchProcessor.cc src/protocols/match/output/PDBWriter.cc src/protocols/match/output/ProcessorFactory.cc src/protocols/match/output/SameChiBinComboGrouper.cc src/protocols/match/output/SameSequenceGrouper.cc src/protocols/match/output/UpstreamCollisionFilter.cc src/protocols/match/output/UpstreamDownstreamCollisionFilter.cc src/protocols/match/output/UpstreamHitCacher.cc src/protocols/match/output/WriteKinemageOutputter.cc src/protocols/match/output/WriteUpstreamCoordinateKineamge.cc src/protocols/match/upstream/OriginalScaffoldBuildPoint.cc src/protocols/match/upstream/ProteinSCSampler.cc src/protocols/match/upstream/ProteinUpstreamBuilder.cc src/protocols/match/upstream/UpstreamResTypeGeometry.cc src/protocols/matdes/BuildingBlockInterfaceOperation.cc src/protocols/matdes/ClashCheckFilter.cc src/protocols/matdes/ExtractSubposeMover.cc src/protocols/matdes/GetRBDOFValues.cc src/protocols/matdes/InterfacePackingFilter.cc src/protocols/matdes/MatDesGreedyOptMutationMover.cc src/protocols/matdes/MatDesPointMutationCalculator.cc src/protocols/matdes/MotifHitsRotamersOperation.cc src/protocols/matdes/OligomericAverageDegreeFilter.cc src/protocols/matdes/SchemePlaceMotifsMover.cc src/protocols/matdes/SymDofMover.cc src/protocols/matdes/SymUnsatHbondFilter.cc src/protocols/md/CartesianMD.cc src/protocols/md/MDBase.cc src/protocols/mean_field/AAMatrix.cc src/protocols/mean_field/AAProb.cc src/protocols/mean_field/DesignMeanField.cc src/protocols/mean_field/EnergiesByTaskCalculator.cc src/protocols/mean_field/FlexBBDesignMeanField.cc src/protocols/mean_field/FlexBBMeanField.cc src/protocols/mean_field/GenMeanFieldMover.cc src/protocols/mean_field/MeanField.cc src/protocols/mean_field/MeanFieldFactory.cc src/protocols/mean_field/ResHashMap.cc src/protocols/mean_field/RotMatrix.cc src/protocols/mean_field/RotProb.cc src/protocols/medal/MedalExchangeMover.cc src/protocols/medal/MedalMover.cc src/protocols/membrane/AddMPLigandMover.cc src/protocols/membrane/AddMembraneMover.cc src/protocols/membrane/AddMembraneSpanConstraint.cc src/protocols/membrane/AddMembraneSpanTermZConstraint.cc src/protocols/membrane/AqueousPoreFinder.cc src/protocols/membrane/FlipMover.cc src/protocols/membrane/MPLipidAccessibility.cc src/protocols/membrane/MPQuickRelaxMover.cc src/protocols/membrane/MembranePositionFromTopologyMover.cc src/protocols/membrane/OptimizeMembranePositionMover.cc src/protocols/membrane/OptimizeProteinEmbeddingMover.cc src/protocols/membrane/RandomMembranePositionMover.cc src/protocols/membrane/SetMembranePositionMover.cc src/protocols/membrane/SpinAroundPartnerMover.cc src/protocols/membrane/TiltMover.cc src/protocols/membrane/TransformIntoMembraneMover.cc src/protocols/membrane/TranslationRotationMover.cc src/protocols/membrane/benchmark/MakeCanonicalHelix.cc src/protocols/membrane/benchmark/SampleTiltAngles.cc src/protocols/membrane/geometry/Embedding.cc src/protocols/membrane/geometry/EmbeddingDef.cc src/protocols/membrane/scoring/FaWaterToBilayerEnergy.cc src/protocols/membrane/symmetry/SymmetricAddMembraneMover.cc src/protocols/membrane/symmetry/util.cc src/protocols/membrane/util.cc src/protocols/membrane/visualize/VisualizeEmbeddingMover.cc src/protocols/membrane/visualize/VisualizeMembraneMover.cc src/protocols/membrane_benchmark/MembraneEnergyLandscapeSampler.cc src/protocols/membrane_benchmark/PeptideOrientationMover.cc src/protocols/metal_interface/AddZincSiteConstraints.cc src/protocols/metal_interface/FindClosestAtom.cc src/protocols/metal_interface/MatchGrafter.cc src/protocols/metal_interface/ZincHeterodimerMover.cc src/protocols/metal_interface/ZincSiteFinder.cc src/protocols/minimization_packing/BoltzmannRotamerMover.cc src/protocols/minimization_packing/DisulfideOptimizationMover.cc src/protocols/minimization_packing/GreenPacker.cc src/protocols/minimization_packing/MinMover.cc src/protocols/minimization_packing/MinPackMover.cc src/protocols/minimization_packing/PackRotamersMover.cc src/protocols/minimization_packing/PackRotamersMoverLazy.cc src/protocols/minimization_packing/PertMinMover.cc src/protocols/minimization_packing/RepackSidechainsMover.cc src/protocols/minimization_packing/RotamerTrialsMinMover.cc src/protocols/minimization_packing/RotamerTrialsMover.cc src/protocols/minimization_packing/RotamerizeMover.cc src/protocols/minimization_packing/SetReturningPackRotamersMover.cc src/protocols/minimization_packing/TaskAwareMinMover.cc src/protocols/minimization_packing/symmetry/SymMinMover.cc src/protocols/minimization_packing/symmetry/SymRotamerTrialsMover.cc src/protocols/minimization_packing/symmetry/TaskAwareSymMinMover.cc src/protocols/monte_carlo/GenericMonteCarloMover.cc src/protocols/monte_carlo/GenericSimulatedAnnealer.cc src/protocols/motif_grafting/movers/MotifGraftMover.cc src/protocols/motifs/BuildPosition.cc src/protocols/motifs/IRCollection.cc src/protocols/motifs/LigandMotifSearch.cc src/protocols/motifs/Motif.cc src/protocols/motifs/MotifDnaPacker.cc src/protocols/motifs/MotifHit.cc src/protocols/motifs/MotifSearch.cc src/protocols/motifs/SingleMotif.cc src/protocols/motifs/motif_utils.cc src/protocols/moves/FilterReportAsPoseExtraScoresMover.cc src/protocols/moves/MoverContainer.cc src/protocols/moves/PyMOLMover.cc src/protocols/moves/StructureRestrictor.cc src/protocols/mpi_refinement/Clusterer.cc src/protocols/mpi_refinement/MPI_Refine_Master.cc src/protocols/mpi_refinement/MPI_Refinement.cc src/protocols/mpi_refinement/MultiObjective.cc src/protocols/mpi_refinement/Scheduler.cc src/protocols/mpi_refinement/Serial_Refine.cc src/protocols/mpi_refinement/StructAvrgMover.cc src/protocols/mpi_refinement/WorkUnit_Aggressive.cc src/protocols/mpi_refinement/WorkUnit_Loop.cc src/protocols/mpi_refinement/WorkUnit_Relax.cc src/protocols/mpi_refinement/WorkUnit_Sampler.cc src/protocols/mpi_refinement/util.cc src/protocols/multistage_rosetta_scripts/MRSJobQueen.cc src/protocols/multistate_design/MultiStatePacker.cc src/protocols/multistate_design/PackingState.cc src/protocols/multistate_design/util.cc src/protocols/ncbb/NcbbDockDesignProtocol.cc src/protocols/ncbb/PeptideStapleMover.cc src/protocols/ncbb/ResidueReplacementRebuildMover.cc src/protocols/ncbb/SecStructFinder.cc src/protocols/ncbb/SecStructMinimizeMover.cc src/protocols/ncbb/SecStructMinimizeMultiFunc.cc src/protocols/ncbb/a3b_hbs/A3BHbsPatcher.cc src/protocols/ncbb/hbs/HbsPatcher.cc src/protocols/ncbb/oop/OopCreatorMover.cc src/protocols/ncbb/oop/OopDockDesignProtocol.cc src/protocols/ncbb/oop/OopMover.cc src/protocols/ncbb/oop/OopPatcher.cc src/protocols/ncbb/oop/OopPuckMover.cc src/protocols/ncbb/oop/OopRandomPuckMover.cc src/protocols/ncbb/oop/OopRandomSmallMover.cc src/protocols/ncbb/triazolamer/TriazolamerMover.cc src/protocols/ncbb/triazolamer/TriazolamerRandomSmallMover.cc src/protocols/ncbb/util.cc src/protocols/neighbor/Neighborhood.cc src/protocols/nmr/ParaNMRScoreMover.cc src/protocols/nmr/nmrspinlabel_util.cc src/protocols/nmr/pcs/PCSEnergy.cc src/protocols/nmr/pcs/PCSLigandTransformMover.cc src/protocols/nmr/pre/PREEnergy.cc src/protocols/nmr/pre/PREMover.cc src/protocols/nmr/rdc/RDCEnergy.cc src/protocols/noesy_assign/CrossPeakList.cc src/protocols/noesy_assign/FragsToAtomDist.cc src/protocols/nonlocal/HelixRotate.cc src/protocols/nonlocal/SheetTranslate.cc src/protocols/nonlocal/StarTreeBuilder.cc src/protocols/nonlocal/util.cc src/protocols/normalmode/NormalMode.cc src/protocols/normalmode/NormalModeMultiFunc.cc src/protocols/normalmode/NormalModeRelaxMover.cc src/protocols/optimize_weights/IterativeOptEDriver.cc src/protocols/pack_daemon/PackDaemon.cc src/protocols/pack_daemon/util.cc src/protocols/pack_interface/ProteinProteinInterfaceUpweighterTaskOperation.cc src/protocols/parser/FragmentReader.cc src/protocols/parser/PackerPaletteLoader.cc src/protocols/pb_potential/SetupPoissonBoltzmannPotential.cc src/protocols/peptide_deriver/PeptideDeriverFilter.cc src/protocols/peptide_deriver/PeptideDeriverMarkdownStreamOutputter.cc src/protocols/pmut_scan/AlterSpecDisruptionDriver.cc src/protocols/pmut_scan/PointMutScanDriver.cc src/protocols/pockets/DarcParticleSwarmMinimizer.cc src/protocols/pockets/Fingerprint.cc src/protocols/pockets/FingerprintMultifunc.cc src/protocols/pockets/GenPharmacophore.cc src/protocols/pockets/PocketConstraint.cc src/protocols/pockets/PocketExemplarMultifunc.cc src/protocols/pockets/PocketGrid.cc src/protocols/pose_creation/ExtendedPoseMover.cc src/protocols/pose_creation/LoadPDBMover.cc src/protocols/pose_creation/MakeJunctionsMover.cc src/protocols/pose_creation/MakePolyXMover.cc src/protocols/pose_creation/MergePDBMover.cc src/protocols/pose_creation/MergePDBatOverlapMover.cc src/protocols/pose_creation/RepeatPropagationMover.cc src/protocols/pose_creation/SliceToMiniProteinMover.cc src/protocols/pose_length_moves/AnalyzeLoopModeling.cc src/protocols/pose_length_moves/ConnectChainsMover.cc src/protocols/pose_length_moves/FixAllLoopsMover.cc src/protocols/pose_length_moves/InsertResMover.cc src/protocols/pose_length_moves/NearNativeLoopCloser.cc src/protocols/pose_metric_calculators/CatPiCalculator.cc src/protocols/pose_metric_calculators/ChargeCalculator.cc src/protocols/pose_metric_calculators/ClashCountCalculator.cc src/protocols/pose_metric_calculators/FragQualCalculator.cc src/protocols/pose_metric_calculators/HPatchCalculator.cc src/protocols/pose_metric_calculators/NonlocalContactsCalculator.cc src/protocols/pose_metric_calculators/PackstatCalculator.cc src/protocols/pose_metric_calculators/PiPiCalculator.cc src/protocols/pose_metric_calculators/ResidueDecompositionByChainCalculator.cc src/protocols/pose_metric_calculators/RotamerBoltzCalculator.cc src/protocols/pose_metric_calculators/RotamerRecovery.cc src/protocols/pose_metric_calculators/SHOBuriedUnsatisfiedPolarsCalculator.cc src/protocols/pose_metric_calculators/SaltBridgeCalculator.cc src/protocols/pose_metric_calculators/SemiExplicitWaterUnsatisfiedPolarsCalculator.cc src/protocols/pose_metric_calculators/SequenceComparison.cc src/protocols/pose_metric_calculators/SurfaceCalculator.cc src/protocols/pose_reporters/BasicPosePropertyReporters.cc src/protocols/pose_selectors/BasicPoseSelectors.cc src/protocols/protein_interface_design/ReportPSSMDifference.cc src/protocols/protein_interface_design/design_utils.cc src/protocols/protein_interface_design/filters/AtomicContactCountFilter.cc src/protocols/protein_interface_design/filters/AverageDegreeFilter.cc src/protocols/protein_interface_design/filters/BindingStrainFilter.cc src/protocols/protein_interface_design/filters/BoltzmannFilter.cc src/protocols/protein_interface_design/filters/ClashWithTargetFilter.cc src/protocols/protein_interface_design/filters/DesignableResiduesFilter.cc src/protocols/protein_interface_design/filters/FNatFilter.cc src/protocols/protein_interface_design/filters/FilterScan.cc src/protocols/protein_interface_design/filters/HbondsToAtomFilter.cc src/protocols/protein_interface_design/filters/HbondsToResidueFilter.cc src/protocols/protein_interface_design/filters/IRmsdFilter.cc src/protocols/protein_interface_design/filters/LRmsdFilter.cc src/protocols/protein_interface_design/filters/RmsdFilter.cc src/protocols/protein_interface_design/filters/RmsdSimpleFilter.cc src/protocols/protein_interface_design/filters/SSamountFilter.cc src/protocols/protein_interface_design/filters/SequenceRecoveryFilter.cc src/protocols/protein_interface_design/filters/SpecificResiduesNearInterfaceFilter.cc src/protocols/protein_interface_design/filters/StubScoreFilter.cc src/protocols/protein_interface_design/filters/StubScoreLoopsFilter.cc src/protocols/protein_interface_design/filters/TorsionFilter.cc src/protocols/protein_interface_design/movers/AddChainBreak.cc src/protocols/protein_interface_design/movers/AddSidechainConstraintsToHotspots.cc src/protocols/protein_interface_design/movers/BackrubDDMover.cc src/protocols/protein_interface_design/movers/BestHotspotCstMover.cc src/protocols/protein_interface_design/movers/BuildAlaPose.cc src/protocols/protein_interface_design/movers/DesignMinimizeHbonds.cc src/protocols/protein_interface_design/movers/DisulfideMover.cc src/protocols/protein_interface_design/movers/DockAndRetrieveSidechains.cc src/protocols/protein_interface_design/movers/DockWithHotspotMover.cc src/protocols/protein_interface_design/movers/HotspotDisjointedFoldTreeMover.cc src/protocols/protein_interface_design/movers/InterfaceRecapitulationMover.cc src/protocols/protein_interface_design/movers/LoopFinder.cc src/protocols/protein_interface_design/movers/LoopLengthChange.cc src/protocols/protein_interface_design/movers/LoopMoverFromCommandLine.cc src/protocols/protein_interface_design/movers/LoopRemodel.cc src/protocols/protein_interface_design/movers/MapHotspot.cc src/protocols/protein_interface_design/movers/PlaceOnLoop.cc src/protocols/protein_interface_design/movers/PlaceSimultaneouslyMover.cc src/protocols/protein_interface_design/movers/PlaceStubMover.cc src/protocols/protein_interface_design/movers/PlaceUtils.cc src/protocols/protein_interface_design/movers/PlacementAuctionMover.cc src/protocols/protein_interface_design/movers/PlacementMinimizationMover.cc src/protocols/protein_interface_design/movers/PrepackMover.cc src/protocols/protein_interface_design/movers/ProteinInterfaceMultiStateDesignMover.cc src/protocols/protein_interface_design/movers/RandomMutation.cc src/protocols/protein_interface_design/movers/RepackMinimize.cc src/protocols/protein_interface_design/movers/SaveAndRetrieveSidechains.cc src/protocols/protein_interface_design/movers/SetAtomTree.cc src/protocols/protein_interface_design/movers/SetTemperatureFactor.cc src/protocols/protein_interface_design/movers/SetupHotspotConstraintsLoopsMover.cc src/protocols/protein_interface_design/movers/SetupHotspotConstraintsMover.cc src/protocols/protein_interface_design/movers/ShoveResidueMover.cc src/protocols/protein_interface_design/movers/SpinMover.cc src/protocols/protein_interface_design/movers/TaskAwareCsts.cc src/protocols/protein_interface_design/movers/TopologyBrokerMover.cc src/protocols/protein_interface_design/movers/TryRotamers.cc src/protocols/protein_interface_design/read_patchdock.cc src/protocols/protein_interface_design/util.cc src/protocols/qsar/RenderGridsToKinemage.cc src/protocols/qsar/qsarMap.cc src/protocols/qsar/qsarMover.cc src/protocols/qsar/scoring_grid/AtrGrid.cc src/protocols/qsar/scoring_grid/ChargeGrid.cc src/protocols/qsar/scoring_grid/ClassicGrid.cc src/protocols/qsar/scoring_grid/GridManager.cc src/protocols/qsar/scoring_grid/GridSet.cc src/protocols/qsar/scoring_grid/HbaGrid.cc src/protocols/qsar/scoring_grid/HbdGrid.cc src/protocols/qsar/scoring_grid/LigandPropertyScore.cc src/protocols/qsar/scoring_grid/PCSMultiGrid.cc src/protocols/qsar/scoring_grid/PCSSingleGrid.cc src/protocols/qsar/scoring_grid/RepGrid.cc src/protocols/qsar/scoring_grid/ScoreNormalization.cc src/protocols/qsar/scoring_grid/ShapeGrid.cc src/protocols/qsar/scoring_grid/SingleGrid.cc src/protocols/qsar/scoring_grid/SiteGrid.cc src/protocols/qsar/scoring_grid/SolvationGrid.cc src/protocols/qsar/scoring_grid/SolvationMetaGrid.cc src/protocols/qsar/scoring_grid/VdwGrid.cc src/protocols/quantum_annealing/InteractionGraphSummaryMetric.cc src/protocols/rbsegment_relax/AutoRBRelaxMover.cc src/protocols/rbsegment_relax/FragInsertAndAlignMover.cc src/protocols/rbsegment_relax/IdealizeHelices.cc src/protocols/rbsegment_relax/MakeStarTopology.cc src/protocols/rbsegment_relax/OptimizeThreading.cc src/protocols/rbsegment_relax/RBSegmentMover.cc src/protocols/rbsegment_relax/RBSegmentRelax.cc src/protocols/rbsegment_relax/RBSegmentRelax_main.cc src/protocols/rbsegment_relax/util.cc src/protocols/recces/sampler/rna/MC_RNA_OneJump.cc src/protocols/recces/sampler/util.cc src/protocols/recces/scratch/ThermalMinimizer.cc src/protocols/recces/scratch/ThermalSamplingMover.cc src/protocols/recces/scratch/thermal_sampler.cc src/protocols/recces/setup_util.cc src/protocols/recces/util.cc src/protocols/recon_design/FindConsensusSequence.cc src/protocols/recon_design/FitnessFilter.cc src/protocols/recon_design/MSDMover.cc src/protocols/recon_design/recon_util.cc src/protocols/relax/AcceptToBestMover.cc src/protocols/relax/AtomCoordinateCstMover.cc src/protocols/relax/CentroidRelax.cc src/protocols/relax/ClassicRelax.cc src/protocols/relax/FastRelax.cc src/protocols/relax/LocalRelax.cc src/protocols/relax/MiniRelax.cc src/protocols/relax/Ramady.cc src/protocols/relax/RangeRelaxMover.cc src/protocols/relax/RelaxProtocolBase.cc src/protocols/relax/RepeatProteinRelax.cc src/protocols/relax/WorkUnit_BatchRelax.cc src/protocols/relax/cst_util.cc src/protocols/relax/loop_closure/FASelectSlidingWindowLoopClosure.cc src/protocols/relax/membrane/MPFastRelaxMover.cc src/protocols/relax/membrane/MPMutateRelaxMover.cc src/protocols/relax/membrane/MPRangeRelaxMover.cc src/protocols/relax/membrane/util.cc src/protocols/relax/util.cc src/protocols/residue_optimization/MetapatchEnumeration.cc src/protocols/residue_selectors/NativeSelector.cc src/protocols/residue_selectors/TaskSelector.cc src/protocols/rigid/PoseMembraneRigidBodyMover.cc src/protocols/rigid/RB_geometry.cc src/protocols/rigid/RigidBodyMover.cc src/protocols/rigid/RollMover.cc src/protocols/rigid/RotateJumpAxisMover.cc src/protocols/rigid/UniformRigidBodyCM.cc src/protocols/rigid/UniformRigidBodyMover.cc src/protocols/rna/AlignmentEnergy.cc src/protocols/rna/denovo/RNA_DeNovoPoseInitializer.cc src/protocols/rna/denovo/RNA_DeNovoProtocol.cc src/protocols/rna/denovo/RNA_FragmentMonteCarlo.cc src/protocols/rna/denovo/coarse/CoarseRNA_Fragments.cc src/protocols/rna/denovo/coarse/CoarseRNA_LoopCloser.cc src/protocols/rna/denovo/coarse/MultipleDomainMover.cc src/protocols/rna/denovo/movers/RNA_DeNovoMasterMover.cc src/protocols/rna/denovo/movers/RNA_DeNovoProtocolMover.cc src/protocols/rna/denovo/movers/RNA_FragmentMover.cc src/protocols/rna/denovo/movers/RNA_HelixMover.cc src/protocols/rna/denovo/movers/RNA_Minimizer.cc src/protocols/rna/denovo/movers/RNP_HighResMover.cc src/protocols/rna/denovo/util.cc src/protocols/rna/movers/ERRASER2Protocol.cc src/protocols/rna/movers/ErraserMinimizerMover.cc src/protocols/rna/movers/RNAIdealizeMover.cc src/protocols/rna/movers/RNAThreadAndMinimizeMover.cc src/protocols/rna/movers/RNA_LoopCloser.cc src/protocols/rosetta_scripts/ParsedProtocol.cc src/protocols/rosetta_scripts/RosettaScriptsParser.cc src/protocols/rosetta_scripts/util.cc src/protocols/rotamer_recovery/RRComparer.cc src/protocols/rotamer_recovery/RRComparerAutomorphicRMSD.cc src/protocols/rotamer_recovery/RRComparerElecDensDiff.cc src/protocols/rotamer_recovery/RRProtocolMinPack.cc src/protocols/rotamer_recovery/RRProtocolMover.cc src/protocols/rotamer_recovery/RRProtocolPackRotamers.cc src/protocols/rotamer_recovery/RRProtocolRTMin.cc src/protocols/rotamer_recovery/RRProtocolReferenceStructure.cc src/protocols/rotamer_recovery/RRProtocolRelax.cc src/protocols/rotamer_recovery/RRProtocolRotamerTrials.cc src/protocols/rotamer_recovery/RRReporterHuman.cc src/protocols/rotamer_recovery/RRReporterSQLite.cc src/protocols/rotamer_recovery/RotamerRecoveryMover.cc src/protocols/rpc/rpc.cc src/protocols/sasa_scores/sasapack.cc src/protocols/score_filters/GeometryFilter.cc src/protocols/score_filters/ScoreCutoffFilter.cc src/protocols/score_filters/ScoreTypeFilter.cc src/protocols/scoring/ImplicitFastClashCheck.cc src/protocols/scoring/InterchainPotential.cc src/protocols/scoring/Interface.cc src/protocols/scoring/InterfaceInfo.cc src/protocols/scoring/VDW_GridEnergy.cc src/protocols/scoring/methods/InterchainEnvEnergy.cc src/protocols/scoring/methods/InterchainPairEnergy.cc src/protocols/scoring/methods/SpecialRotamerEnergy.cc src/protocols/scoring/methods/TargetClashEnergy.cc src/protocols/scoring/methods/pcs/PseudocontactShiftData.cc src/protocols/scoring/methods/pcs/PseudocontactShiftEnergy.cc src/protocols/scoring/methods/pcs2/GridSearchIteratorCA.cc src/protocols/scoring/methods/pcs2/PcsDataCenter.cc src/protocols/scoring/methods/pcs2/PcsEnergy.cc src/protocols/scoring/methods/pcsTs1/PseudocontactShiftData.cc src/protocols/scoring/methods/pcsTs1/PseudocontactShiftEnergy.cc src/protocols/scoring/methods/pcsTs2/PseudocontactShiftData.cc src/protocols/scoring/methods/pcsTs2/PseudocontactShiftEnergy.cc src/protocols/scoring/methods/pcsTs3/PseudocontactShiftData.cc src/protocols/scoring/methods/pcsTs3/PseudocontactShiftEnergy.cc src/protocols/scoring/methods/pcsTs4/PseudocontactShiftData.cc src/protocols/scoring/methods/pcsTs4/PseudocontactShiftEnergy.cc src/protocols/scoring/methods/saxs/PDDFEnergy.cc src/protocols/seeded_abinitio/CAcstGenerator.cc src/protocols/seeded_abinitio/CloseFold.cc src/protocols/seeded_abinitio/CoordinateCst.cc src/protocols/seeded_abinitio/DefineMovableLoops.cc src/protocols/seeded_abinitio/GrowPeptides.cc src/protocols/seeded_abinitio/SeedFoldTree.cc src/protocols/seeded_abinitio/SeedSetupMover.cc src/protocols/seeded_abinitio/SeededAbinitio_util.cc src/protocols/seeded_abinitio/SegmentHybridizer.cc src/protocols/seeded_abinitio/SwapSegment.cc src/protocols/sewing/data_storage/SmartAssembly.cc src/protocols/sewing/hashing/AlignmentFileGeneratorMover.cc src/protocols/sewing/hashing/LigandBindingResPlacer.cc src/protocols/sewing/movers/AssemblyMover.cc src/protocols/sewing/requirements/ClashRequirement.cc src/protocols/sewing/requirements/DsspSpecificLengthRequirement.cc src/protocols/sewing/requirements/KeepLigandContactsRequirement.cc src/protocols/sewing/requirements/LengthInResiduesRequirement.cc src/protocols/sewing/requirements/LigandClashRequirement.cc src/protocols/sewing/requirements/SizeInSegmentsRequirement.cc src/protocols/sewing/scoring/InterModelMotifScorer.cc src/protocols/sewing/scoring/IntraDesignTerminusMotifScorer.cc src/protocols/sewing/scoring/MotifScorer.cc src/protocols/sewing/scoring/PartnerMotifScorer.cc src/protocols/sewing/scoring/SegmentContactOrderScorer.cc src/protocols/sewing/scoring/StartingNodeMotifScorer.cc src/protocols/sewing/scoring/SubsetPartnerMotifScorer.cc src/protocols/sewing/scoring/TerminusMotifScorer.cc src/protocols/sewing/scoring/TopNMotifScorer.cc src/protocols/sic_dock/RigidScore.cc src/protocols/sic_dock/Rose.cc src/protocols/sic_dock/SICFast.cc src/protocols/sic_dock/designability_score.cc src/protocols/sic_dock/loophash_util.cc src/protocols/sic_dock/read_biounit.cc src/protocols/sic_dock/scores/MotifHashRigidScore.cc src/protocols/sic_dock/scores/TrisBpyScore.cc src/protocols/sic_dock/util.cc src/protocols/simple_ddg/AlaScan.cc src/protocols/simple_ddg/DdGScan.cc src/protocols/simple_ddg/DdgFilter.cc src/protocols/simple_ddg/InterfaceBindingEnergyDensityFilter.cc src/protocols/simple_ddg/SSElementBisectddGFilter.cc src/protocols/simple_ddg/ddG.cc src/protocols/simple_filters/AbinitioBaseFilter.cc src/protocols/simple_filters/AngleToVectorFilter.cc src/protocols/simple_filters/AtomicContactFilter.cc src/protocols/simple_filters/AtomicDistanceFilter.cc src/protocols/simple_filters/AveragePathLengthFilter.cc src/protocols/simple_filters/BuriedSurfaceAreaFilter.cc src/protocols/simple_filters/BuriedUnsatHbondFilter.cc src/protocols/simple_filters/ChainBreakFilter.cc src/protocols/simple_filters/ChainCountFilter.cc src/protocols/simple_filters/ChiWellRmsdEvaluator.cc src/protocols/simple_filters/ContactMapEvaluator.cc src/protocols/simple_filters/ContactMolecularSurfaceFilter.cc src/protocols/simple_filters/DeltaFilter.cc src/protocols/simple_filters/DisulfideEntropyFilter.cc src/protocols/simple_filters/DomainInterfaceFilter.cc src/protocols/simple_filters/EnergyPerResidueFilter.cc src/protocols/simple_filters/EvaluatedTrialMover.cc src/protocols/simple_filters/ExtraScoreEvaluatorCreator.cc src/protocols/simple_filters/HelixHelixAngleFilter.cc src/protocols/simple_filters/HolesFilter.cc src/protocols/simple_filters/InterfaceHbondsFilter.cc src/protocols/simple_filters/InterfaceHydrophobicResidueContactsFilter.cc src/protocols/simple_filters/InterfaceSasaFilter.cc src/protocols/simple_filters/JumpEvaluator.cc src/protocols/simple_filters/LeastNativeLike9merFilter.cc src/protocols/simple_filters/LongestContinuousApolarSegmentFilter.cc src/protocols/simple_filters/LongestContinuousPolarSegmentFilter.cc src/protocols/simple_filters/MPSpanAngleFilter.cc src/protocols/simple_filters/MembAccesResidueLipophilicityFilter.cc src/protocols/simple_filters/MotifScoreFilter.cc src/protocols/simple_filters/MutationsFilter.cc src/protocols/simple_filters/NMerPSSMEnergyFilter.cc src/protocols/simple_filters/NMerSVMEnergyFilter.cc src/protocols/simple_filters/NativeEvaluatorCreator.cc src/protocols/simple_filters/NeighborTypeFilter.cc src/protocols/simple_filters/NetChargeFilter.cc src/protocols/simple_filters/NonSequentialNeighborsFilter.cc src/protocols/simple_filters/PackStatFilter.cc src/protocols/simple_filters/PackerNeighborGraphFilter.cc src/protocols/simple_filters/PoseCommentFilter.cc src/protocols/simple_filters/PredictedBurialEvaluator.cc src/protocols/simple_filters/RdcEvaluatorCreator.cc src/protocols/simple_filters/ReadPoseExtraScoreFilter.cc src/protocols/simple_filters/RepeatParameterFilter.cc src/protocols/simple_filters/ResidueBurialFilter.cc src/protocols/simple_filters/ResidueChiralityFilter.cc src/protocols/simple_filters/ResidueCountFilter.cc src/protocols/simple_filters/ResidueDepthFilter.cc src/protocols/simple_filters/ResidueDistanceFilter.cc src/protocols/simple_filters/ResidueIEFilter.cc src/protocols/simple_filters/ResidueLipophilicityFilter.cc src/protocols/simple_filters/ResidueSelectionDistanceFilter.cc src/protocols/simple_filters/ResidueSetChainEnergyFilter.cc src/protocols/simple_filters/ResiduesInInterfaceFilter.cc src/protocols/simple_filters/RmsdTargetEvaluatorCreator.cc src/protocols/simple_filters/SAXSScoreFilter.cc src/protocols/simple_filters/SSElementLengthFilter.cc src/protocols/simple_filters/SSElementMotifContactFilter.cc src/protocols/simple_filters/SSMotifFinderFilter.cc src/protocols/simple_filters/SaveResfileToDiskFilter.cc src/protocols/simple_filters/SecretionPredictionFilter.cc src/protocols/simple_filters/SequenceDistanceFilter.cc src/protocols/simple_filters/ShapeComplementarityFilter.cc src/protocols/simple_filters/SheetFilter.cc src/protocols/simple_filters/SidechainRmsdFilter.cc src/protocols/simple_filters/SimpleHbondsToAtomFilter.cc src/protocols/simple_filters/SimpleMetricFilter.cc src/protocols/simple_filters/SpanTopologyMatchPoseFilter.cc src/protocols/simple_filters/StemFinderFilter.cc src/protocols/simple_filters/StructuralSimilarityEvaluator.cc src/protocols/simple_filters/SymmetricMotifFilter.cc src/protocols/simple_filters/TMsAACompFilter.cc src/protocols/simple_filters/TMsSpanMembraneFilter.cc src/protocols/simple_filters/TaskAwareSASAFilter.cc src/protocols/simple_filters/TaskAwareScoreTypeFilter.cc src/protocols/simple_filters/TerminusDistanceFilter.cc src/protocols/simple_filters/TotalSasaFilter.cc src/protocols/simple_moves/AddCavitiesMover.cc src/protocols/simple_moves/AddChainMover.cc src/protocols/simple_moves/AddJobPairData.cc src/protocols/simple_moves/AddPDBInfoMover.cc src/protocols/simple_moves/AddResidueCouplingConstraint.cc src/protocols/simple_moves/AddResidueLabelMover.cc src/protocols/simple_moves/AlignChainMover.cc src/protocols/simple_moves/BBConRotMover.cc src/protocols/simple_moves/BBGaussianMover.cc src/protocols/simple_moves/BackboneMover.cc src/protocols/simple_moves/ChainSplitMover.cc src/protocols/simple_moves/CombinePoseMover.cc src/protocols/simple_moves/ConcatenatePosesMover.cc src/protocols/simple_moves/ConstrainToIdealMover.cc src/protocols/simple_moves/ContingentAcceptMover.cc src/protocols/simple_moves/ConvertRealToVirtualMover.cc src/protocols/simple_moves/ConvertVirtualToRealMover.cc src/protocols/simple_moves/CopyDofMover.cc src/protocols/simple_moves/CopyRotamerMover.cc src/protocols/simple_moves/CoupledMover.cc src/protocols/simple_moves/CutChainMover.cc src/protocols/simple_moves/CyclizationMover.cc src/protocols/simple_moves/DME_FilterMover.cc src/protocols/simple_moves/DOFHistogramRecorder.cc src/protocols/simple_moves/DeleteChainMover.cc src/protocols/simple_moves/DeleteChainsMover.cc src/protocols/simple_moves/DisulfideInsertionMover.cc src/protocols/simple_moves/DumpPdb.cc src/protocols/simple_moves/DumpSingleResidueRotamers.cc src/protocols/simple_moves/ExplicitWaterMover.cc src/protocols/simple_moves/FavorSequenceProfile.cc src/protocols/simple_moves/FoldTreeFromMotif.cc src/protocols/simple_moves/GunnCost.cc src/protocols/simple_moves/MissingDensityToJumpMover.cc src/protocols/simple_moves/ModifyVariantTypeMover.cc src/protocols/simple_moves/MutateResidue.cc src/protocols/simple_moves/PDBReloadMover.cc src/protocols/simple_moves/PSSM2BfactorMover.cc src/protocols/simple_moves/PeriodicBoxMover.cc src/protocols/simple_moves/ProlineFixMover.cc src/protocols/simple_moves/RandomOmegaFlipMover.cc src/protocols/simple_moves/RandomTorsionMover.cc src/protocols/simple_moves/ReportEffectivePKA.cc src/protocols/simple_moves/ReportXYZ.cc src/protocols/simple_moves/RepulsiveOnlyMover.cc src/protocols/simple_moves/ResTypeFragmentMover.cc src/protocols/simple_moves/ResetFoldTree.cc src/protocols/simple_moves/ReturnSidechainMover.cc src/protocols/simple_moves/RingConformationMover.cc src/protocols/simple_moves/SaveSequenceToCommentsMover.cc src/protocols/simple_moves/ScoreMover.cc src/protocols/simple_moves/SetTorsion.cc src/protocols/simple_moves/SetupMetalsMover.cc src/protocols/simple_moves/ShakeStructureMover.cc src/protocols/simple_moves/ShortBackrubMover.cc src/protocols/simple_moves/SimpleThreadingMover.cc src/protocols/simple_moves/StructProfileMover.cc src/protocols/simple_moves/SuperimposeMover.cc src/protocols/simple_moves/SwitchChainOrderMover.cc src/protocols/simple_moves/SwitchResidueTypeSetMover.cc src/protocols/simple_moves/TailsScoreMover.cc src/protocols/simple_moves/TorsionDOFMover.cc src/protocols/simple_moves/Tumble.cc src/protocols/simple_moves/UniformPositionMover.cc src/protocols/simple_moves/VirtualRootMover.cc src/protocols/simple_moves/WriteFiltersToPose.cc src/protocols/simple_moves/WriteSSEMover.cc src/protocols/simple_moves/asym_fold_and_dock/AsymFoldandDockMoveRbJumpMover.cc src/protocols/simple_moves/bb_sampler/SmallBBSampler.cc src/protocols/simple_moves/bb_sampler/SugarBBSampler.cc src/protocols/simple_moves/bin_transitions/InitializeByBins.cc src/protocols/simple_moves/bin_transitions/PerturbByBins.cc src/protocols/simple_moves/chiral/ChiralMover.cc src/protocols/simple_moves/sidechain_moves/JumpRotamerSidechainMover.cc src/protocols/simple_moves/sidechain_moves/PerturbChiSidechainMover.cc src/protocols/simple_moves/sidechain_moves/PerturbRotamerSidechainMover.cc src/protocols/simple_moves/sidechain_moves/SetChiMover.cc src/protocols/simple_moves/sidechain_moves/SidechainMCMover.cc src/protocols/simple_moves/sidechain_moves/SidechainMover.cc src/protocols/simple_moves/sidechain_moves/SidechainMoverBase.cc src/protocols/simple_pose_metric_calculators/BuriedUnsatisfiedPolarsCalculator.cc src/protocols/simple_pose_metric_calculators/NumberHBondsCalculator.cc src/protocols/simple_task_operations/RestrictToInterface.cc src/protocols/simple_task_operations/RestrictToLoops.cc src/protocols/simple_task_operations/RestrictToLoopsAndNeighbors.cc src/protocols/splice/AlignEndsMover.cc src/protocols/splice/DesignInterfacesOperation.cc src/protocols/splice/FindEndpointsOperation.cc src/protocols/splice/RBInMover.cc src/protocols/splice/RBOutMover.cc src/protocols/splice/RotLibOut.cc src/protocols/splice/SampleRotamersFromPDB.cc src/protocols/splice/Splice.cc src/protocols/splice/SpliceIn.cc src/protocols/splice/SpliceInAntibody.cc src/protocols/splice/SpliceInTail.cc src/protocols/splice/SpliceManager.cc src/protocols/splice/SpliceOut.cc src/protocols/splice/SpliceOutAntibody.cc src/protocols/splice/SpliceOutTail.cc src/protocols/splice/SpliceSegment.cc src/protocols/splice/TailSegmentMover.cc src/protocols/splice/util.cc src/protocols/star/Extender.cc src/protocols/star/StarAbinitio.cc src/protocols/stepwise/StepWiseSampleAndScreen.cc src/protocols/stepwise/legacy/modeler/protein/StepWiseProteinMinimizer.cc src/protocols/stepwise/legacy/modeler/protein/StepWiseProteinPoseSetup.cc src/protocols/stepwise/legacy/modeler/protein/util.cc src/protocols/stepwise/legacy/modeler/rna/RNA_AnalyticLoopCloser.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_Clusterer.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_PoseSelection.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_PoseSetup.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_PoseSetupFromCommandLine.cc src/protocols/stepwise/legacy/modeler/rna/StepWiseRNA_WorkingParametersSetup.cc src/protocols/stepwise/legacy/modeler/rna/util.cc src/protocols/stepwise/legacy/screener/SimpleRMSD_Screener.cc src/protocols/stepwise/modeler/StepWiseConnectionSampler.cc src/protocols/stepwise/modeler/StepWiseMinimizer.cc src/protocols/stepwise/modeler/StepWiseModeler.cc src/protocols/stepwise/modeler/align/StepWiseClusterer.cc src/protocols/stepwise/modeler/align/StepWiseLegacyClusterer.cc src/protocols/stepwise/modeler/align/StepWiseLegacyClustererSilentBased.cc src/protocols/stepwise/modeler/align/StepWisePoseAligner.cc src/protocols/stepwise/modeler/align/util.cc src/protocols/stepwise/modeler/constraint_util.cc src/protocols/stepwise/modeler/movemap/util.cc src/protocols/stepwise/modeler/options/StepWiseModelerOptions.cc src/protocols/stepwise/modeler/output_util.cc src/protocols/stepwise/modeler/packer/SideChainCopier.cc src/protocols/stepwise/modeler/packer/StepWiseMasterPacker.cc src/protocols/stepwise/modeler/packer/StepWisePacker.cc src/protocols/stepwise/modeler/packer/util.cc src/protocols/stepwise/modeler/polar_hydrogens/PolarHydrogenPacker.cc src/protocols/stepwise/modeler/polar_hydrogens/util.cc src/protocols/stepwise/modeler/precomputed/PrecomputedLibraryMover.cc src/protocols/stepwise/modeler/protein/InputStreamWithResidueInfo.cc src/protocols/stepwise/modeler/protein/StepWiseProteinBackboneSampler.cc src/protocols/stepwise/modeler/protein/checker/ProteinAtrRepChecker.cc src/protocols/stepwise/modeler/protein/loop_close/StepWiseProteinCCD_Closer.cc src/protocols/stepwise/modeler/protein/loop_close/StepWiseProteinKIC_LoopBridger.cc src/protocols/stepwise/modeler/protein/util.cc src/protocols/stepwise/modeler/rna/StepWiseRNA_CombineLongLoopFilterer.cc src/protocols/stepwise/modeler/rna/StepWiseRNA_OutputData.cc src/protocols/stepwise/modeler/rna/StepWiseRNA_ResidueInfo.cc src/protocols/stepwise/modeler/rna/bulge/BulgeApplyMover.cc src/protocols/stepwise/modeler/rna/bulge/BulgeUnApplyMover.cc src/protocols/stepwise/modeler/rna/checker/RNA_AtrRepChecker.cc src/protocols/stepwise/modeler/rna/checker/RNA_BaseCentroidChecker.cc src/protocols/stepwise/modeler/rna/checker/RNA_ChainClosableGeometryChecker.cc src/protocols/stepwise/modeler/rna/checker/RNA_ChainClosureChecker.cc src/protocols/stepwise/modeler/rna/checker/RNA_VDW_BinChecker.cc src/protocols/stepwise/modeler/rna/o2prime/O2PrimePacker.cc src/protocols/stepwise/modeler/rna/phosphate/MultiPhosphateSampler.cc src/protocols/stepwise/modeler/rna/phosphate/PhosphateMover.cc src/protocols/stepwise/modeler/rna/phosphate/util.cc src/protocols/stepwise/modeler/rna/rigid_body/util.cc src/protocols/stepwise/modeler/rna/sugar/SugarInstantiateMover.cc src/protocols/stepwise/modeler/rna/sugar/SugarModeling.cc src/protocols/stepwise/modeler/rna/sugar/SugarVirtualizeMover.cc src/protocols/stepwise/modeler/rna/sugar/VirtualSugarJustInTimeInstantiator.cc src/protocols/stepwise/modeler/rna/sugar/VirtualSugarSampler.cc src/protocols/stepwise/modeler/rna/sugar/VirtualSugarSamplerFromStringList.cc src/protocols/stepwise/modeler/rna/sugar/util.cc src/protocols/stepwise/modeler/rna/util.cc src/protocols/stepwise/modeler/util.cc src/protocols/stepwise/modeler/working_parameters/StepWiseWorkingParameters.cc src/protocols/stepwise/modeler/working_parameters/util.cc src/protocols/stepwise/monte_carlo/StepWiseMonteCarlo.cc src/protocols/stepwise/monte_carlo/mover/AddMover.cc src/protocols/stepwise/monte_carlo/mover/AddOrDeleteMover.cc src/protocols/stepwise/monte_carlo/mover/DeleteMover.cc src/protocols/stepwise/monte_carlo/mover/FromScratchMover.cc src/protocols/stepwise/monte_carlo/mover/ResampleMover.cc src/protocols/stepwise/monte_carlo/mover/StepWiseMasterMover.cc src/protocols/stepwise/monte_carlo/mover/StepWiseMoveSelector.cc src/protocols/stepwise/monte_carlo/mover/TransientCutpointHandler.cc src/protocols/stepwise/monte_carlo/rna/RNA_AddDeleteMonteCarlo.cc src/protocols/stepwise/monte_carlo/rna/RNA_O2PrimeMover.cc src/protocols/stepwise/monte_carlo/rna/RNA_TorsionMover.cc src/protocols/stepwise/monte_carlo/submotif/SubMotifLibrary.cc src/protocols/stepwise/sampler/copy_dofs/ResidueAlternativeStepWiseSampler.cc src/protocols/stepwise/sampler/copy_dofs/ResidueListStepWiseSampler.cc src/protocols/stepwise/sampler/protein/util.cc src/protocols/stepwise/sampler/rigid_body/RigidBodyStepWiseSampler.cc src/protocols/stepwise/sampler/rigid_body/RigidBodyStepWiseSamplerWithResidueAlternatives.cc src/protocols/stepwise/sampler/rigid_body/RigidBodyStepWiseSamplerWithResidueList.cc src/protocols/stepwise/sampler/rna/RNA_KinematicCloser.cc src/protocols/stepwise/sampler/rna/RNA_SugarStepWiseSampler.cc src/protocols/stepwise/sampler/rna/util.cc src/protocols/stepwise/sampler/screener/RNA_TorsionScreener.cc src/protocols/stepwise/screener/BaseBinMapUpdater.cc src/protocols/stepwise/screener/BaseCentroidScreener.cc src/protocols/stepwise/screener/CentroidDistanceScreener.cc src/protocols/stepwise/screener/FastForwardToNextResidueAlternative.cc src/protocols/stepwise/screener/FastForwardToNextRigidBody.cc src/protocols/stepwise/screener/IntegrationTestBreaker.cc src/protocols/stepwise/screener/PartitionContactScreener.cc src/protocols/stepwise/screener/RNA_ChainClosableGeometryResidueBasedScreener.cc src/protocols/stepwise/screener/RNA_ChainClosableGeometryStubBasedScreener.cc src/protocols/stepwise/screener/ResidueContactScreener.cc src/protocols/stepwise/screener/SampleApplier.cc src/protocols/stepwise/screener/StubApplier.cc src/protocols/stepwise/screener/StubDistanceScreener.cc src/protocols/stepwise/screener/SugarInstantiator.cc src/protocols/stepwise/screener/TagDefinition.cc src/protocols/stepwise/screener/VDW_BinScreener.cc src/protocols/stepwise/screener/util.cc src/protocols/struct_fragment/StructFragmentMover.cc src/protocols/surface_docking/CentroidRelaxMover.cc src/protocols/surface_docking/FullatomRelaxMover.cc src/protocols/surface_docking/SurfaceDockingProtocol.cc src/protocols/switches/GraftSwitchMover.cc src/protocols/symmetric_docking/SymDockProtocol.cc src/protocols/symmetric_docking/SymDockingHiRes.cc src/protocols/symmetric_docking/SymDockingLowRes.cc src/protocols/symmetric_docking/SymFoldandDockRbTrialMover.cc src/protocols/symmetric_docking/SymFoldandDockSlideTrialMover.cc src/protocols/symmetric_docking/SymRestrictTaskForDocking.cc src/protocols/symmetric_docking/SymSidechainMinMover.cc src/protocols/symmetric_docking/membrane/MPSymDockMover.cc src/protocols/symmetry/DetectSymmetryMover.cc src/protocols/symmetry/SetupForSymmetryMover.cc src/protocols/symmetry/SetupNCSMover.cc src/protocols/symmetry/SymDockingInitialPerturbation.cc src/protocols/symmetry/SymmetricRMSMover.cc src/protocols/task_operations/AlignedThreadOperation.cc src/protocols/task_operations/ConservativeDesignOperation.cc src/protocols/task_operations/CrystalContactsOperation.cc src/protocols/task_operations/DatabaseThread.cc src/protocols/task_operations/DesignAroundOperation.cc src/protocols/task_operations/DsspDesignOperation.cc src/protocols/task_operations/ImportUnboundRotamersOperation.cc src/protocols/task_operations/InteractingRotamerExplosion.cc src/protocols/task_operations/JointSequenceOperation.cc src/protocols/task_operations/LimitAromaChi2Operation.cc src/protocols/task_operations/LinkResidues.cc src/protocols/task_operations/ModifyAnnealer.cc src/protocols/task_operations/MutationSetDesignOperation.cc src/protocols/task_operations/PreventChainFromRepackingOperation.cc src/protocols/task_operations/PreventResiduesFromRepackingOperation.cc src/protocols/task_operations/ProteinInterfaceDesignOperation.cc src/protocols/task_operations/PruneBuriedUnsatsOperation.cc src/protocols/task_operations/ReadResfileFromDB.cc src/protocols/task_operations/ResfileCommandOperation.cc src/protocols/task_operations/ResidueProbDesignOperation.cc src/protocols/task_operations/RestrictByCalculatorsOperation.cc src/protocols/task_operations/RestrictChainToRepackingOperation.cc src/protocols/task_operations/RestrictIdentitiesAtAlignedPositions.cc src/protocols/task_operations/RestrictIdentitiesOperation.cc src/protocols/task_operations/RestrictInterGroupVectorOperation.cc src/protocols/task_operations/RestrictNativeResiduesOperation.cc src/protocols/task_operations/RestrictNonSurfaceToRepackingOperation.cc src/protocols/task_operations/RestrictResiduesToRepackingOperation.cc src/protocols/task_operations/RestrictToAlignedSegments.cc src/protocols/task_operations/RestrictToCDRH3Loop.cc src/protocols/task_operations/RestrictToInterfaceOperation.cc src/protocols/task_operations/RestrictToInterfaceVectorOperation.cc src/protocols/task_operations/RestrictToMoveMapChiOperation.cc src/protocols/task_operations/RestrictToNeighborhoodOperation.cc src/protocols/task_operations/RestrictToTerminiOperation.cc src/protocols/task_operations/RetrieveStoredTaskOperation.cc src/protocols/task_operations/STMStoredTask.cc src/protocols/task_operations/SelectByDeltaScoreOperation.cc src/protocols/task_operations/SelectByDensityFitOperation.cc src/protocols/task_operations/SelectBySASAOperation.cc src/protocols/task_operations/SelectResiduesWithinChain.cc src/protocols/task_operations/SeqprofConsensusOperation.cc src/protocols/task_operations/SequenceMotifTaskOperation.cc src/protocols/task_operations/SetIGTypeOperation.cc src/protocols/task_operations/StoreCombinedStoredTasksMover.cc src/protocols/task_operations/StoreCompoundTaskMover.cc src/protocols/task_operations/StoreTaskMover.cc src/protocols/task_operations/ThreadSequenceOperation.cc src/protocols/task_operations/pHVariantTaskOperation.cc src/protocols/tcr/TCRmodel.cc src/protocols/tcr/grafting_util.cc src/protocols/tcr/modeling_util.cc src/protocols/tcr/util.cc src/protocols/toolbox/DecoySetEvaluation.cc src/protocols/toolbox/IGEdgeReweighters.cc src/protocols/toolbox/NetworkAlgorithms.cc src/protocols/toolbox/match_enzdes_util/AlignPoseToInvrotTreeMover.cc src/protocols/toolbox/match_enzdes_util/AllowedSeqposForGeomCst.cc src/protocols/toolbox/match_enzdes_util/EnzConstraintIO.cc src/protocols/toolbox/match_enzdes_util/EnzConstraintParameters.cc src/protocols/toolbox/match_enzdes_util/EnzCstTemplateRes.cc src/protocols/toolbox/match_enzdes_util/EnzdesCacheableObserver.cc src/protocols/toolbox/match_enzdes_util/EnzdesCstCache.cc src/protocols/toolbox/match_enzdes_util/EnzdesSeqRecoveryCache.cc src/protocols/toolbox/match_enzdes_util/InvrotTarget.cc src/protocols/toolbox/match_enzdes_util/InvrotTree.cc src/protocols/toolbox/match_enzdes_util/InvrotTreeNode.cc src/protocols/toolbox/match_enzdes_util/InvrotTreeNodeBase.cc src/protocols/toolbox/match_enzdes_util/LigandConformer.cc src/protocols/toolbox/match_enzdes_util/MatchConstraintFileInfo.cc src/protocols/toolbox/match_enzdes_util/util_functions.cc src/protocols/toolbox/pose_manipulation/pose_manipulation.cc src/protocols/toolbox/rigid_body/util.cc src/protocols/toolbox/rotamer_set_operations/AddGood2BPairEnergyRotamers.cc src/protocols/toolbox/rotamer_set_operations/RigidBodyMoveRotSetOps.cc src/protocols/toolbox/rotamer_set_operations/SpecialRotamerRotSetOps.cc src/protocols/toolbox/sample_around/util.cc src/protocols/toolbox/superimpose.cc src/protocols/topology_broker/AsymFoldandDockClaimer.cc src/protocols/topology_broker/CoordConstraintClaimer.cc src/protocols/topology_broker/FibrilModelingClaimer.cc src/protocols/topology_broker/FoldandDockClaimer.cc src/protocols/topology_broker/MembraneTopologyClaimer.cc src/protocols/topology_broker/MetalloClaimer.cc src/protocols/topology_broker/RigidBodyRandomTMHMover.cc src/protocols/topology_broker/RigidChunkClaimer.cc src/protocols/topology_broker/SequenceClaimer.cc src/protocols/topology_broker/SymmetryClaimer.cc src/protocols/topology_broker/TMHTopologySamplerClaimer.cc src/protocols/topology_broker/TopologyBroker.cc src/protocols/topology_broker/TopologyClaimerFactory.cc src/protocols/unfolded_state_energy_calculator/UnfoldedStateEnergyCalculatorMover.cc src/protocols/vardist_solaccess/VarSolDRotamerDots.cc src/protocols/viewer/viewers.cc src/protocols/viewer/visualize.cc src/protocols/vip/VIP_Mover.cc src/protocols/vip/VIP_Report.cc src/protocols/wum/SilentStructStore.cc
Test: ubuntu.gcc.code_quality.cppcheck

Failed sub-tests (click for more details):
core/chemical/ResidueProperty.hh
Test: linux.clang.code_quality.submodule_regression

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Test: linux.gcc.mpi.serialization.integration.mpi

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Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
AddConstraintsToCurrentConformationMover AlignPDBInfoToSequences AlterSpecDisruption AnchorFinder AnchoredDesign AnchoredPDBCreator BuildPeptide CCD_loop_closure ConsensusLoopDesign ContactMolecularSurface DARC_electrostatics DARC_make_ray_files DARC_sampling_on_the_fly DARC_shapeonly DNA_methylation DumpTrajectoryEnergy DumpTrajectoryEnergy_packing Enzrevert_xml FilterReportAsPoseExtraScoresMover FlipChirality FloppyTail HelixBendFilter InterfaceAnalyzer InterfaceAnalyzer_allscores InterfaceAnalyzer_bothpack InterfaceAnalyzer_ligand InterfaceAnalyzer_prepack InterfaceAnalyzer_resfile InterfaceAnalyzer_tracer InterfaceDdG KIC_refine KIC_vicinity KIC_with_fragments LayerDesign LayerDesign_symm LayerSelector LoopAnalyzer LoopLengthChange ModifyVariantTypeMover MutateResidue_selector N-terminal_acetylation OversaturatedHbondAcceptorFilter PDB_diagnostic PeptideCyclizeMover PeptideStubMover_prependRepeat PolarDesign2019 ProQ RBOut ReadResfile_with_selector RescorePDDF ResidueDisorder SID_rescore SSElementSelector SecondaryStructureFilter SnugDock StrandCurvatureByLevels StrandHelixGeometryFilter ThreadingInputter TryDisulfPermutations UBQ_E2_thioester UBQ_E2_thioester_extra_bodies UBQ_E2_thioester_two_ubiquitins UBQ_Gp_CYD-CYD UBQ_Gp_LYX-Cterm UnsatSelector abinitio add_constraints_to_current_conformation add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup add_job_pair_data angle_recovery_stats antibody_H3 antibody_H3_camelid antibody_designer antibody_designer_camelid antibody_designer_xml antibody_graft antibody_numbering_converter assemble_domains_jd2 auto-drrafter_final_results auto-drrafter_setup_run_R1 auto-drrafter_setup_run_R2 auto-drrafter_setup_run_R3 autoNOE_rosetta autosetup_metals_centroid backbonegridsampler backbonegridsampler_multiresidue backbonegridsampler_nstruct_mode backrub backrub_interface_ddG backrub_pilot batch_relax beta_strand_homodimer bin_initialization bin_perturbation binselector binselector_probins broker broker_membrane bundlegridsampler bundlegridsampler_composition_energy bundlegridsampler_composition_energy_fract_range bundlegridsampler_copy_pitch bundlegridsampler_design bundlegridsampler_design_nstruct_mode bundlegridsampler_epsilon bundlegridsampler_multirepeat bundlegridsampler_z0_offset bundlegridsampler_z1_offset bundlereporter_filter burial_measure_centroid buried_area_filter buried_unsat_kinemage buried_unsat_voids_hbnet_design buried_unsat_voids_hbnet_design_symm c-term_conjugation calculate_sasa carbohydrates cart_min_glycans cartesianddg ccd_ends_graft_mover_rs centroid_disulfide_scores centroid_from_fullatom classic_relax_1a19 cleanAlignment cluster cluster_alns cluster_calibur cluster_filter coenzymes combine_silent composition_energy_layers constel contactMap copy_rotamer_mover count_cycpep_sequences coupled_moves create_clash-based_repack_shell create_sequence_motif crossaln crosslinkermover_octahedral crosslinkermover_octahedral_s2_symm crosslinkermover_square_planar crosslinkermover_square_planar_d2_symm crosslinkermover_square_pyramidal crosslinkermover_tetrahedral_metal crosslinkermover_tetrahedral_metal_asp crosslinkermover_tetrahedral_metal_c2_symmetry crosslinkermover_tetrahedral_metal_d2_symmetry crosslinkermover_tma crosslinkermover_tma_symm crosslinkermover_trigonal_planar crosslinkermover_trigonal_planar_c3_symm crosslinkermover_trigonal_pyramidal crosslinkermover_trigonal_pyramidal_c3_symm cs_rosetta_rna cst_info cstfile_to_theozyme_pdb custom_basetype_packer_palette cyclization cycpep_design_pipeline cycpep_symmetry_filter d_workflow database_jd2_compact_io database_jd2_io database_md5 database_session_resource ddG_ensemble ddG_of_mutation ddG_scan ddG_sym density_denovo density_refine density_refine_symm density_tools design_glycans design_w_custom_palette-CAAs design_w_custom_palette-NCAAs design_w_custom_palette-RNA distances disulfidize_beta_cys dna_interface_design dock_glycans dock_with_hotspot_place_simultaneously docking_distance_constraints docking_ensemble docking_ensemble_prepack docking_full_protocol docking_local_refine docking_local_refine_min docking_low_res docking_prepack docking_site_constraints doug_dock_design_min_mod2_cal_cal drrafter_error_estimation drrafter_run energy_based_clustering_alpha_aa energy_based_clustering_alpha_aa_bin_analysis energy_based_clustering_alpha_aa_dihedral entropy_correction enumerative_sampling enzdes enzscore_filter_dimetal enzscore_filter_dimetal_sym enzscore_filter_ligand enzscore_filter_metal enzscore_filter_metal_sym erraser_minimize evolution explicit_membrane extract_atomtree_diffs extract_pdbs farfar_mrna farnesyl fast_relax fast_relax_scripts favor_coupling_tensor favor_native_residue features features_database_schema features_parallel features_pdb features_postgres fiber_diffraction fiber_diffraction_fad fit_helixparams fit_helixparams_a3b fit_helixparams_rms fix_alignment_to_match_pdb fixbb flexpepdock flexpepdock_abinitio fold_and_dock fold_cst_new fold_from_loops fragment_picker fragmentpicker_integration_demo fuzzy ga_ligand_dock gen_apo_grids gen_lig_grids generate_6Dloopclose genkic_bin_perturbing genkic_bin_sampling genkic_bin_setting genkic_dihedral_copying genkic_lowmemory_mode genkic_rama_filter genkic_ramaprepro_sampling genkic_sugars geometric_solvation glycan_anomers glycan_clash_check glycan_refinment glycan_relax glycan_sequon_scanner glycan_tree_relax glycomutagenesis glycosylation grid_scores_features hbnet hbnet_asymm hbnet_energy hbnet_energy_rosettascripts_linear hbnet_energy_symm hbnet_use_input_rot hbonds hbonds_sp2 hbondstoresidue_selector hbs_design helical_bundle helical_bundle_nonideal helical_bundle_predict helical_bundle_predict_sequence helical_bundle_predict_skipping_residues helix_from_sequence hierarchical_clustering homodimer_fnd_ref2015_memb hotspot_graft hotspot_hashing hotspot_stub_constraints hshash_utils hts_io hybridization hydrate hydrate_relax identify_cdr_clusters ig_dump interaction_graph_summary_metric interface_energy inv_kin_lig_loop_design jd2test_PDBIO jd2test_PDBin_mmCIFout jd2test_PDBin_mmCIFout_extra_data_separate jd2test_mmCIFIO jd2test_mmCIFin_PDBout job_definition_script_vars jrelax jscore kinemage_grid_output kinematic_looprelax ld_converter ligand_database_io ligand_dock_7cpa ligand_dock_ensemble ligand_dock_grid ligand_dock_script ligand_motif_design ligand_water_docking longest_continuous_polar_segment_filter loop_creation loop_grower_N_term_symm loop_hash loop_modeling make_and_perturb_bundle_multirepeat make_exemplar make_mainchain_potential make_mainchain_potential_symm make_mainchain_potential_symm_preproline make_rot_lib make_symmdef_file match_1c2t match_1n9l match_6cpa match_xml measure_lcaa_radii membrane_abinitio metal_setup metalloprotein_abrelax metalloprotein_broker metropolis_hastings mf_fixbb_des mf_fixbb_sc mf_flexbb_sc mg_modeler mg_modeler_lores mhc_epitope mhc_epitope_nmer_preload min_pack_min minimize_6Dloopclose minimize_with_elec_dens mirror_symm mm_params mmtfIO_score_test motif_dna_packer_design motif_extraction motif_score_filter mp_dock mp_dock_prepack mp_dock_setup mp_domain_assembly mp_domain_assembly_FtsQ mp_find_interface mp_interface_statistics mp_ligand_interface mp_loadtime mp_mutate_relax mp_mutate_repack mp_quick_relax_ref2015_memb mp_range_relax mp_relax mp_score_jd2 mp_span_ang_ref2015_memb mp_span_from_pdb mp_symdock mp_symmetry_load mp_transform mp_transform_optimize mp_vis_emb mpi_multistate_design mpil_find_pore_ahelical mpil_find_pore_bbarrel mpil_load_implicit_lipids mr_protocols multistage_rosetta_scripts multistage_rosetta_scripts_clustering mutate ncaa_fixbb ncbb_packer_palette netcharge_design netcharge_design_symm next_generation_KIC noe_assignment non-canonical_connectivities nonideal_rtmin nucleobase_sample_around number_of_residuetypes oligourea_design oligourea_predict oop_create oop_design oop_dock_design orbitals pH_mode pepspec_anchor_dock peptiderive per_residue_energies per_residue_sc_sasa per_residue_solvent_exposure pertmin perturb_helical_bundle perturb_helical_bundle_copying_pitch perturb_helical_bundle_epsilon perturb_helical_bundle_setting perturb_helical_bundle_z_offset phiselector phosphonate phosphorylation place_simultaneously pmut_scan pna pna_base_pairs pocket_measure pocket_relax pocket_suggest_targets polyaramid_test_trivial posttranslationalmod_io ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG ppk protocol_metric pwsho pymol_cif r_pdb2top r_rmsf ralford_dump_rotamers rama_mutation_selector range_relax_w_cst rb_recces read_polymeric_components readin_dna_rna_protein real_virt_mover recces_turner recon_design referencepose_mutateresidue relax_w_allatom_cst remodel_disulfides_rosettascripts remodel_helical_repeat repack_with_elec_dens repeat_propagate repeat_propagate_v2 repeat_propagate_v3 repeat_relax report_hbonds_for_plugin res_lipo_ref2015_memb residue_energy_breakdown resource_database_locator restype_converter rings rna_add_WC_stats rna_assemble rna_cluster rna_denovo rna_denovo_RNP_low_res rna_denovo_RNP_refine_native rna_denovo_base_pair_constraints rna_denovo_base_pair_setup rna_denovo_bps rna_denovo_bps_fixed_ends rna_denovo_bps_helix_ends rna_denovo_dna_bridge rna_denovo_fragment_homology_exclusion rna_denovo_grid_vdw rna_denovo_lariat rna_denovo_new_FT_2in_dens rna_denovo_new_FT_5P_j12_leadzyme rna_denovo_new_FT_RNP_2prot_dens rna_denovo_new_FT_rna_two_chains rna_denovo_new_libs rna_denovo_symm_hack rna_design rna_farfar_block_stack rna_farfar_noncanonical_hairpin rna_farfar_syn_chi_res rna_helix rna_minimize rna_minimize_6D_loop_close rna_motif rna_predict_chem_map rna_puzzle11_H2H3H4_run3_connectU40 rna_puzzle12_P5P6P7_DMS rna_puzzle5_P15P3P8_noP4P6_4RB_G208phosphate_ligation rna_puzzle5_p2_GAAA_mini rna_puzzle6_U75G76A77_on_thread1 rna_puzzle6_j67_into_p6p7rigidbody_thread1 rna_ribosome_tether rna_score rna_screen_phosphates rna_suitename rnp_ddg_calc_mut rnp_ddg_calc_wt rnp_ddg_relax_command_1 rnp_ddg_relax_command_2 rollmover rosetta_scripts_hbond_options rosetta_scripts_include rosetta_scripts_info rosetta_scripts_jd3 rosetta_scripts_loops rosetta_scripts_setup rosie_ligand_docking rotamer_probability rotamer_recovery rotamer_recovery_compare_two_structures rs_flexbbmoves rs_loophash sasa_metric_options score12_docking score_aln score_jd2 score_only_silence sdf_reader secondary_structure_output seed_ensemble_JD2_JI select_best_unique_ligand_poses selected_residue_count_metric sequence_profile_constraints sequence_recovery sequence_tolerance set_torsion shobuns silent2frag simple_cycpep_predict simple_cycpep_predict_angle simple_cycpep_predict_anglelength simple_cycpep_predict_bondangle_bondlength simple_cycpep_predict_cartesian simple_cycpep_predict_cispro simple_cycpep_predict_cterm_isopeptide_lariat simple_cycpep_predict_cterm_isopeptide_lariat_tailless simple_cycpep_predict_design simple_cycpep_predict_nmethyl simple_cycpep_predict_nterm_isopeptide_lariat simple_cycpep_predict_nterm_isopeptide_lariat_tailless simple_cycpep_predict_octahedral_metal simple_cycpep_predict_peptoid simple_cycpep_predict_setting simple_cycpep_predict_sidechain_isopeptide simple_cycpep_predict_sidechain_isopeptide_reverse simple_cycpep_predict_square_planar_metal simple_cycpep_predict_square_pyramidal_metal simple_cycpep_predict_symm_gly simple_cycpep_predict_symmetric_sampling simple_cycpep_predict_tbmb simple_cycpep_predict_terminal_disulfide simple_cycpep_predict_terminal_disulfide_internal_permutations simple_cycpep_predict_terminal_disulfide_tails simple_cycpep_predict_tetrahedral_metal simple_cycpep_predict_tetrahedral_metal_asp simple_cycpep_predict_tma simple_cycpep_predict_trigonal_planar_metal simple_cycpep_predict_trigonal_pyramidal_metal simple_dna_test simple_glycosylation simple_grafting_movers simple_hbondstoatom simple_metric_cache simple_metric_features simple_metric_filter simple_metrics simple_metrics_per_residue site_constraint small_molecule_lattice_dock smallmover_resselector splice_in_4loops_longer splice_in_4loops_shorter splice_out_H1_H2_longer splice_out_H1_H2_same splice_out_H1_H2_shorter splice_out_H3_longer splice_out_H3_same splice_out_H3_shorter splice_out_L1_L2_longer splice_out_L1_L2_same splice_out_L1_L2_shorter splice_out_L3_longer splice_out_L3_same splice_out_L3_shorter startfrom_file stepwise_lores stored_residue_subset struc_set_fragment_picker super_aln supercharge surface_docking swa_protein_CCDclose swa_protein_build_at_Cterminus swa_protein_build_at_Nterminus swa_protein_cluster swa_protein_combine_loops swa_protein_loop_sampler swa_protein_prepack swa_rna_erraser swa_rna_gagu_01_append swa_rna_gagu_02_prepend swa_rna_gagu_03_append_to_silent swa_rna_gagu_04_clustering swa_rna_gagu_05_prepend_to_5primeterminus swa_rna_gagu_06_append_to_3primeterminus swa_rna_gagu_07_prepend_dinucleotide swa_rna_gagu_08_append_dinucleotide swa_rna_gagu_09_sample_virtual_ribose swa_rna_gagu_10_prepend_and_ccd_close swa_rna_gagu_11_append_and_ccd_close swa_rna_gagu_12_helix_addition swa_rna_gagu_13_chunk_combination_and_closure swa_rna_gagu_14_combine_long_loop_filtering swa_rna_gagu_15_combine_long_loop_sampling swa_rna_gagu_16_prepend_dinucleotide_on_dinucleotide swa_rna_gagu_17_append_floating_base swa_rna_gagu_18_rebuild_bulge swa_rna_gagu_19_prepend_floating_base_by_jump swa_rna_gagu_20_append_floating_base_by_jump swa_rna_gagu_21_prepend_dinucleotide_on_dinucleotide_by_jump swa_rna_gagu_22_prepend_and_kic_close swa_rna_gagu_23_append_and_kic_close swa_rna_loop_clusterer swa_rna_loop_sampler sweep_respair_energies swm_add_rosettascripts swm_beta_peptide_loop swm_build_full_model swm_dna_bridge swm_dna_loop swm_general_polymer_sampler swm_l_rna swm_protein_CCDmove swm_protein_from_scratch swm_protein_loop_sampler swm_protein_move_inside_coiledcoil_by_bond swm_protein_move_inside_helix_by_bond swm_protein_preminimize swm_rna_base_pair_constraints swm_rna_checkpoint_partition swm_rna_fourwayjunction swm_rna_loop_design swm_rna_move_align_dock swm_rna_move_inside_helix_by_bond swm_rna_move_inside_helix_by_jump swm_rna_move_two_strands swm_rna_nickedhelix swm_rna_protonated_adenosine swm_rna_singleloop swm_rna_srl_triplet symm_disulfidize symm_rotamer_boltzmann symmetric_cycpep_align_and_symmetrize symmetric_docking symmetrical_residue_selector symmetry_data_resource symmetry_multicomponent target_clash task_selector tcrmodel template_features test1_benchmark test_computed_saxs_spectrum test_d_l_readin test_energy_method_options test_idealize thermal_sampler threefold_symm_peptide_design threefoldlinkermover_tbmb threefoldlinkermover_tbmb_symmetric tna_base_pairs torsion_restricted_sampling unfolded_state_energy_calc validate_database vancomycin vip voids_penalty_energy_design voids_penalty_energy_design_symmetry write_mol_file zinc_heterodimer zinc_homodimer_design zinc_homodimer_setup
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